Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Directed Molecular Evolution: 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.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Molecular Sequence Data: 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.Cultural Evolution: The continuous developmental process of a culture from simple to complex forms and from homogeneous to heterogeneous qualities.Models, Genetic: 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.Species Specificity: 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.Genetic Variation: Genotypic differences observed among individuals in a population.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Amino Acid 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.Clonal Evolution: The process of accumulation of genetic and epigenetic changes over time in individual cells and the effect of the changes on CELL PROLIFERATION.Adaptation, Biological: Changes in biological features that help an organism cope with its ENVIRONMENT. These changes include physiological (ADAPTATION, PHYSIOLOGICAL), phenotypic and genetic changes.Sequence Alignment: 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.Multigene Family: 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)PrimatesFossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Mutation: 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.Evolution, Chemical: 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.Hominidae: 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).Likelihood Functions: 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.Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.Gene Transfer, Horizontal: 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).Conserved Sequence: 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.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Adaptation, Physiological: The non-genetic biological changes of an organism in response to challenges in its ENVIRONMENT.Genetic Speciation: 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.Models, Biological: 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.Angiosperms: 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.Synteny: 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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Sequence Homology, Nucleic Acid: 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.Invertebrates: Animals that have no