The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The relationships of groups of organisms as reflected by their genetic makeup.
The techniques used to produce molecules exhibiting properties that conform to the demands of the experimenter. These techniques combine methods of generating structural changes with methods of selection. They are also used to examine proposed mechanisms of evolution under in vitro selection conditions.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The continuous developmental process of a culture from simple to complex forms and from homogeneous to heterogeneous qualities.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Genotypic differences observed among individuals in a population.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The process of accumulation of genetic and epigenetic changes over time in individual cells and the effect of the changes on CELL PROLIFERATION.
Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Chemical and physical transformation of the biogenic elements from their nucleosynthesis in stars to their incorporation and subsequent modification in planetary bodies and terrestrial biochemistry. It includes the mechanism of incorporation of biogenic elements into complex molecules and molecular systems, leading up to the origin of life.
Family of the suborder HAPLORHINI (Anthropoidea) comprising bipedal primate MAMMALS. It includes modern man (HOMO SAPIENS) and the great apes: gorillas (GORILLA GORILLA), chimpanzees (PAN PANISCUS and PAN TROGLODYTES), and orangutans (PONGO PYGMAEUS).
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.
The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
The genetic complement of a BACTERIA as represented in its DNA.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
Animals that have no spinal column.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The total process by which organisms produce offspring. (Stedman, 25th ed)
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The fluctuation of the ALLELE FREQUENCY from one generation to the next.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
The genetic complement of a plant (PLANTS) as represented in its DNA.
A portion of the animal phylum Chordata comprised of the subphyla CEPHALOCHORDATA; UROCHORDATA, and HYPEROTRETI, but not including the Vertebrata (VERTEBRATES). It includes nonvertebrate animals having a NOTOCHORD during some developmental stage.
The capability of an organism to survive and reproduce. The phenotypic expression of the genotype in a particular environment determines how genetically fit an organism will be.
Creation and development of bodies within solar systems, includes study of early planetary geology.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The functional hereditary units of PLANTS.
A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.
The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.
Computer-based representation of physical systems and phenomena such as chemical processes.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The origin of life. It includes studies of the potential basis for life in organic compounds but excludes studies of the development of altered forms of life through mutation and natural selection, which is BIOLOGICAL EVOLUTION.
Any method used for determining the location of and relative distances between genes on a chromosome.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
Members of the phylum Arthropoda, composed of organisms having a hard, jointed exoskeleton and paired jointed legs. It includes the class INSECTS and the subclass ARACHNIDA, many species of which are important medically as parasites or as vectors of organisms capable of causing disease in man.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The functional hereditary units of INSECTS.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Phylum in the domain Eukarya, comprised of animals either with fully developed backbones (VERTEBRATES), or those with notochords only during some developmental stage (CHORDATA, NONVERTEBRATE).
Elements of limited time intervals, contributing to particular results or situations.
Deoxyribonucleic acid that makes up the genetic material of plants.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
The study of early forms of life through fossil remains.
Sexual activities of animals.
Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The external elements and conditions which surround, influence, and affect the life and development of an organism or population.
The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The branch of science concerned with the interrelationship of organisms and their ENVIRONMENT, especially as manifested by natural cycles and rhythms, community development and structure, interactions between different kinds of organisms, geographic distributions, and population alterations. (Webster's, 3d ed)
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Theoretical construct used in applied mathematics to analyze certain situations in which there is an interplay between parties that may have similar, opposed, or mixed interests. In a typical game, decision-making "players," who each have their own goals, try to gain advantage over the other parties by anticipating each other's decisions; the game is finally resolved as a consequence of the players' decisions.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The sequential location of genes on a chromosome.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
Coloration or discoloration of a part by a pigment.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
The genetic complement of an insect (INSECTS) as represented in its DNA.
General name for two extinct orders of reptiles from the Mesozoic era: Saurischia and Ornithischia.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The reproductive organs of plants.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
This single species of Gorilla, which is a member of the HOMINIDAE family, is the largest and most powerful of the PRIMATES. It is distributed in isolated scattered populations throughout forests of equatorial Africa.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
The complete gene complement contained in a set of chromosomes in a fungus.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The homologous chromosomes that are dissimilar in the heterogametic sex. There are the X CHROMOSOME, the Y CHROMOSOME, and the W, Z chromosomes (in animals in which the female is the heterogametic sex (the silkworm moth Bombyx mori, for example)). In such cases the W chromosome is the female-determining and the male is ZZ. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
A species of orangutan, family HOMINIDAE, found in the forests on the island of Borneo.
The use of DNA recombination (RECOMBINATION, GENETIC) to prepare a large gene library of novel, chimeric genes from a population of randomly fragmented DNA from related gene sequences.
A small aquatic oviparous mammal of the order Monotremata found in Australia and Tasmania.
Proteins found in any species of bacterium.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
The selection or choice of sexual partner in animals. Often this reproductive preference is based on traits in the potential mate, such as coloration, size, or behavioral boldness. If the chosen ones are genetically different from the rejected ones, then NATURAL SELECTION is occurring.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
The comparative study of animal structure with regard to homologous organs or parts. (Stedman, 25th ed)
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The relationship between an invertebrate and another organism (the host), one of which lives at the expense of the other. Traditionally excluded from definition of parasites are pathogenic BACTERIA; FUNGI; VIRUSES; and PLANTS; though they may live parasitically.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Group of fish under the superorder Acanthopterygii, separate from the PERCIFORMES, which includes swamp eels, mullets, sticklebacks, seahorses, spiny eels, rainbowfishes, and KILLIFISHES. The name is derived from the six taxa which comprise the group. (From, 8/4/2000)
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
A class of unsegmented helminths with fundamental bilateral symmetry and secondary triradiate symmetry of the oral and esophageal structures. Many species are parasites.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The functional hereditary units of BACTERIA.
A plant family of the order Capparales, subclass Dilleniidae, class Magnoliopsida. They are mostly herbaceous plants with peppery-flavored leaves, due to gluconapin (GLUCOSINOLATES) and its hydrolysis product butenylisotrhiocyanate. The family includes many plants of economic importance that have been extensively altered and domesticated by humans. Flowers have 4 petals. Podlike fruits contain a number of seeds. Cress is a general term used for many in the Brassicacea family. Rockcress is usually ARABIS; Bittercress is usually CARDAMINE; Yellowcress is usually RORIPPA; Pennycress is usually THLASPI; Watercress refers to NASTURTIUM; or RORIPPA or TROPAEOLUM; Gardencress refers to LEPIDIUM; Indiancress refers to TROPAEOLUM.
Any behavior caused by or affecting another individual, usually of the same species.
Time period from 1901 through 2000 of the common era.
The family of Old World monkeys and baboons consisting of two subfamilies: CERCOPITHECINAE and COLOBINAE. They are found in Africa and part of Asia.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Instinctual behavior pattern in which food is obtained by killing and consuming other species.
Bony structure of the mouth that holds the teeth. It consists of the MANDIBLE and the MAXILLA.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.
An order of wholly aquatic MAMMALS occurring in all the OCEANS and adjoining seas of the world, as well as in certain river systems. They feed generally on FISHES, cephalopods, and crustaceans. Most are gregarious and most have a relatively long period of parental care and maturation. Included are DOLPHINS; PORPOISES; and WHALES. (From Walker's Mammals of the World, 5th ed, pp969-70)
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A mammalian order which consists of 29 families and many genera.
An infraclass of MAMMALS, also called Metatheria, where the young are born at an early stage of development and continue to develop in a pouch (marsupium). In contrast to Eutheria (placentals), marsupials have an incomplete PLACENTA.
Communication between animals involving the giving off by one individual of some chemical or physical signal, that, on being received by another, influences its behavior.
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide using energy obtained from light rather than from the oxidation of chemical compounds. Photosynthesis comprises two separate processes: the light reactions and the dark reactions. In higher plants; GREEN ALGAE; and CYANOBACTERIA; NADPH and ATP formed by the light reactions drive the dark reactions which result in the fixation of carbon dioxide. (from Oxford Dictionary of Biochemistry and Molecular Biology, 2001)
Slender-bodies diurnal insects having large, broad wings often strikingly colored and patterned.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.
Reproduction without fusion of two types of cells, mostly found in ALGAE; FUNGI; and PLANTS. Asexual reproduction occurs in several ways, such as budding, fission, or splitting from "parent" cells. Only few groups of ANIMALS reproduce asexually or unisexually (PARTHENOGENESIS).
Common name for the only family (Petromyzontidae) of eellike fish in the order Petromyzontiformes. They are jawless but have a sucking mouth with horny teeth.
Consideration and concern for others, as opposed to self-love or egoism, which can be a motivating influence.
The period of history before 500 of the common era.
The ceasing of existence of a species or taxonomic groups of organisms.
The totality of characteristics of reproductive structure, functions, PHENOTYPE, and GENOTYPE, differentiating the MALE from the FEMALE organism.
Common name for perch-like fish of the family Cichlidae, belonging to the suborder Labroidei, order PERCIFORMES.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
A phylum of radially symmetrical invertebrates characterized by possession of stinging cells called nematocysts. It includes the classes ANTHOZOA; CUBOZOA; HYDROZOA, and SCYPHOZOA. Members carry CNIDARIAN VENOMS.
The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).
Proteins found in any species of insect.
A kingdom of eukaryotic, heterotrophic organisms that live parasitically as saprobes, including MUSHROOMS; YEASTS; smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi, commonly known as molds, refer to those that grow as multicellular colonies.
Insects of the family Formicidae, very common and widespread, probably the most successful of all the insect groups. All ants are social insects, and most colonies contain three castes, queens, males, and workers. Their habits are often very elaborate and a great many studies have been made of ant behavior. Ants produce a number of secretions that function in offense, defense, and communication. (From Borror, et al., An Introduction to the Study of Insects, 4th ed, p676)
Time period from 1801 through 1900 of the common era.
The direct struggle between individuals for environmental necessities or for a common goal.
Genes that encode highly conserved TRANSCRIPTION FACTORS that control positional identity of cells (BODY PATTERNING) and MORPHOGENESIS throughout development. Their sequences contain a 180 nucleotide sequence designated the homeobox, so called because mutations of these genes often results in homeotic transformations, in which one body structure replaces another. The proteins encoded by homeobox genes are called HOMEODOMAIN PROTEINS.
Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.
Number of individuals in a population relative to space.
A phylum of photosynthetic EUKARYOTA bearing double membrane-bound plastids containing chlorophyll a and b. They comprise the classical green algae, and represent over 7000 species that live in a variety of primarily aquatic habitats. Only about ten percent are marine species, most live in freshwater.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
The field of biology which deals with the process of the growth and differentiation of an organism.
Invertebrate organisms that live on or in another organism (the host), and benefit at the expense of the other. Traditionally excluded from definition of parasites are pathogenic BACTERIA; FUNGI; VIRUSES; and PLANTS; though they may live parasitically.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
A genus of pufferfish commonly used for research.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)
An extensive order of highly specialized insects including bees, wasps, and ants.
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
The amount of DNA (or RNA) in one copy of a genome.
Databases devoted to knowledge about specific genes and gene products.
The only species of a cosmopolitan ascidian.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
INSECTS of the order Coleoptera, containing over 350,000 species in 150 families. They possess hard bodies and their mouthparts are adapted for chewing.
The SKELETON of the HEAD including the FACIAL BONES and the bones enclosing the BRAIN.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Time period from 2001 through 2100 of the common era.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
The mechanisms by which the SEX of an individual's GONADS are fixed.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Photosensitive proteins in the membranes of PHOTORECEPTOR CELLS such as the rods and the cones. Opsins have varied light absorption properties and are members of the G-PROTEIN-COUPLED RECEPTORS family. Their ligands are VITAMIN A-based chromophores.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.

Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (1/24558)

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

Molecular chaperones: small heat shock proteins in the limelight. (2/24558)

Small heat shock proteins have been the Cinderellas of the molecular chaperone world, but now the crystal structure of a small heat shock protein has been solved and mutation of two human homologues implicated in genetic disease. Intermediate filaments appear to be one of the key targets of their chaperone activity.  (+info)

Insect evolution: Redesigning the fruitfly. (3/24558)

Homeotic mutations in Drosophila can result in dramatic phenotypes that suggest the possibility for rapid morphological evolution, but dissection of the genetic pathway downstream of Ultrabithorax is beginning to reveal how wing morphology may have evolved by more gradual transformations.  (+info)

Ultrabithorax function in butterfly wings and the evolution of insect wing patterns. (4/24558)

BACKGROUND: . The morphological and functional evolution of appendages has played a critical role in animal evolution, but the developmental genetic mechanisms underlying appendage diversity are not understood. Given that homologous appendage development is controlled by the same Hox gene in different organisms, and that Hox genes are transcription factors, diversity may evolve from changes in the regulation of Hox target genes. Two impediments to understanding the role of Hox genes in morphological evolution have been the limited number of organisms in which Hox gene function can be studied and the paucity of known Hox-regulated target genes. We have therefore analyzed a butterfly homeotic mutant 'Hindsight', in which portions of the ventral hindwing pattern are transformed to ventral forewing identity, and we have compared the regulation of target genes by the Ultrabithorax (Ubx) gene product in Lepidopteran and Dipteran hindwings. RESULTS: . We show that Ubx gene expression is lost from patches of cells in developing Hindsight hindwings, correlating with changes in wing pigmentation, color pattern elements, and scale morphology. We use this mutant to study how regulation of target genes by Ubx protein differs between species. We find that several Ubx-regulated genes in the Drosophila haltere are not repressed by Ubx in butterfly hindwings, but that Distal-less (Dll) expression is regulated by Ubx in a unique manner in butterflies. CONCLUSIONS: . The morphological diversification of insect hindwings has involved the acquisition of different sets of target genes by Ubx in different lineages. Changes in Hox-regulated target gene sets are, in general, likely to underlie the morphological divergence of homologous structures between animals.  (+info)

Molecular phylogeny of the ETS gene family. (5/24558)

We have constructed a molecular phylogeny of the ETS gene family. By distance and parsimony analysis of the ETS conserved domains we show that the family containing so far 29 different genes in vertebrates can be divided into 13 groups of genes namely ETS, ER71, GABP, PEA3, ERG, ERF, ELK, DETS4, ELF, ESE, TEL, YAN, SPI. Since the three dimensional structure of the ETS domain has revealed a similarity with the winged-helix-turn-helix proteins, we used two of them (CAP and HSF) to root the tree. This allowed us to show that the family can be divided into five subfamilies: ETS, DETS4, ELF, TEL and SPI. The ETS subfamily comprises the ETS, ER71, GABP, PEA3, ERG, ERF and the ELK groups which appear more related to each other than to any other ETS family members. The fact that some members of these subfamilies were identified in early metazoans such as diploblasts and sponges suggests that the diversification of ETS family genes predates the diversification of metazoans. By the combined analysis of both the ETS and the PNT domains, which are conserved in some members of the family, we showed that the GABP group, and not the ERG group, is the one most closely related to the ETS group. We also observed that the speed of accumulation of mutations in the various genes of the family is highly variable. Noticeably, paralogous members of the ELK group exhibit strikingly different evolutionary speed suggesting that the evolutionary pressure they support is very different.  (+info)

Anopheles gambiae Ag-STAT, a new insect member of the STAT family, is activated in response to bacterial infection. (6/24558)

A new insect member of the STAT family of transcription factors (Ag-STAT) has been cloned from the human malaria vector Anopheles gambiae. The domain involved in DNA interaction and the SH2 domain are well conserved. Ag-STAT is most similar to Drosophila D-STAT and to vertebrate STATs 5 and 6, constituting a proposed ancient class A of the STAT family. The mRNA is expressed at all developmental stages, and the protein is present in hemocytes, pericardial cells, midgut, skeletal muscle and fat body cells. There is no evidence of transcriptional activation following bacterial challenge. However, bacterial challenge results in nuclear translocation of Ag-STAT protein in fat body cells and induction of DNA-binding activity that recognizes a STAT target site. In vitro treatment with pervanadate (vanadate and H2O2) translocates Ag-STAT to the nucleus in midgut epithelial cells. This is the first evidence of direct participation of the STAT pathway in immune responses in insects.  (+info)

Analysis of a ubiquitous promoter element in a primitive eukaryote: early evolution of the initiator element. (7/24558)

Typical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protist Trichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examined T. vaginalis genes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found in T. vaginalis protein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.  (+info)

The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. (8/24558)

The nuclear receptor (NR) superfamily is the most abundant class of transcriptional regulators encoded in the Caenorhabditis elegans genome, with >200 predicted genes revealed by the screens and analysis of genomic sequence reported here. This is the largest number of NR genes yet described from a single species, although our analysis of available genomic sequence from the related nematode Caenorhabditis briggsae indicates that it also has a large number. Existing data demonstrate expression for 25% of the C. elegans NR sequences. Sequence conservation and statistical arguments suggest that the majority represent functional genes. An analysis of these genes based on the DNA-binding domain motif revealed that several NR classes conserved in both vertebrates and insects are also represented among the nematode genes, consistent with the existence of ancient NR classes shared among most, and perhaps all, metazoans. Most of the nematode NR sequences, however, are distinct from those currently known in other phyla, and reveal a previously unobserved diversity within the NR superfamily. In C. elegans, extensive proliferation and diversification of NR sequences have occurred on chromosome V, accounting for > 50% of the predicted NR genes.  (+info)

That is absurd. Even evolutionists are now agreeing that what they once rejected as impossible, and then grudgingly admitted as rare, now must be treated as a significant mode of the origins of new genes. As Light, Basile and Elofsson write in their 2014 review which I referenced, It has even been proposed that the creation of novel genes, a continuous process where most de novo genes are short-lived, is as frequent as gene duplications. Likewise Neme and Tautz explain, there is now rapidly increasing evidence that de novo evolution of transcripts and genes is not only a theoretical possibility, but might even have been a rather active process throughout evolution. And even Zimmer admitted in the NY Times piece, Far from being a fluke, these studies suggest that de novo genes are abundant. Nick you have an ax to grind that wont let acknowledge the clear evidence ...
TY - JOUR. T1 - Synonymous substitution rates in Drosophila. T2 - Mitochondrial versus nuclear genes. AU - Moriyama, Etsuko N.. AU - Powell, Jeffrey R.. PY - 1997. Y1 - 1997. N2 - Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 ...
De novo genes are new genes that arise spontaneously from junk DNA [De novo gene birth]. The frequency of de novo gene creation is important for an understanding of evolution. If its a frequent event, then species with a large amount of junk DNA might have a selective advantage over species with less junk DNA, especially in a changing environment.. Last week I read a short Nature article on de novo genes [Levy, 2019] and I think the subject deserves more attention. Most new genes in a species appear to arise by gene duplication and subsequent divergence but de novo genes are genes that are unrelated to genes in any other clade so we can assume that they are created from junk DNA that accidentally becomes associated with a promoter causing the DNA to be transcribed. A new gene is formed if the RNA acquires a function. If the transcript contains an open reading frame then it may be translated to produce a polypeptide and if the polypeptide performs a new function then the resulting de novo gene ...
The distribution of fitness effects (DFE) encompasses the fraction of deleterious, neutral, and beneficial mutations. It conditions the evolutionary trajectory of populations, as well as the rate of adaptive molecular evolution (alpha). Inferring DFE and a from patterns of polymorphism, as given through the site frequency spectrum (SFS) and divergence data, has been a longstanding goal of evolutionary genetics. A widespread assumption shared by previous inference methods is that beneficial mutations only contribute negligibly to the polymorphism data. Hence, a DFE comprising only deleterious mutations tends to be estimated from SFS data, and alpha is then predicted by contrasting the SFS with divergence data from an outgroup. We develop a hierarchical probabilistic framework that extends previous methods to infer DFE and alpha from polymorphism data alone. We use extensive simulations to examine the performance of our method. While an outgroup is still needed to obtain an unfolded SFS, we show ...
Graduate Student (PhD) positions are available in Dr. Eirin-Lopezs Chromatin Structure & Evolution Lab at the Department of Biological Sciences in Florida International University ( starting in Fall 2015.. We are looking for enthusiastic, dynamic and independent students broadly interested in studying the interface between evolution, epigenetics and adaptation. Students would ideally have a B.S. degree in Biology or related discipline (academic training in biology, statistics, genetics and evolution) and must be proficient in English (both spoken and written). Candidates with additional knowledge on computer science and/or bioinformatics are encouraged to apply. Our research addresses the study of chromatin and epigenetics from different perspectives, most notably evolution, development and adaptation. To this end we use marine invertebrates as model systems in the lab, as well as a wide range of eukaryote groups in molecular evolutionary analyses. Our current projects combine ...
The recombinational environment is predicted to influence patterns of protein sequence evolution through the effects of Hill-Robertson interference among linked sites subject to selection. In freely recombining regions of the genome, selection should more effectively incorporate new beneficial mutations, and eliminate deleterious ones, than in regions with low rates of genetic recombination. We examined the effects of recombinational environment on patterns of evolution using a genome-wide comparison of Drosophila melanogaster and D. yakuba. In regions of the genome with no crossing over, we find elevated divergence at nonsynonymous sites and in long introns, a virtual absence of codon usage bias, and an increase in gene length. However, we find little evidence for differences in patterns of evolution between regions with high, intermediate, and low crossover frequencies. In addition, genes on the fourth chromosome exhibit more extreme deviations from regions with crossing over than do other, no
Bgee allows to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships between them.
Genotyping and sequencing of a number of eukaryotic genomes provide us with an opportunity to study the temporal and functional character of evolutionary changes in metazoans. Here we provide a framework for identifying changes in evolutionary constraints on mutated positions in the human genome. Due to lack of SNP data, in the current analysis we captured only higher order patterns at the level of functional categories. But upon availability of resequencing data, using BaseDiver it is possible to achieve higher resolution. In this work we restricted the use of BaseDiver to coding regions only, where most of the base positions are under selection and the effects of hitchhiking are small, it can be used to identify changes in constraints in non-coding regions as well.. Recently outliers of evolutionary patterns like ultra-conserved elements in higher eukaryotes and highly accelerated regions in humans have been identified [4, 7]; here we attempt to capture the comprehensive spectrum of evolution ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new relaxed-clock phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the detrimental effects of
Abstract: Using genomic information from mosquito, red flour beetle, honeybee, mouse, and sea anemone, we have studied the molecular evolution of 91 Drosophila genes involved in eye primordium determination, retinal differentiation, and phototransduction. Our results show that the majority of these gene sequences predate the diversification of endopterygote insects. However, all three functional groups contain a conspicuous fraction of evolutionarily younger genes, which originated by tandem duplication in the lineage leading to Drosophila, whereas gene duplications are rare in other insect lineages. We conclude that the retention of duplicated genes spiked during the early diversification of the higher Diptera possibly due to an extended period of exceptional population size reduction. Genetic data suggest that gene duplication played an important role in the evolution of visual performance in the fast flying higher Diptera by spatial or intracellular subfunctionalization. Developmental gene ...
Once they had finished their analysis, Bill Martins team was left with just 355 genes from the original 11,000, and they argue that these 355 definitely belonged to LUCA and can tell us something about how LUCA lived.. Such a small number of genes, of course, would not support life as we know it, and critics immediately latched onto this apparent gene shortage, pointing out that essential components capable of nucleotide and amino acid biosynthesis, for example, were missing. We didnt even have a complete ribosome, admits Martin.. However, their methodology required that they omit all genes that have undergone LGT, so had a ribosomal protein undergone LGT, it wouldnt be included in the list of LUCAs genes. They also speculated that LUCA could have gotten by using molecules in the environment to fill the functions of lacking genes, for example molecules that can synthesize amino acids. After all, says Martin, biochemistry at this early stage in lifes evolution was still primitive and all ...
Biological systems are resistant to perturbations caused by the environment and by the intrinsic noise of the system. Robustness to mutations is a particular aspect of robustness in which the phenotype is resistant to genotypic variation. Mutational robustness has been linked to the ability of the system to generate heritable genetic variation (a property known as evolvability). It is known that greater robustness leads to increased evolvability. Therefore, mechanisms that increase mutational robustness fuel evolvability. Two such mechanisms, molecular chaperones and gene duplication, have been credited with enormous importance in generating functional diversity through the increase of systems robustness to mutational insults. However, the way in which such mechanisms regulate robustness remains largely uncharacterized. In this review, I provide evidence in support of the role of molecular chaperones and gene duplication in innovation. Specifically, I present evidence that these mechanisms ...
Molecular evolution is not based on scientific authority. . . . There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculations. Since no one knows molecular evolution by direct experience, and since there is no authority on which to base claims of knowledge, it can truly be said that . . . the assertion of Darwinian molecular evolution is merely bluster. - quote by Michael Behe on YourDictionary.
One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost one year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over one year in each evolution line. Many majority mutations appeared in more than one evolution line, i.e. our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by ...
Gene duplication and loss are predicted to be at least of the order of the substitution rate and are key contributors to the development of novel gene function and overall genome evolution. Although it has been established that proteins evolve more rapidly after gene duplication, we were interested in testing to what extent this reflects causation or association. Therefore, we investigated the rate of evolution prior to gene duplication in chordates. Two patterns emerged; firstly, branches, which are both preceded by a duplication and followed by a duplication, display an elevated rate of amino acid replacement. This is reflected in the ratio of nonsynonymous to synonymous substitution (mean nonsynonymous to synonymous nucleotide substitution rate ratio [Ka:Ks]) of 0.44 compared with branches preceded by and followed by a speciation (mean Ka:Ks of 0.23). The observed patterns suggest that there can be simultaneous alteration in the selection pressures on both gene duplication and amino acid ...
How does nature make new things that have new functions? How does it make something simple into something more complex? Evolution.. In nature, evolution is manifested in the progression of changes in the genetic composition of all organisms over generations as they adapt to altered living conditions. Researchers have been studying natures process of change for more than a century in a desire to understand it and, in the lab, control or direct evolution at the molecular level at an unprecedented rate.. Molecular evolution (the process of evolution at the DNA, RNA, and protein level) emerged as a field in the 1960s, so its inevitable that the field itself has also evolved.. Over the past 30 years or so, scientists have figured out how to use some of the mechanisms that biology uses for evolution - extracting the tools for evolving molecules out of biological systems and putting them into the hands of laboratory investigators, says M.G. Finn, professor and chair in the School of Chemistry and ...
If you have a question about this talk, please contact Xin Wang.. Differences in the gene regulatory network are hypothesized to contribute significantly to phenotypic divergence between and within species. Non-coding sequences with bursts of lineage-specific changes are promising candidates, because clusters of nearby substitutions are a hallmark of selection potentially modify evolutionarily conserved regulatory elements. Performing a comprehensive, genome-wide analysis, we find that genomic loci with high substitution rates in the human-chimp lineage are over-represented near genes that duplicated in the human-chimp ancestor. We also developed a method to screen for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in non-coding sequences near duplicated loci with accelerated substitution rates. Finally, GC-biased gene conversion (gBGC) is a non-adaptive, recombination-associated explanation for accelerated substitution ...
Abstract: A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects-modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the ...
Page 1 of 5 - Does The E. Coli Long-term Evolution Experiment Evolution - posted in Best all time threads.: The E. Coli long-term evolution experiment is an ongoing study led by Richard Lenski. The study tracks genetic changes in 12 initially nearly identical populations of asexual Escherichia coli bacteria. The experiment started on February 24, 1988 and on February 14, 2010 the populations reached the milestone of 50,000 generations.QUESTIONS:What implications does this study have on the...
Evolution is defined as adapted set of positively favorable changes across successive generations in heritable characteristics of different biological species [1]. It often imposes divergence in the organisms at every evolutionary level, be it genetic or epigenetic [2]. Canalization thus study the genotypic variants contributing to the similar phenotype [3]. Hence irrespective of genotypes, genetic alterations assisting the individuals phenotype solely guides the evolutionary adaptation. In this regard, the molecular clock hypothesis proposed by Zuckerkandl & Pauling [4] seems to be correct. Sarich & Wilson [5,6] also demonstrated the divergence of humans and apes approximately 5 million years ago through the same hypothesis. Evolutionary factors Evolution being highly dimensional phenomenon is almost impossible to explain simply. Even the mathematical analysis fails to correctly track the evolutionary rate in a population [7,8]. While diversions exist for every evolved factor among different ...
The neutral theory of molecular evolution has been instrumental in organizing our thinking about the nature of evolutionary forces shaping variation at the DNA level. More importantly, it has provided empiricists with a strong set of testable predictions and hence, a useful null hypothesis against which to test for the presence of selection. Evidence indicates that the neutral theory cannot explain key features of protein evolution nor patterns of biased codon usage in certain species. Whereas we now have a reasonable model of selection acting on synonymous changes in Drosophila, protein evolution remains poorly understood. Despite limitations in the applicability of the neutral theory, it is likely to remain an integral part of the quest to understand molecular evolution. ...
Transcript of 1963 Macy Conference The Fifth Macy Conference on Genetics, held November 3-6, 1963 at Princeton University, brought together several well-known geneticists of that time period to discuss important issues in population genetics. This conference took place just before the emergence of the field of molecular evolution. Attendees included: Walter Bodmer, James Crow, Everett Dempster, Theodosius Dobzhansky, L.C. Dunn, Barry Falconer, Dick Lewontin, Howard Levene, H.J. Muller, James Neel, Bruce Wallace, and Jack Schull, among others. The format of the conference was short individual presentations followed by an informal free-for-all discussion. Fortunately, a stenographer was present throughout the conference to preserve the interactions of these scientists. We have posted the entire transcript, dividing it up by sessions. Although we have only listed the paper titles, there is extensive discussion and debate among the scientists recorded throughout the transcript. (To get to the Table ... - (Convergent_evolution) CONVERGENT EVOLUTION is the independent evolution of similar features in species of different lineages. CONVERGENT EVOLUTION Convergent evolution creates ANALOGOUS STRUCTURES that have similar form or function but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy
Is the rate of insertion and deletion mutation male-biased? - Molecular evolutionary analysis of avian and primate sex chromosome sequence. ...
Encontre molecular evolution com ótimos preços e condições na Saraiva. Temos Molecular Systematics and Plant Evolution, Molecular Evolution and Phylogenetics e muito mais.
TY - JOUR. T1 - Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution. AU - Gojobori, Jun. AU - Tang, Hua. AU - Akey, Joshua M.. AU - Wu, Chung I.. PY - 2007/3/6. Y1 - 2007/3/6. N2 - The selective forces acting on amino acid substitutions may be different in the two phases of molecular evolution: polymorphism and fixation. Negative selection and genetic drift may dominate the first phase, whereas positive selection may become much more significant in the second phase. However, the conventional dichotomy of synonymous vs. nonsynonymous changes does not offer the resolution needed to study the dynamics of these two phases. Following previously published methods, we separated amino acid changes into 75 elementary types (1-bp substitution between their respective codons). The likelihood of each type of amino acid change becoming polymorphic (PI, which stands for polymorphic index), relative to synonymous changes, can then be ...
Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli Caroline B. Turner, Zachary D. Blount, Daniel H. Mitchell, Richard E. Lenski doi: Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the…
Abstract A protein domain is a well-defined region within a protein that performs a specific function. Thus duplication of a protein domain may enhance the function of the protein. The fact that many extant proteins contain duplicated domains suggests that present-day complex proteins have evolved from simple proteins mainly via domain duplication.
The ratio of non-synonymous to synonymous substitutions, known as the Ka/Ks ratio,is used to estimate both purifying and positive Darwinian selection.A Ka/Ks ratio significantly greater than 1 is indicative of positive selection, whereas values significantly smaller than 1 are indicative of purifying selection.We present an algorithmic web-based tool which calculates the Ka/Ks ratio for each codon site in a codon-based multiple sequence alignment (Doron-Faigenboim et al. 2005;Stern et al.2006).Selecton implements both an empirical Bayesian algorithm (Yang et al.2000)as well as a maximum-likelihood algorithm (Goldman and Yang 1994),which the user may choose (the default algorithm is the Bayesian one).On the one hand,through its user-friendly interface Selecton enables simplicity of use for non-expert users.The minimal input to the server consists of merely a file of homologous DNA coding sequences.On the other hand,Selecton further implements a wide variety of user options which enable maximal ...
We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods. ...
The rapid accumulation of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the new genomes. To avoid informational overflow from the constant influx of new genome sequences, a comprehensive evolutionary classification of the genes from all sequenced genomes is required. Such classifications are based on two fundamental notions from evolutionary biology: orthology and paralogy, which describe the two fundamentally different types of homologous relationships between genes [1-4]. Orthologs are homologous genes derived by vertical descent from a single ancestral gene in the last common ancestor of the compared species. Paralogs, in contrast, are homologous genes, which, at some stage of evolution of the respective gene family, have evolved by duplication of an ancestral gene. The notions of orthology and paralogy are intimately linked because, if a duplication (s) occurred after the speciation event that separated the ...
MBLs Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of ...
MBLs Workshop on Molecular Evolution is the most prestigious workshop serving the field of evolutionary studies. Founded in 1988, it is the longest-running workshop if its kind, and it has earned worldwide recognition for its rich and intensive learning experience. Students work closely with internationally-recognized scientists, receiving (i) high-level instruction in the principles of molecular evolution and evolutionary genomics, (ii) advanced training in statistical methods best suited to modern datasets, and (iii) hands-on experience with the latest software tools (often from the authors of the programs they are using). The material is delivered via lectures, discussions, and bioinformatic exercises motivated by contemporary topics in molecular evolution. A hallmark of this workshop is the direct interaction between students and field-leading scientists. The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of ...
Why some individuals develop AIDS rapidly whereas others remain healthy without treatment for many years remains a central question of HIV research. An evolutionary perspective reveals an apparent conflict between two levels of selection on the virus. On the one hand, there is rapid evolution of the virus in the host, and on the other, new observations indicate the existence of virus factors that affect the virulence of infection whose influence persists over years in infected individuals and across transmission events. Here, we review recent evidence that shows that viral genetic factors play a larger role in modulating disease severity than anticipated. We propose conceptual models that reconcile adaptive evolution at both levels of selection. Evolutionary analysis provides new insight into HIV pathogenesis.. ...
Although positive selection has been detected in many genes, its overall contribution to protein evolution is debatable. If the bulk of molecular evolution is neutral, then the ratio of amino-acid (A) to synonymous (S) polymorphism should, on average, equal that of divergence. A comparison of the A/ …
Packing flaws create sticky, interactive proteins that spread in small populations. Over four billion years of evolution, plants and animals grew far more complex than their single-celled ancestors. But a new comparison of proteins shared across species finds that complex organisms, including humans, have accumulated structural weaknesses that may have actually launched the long journey from microbe to man.. The study, published in Nature, suggests that the random introduction of errors into proteins, rather than traditional natural selection, may have boosted the evolution of biological complexity. Flaws in the packing of proteins that make them more unstable in water could have promoted protein interactions and intracellular teamwork, expanding the possibilities of life.. Everybody wants to say that evolution is equivalent to natural selection and that things that are sophisticated and complex have been absolutely selected for, said study co-author Ariel Fernández, PhD, a visiting ...
On the Evolution of Species was published in the year 1859 and it went on to becoming one of the most influential books of the time. The theory came to be widely accepted by the scientific community and overthrew many other popular streams of thought and Philosophy on evolution. Many of these theories had theological bases. The strong scientific backing of Darwins ideas convinced most people about the soundness of his theory. Although as the body of scientific knowledge grew and more and more data on obscure species emerged, the Darwinian thought has been challenged more than once, the theory of evolution remains the single most important thought behind our attempts to explain our evolution on this planet. Today there are groups of scientists who have put Darwin in the perspective of genes, namely have explained or tried to the evolution of species in terms of genetics. This new breed of Darwinism has come to be known as Neo-Darwinism. Richard Dawkins is arguably the most well-known and witty ...
TY - JOUR. T1 - Molecular evolution of a developmental pathway. T2 - Phylogenetic analyses of transforming growth factor-β family ligands, receptors and Smad signal transducers. AU - Newfeld, Stuart. AU - Wisotzkey, Robert G.. AU - Kumar, Sudhir. PY - 1999/6/1. Y1 - 1999/6/1. N2 - Intercellular signaling by transforming growth factor-β (TGF-β) proteins coordinates developmental decisions in many organisms. A receptor complex and Smad signal transducers are required for proper responses to TGF- β signals. We have taken a phylogenetic approach to understanding the developmental evolutionary history of TGF-β signaling pathways. We were interested in detecting evolutionary influences among the physically interacting multigene families encoding TGF-β ligands, receptors, and Smads. Our analyses included new ligands and Smads identified from genomic sequence as well as the newest published family members. From an evolutionary perspective we find that (I) TGF-β pathways do not predate the ...
The significance of N-glycosylation of the TGF-β-type ligands has been studied previously. For example, N-glycosylation of the BMP2 prodomain affects the folding and secretion of ligands, and non-glycosylated BMP2 and BMP6 produced in bacterial cells appear to be less active than the glycosylated ligands (Schmoekel et al., 2004; Saremba et al., 2008; van de Watering et al., 2012; Hang et al., 2014). Addition of an N-glycosylation motif in Nodal changes the stability of ligands, resulting in an increased signaling range (Le Good et al., 2005). These facts suggest that N-glycosylation of ligands may play significant roles in vivo. However, these roles have been largely unexplored because of a lack of in vivo model systems. By employing both in vivo studies and cell-based experiments, we investigated how N-glycosylation modifications of the BMP-type ligands impact developmental processes. The in vivo rescue experiments revealed that these motifs are crucial for fly viability and are required to ...
The global effects of epistasis on protein and RNA function are revealed by an unsupervised model of amino acid co-conservation in evolutionary sequence variation. Many high-throughput experimental technologies have been developed to assess the effects of large numbers of mutations (variation) on phenotypes. However, designing functional assays for these methods is challenging, and systematic testing of all combinations is impossible, so robust methods to predict the effects of genetic variation are needed. Most prediction methods exploit evolutionary sequence conservation but do not consider the interdependencies of residues or bases. We present EVmutation, an unsupervised statistical method for predicting the effects of mutations that explicitly captures residue dependencies between positions. We validate EVmutation by comparing its predictions with outcomes of high-throughput mutagenesis experiments and measurements of human disease mutations and show that it outperforms methods that do not account
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBIs GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions drawn about DA evolution of
When the coding regions of 11 genes from rodents (mouse or rat) and man are compared with those from another mammalian species (usually bovine), it is found that rodents evolve significantly faster than man. The ratio of the number of nucleotide substitutions in the rodent lineage to that in the human lineage since their divergence is 2.0 for synonymous substitutions and 1.3 for nonsynonymous substitutions. Rodents also evolve faster in the 5 and 3 untranslated regions of five different mRNAs; the ratios are 2.6 and 3.1, respectively. The numbers of nucleotide substitutions between members of the beta-globin gene family that were duplicated before the man-mouse split are also higher in mouse than in man. The difference is, again, greater for synonymous substitutions than for nonsynonymous substitutions. This tendency is more consistent with the neutralist view of molecular evolution than with the selectionist view. A simple explanation for the higher rates in rodents is that rodents have ...
Life: The Science of Biology 11th Edition answers to Chapter 23 - Evolution of Genes and Genomes - 23.4 - Molecular Evolution Has Many Practical Applications - 23.4 Recap - Learning Outcomes - Page 504 3 including work step by step written by community members like you. Textbook Authors: Sadava, David E.; Hillis, David M.; Heller, H. Craig; Hacker, Sally D. , ISBN-10: 1-31901-016-4, ISBN-13: 978-1-31901-016-4, Publisher: W. H. Freeman
Key innovations in the history of life are often caused by the acquisition of a qualitatively new trait that is an evolutionary novelty which allows the exploitation of new resources or habitats and thus triggers an adaptive radiation. Such innovations are typically rare and difficult to predict because they result from complex nonadditive (i.e., epistatic) genetic interactions or ecological interactions, within or between species, that develop only over the course of long evolutionary trajectories. Evolution of a new trait can be conceptually divided into three steps: potentiation, actualization, and refinement. First, one or more potentiating events may be necessary to generate a genetic background or environmental conditions that make a new trait accessible to evolution. Genetic potentiation, for example, may involve a period of nonadaptive genetic drift wherein a phenotype stays constant or the accumulation of mutations that are immediately advantageous for reasons unrelated to the new ...
While the theory of descent with modification in the broad sense is supported, the conventional paradigm that the history of life maps as the tree of life-a tree beginning with one universal common ancestor as the trunk and then progressively branching, with modern species at the twig ends-is being re-drawn at both the base of the trunk and the branches. These revisions arise as scientists gain more understanding about the hidden world of microbes (unicellular organisms and viruses).. The great diversity, abundance, and ubiquity of the single-celled organisms (bacteria, archaea, and some protists) has gained widespread recognition in recent years, and considerable progress has been made in incorporating that knowledge into the story of evolution. In contrast, the place of viruses in the story of evolution remains much more speculative.. There are proposals that the tree of life instead of being simple at its base, may be considerably more complex. Sequencing the genomes of specific organisms ...
Author Summary The relationship between morphological and molecular evolution is a central issue to the understanding of eukaryote evolution. In particular, there is much interest in how duplicate genes have contributed to morphological diversification during evolution. As a mechanism of functionalization of duplicate genes, differentiation of both gene expression and protein function are believed to be important. Although it has been reported that both expression and protein divergence tend to increase as a duplication ages, it is unclear whether expression or protein divergence in duplicate genes is greater in those genes that have undergone functionalization compared with those that have not. Here, we studied 492 duplicate gene pairs associated with various degrees of morphological diversification in Arabidopsis thaliana. Using these data, we found that the divergence of both expression and protein sequence were important sources for morphological diversification of duplicate genes. Although both
TY - JOUR. T1 - Photoemission study of electronic structure evolution across the metalinsulator transition of heavily B-doped diamond. AU - Okazaki, H.. AU - Arakane, T.. AU - Sugawara, K.. AU - Sato, T.. AU - Takahashi, T.. AU - Wakita, T.. AU - Hirai, M.. AU - Muraoka, Y.. AU - Takano, Y.. AU - Ishii, S.. AU - Iriyama, S.. AU - Kawarada, H.. AU - Yokoya, T.. N1 - Funding Information: This work was supported partly by a Grant-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science, and Technology, Japan ( 20340091 ). PY - 2011/5. Y1 - 2011/5. N2 - We studied the electronic structure evolution of heavily B-doped diamond films across the metalinsulator transition (MIT) using ultraviolet photoemission spectroscopy (UPS). From higherature UPS, through which electronic states near the Fermi level (EF) up to ∼5kBT can be observed (kB is the Boltzmann constant and T the temperature), we observed the carrier concentration dependence of spectral shapes near EF. Using ...
Proteins often differ in amino-acid sequence across species. This difference has evolved by the accumulation of neutral mutations by random drift, the fixation of adaptive mutations by selection, or a mixture of the two. Here we propose a simple statistical test of the neutral protein evolution hypothesis based on a comparison of the number of amino-acid replacement substitutions to synonymous substitutions in the coding region of a locus. If the observed substitutions are neutral, the ratio of replacement to synonymous fixed differences between species should be the same as the ratio of replacement to synonymous polymorphisms within species. DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC in three species in the Drosophila melanogaster species subgroup do not fit this expectation; instead, there are more fixed replacement differences between species than expected. We suggest that these excess replacement substitutions result from adaptive fixation of selectively ...
Gene duplication provide a means to evolve novel biological functions and changes in protein functions may then provide different evolutionary constraints on duplicated genes. Functional divergence of a protein family can occur after major evolutionary events such as gene duplication or speciation. Some of them result in different evolutionary rates at certain amino acid residues, which is termed type I functional divergence [33, 34]. To estimate functional divergence in the vertebrate anoctamin family, we have conducted pair-wise functional divergence analysis between anoctamin paralogous genes using DIVERGE [35]. Table 1 shows the coefficient of functional divergence (θ) of pair-wise comparisons between the members of the anoctamin family. All comparisons showed θ , 0 with p , 0.05, suggesting that a site-specific rate shift after gene duplication is a common phenomenon in the evolution of the anoctamin family. Further analysis was subsequently focused on ano1/ano2, and ano1/ano4. Amino ...
An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for
The known functions of RNA structures have expanded of late, such that RNA is considered a more active player in molecular biology. The presence of RNA secondary structure in a sequence should constrain evolution of its constituent nucleotides because of the requirement to maintain the base-pairing regions in the structure. In a previous work, we found support for this hypothesis in nine molecules from various organisms, the exception being a structure found in a protein-coding region of the HIV-1 genome. In this work, I examine the interaction of constraints imposed by RNA structures and host-induced hypermutation on molecular evolution in HIV-1. I conclude that RNA structures in HIV do evolve via compensatory evolution, but that hypermutation can obscure the expected signal. Since RNAs known roles have increased, so have the methods for identification and prediction of RNA structures in genetic sequence. I use a method adapted for searching in multiple coding regions to identify conserved RNA ...
Any change in the molecular structure is harmful. The origins of the neutral theory of molecular evolution Michael R. Dietrich 1 Journal of the History of Biology volume 27 , pages 21 - 59 ( 1994 ) Cite this article 1983. Hubbells original model has been extensively tested, and maximum likelihood techniques have added a rigorous backbone to the estimation of neutral model parameters. Alternatively, molecular evolution may be mainly driven by natural selection. He is most known as an advocate of the, International Encyclopedia of the Social & Behavioral Sciences. Darwins core insight was that organisms with disadvantageous traits would slowly be weeded out through negative (or purifying) selection, while those with advantageous features would reproduce more often and pass those features on to the next generation (positive selection). Motoo Kimura, as founder of the neutral theory, is uniquely placed to write this book. As such, these models can detect positive selection at individual sites only ...
Adaptive protein evolution at the Adh locus in Drosophila.: Proteins often differ in amino-acid sequence across species. This difference has evolved by the accu
Certain techniques of molecular evolution - the generation and selection of functional molecules using biological mechanisms in the test tube - are well established, but still only used by laboratories expert in the art. Principal examples include directed evolution, SELEX, and yeast, bacterial and phage surface display selection methods. These techniques provide access to peptides and polynucleotides with an enormous range of properties. Many labs at Tech (and everywhere else) often want to gain access to these tools, but make do without them because it is too difficult and time consuming to get started.. The Molecular Evolution Core Facility is housed in two convenient locations for researchers across the biotechnology campus at Georgia Tech. One is an 800-sq.-ft. suite on the second floor of the Krone Engineered Biosystems Building and another is a multi-functional lab on the third floor of the Petit H. Parker Institute of Bioengineering and Bioscience building . The purpose of the facility ...
1. BaackEJ. WhitneyKD. RiesebergLH. 2005 Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species. New Phytol 167 623 630. 2. GregoryTR. 2005 The evolution of the genome. Amsterdam Elsevier. 3. GregoryTR. NicolJA. TammH. KullmanB. KullmanK. 2007 Eukaryotic genome size databases. Nucleic Acids Res 35 D332 D338. 4. Center for Biological Sequence Analysis 2010 Genome Atlas Database. Lyngby, Denmark Technical University of Denmark 5. LynchM. 2007 The origins of genome architecture. Sunderland, , Massachusetts, USA Sinauer Associates. 6. LynchM. 2007 The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA 104 8597 8604. 7. LynchM. ConeryJS. 2003 The origins of genome complexity. Science 302 1401 1404. 8. BennettMD. LeitchIJ. 2005 Genome size evolution in plants. GregoryTR. The evolution of the genome Amsterdam Elsevier 89 162. 9. ...
Ancestral reconstruction (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the ...
Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of
Gene loss pattern after teleost-specific whole genome duplication. Figure 2. Gene loss pattern after teleost-specific whole genome duplication.. A: Species tree showing major vertebrate groups and their evolutionary relationships.. B: The comparison of genomes between two species with the coloured lines showing corresponding genes between human and medaka (upper circle) and between zebrafish and medaka (lower circle). The structure is quite different between human and medaka, while it is similar between zebrafish and medaka.. C: Gene loss pattern showing the two-phase loss of duplicate genes in teleost fishes. A and C use the same timeline.. The results of this study suggest that approximately 80% of the duplicate genes were lost in the first 60 million years after the whole genome duplication event (Fig. 2C). Considering that the first vertebrates appeared on Earth about 500 million years ago (Fig. 2A), 60 million years is a very short time. Dr Inoue states that it is possible that genome ...
In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific
The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases ...
TY - JOUR. T1 - Molecular evolutionary rates of oncogenes. AU - Gojobori, Takashi. AU - Yokoyama, Shozo. PY - 1987/11/1. Y1 - 1987/11/1. N2 - Using nine sets of viral and cellular oncogenes, the rates of nucleotide substitutions were computed by using Gojobori and Yokoyamas (1985) method. The results obtained confirmed our previous conclusion that the rates of nucleotide substitution for the viral oncogenes are about a million times higher than those for their cellular counterparts. For cellular oncogenes and most viral oncogenes, however, the rate of synonymous substitution is higher than that of nonsynonymous substitution. Moreover, the pattern of nucleotide substitutions for viral oncogenes is more similar to that for functional genes (such as cellular oncongenes) than for pseudogenes. This implies that nucleotide substitutions in viral oncogenes may be functionally constrained. Thus, our observation supports that nucleotide substitutions for the oncogenes in those DNA and RNA genomes are ...
How does nature make new things that have new functions? How does it make something simple into something more complex? Evolution.. In nature, evolution is manifested in the progression of changes in the genetic composition of all organisms over generations as they adapt to altered living conditions. Researchers have been studying natures process of change for more than a century in a desire to understand it and, in the lab, control or direct evolution at the molecular level at an unprecedented rate.. Molecular evolution (the process of evolution at the DNA, RNA, and protein level) emerged as a field in the 1960s, so its inevitable that the field itself has also evolved.. Over the past 30 years or so, scientists have figured out how to use some of the mechanisms that biology uses for evolution - extracting the tools for evolving molecules out of biological systems and putting them into the hands of laboratory investigators, says M.G. Finn, professor and chair in the School of Chemistry and ...
From millions of real job salary data. Foundation For Applied Molecular Evolution Postdoctoral Associate salary data. Average Foundation For Applied Molecular Evolution Postdoctoral Associate salary is Detailed Foundation For Applied Molecular Evolution Postdoctoral Associate starting salary, median salary, pay scale, bonus data report
Biologists have long noted the tremendous diversity of behaviors, morphological traits and molecules involved in mating and reproduction. In this thesis, I investigate the molecular evolution of reproductive proteins in the vinegar fly Drosophila melanogaster, focusing on a class of ejaculate proteins known as accessory gland proteins (?Acps?). Previous work has documented extensive evidence for rapid, adaptive evolution of some Acps. It is generally thought that male-female interactions, e.g., sexual conflict and cryptic female choice, drive rapid Acp evolution, although evidence specifically favoring this hypothesis in D. melanogaster is limited. Here, I describe biochemical and structural studies on a particularly rapidly evolving Acp, ovulin. I argue that structural features of ovulin may contribute to its ability to tolerate high sequence diversity. I also investigate the molecular evolution of a class of Acps and female reproductive tract proteins that (I argue) are particularly likely to ...
BACKGROUND: Although homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species. RESULTS: Recombination rate is negatively correlated with genome size, which is likely caused by the ...
Molecular evolution is the process of evolution at the scale of DNA, RNA and proteins. Our goal was to study molecular evolution of viruses with special reference to Influenza A Virus. The recent Influenza A/H1N1(2009) outbreak has been the focus of intense research because of its high level of infectivity across the globe. Analysis of nucleotide sequence polymorphism in the genomic segments encoding the two most immunologically important proteins of influenza A, neuraminidase (NA) and hemagglutinin (HA), showed that the H1N1 (2009) has resulted from the spread of an HA segment of recent origin and low diversity through a population of ancient and much more diverse NA segments. We also studied about the selection pattern of CTL epitope and CTL non-epitope regions of different proteins of Influenza and found that natural selection is the main pattern of selection with epitope regions being more conserved than non-epitope regions. This dissertation also focuses on implementation of a methodology to study
Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do
Models of molecular evolution that incorporate the ratio of nonsynonymous to synonymous polymorphism (dN/dS ratio) as a parameter can be used to identify sites that are under diversifying selection or functional constraint in a sample of gene sequences. However, when there has been recombination in the evolutionary history of the sequences, reconstructing a single phylogenetic tree is not appropriate, and inference based on a single tree can give misleading results. In the presence of high levels of recombination, the identification of sites experiencing diversifying selection can suffer from a false-positive rate as high as 90%. We present a model that uses a population genetics approximation to the coalescent with recombination and use reversible-jump MCMC to perform Bayesian inference on both the dN/dS ratio and the recombination rate, allowing each to vary along the sequence. We demonstrate that the method has the power to detect variation in the dN/dS ratio and the recombination rate and does not
Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing lateral gene transfer. When Jonathan Eisen originally coined phylogenomics, it applied to prediction of gene function. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. When several genes with similar ...
Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing these models via flux balance analysis (FBA) cannot predict many evolutionary outcomes including adaptive diversification, whereby an ancestral lineage diverges to fill multiple niches. Here we combine in silico evolution with FBA and apply this modelling framework, evoFBA, to a long-term evolution experiment with Escherichia coli. Simulations predicted the adaptive diversification that occurred in one experimental population and generated hypotheses about the mechanisms that promoted coexistence of the diverged lineages. We experimentally tested and, on balance, verified these mechanisms, showing that diversification involved niche construction and character displacement through differential nutrient uptake and altered metabolic regulation. The evoFBA framework represents a promising new way to
Symposium: Genome Evolution in Microbial Eukaryotes June 2nd, Smithfield Rhode Island To elucidate principles of eukaryotic genome evolution, we must increase studies of microbial eukaryotes. The bulk of eukaryotic diversity is microbial yet our current knowledge of eukaryotic genome evolution comes largely from studies of plants, animals and fungi. Our intention in this one-day symposium is to highlight recent achievements in understanding the diversity of eukaryotic genomes, and to expose relevant researchers to advances in techniques for both data acquisition and data analysis. Speakers and titles appear below. Travel funds are available for undergraduates, graduate students and postdocs. These funds will offset costs of those currently working on molecular evolution/genomics of microbial eukaryotes, and those switching into the field. Students and postdocs are encouraged to bring a poster of their work. For more information, visit: ...
Often after natural selection increases the frequency of beneficial alleles in an evolving species, it then maintains the high frequency of these alleles by rejecting harmful or less beneficial alleles. This transformation of positive selection into purifying selection (35) is more likely to occur at nonsynonymous sites than at synonymous sites, where theory predicts synonymous substitutions steadily accumulate over time. Thus, considering the many millions of years of time involved in the descent of the elephant or tenrec lineage (about 78 Ma) and the human or mouse lineage (about 91 Ma), it is not surprising that ,1.4% of the thousands of genes examined have dN/dS ,1 (Table S4) and that the percentage of such likely positively selected genes is smallest for mouse (0.12%). To increase our chances of detecting gene sets that were likely targets of positive selection, we examined by the functional annotation clustering tool (30) the 5% of RefSeqs (389) with the more elevated dN/dS ratios, these ...
Sex chromosomes have evolved from non-sex-determining chromosomes (autosomes) many times throughout the tree of life. Ever since their discovery, these chromosomes have captivated researchers because of their obvious involvement in fundamental aspects of an organisms life, such as sex determination, sexual reproduction and sexual conflicts. Despite this long-lasting fascination, their biology remains unclear in several central aspects, in particular regarding their almost ubiquitous evolution of recombination cessation and impoverished gene content, and the multifaceted consequences thereof. This lack of detailed knowledge about sex chromosome evolution compromises our understanding of fundamental biological questions (e.g. the evolution of sexual conflicts) as well as more practical ones (e.g. about sex-linked genetic diseases).. Our research focuses mainly on Sylvioidea passerine birds where we have recently detected a new sex chromosome, a neo-sex chromosome, which has been formed by a ...
TY - JOUR. T1 - Molecular evolution of aerobic energy metabolism in primates. AU - Grossman, Lawrence I.. AU - Schmidt, Timothy R.. AU - Wildman, Derek E.. AU - Goodman, Morris. PY - 2001. Y1 - 2001. N2 - As part of our goal to reconstruct human evolution at the DNA level, we have been examining Changes in the biochemical machinery for aerobic energy metabolism. We find that protein subunits of two of the electron transfer complexes, complex III and complex IV, and cytochrome c, the protein carrier that connects them, have all undergone a period of rapid protein evolution in the anthropoid lineage that ultimately led to humans. Indeed, subunit IV of cytochrome c oxidase (COX; complex IV) provides one of the best examples of positively selected changes of any protein studied. The rate of subunit IV evolution accelerated in our catarrhine ancestors in the period between 40 to 18 million years ago and then decelerated in the descendant hominid lineages, a pattern of rate changes indicative of ...
Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.
The powerful pressures of sexual and natural selection associated with species recognition and reproduction are thought to manifest in a faster rate of evolution in sex-biased genes, an effect that has been documented particularly for male-biased genes expressed in the reproductive tract. However, little is known about the rate of evolution for genes involved in sexually dimorphic behaviors, which often form the neurological basis of intrasexual competition and mate choice. We used microarray data, designed to uncover sex-biased expression patterns in embryonic chicken brain, in conjunction with data on the rate of sequence evolution for ,4,000 coding regions aligned between chicken and zebra finch in order to study the role of selection in governing the molecular evolution for sex-biased and unbiased genes. Surprisingly, we found that female-biased genes, defined across a range of cutoff values, show a higher rate of functional evolution than both male-biased and unbiased genes. Autosomal ...
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of
The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in ...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (, a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic ...
Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively
It is widely accepted that during vertebrate evolution two whole genome duplication (WGD) events occurred, followed by another in the lineage leading to teleosts (Amores et al., 1998; Dehal and Boore, 2005; Holland et al., 1994; Ohno et al., 1968; Taylor et al., 2003; Wittbrodt and Schartl, 1998). These events coincided with a rapid expansion in organismal complexity particularly in teleosts, a lineage that constitutes half of extant vertebrates. The persistence of many duplicate genes after these WGD events forms the basis of the duplication-degeneration-complementation (DDC) model of gene evolution (Force et al., 1999). The DDC model predicts that at least some aspects of ancestral gene function are sub-partitioned between duplicate genes in a complementary manner, such that each copy remains indispensable. At the same time, redundancy of associated cis-regulatory elements may increase the evolvability of these sequences (Jimenez-Delgado et al., 2009) and their potential to direct novel gene ...
Maternal RNAs play a critical role in early development. Variation in the diversity and levels of maternally derived gene transcripts may be central to the origin of phenotypic novelty -- a longstanding problem in evolution and development. By studying maternal transcriptomes within and between divergent species, a better understanding of the evolutionary forces acting on maternal RNA allocation is possible. We present the first maternal transcriptome of the red flour beetle, Tribolium castaneum. Using a tiled whole-genome microarray, we found that 58.2% of T. castaneum genes are maternally loaded into eggs. Comparison of known Drosophila melanogaster maternal genes to our results showed widespread conservation of maternal expression with T. castaneum. Additionally, we found that many genes previously reported as having sex or tissue specific expression in T. castaneum were also maternally loaded. Identification of such pleiotropy is vital for proper modeling and testing of evolutionary theory using
Background Comparative approaches using protostome and deuterostome data have greatly contributed to understanding gene function and organismal complexity. The family 2 G-protein coupled receptors (GPCRs) are one of the largest and best studied hormone and neuropeptide receptor families. They are suggested to have arisen from a single ancestral gene via duplication events. Despite the recent identification of receptor members in protostome and early deuterostome genomes, relatively little is known about their function or origin during metazoan divergence. In this study a comprehensive description of family 2 GPCR evolution is given based on in silico and expression analyses of the invertebrate receptor genes. Results Family 2 GPCR members were identified in the invertebrate genomes of the nematodes C. elegans and C. briggsae, the arthropods D. melanogaster and A. gambiae (mosquito) and in the tunicate C. intestinalis. This suggests that they are of ancient origin and have evolved through ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...
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"Molecular Phylogenetics and Evolution. 70: 402-411. doi:10.1016/j.ympev.2013.08.008. ISSN 1095-9513. PMID 23994490.. ... "Frontiers in Ecology and Evolution. 5. doi:10.3389/fevo.2017.00025. ISSN 2296-701X.. ... McCracken, Kevin G.; Johnson, William P.; Sheldon, Frederick H. (2001). "Molecular population genetics, phylogeography, and ... Molecular Ecology (published January 2013). 22 (1): 41-55. doi:10.1111/mec.12098. PMID 23110616.. ...
Hasegawa, Masami (2017). "Phylogeny mandalas for illustrating the Tree of Life". Molecular Phylogenetics and Evolution. 117: ... Cowen, Painton (2005). The Rose Window, London and New York, (offers the most complete overview of the evolution and meaning of ...
Molecular Biology and Evolution. 28 (1): 407-22. doi:10.1093/molbev/msq209. PMID 20702568.. ... Molecular structureEdit. The 154 kb chloroplast DNA map of a model flowering plant (Arabidopsis thaliana: Brassicaceae) showing ... "Genome Biology and Evolution. 10 (10): 2669-2571. doi:10.1093/gbe/evy189. PMC 6166771. PMID 30165616.. ... Alberts B (2002). Molecular biology of the cell (4. ed.). New York [u.a.]: Garland. ISBN 978-0-8153-4072-0. .. ...
Molecular Phylogenetics and Evolution 40: 389-399. doi:10.1016/j.ympev.2006.02.021 PMID 16635580 (HTML abstract) ... Systematics and evolutionEdit. Although not well known from fossils, the evolution of piculets is now considered rather ... Molecular dating, calibrated with geographic events in the absence of a good fossil record, points at the Late Miocene, c. 8 ... Fuchs, J.; Ohlson, J. I.; Ericson, Per G. P. & Pasquet, E. (2006): Molecular phylogeny and biogeographic history of the ...
Distinguished for his work on molecular evolution, in particular on the role of stochastic events in determining the rate of ... This means evolution, population biology, organismal biology and biological diversity. It was first awarded in 1890. It comes ... They have combined molecular and genetic approaches to answer some of Darwins key questions about the natural variation of ... for their fundamental work on the ecology, breeding and evolution of Darwin's finches on the Galapagos islands. This work has ...
"Human Evolution (Netherlands: Springer) 3 (4): 297-308. ISSN (Print) 1824-310X (Online) 0393-9375 (Print) 1824-310X (Online). ... Russo J, Russo I (1987). "Biological and molecular bases of mammary carcinogenesis". Laboratory Investigation 57 (2): 112-37. ...
Evolution. Further information: Evolution of cephalopods. Fossil history and phylogeny. Cephalopods have existed for 500 ... The California two-spot octopus has had its genome sequenced, allowing exploration of its molecular adaptations.[151] Having ... Hence, greater transcriptome plasticity has come as the cost of slower genome evolution. High levels of RNA editing do not ... Strugnell, J.; Nishiguchi, M. K. (2007). "Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from ...
The brolga was formerly placed in the genus Grus but a molecular phylogenetic study published in 2010 found that the genus, as ... Evolution. *Origin of birds. *Origin of flight. *Evolution of birds. *Darwin's finches ... This was further confirmed by molecular studies of their DNA.[6] These also showed that the brolga is more closely related to ...
The evolution of stalk positioning in the Caulobacter cladeEdit. Diverse positioning of the stalks. Caulobacter crescentus ( ... "Journal of Molecular Biology. 409 (1): 28-35. doi:10.1016/j.jmb.2011.02.041. PMC 3108490. PMID 21371478.. ... Detailed study of the molecular development of these cells as they progress through the cell cycle has enabled researchers to ... The "housekeeping" metabolic and catabolic subsystems provide the energy and the molecular raw materials for protein synthesis ...
... and the development of techniques in molecular biology, evolution, and genetics are influencing medical technology, practice ... Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the ... Many modern molecular tests such as flow cytometry, polymerase chain reaction (PCR), immunohistochemistry, cytogenetics, gene ... Genomics and knowledge of human genetics and human evolution is having increasingly significant influence on medicine, as the ...
Evolution[change , change source]. Evidence on their evolution comes from comparative anatomy, the fossil record and molecular ...
The evolution of bird-dispersed pines. Evolutionary Ecology 4: 185-219 *^ a b "South Island wilding conifer strategy". ... A new classification and linear sequence based on molecular data can be found in an article by Christenhusz et al.[7] ... a b c Henry, R.J.(2005) Plant Diversity and evolution. London: CABI. ... Phylogeny of the Pinophyta based on cladistic analysis of molecular data.[5] ...
"Genome Biology and Evolution. 6 (4): 974-980. doi:10.1093/gbe/evu071. ISSN 1759-6653. PMC 4007541 . PMID 24709562.. ... Studies of the genomic organization and of the molecular phylogeny have shown that the nucleomorph of the cryptomonads used to ... Archibald, John M (2007). "Nucleomorph Genomes: Structure, Function, Origin and Evolution". BioEssays. 29 (4): 392-402. doi: ...
... is dedicated to bringing Darwins dream within grasp - to have fairly true genealogical ... Special issues published in Molecular Phylogenetics and Evolution. * 25th Anniversary Issue of Molecular Phylogenetics and ... understanding of the mechanisms and processes of molecular evolution should lead to more accurate models of molecular evolution ... Molecular Phylogenetics and Evolution is dedicated to bringing Darwins dream within grasp - to have fairly true genealogical ...
Molecular All life on Earth [1] is cellular and uses DNA to store genetic information. However, evidence suggests that, on ... Evolution, Molecular Genetics Copyright Genetics Society of America. Evolution, Molecular. All life on Earth is cellular and ... "Directed Molecular Evolution." Scientific American 267 (Dec. 1992): 90-97. Orgel, Leslie E. "Molecular Replication." Nature 358 ... According to the neutral mutation theory of molecular evolution, the variability at the molecular level which results from ...
Molecular evolution. Evolution, at the molecular level, is observableas nucleotide changes in the DNA and amino acid changes in ... In the evolution of modern species, there have been millions of molecular changes. Natural selection and neutral drift could ...
Evolution and the Molecular Revolution, on Friday at UCLA.An international roster of ... New discoveries about the molecular bases of the evolution of life will be explored in a one-day symposium, ... New discoveries about the molecular bases of the evolution of life will be explored in a one-day symposium, "Evolution and the ... how the molecular revolution began, biomedical research and genes, sequences and other molecular clues to the history of life. ...
The neutralist view of evolution suggests that, of all these possible molecules, the great majority would fail to carry oxygen ... Evolution consists of the substitution of one variant for another when the environment changes. ... What we observe as evolution consists of shuffling round within this limited set of equivalent sequences. ...
... "molecular evolution." The molecular evolution of an organism can be very different from its morphological (body features) ... Two hypotheses have been put forward to explain these molecular changes. One hypothesis suggests that most molecular evolution ... We can observe molecular evolution in DNA, and also in amino acid changes in proteins. This table (page 4 of the document) ... Credits: From The Neutral Theory of Molecular Evolution, by Motoo Kimura. Reprinted with the permission of Cambridge University ...
Molecular evolution. [Wen-Hsiung Li] -- This book represents the authors effort to provide a synthesis of the exciting ... developments in molecular evolution in the past two decades. It describes the dynamics of evolutionary change at the ... ... molecular> # Evolution, Molecular a schema:Intangible ;. schema:name "Evolution, Molecular"@en ;. . ... Molecular evolution a schema:Intangible ;. schema:name "Molecular evolution"@en ;. . ...
... do14 David_A_OBROCHTA at UMAIL.UMD.EDU Tue Oct 18 14:47:33 EST 1994 *Previous message: Marine molecular ... Postdoctoral Research Fellow In Molecular Evolution Dr. David OBrochta, University of Maryland Biotechnology Institute, Center ... wishes to sponsor highly qualified recent Ph.D.s interested in applying for a postdoctoral fellowships in Molecular Evolution ... OBrochtaUs laboratory is adjacent to a large molecular systematics laboratory ion of DNA from know species of heliothines is ...
... Howard Lasker biolask at Tue Oct 18 08:34:00 EST 1994 *Previous message: ... Speciation in abalone is linked to the molecular evolution of sperm lysin. Steven Palumbi - University of Hawaii Evolution of ... Dear Colleague, We are organizing a Keystone Symposium entitled, Molecular Approaches to Marine Ecology and Evolution. The ... MOLECULAR APPROACHES TO MARINE ECOLOGY AND EVOLUTION INTRODUCTION Howard R. Lasker - SUNY at Buffalo Introductory remarks - ...
With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and ... inferences about past evolutionary events are made using molecular data from currently living species. ... In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently ... This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular ...
Molecular Basis of Virus Evolution, Edited by Adrian J. Gibbs, Charles H. Calisher, Fernando García-Arenal, 9780521022897, ... Genetic variation and evolution of satellite viruses and satellite RNAs G. Kurath and C. Robaglia; 27. Molecular evolution of ... Molecular evolution of papillomaviruses Marc Van Ranst, Jeffrey B. Kaplan, John P. Sundberg and Robert D. Burk; 32. Molecular ... Evolution of alphaviruses Scott C. Weaver; 34. Evolution of influenza viruses: rapid evolution and stasis R. G. Webster, W. J. ...
Lysine Arginine Leucine Biosynthetic Pathway Molecular Evolution These keywords were added by machine and not by the authors. ...
I have often neglected to consider evolution when trying to understand the molecular basis of a given cellular process. ... Molecular Lego As we obtain more and more protein structures, we see that certain folds are used to achieve distantly related ... Brodsky added, "Molecular cell biologists interested in the evolutionary origins of pathways we study can learn a lot from ... for Biochemistry and Molecular Biology. 11200 Rockville Pike, Suite 302, Rockville, MD 20852. 240-283-6614 , [email protected] ...
Molecular evolution of the synapsin gene family.. Kao HT1, Porton B, Hilfiker S, Stefani G, Pieribone VA, DeSalle R, Greengard ... Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York 10021, USA. [email protected] ... In invertebrate synapsins, the most conserved domains are C and E. During the evolution of vertebrates, at least two gene ... Synapsins possess multiple domains, which have evolved at different rates throughout evolution. ...
1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286. ... 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, New York. ... Their monograph remains as the earliest landmark in the history of molecular evolution. Hemin crystals obtained from different ... The concept that each protein from each species of animal was a single chemical substance at the molecular level was implicit ...
Kyoichi Sawamura, "Chromatin Evolution and Molecular Drive in Speciation," International Journal of Evolutionary Biology, vol. ... Chromatin Evolution and Molecular Drive in Speciation. Kyoichi Sawamura Graduate School of Life and Environmental Sciences, ...
Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance ... Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light ... Reductive evolution in CenAsiaIII S. sonnei Reductive evolution has played an important role in shaping the long-term evolution ... Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. *Hao Chung The ORCID: ...
POPULATION GENETICS AND EVOLUTION. Molecular Evolution of the Helicobacter pylori Vacuolating Toxin Gene vacA Kelly A. Gangwer ... POPULATION GENETICS AND EVOLUTION. Evolution and Population Structure of Salmonella enterica Serovar Newport Vartul Sangal, ... POPULATION GENETICS AND EVOLUTION. Genomic Identification of a Novel Mutation in hfq That Provides Multiple Benefits in ... The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli Nicola K. Petty, ...
... should drive molecular evolution through continual natural selection for adaptation and counter-adaptation. Although the ... Antagonistic coevolution accelerates molecular evolution Nature. 2010 Mar 11;464(7286):275-8. doi: 10.1038/nature08798. Epub ... that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than ... should drive molecular evolution through continual natural selection for adaptation and counter-adaptation. Although the ...
... stability and binding affinities in phylogenetic evolution and causation of human disease. ... Neutral theory of molecular evolution - ( ... Biological evolution employs genetic alterations or mutations as its basic working material. The current study of molecular ... Fruit Fly Neurons Hold Key to Molecular Causes of Mental Diseases. A neuron is a cell that processes and transmits information ...
Molecular evolution of rifampicin resistance in Streptococcus pneumoniae.. Enright M1, Zawadski P, Pickerill P, Dowson CG. ... of rpoB from one isolate examined suggests that interspecies gene transfer may also have played a role in the evolution of ...
... new genes and their proteins that revealed striking new insights into the early evolution of multicellular animals have been ... Sponges (Porifera) Molecular Model Systems to Study Cellular Differentiation in Metazoa W. E. G. Müller, C. Wagner, C. C. ... amino acid apoptosis cell cellular differentiation classification evolution genome membrane mitochondria primary structure ... Evolution of Early Metazoa: Phylogenetic Status of the Hexactinellida Within the Phylum of Porifera (Sponges) ...
Molecular Machine Protein Import by Mitochondria If a cell is irreducibly complex, this means that if the component parts are ... What is Evolution?. Evolution is a gradual process in which a biological organism changes into a different and usually more ... Recently in 2009, however, scientists have been able to show that a cell is composed of "molecular machines." These molecular ... Evolution works at the DNA level. This has been known for a long time. Darwin did not know it, but he was prescient enough to ...
... J Mol Biol. 2004 May 28;339(2):327-35. doi: 10.1016/j.jmb.2004.03.065. ... The complex history of the mir17 microRNA family appears to be closely linked to the early evolution of the vertebrate lineage ...
The molecular evolution of feathers with direct evidence from fossils. Yanhong Pan, Wenxia Zheng, Roger H. Sawyer, Michael W. ... The molecular evolution of feathers with direct evidence from fossils. Yanhong Pan, Wenxia Zheng, Roger H. Sawyer, Michael W. ... The molecular evolution of feathers with direct evidence from fossils. Yanhong Pan, Wenxia Zheng, Roger H. Sawyer, Michael W. ... The molecular evolution of feathers with direct evidence from fossils Message Subject (Your Name) has sent you a message from ...
Evidence for an ancient adaptive episode of convergent molecular evolution. Todd A. Castoe, A. P. Jason de Koning, Hyun-Min Kim ... Evidence for an ancient adaptive episode of convergent molecular evolution. Todd A. Castoe, A. P. Jason de Koning, Hyun-Min Kim ... Evidence for an ancient adaptive episode of convergent molecular evolution. Todd A. Castoe, A. P. Jason de Koning, Hyun-Min Kim ... Evidence for an ancient adaptive episode of convergent molecular evolution Message Subject (Your Name) has sent you a message ...
Many bioinformatics applications are based on principles of molecular evolution, and to study molecular evolution is ... giving detailed treatments of molecular evolution and molecular phylogenetics and discussing evolution at the whole-genome ... places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular ... Bioinformatics and Molecular Evolution. Paul G. Higgs, Teresa K. Attwood. ISBN: 978-1-118-69707-8 June 2013 Wiley-Blackwell 448 ...
It looks at population genetics, phylogeny (history of evolution) and developmental genetics, to provide a framework from which ... Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. ... Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. It looks ... Molecular Systematics and Plant Evolution. 1st Edition. Edited by Peter M. Hollingsworth, Richard M. Bateman, Richard J. ...
... is the process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution ... Journals dedicated to molecular evolution include Molecular Biology and Evolution, Journal of Molecular Evolution, and ... Molecular evolution is the process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a ... The Society for Molecular Biology and Evolution publishes the journal "Molecular Biology and Evolution" and holds an annual ...
Molecular characterization of the klebicin B plasmid of Klebsiella pneumoniae.. *Molecular evolution of bacteriocins in gram- ... Home » About the Lab » Research » Publications » Molecular Mechanisms of Colicin Evolution. Molecular Mechanisms of Colicin ... Molecular mechanisms of bacteriocin evolution.. *Nucleotide Polymorphism at the Xanthine Dehydrogenase Locus in Drosophila ... Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. ...
  • The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution , further the development. (
  • The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution , further the development of phylogenetically more accurate taxonomic classifications , and ultimately bring a unified classification for all the ramifying lines of life. (
  • Synapsin protein sequences from all these species were then used to explore the molecular phylogeny of these important neuronal phosphoproteins. (
  • It looks at population genetics, phylogeny (history of evolution) and developmental genetics, to provide a framework from which to understand evolutionary patterns and relationships amongst plants. (
  • Molecular systematics is the process of using data on the DNA, RNA, or proteins to resolve questions in phylogeny and taxonomy . (
  • We have generated and collected multilocus sequence data (mtSSU, nrITS, nrLSU, RPB1 , RPB2 ) for 149 species associated with the Ramalinaceae and present the first comprehensive molecular phylogeny of the family. (
  • We used ancestral state reconstructions on our molecular family phylogeny to trace the evolution of character states. (
  • Persoonia aims to publish papers dealing with molecular phylogeny and evolution of fungi. (
  • This computer simulation demonstrates the phylogeny reconstruction using virus evolution. (
  • She works in the project "Phylogeny, historic biogeography and niche evolution of the neotropical Marcgraviaceae - a model case of swift morphological diversification and speciation by flower-pollinator-interaction" (project leader: Dr. Stefan Dressler) with funding from DFG (Deutsche Forschungsgemeinschaft). (
  • Molecular phylogeny of Chaetodon (Teleostei: Chaetodontidae) in the Indo-West Pacific: evolution in geminate species pairs and species groups" (PDF). (
  • Dr. OBrochtaUs laboratory is adjacent to a large molecular systematics laboratory ion of DNA from know species of heliothines is available for this project. (
  • Case Studies of Viral Taxa: Their Systematics and Evolution: 18. (
  • Molecular Systematics and Plant Evolution discusses the diversity and evolution of plants with a molecular approach. (
  • Molecular systematics is a product of the traditional field of systematics and molecular genetics . (
  • It is the process of using data on the molecular constitution of biological organisms' DNA , RNA , or both, in order to resolve questions in systematics, i.e. about their correct scientific classification or taxonomy from the point of view of evolutionary biology . (
  • Molecular systematics has been made possible by the availability of techniques for DNA sequencing , which allow the determination of the exact sequence of nucleotides or bases in either DNA or RNA. (
  • Molecular systematics has been made possible by techniques for sequence analysis . (
  • Molecular systematics and character evolution in the lichen famil. (
  • This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. (
  • Global diversity and molecular systematics of Wrightoporia s.l. (
  • Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream within grasp - to 'have fairly true genealogical trees of each great kingdom of Nature. (
  • His current research interests include RNA structure and sequence evolution, molecular phylogenetics, theoretical evolutionary biology, and population genetics. (
  • Further Topics in Molecular Evolution and Phylogenetics. (
  • Molecular Phylogenetics and Evolution, 44 (1): 15-25. (
  • Molecular Phylogenetics and Evolution , 63: 521-526. (
  • Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. (
  • Molecular Phylogenetics and Evolution is a peer-reviewed scientific journal of evolutionary biology and phylogenetics. (
  • It will be of relevance and use to students and professional researchers (both empiricists and theoreticians) in the fields of molecular phylogenetics, evolutionary biology, population genetics, mathematics, statistics and computer science. (
  • An international roster of scientists will discuss topics such as Darwinism in an age of molecular revolution, how the molecular revolution began, biomedical research and genes, sequences and other molecular clues to the history of life. (
  • One hypothesis suggests that most molecular evolution is driven by random changes in genes, or "neutral drift. (
  • It describes the dynamics of evolutionary change at the molecular level, the driving forces behind the evolutionary process, novel evolutionary phenomena revealed by molecular data, the effects of various molecular mechanisms on the structure of genes and genomes, and the methodology involved in the statistical analysis of molecular data from an evolutionary perspective. (
  • This text describes the dynamics of evolutionary change at the molecular level, the driving forces behind the evolutionary process, and the effects of the various molecular mechanisms on the structure of genes and genomes. (
  • Bringing together molecular cell biologists, immunologists and evolutionary biologists who appeared ready to candidly discuss their favorite cellular processes and structures and debate the origins of cellular compartments and cellular immunity in the context of new ideas about genes and their capacity for evolution was a risky experiment for us as organizers of this conference," said Mayor. (
  • Recently, new genes and their proteins that revealed striking new insights into the early evolution of multicellular animals have been identified and characterized from members of the lowest metazoan phylum, the porifera (sponges). (
  • Molecular phylogenetic estimates among 34 squamate reptile species plus 6 tetrapod outgroup species were examined based on 2 nucleotide datasets: a nuclear dataset with 2 nuclear genes (3,411 bp) and a mitochondrial dataset including all 13 protein-coding mitochondrial genes (11,727 bp). (
  • Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes. (
  • Evidence suggests that stable long-term acquisitive evolution results from minor increases in mutation rates of genes related to a particular stress, with minimal disturbance to the balanced and resilient metabolism critical for responding to an unpredictable environment. (
  • Scientists believe that the study of genes that encode the proteins for molecular motors will help solve the mysteries of evolution. (
  • Specifically, the ideas of convergent evolution and lineage-specific expansions are nothing more than fancy terms for the fact that these different types of myosin genes appeared suddenly in unrelated creatures at the same time. (
  • By comparing the relative rate of molecular evolution between humans and chimps with that of their lice, a new study published in the Proceedings of the Royal Society B is attempting to discover whether evolution marches on a same rate of speed in all creatures or whether subtle changes in genes occur rapidly in some species than in others. (
  • Previous studies had looked at the rate of molecular changes between parasites and their hosts, but most focused on single genes in the mitochondria, tiny energy-generating structures outside the nucleus of the cell that are easier to study. (
  • He is especially interested in problems related to understanding the evolution of genes, genomes, and species. (
  • We concluded that heterogeneous alterations in the p53 gene and occasionally in the N-RAS genes accompany the evolution of chronic phase CML to blast crisis. (
  • We have investigated the molecular evolution of one such group of seven Avh genes. (
  • We have also been able to obtain the sequence of homologous Avh genes in the sister taxa P. hibernalis , P. lateralis , and P. foliorum allowing for examination of the evolution of these genes across species. (
  • This study focuses on the evolution of mammalian TET genes. (
  • Genetic change, and hence the evolution of new species, is commonly thought to result from small, random mutations in individual genes, but a growing wealth of data emphasizes that that perception is wrong. (
  • Like many others--Nobel laureate Barbara McClintock was a notable exception--Thomas thought that genetic change, and hence the evolution of new species, results from small, random mutations in individual genes. (
  • This study traces the evolution of LOX genes which have been differentially retained and expanded in rosid plants. (
  • Polyploidy has been and continues to have an extensive effect on the number or type of genes in plant evolution ( Adams and Wendel, 2005 ). (
  • Given this limitation, there are very few opportunities to examine the co-evolution of genes in the genome of living organisms and morphological features preserved in the fossil record. (
  • We predicted that enamel-specific genes such as enamelin would show evidence in living organisms of molecular decay because these genes are vestigial and no longer necessary for survival. (
  • The molecular counterpart to vestigial organs is pseudogenes that are descended from formerly functional genes," Springer explained. (
  • Yang describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. (
  • Integrating Molecular Phylogenies and Developmental Genetics: a Gesneriaceae Case Study M. Möller, M. Clokie, P. Cubas and Q.C.B. Cronk 18. (
  • Hamilton, P.B., Gibson, W.C. and Stevens, J.R. (2007) Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies. (
  • The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last universal common ancestor. (
  • The temporal signal of the ML trees and compatibility with molecular clock phylogenies were assessed with TempEst v1.5.3 ( 7 ). (
  • It will be a major source for insight and enormously helpful for anyone who wants to understand molecular phylogenies. (
  • Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology , evolutionary biology and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. (
  • The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. (
  • The neutral theory is based on simple assumptions, enabling us to develop mathematical theories based on population genetics to treat molecular evolution and variation in quantitative terms. (
  • In the evolution of modern species, there have been millions of molecular changes. (
  • In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. (
  • With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. (
  • The concept that each protein from each species of animal was a single chemical substance at the molecular level was implicit for the hemoglobins in the report by Reichert and Brown. (
  • In the meantime, Kimura had published a short note in Nature ( K imura 1968 ) in which he pointed out that the rate of random fixation of neutral mutation in evolution, per species per generation, is equal to the rate of occurrence of neutral mutation per species per generation and is independent of population size. (
  • The Red Queen hypothesis proposes that coevolution of interacting species (such as hosts and parasites) should drive molecular evolution through continual natural selection for adaptation and counter-adaptation. (
  • These results demonstrate, at both the genomic and phenotypic level, that antagonistic coevolution is a cause of rapid and divergent evolution, and is likely to be a major driver of evolutionary change within species. (
  • Explain creation and sustenance of life to keep in tune with the changing environment, a factor critical in the evolution of species over time. (
  • Thus the protein models in the study inspired by the protein misfolding disease show how altered protein structure can bring about newer and useful functions as well which is critical for the phylogenetic evolution of species. (
  • Reticulate Evolution in the Mediterranean Species Complex of Senecio Sect. (
  • Some of the key topics that spurred development of the field have been the evolution of enzyme function, the use of nucleic acid divergence as a " molecular clock " to study species divergence, and the origin of non-functional or junk DNA . (
  • On the Origins of Species: Does Evolution Repeat Itself in Polyploid Populations of Independent Origin? (
  • This page includes an archive of materials from the 150th anniversary of the publication of "The Origin of Species" as well as recent columns by Olivia Judson and Sean Carroll on evolution. (
  • The so-called 'molecular clock' hypothesis, which states that the rate of molecular evolution is constant in time and across lineages, is only rarely met: some species evolve significantly faster than others as far as molecules are concerned ( Bromham & Penny 2003 ). (
  • They predicted that these species would have copies of the gene that codes for the tooth-specific enamelin protein, but this gene would show evidence of molecular decay in these species. (
  • The theory also asserts that most of the genetic variability within species at the molecular level (such as protein and DNA polymorphism) are selectively neutral or very nearly neutral and that they are maintained in the species by the balance between mutational input and random extinction. (
  • The journal encourages articles that are multidisciplinary, especially in areas, such as bioinformatics, computational biology, molecular biology, and organismic biology, that are of interest to the community of systematic and evolutionary biologists. (
  • In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. (
  • This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses. (
  • Much of bioinformatics is based on, yet too often ignores, the underlying principles of molecular evolution. (
  • This book nicely integrates molecular evolution and bioinformatics, two disciplines that go hand in hand, as rightfully claimed by the authors. (
  • Many bioinformatics applications are based on principles of molecular evolution, and to study molecular evolution is unthinkable nowadays without having access to the necessary tools and implementations. (
  • Microscopy, image processing, bioinformatics, in situ hybridization, molecular (epi)genetics and systems biology lets us explore and exploit fundamental processes. (
  • Thanks in advance, Tonu Margus ======================================== Tonu Margus Department of Bioinformatics Institute of Cell and Molecular Biology University of Tartu Riia str. (
  • A molecular evolutionary framework is central to many Bioinformatics approaches used in these analyses, e.g., de novo gene finding from genomic sequences. (
  • Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. (
  • Therefore, by comparing genomes valuable information can be obtained to help explain how millions of years of evolution have generated remarkably complex organisms. (
  • Patterns of alternating GC and AT rich motifs correlated well with hypervariable region recombination sites across the HAdV-D genomes, suggesting foci of DNA instability lead to formulaic patterns of homologous recombination and confer agility to adenovirus evolution. (
  • The new analysis is the first to look at the pace of molecular change across the genomes of different groups. (
  • Biologists at the University of California, Riverside report new evidence for evolutionary change recorded in both the fossil record and the genomes (or genetic blueprints) of living organisms, providing fresh support for Charles Darwin's theory of evolution. (
  • Now his lab has found evidence of such molecular "cavities" in the genomes of living organisms. (
  • Genomes are the ultimate molecular documents, filled with stories that fascinate and instruct, and we can now speed-read them. (
  • However, the result of a study published in the journal Genome Biology and Evolution has only served to support the predictions of special creation-that unique variants of cellular complexity and innovation exist at all levels of life. (
  • Genome Biology and Evolution. (
  • Molecular Biology and Evolution 16: 1315-1328. (
  • Human Longevity: Omega-3 Fatty Acids, Bioenergetics, Molecular Biology, and Evolution is built on the proposition that we age as our mitochondria age. (
  • Genome Evolution. (
  • The topics covered include the appearance of the first genetic material, the origins of cellular life, evolution and development, selection and adaptation, and genome evolution. (
  • His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. (
  • Journal of Molecular Evolution, 40: 190-226. (
  • When we see convergent evolution provide the same solution to a complex problem, we have a better understanding of its importance. (
  • Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. (
  • Although nonneutral convergent evolution of morphological characters has been frequently pointed to as a source of potential bias in phylogenetic inference ( 4 - 6 ), nonneutral convergence at the molecular-genetic level is believed to be relatively rare and limited in scope. (
  • We examined whether the results could be explained by neutral convergence or were instead due to potentially adaptive nonneutral convergent evolution. (
  • This is, therefore, a classic case of convergent evolution: Both groups evolved similar molecular mechanisms for a eusocial lifestyle under similar selection pressures," says genomics expert Dr Mark Harrison, first author of the study. (
  • We do research in molecular genetics, functional genomics, cell biology, developmental biology, biotechnology and biochemistry in established model organisms. (
  • Integrated genomics and comprehensive validation reveal drivers of genomic evolution in esophageal adenocarcinoma. (
  • Research topics in molecular evolution include the characterization of novel hantaviruses harbored by shrews, moles and bats in different geographic locations and investigation of Burkholderia pseudomallei in humans, animal models, and in the environment. (
  • Evolution, at the molecular level, is observableas nucleotide changes in the DNA and amino acid changes in proteins. (
  • We can observe molecular evolution in DNA , and also in amino acid changes in proteins . (
  • Individual proteins placed under similar selective pressures have been observed, however, to respond with convergent molecular changes ( 7 - 12 ). (
  • Molecular evolution is the process of evolution at the scale of DNA , RNA , and proteins . (
  • Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. (
  • The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis and paper chromatography in the 1950s to explore homologous proteins. (
  • After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life. (
  • The rate at which DNA and proteins accumulate substitutions is an important aspect of molecular evolution. (
  • Comparative biochemistry demonstrates that the metabolites, complex biochemical networks, enzymes and regulatory mechanisms essential to all living cells are conserved in amazing detail throughout evolution. (
  • PhD students and scientists with interests on physiology, ecotoxicology, biochemistry, molecular biology, molecular evolution and aquatic science disciplines will find this book very useful, based on the concepts and the relative biomarkers study cases, analyzed from the evolutionary point of view. (
  • While evolution involves changes in organisms that we can observe, they undergo evolution at a deeper level, too. (
  • Evolutionary scientists often use results derived from molecular biology dating methods (based on DNA sequence similarities) to bolster their assumptions that some related organisms may have diverged millions of years ago. (
  • By using these recent methodologies, it could be useful to shed light on the molecular evolution of the biomarkers, and which role and functionality can be better understood based on exploring the relative evolution pathways in several aquatic organisms. (
  • The new study begins to answer fundamental questions about changes at the molecular level that eventually shape the destinies of all organisms, Johnson said. (
  • 1. Using Organelle Markers to Elucidate the History, Ecology and Evolution of Plant Populations R.A. Ennos, W.T. Sinclair, X.-S. Hu and A. Langdon 2. (
  • to assess how the study of genetics and the use of molecular tools can inform biodiversity conservation, animal breeding, animal welfare and our understanding of evolutionary ecology. (
  • Another 2017 publication considers the role of polyploidy or whole genome duplication in ecology and evolution . (
  • A rich ecology of practices and theoretical debates, embedded in some of the political concerns and policies of the postwar period, is part of the emergence of the field of Molecular Evolution. (
  • Here we show, using experimental populations of the bacterium Pseudomonas fluorescens SBW25 and its viral parasite, phage Phi2 (refs 10, 11), that the rate of molecular evolution in the phage was far higher when both bacterium and phage coevolved with each other than when phage evolved against a constant host genotype. (
  • The field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. (
  • The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. (
  • Evolution consists of the substitution of one variant for another when the environment changes. (
  • Gillespie JH (1994) Substitution process in molecular evolution. (
  • A deeper understanding of the mechanisms and processes of molecular evolution should lead to more accurate models of molecular evolution, which in turn should facilitate the development of better algorithms for reconstructing evolutionary history from sequence data. (
  • Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. (
  • To this end, we aim to provide graduate and postgraduate researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data. (
  • Molecular evolution of the synapsin gene family. (
  • In invertebrate synapsins, the most conserved domains are C and E. During the evolution of vertebrates, at least two gene duplication events are hypothesized to have given rise to the synapsin gene family. (
  • However, the nucleotide sequence of rpoB from one isolate examined suggests that interspecies gene transfer may also have played a role in the evolution of rifampicin-resistance in S. pneumoniae. (
  • In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection , disease, and cognition. (
  • Mutations are considered the driving force of evolution , where less favorable (or deleterious ) mutations are removed from the gene pool by natural selection , while more favorable (or beneficial ) ones tend to accumulate. (
  • The near‐neutrality concept may be extended to the evolution of such systems, where epigenetics and robustness are important for gene expression and many mutations are weakly selected. (
  • Khaitovich P, Enard W, Lachmann M and Pääbo S (2006) Evolution of primate gene expression. (
  • We were able to deduce that, long before the evolution of termites, one particular class of transposons led to the expansion of gene families probably involved in communication," added Dr Evelien Jongepier, also first author. (
  • They found that - at the scale of random changes to gene sequence - the lice are winning the molecular evolutionary race. (
  • Molecular phylogenetic analyses using two data sets, derived from DNA sequences of matK, the maturase-encoding gene located in an intron of the chloroplast gene trnK, and ITS (internal transcribed spacer) region of the 18S-26S nuclear ribosomal DNA, were performed to examine relationships among 37 taxa in Cymbidium. (
  • The most common genetic change found in the evolution of typical Ph1 chromosome positive CML to blast crisis was an alteration of the p53 gene involving either a rearrangement, a deletion, or a point mutation in the coding sequence of the gene. (
  • Human Gene Evolution. (
  • Presents the principles of human gene evolution in a concise and easy to understand fashion. (
  • Here we show that some members of the LOX gene family in the Arabidopsis genome are likely to be lost during evolution, leading to a smaller size than that in Populus, Vitis , and Carica . (
  • The researchers were able to correlate the progressive loss of enamel in the fossil record with a simultaneous molecular decay of a gene, called the enamelin gene, that is involved in enamel formation in mammals. (
  • In our research we clearly see the parallel evolution of enamel loss in the fossil record and the molecular decay of the enamelin gene into a pseudogene in representatives of four different orders of mammals that have lost enamel. (
  • Papers based on few taxa, single molecular markers, or that use codon-based methods to test for positive Darwinian selection, but in the absence of experimental evidence that allegedly selected amino acid changes cause an adaptive phenotypic effect, will not be accepted. (
  • Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. (
  • In addition, presentations of new findings on or insights into evolutionary processes and mechanisms as expressed at the molecular level are welcome, as are those that deal with the methodology of reconstructing evolutionary history from molecular data (such as descriptions of new or more powerful computer algorithms for constructing phylogenetic trees from orthologous nucleotide or aminoacid sequences). (
  • What we observe as evolution consists of shuffling round within this limited set of equivalent sequences. (
  • Using the mutation rate per generation and the number of nucleotide differences between two sequences, divergence times can be estimated effectively via the molecular clock. (
  • Nuclear sequences analyzed under maximum parsimony and minimum evolution criteria did not resolve relationships among families and suborders. (
  • We often hear about new 'genome sequences,' commercial kits that can tell you about your ancestry (including pre-human) from your DNA or disease predispositions, debates about the truth of evolution, why animals behave the way they do, and how people found 'genetic evidence for natural selection. (
  • Today, similarities and differences in molecular data (protein and DNA sequences) are also being used. (
  • Next, the researchers analyzed sequences using a variety of molecular evolutionary methods, including new approaches developed by Springer's group. (
  • This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. (
  • Brodsky added, "Molecular cell biologists interested in the evolutionary origins of pathways we study can learn a lot from immunologists who have refined techniques to extract information from the co-evolution of host-pathogen interaction pathways, which are the most rapidly evolving in biology. (
  • In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. (
  • Molecular Biologists recognize that the model is a rough approximation to reality and there is considerable literature on the effects of model deviations. (
  • Abir-Am P (1992) The politics of macromolecules: molecular biologists, biochemists, and rhetoric. (
  • Simpson, A.G.B., Stevens, J.R. and Lukes, J. (2006) The evolution and diversity of kinetoplastid flagellates. (
  • Diversity and evolution of dominant African savanna grasses. (
  • Additionally, explicit use of molecular evolutionary and phylogenetic analyses provide important insights in their own right, e.g., analysis of adaptive evolution in viruses providing clues of their interaction with host immune systems. (
  • In addition, it is theorized that certain chemical reactions may have taken place on early Earth, before true evolution began, and some of these reactions may have helped to form these informational molecules that enabled replication and mutation. (
  • Roles of mutation and selection in molecular evolution. (
  • This session will highlight research into the molecular mechanisms involved in evolutionary processes such as mutation, inheritance, phenotypic plasticity, and more. (
  • They are also learning that the enzymes that copy and maintain the DNA introduce changes in some parts of the genome and not others, creating hotspots of mutation that increase the efficiency of evolution. (
  • This book is one of the first solely devoted to the origins and evolution of viruses, and of the ways in which they interact with their cellular hosts and vectors. (
  • The conference taught me an important lesson: Evolution of a biochemical process can teach us a great deal about how it operates - it can help determine which features are fundamental and which represent cellular or organismal specialization. (
  • I have often neglected to consider evolution when trying to understand the molecular basis of a given cellular process. (
  • The main problem with this idea is that, not only does no such creature exist, but eukaryotes also contain molecular similarities to both bacteria and archaea-prokaryotes that are found in completely separate domains of cellular life. (
  • Another major problem is that many complex molecular and cellular features unique among eukaryotes are not found in any prokaryotes. (
  • Clearly, the only scientific model that predicts this type of molecular and cellular complexity and innovation across all forms of life is one associated with special creation. (
  • Viewing molecular and cellular processes within their evolutionary contexts can reveal key mechanistic information. (
  • Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. (
  • McDonald JH and Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. (
  • Aronson JD (2002) 'Molecules and monkeys': George Gaylord Simpson and the challenge of molecular evolution. (
  • A widely accepted principle is that protein evolution is mainly determined by constraints on activity, specificity, folding, and stability ( 1-4 ). (
  • Thus, we previously proposed that metabolic flows and geochemical budgets might be constraints that were imprinted on protein evolution ( 5 ). (
  • Genome‐wide data on protein evolution are mostly in accord with the nearly neutral theory. (
  • Many observed patterns of protein evolution by measuring synonymous and nonsynonymous divergences are in accord with the nearly neutral theory. (
  • By creating a deeper understanding for the evolutionary dynamics of an important drug targetenzyme, our proposal will develop experimental and computational tools for studying protein evolution with theultimate goal of improving human health. (
  • Our key methods for in situ hybridization are given at this website with more information about methods for molecular cytogenetics and in situ hybridization as well as some other methods used in our laboratory. (
  • Fu, Yun‐Xin(Apr 2001) Neutrality and Selection in Molecular Evolution: Statistical Tests. (
  • The wealth of information contained in colicin sequence comparisons makes this an ideal system with which to explore molecular mechanisms of evolutionary change. (
  • Molecular evolution " is a term used to describe the stages that preceded the origin of life on Earth. (
  • Sponsored by the Center for the Study of Evolution and the Origin of Life, the symposium will be held in Schoenberg Hall from 9 a.m. to 5 p.m. (
  • This review explores features of the origin and evolution of colicins in Escherichia coli. (
  • This site has lesson plans and general information about evolution, the nature of science, origin of life and genetics. (
  • I also discuss such topics as the evolution of deviant coding systems in Mycoplasma , the origin of life and the unified understanding of molecular and phenotypic evolution. (
  • Fay JC (2011) Weighing the evidence for adaptation at the molecular level. (
  • Previous studies in evolutionary biology have provided only limited evidence linking morphological degeneration in the fossil record to molecular decay in the genome. (
  • Therefore, random processes explain most of evolution at the molecular level. (
  • Further chapters detail genetic variation of viruses and the molecular basis of interrelation at the population level and the molecular basis and evolution of this relationship. (
  • Irreducibly complex parts at the molecular level are actually cobbled together by simpler parts and put together as a whole. (
  • Evolution works at the DNA level. (
  • Regardless of the frequency of nonneutral convergence in nature, it is important to identify such cases to understand their impact on phylogenetic inference and to illuminate the mechanisms of functional adaptation at the molecular level. (
  • Nearly neutral theory is an extension of the neutral theory and contends that the borderline mutations, whose effects lie between the selected and the neutral classes, are important at the molecular level. (
  • Introduction to Genetics and Evolution is a college-level class being offered simultaneously to new students at Duke University. (
  • In sharp contrast to the Darwinian theory of evolution by natural selection, the neutral theory claims that the overwhelming majority of evolutionary changes at the molecular level are caused by random fixation (due to random sampling drift in finite populations) of selectively neutral (i.e., selectively equivalent) mutants under continued inputs of mutations. (
  • Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. (
  • This information will prove invaluable as we proceed to dissect, at a molecular level, events associated with Q fever pathogenesis. (
  • This session will highlight research that harnesses the power of experimental evolution, phylogenetic reconstructions, and standing genetic variation to gain insight into molecular systems. (
  • Genetic variation analyses indicate conserved SARS-CoV-2-host interaction and varied genetic adaptation in immune response factors in modern human evolution. (
  • This fact, a mutual divergence that began at the same point in time (roughly 5 million to 6 million years ago) allowed Johnson and his colleagues to determine whether molecular evolution occurs faster in primates or in their parasites. (
  • In retrospect, it might have been better to entitle the article "Non-adaptive evolution," because "non-Darwinian" probably raised the hackles of admirers of Charles Darwin. (
  • up constraint with adaptive evolution and just call it neutral. (
  • Typical molecular systematic analyses require the sequencing of around 1000 base pairs . (
  • Convergent molecular evolution, sometimes referred to as homoplasy, can result from neutral processes or from nonneutral processes such as positive selection and adaptation ( 1 - 3 ). (
  • To assess the hypothesis that nutritional constraints might have influenced the evolution of protein structure, we computed the atomic composition of enzymes involved in elemental assimilation processes in the two model microorganisms E. coli and S. cerevisiae . (
  • We research crop plants and farm animals, studying their evolution and organization at the DNA to genome levels: large-scale processes with chromosomes, polyploidy and DNA sequence. (
  • We undertake research into the evolutionary processes that shape patterns of modern and ancient human molecular and cultural variation. (
  • This GRS seeks to overcome traditional disciplinary divides by bringing together junior scientists from a wide array of fields who share common goals: uncovering molecular mechanisms that drive evolution and/or using evolution and natural variation to better understand molecular processes. (
  • Fitch WM, Bush RM, Bender CA and Cox NJ (1997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proceedings of the National Academy of Sciences of the USA 94: 7712-7718. (
  • Li WH (1997) Molecular Evolution. (
  • At a very early stage in evolution, mitochondria were derived from bacteria that lived within the first eukaryotic cells. (
  • These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution. (
  • Infection, Genetics and Evolution 1: 143-150. (
  • Infection, Genetics and Evolution , 11: 955-959. (
  • Nucleic acids are attractive materials for creating functional molecules that have applications as catalysts, specific binders, and molecular switches. (
  • These methods have helped explore the potential abilities of nucleic acids and steadily contributed to their evolution, i.e . , creation of RNA/DNA enzymes, aptamers, and aptazymes. (
  • This review focuses on the effectiveness of chemical modifications on the evolution of nucleic acids as functional molecules and the outlook for related technologies. (
  • Postdoctoral Research Fellow In Molecular Evolution Dr. David OBrochta, University of Maryland Biotechnology Institute, Center for Agricultural Biotechnology wishes to sponsor highly qualified recent Ph.D.s interested in applying for a postdoctoral fellowships in Molecular Evolution sponsored by the National Science Foundation and Alfred P. Sloan Foundation, of the USDA. (
  • The fellow will be responsible for conducting a research project investigating the evolution of hAT transposable elements in heliothine moths. (
  • Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. (
  • It reviews the latest advances in research into evolution, focusing on the molecular bases for evolutionary change. (
  • The Gordon Research Seminar on Molecular Mechanisms in Evolution is a unique forum for graduate students, post-docs, and other scientists with comparable levels of experience and education to present and exchange new data and cutting edge ideas. (
  • This GRS will be held in conjunction with the "Molecular Mechanisms in Evolution" Gordon Research Conference (GRC). (
  • Due to the Senckenberg-wide regulations and current recommendations in connection with the corona virus epidemic, the Department of Botany and Molecular Evolutionary Research is closed since 16th March 2020 until further notice for volunteers, visiting researchers and interns. (
  • Another important basis for our research and teaching is the Grunelius-Möllgaard Lab, a molecular lab that the division runs for Senckenberg, which is open to Senckenberg and guest researchers. (
  • We hope the work in the current study serves as a resource for both the Coxiella and wider infectious disease research communities interested in the evolution of pathogen virulence. (
  • Coordinated multigene nonneutral molecular convergence events have also been shown to occur in laboratory selection experiments ( 1 ), but have not been observed in nature. (
  • We will use laboratory evolution experiments to identify functional DHFR mutations and reproduciblegenetic trajectories leading to elevated trimethoprim resistance. (
  • Chiang HHH (2009) The laboratory technology of discrete molecular separation: the historical development of gel electrophoresis and the material epistemology of biomolecular science, 1945-1970. (
  • Homologous recombination was identified in at least two of five examined hypervariable regions for every virus, suggesting the evolution of HAdV-Ds has been highly dependent on homologous recombination. (
  • There have been few systematic screens for nonneutral molecular convergence, however, so its true frequency in nature remains largely unknown. (
  • However, molecular systematic investigations of subgroups revealed that current taxonomy is at odds with evolutionary relationships. (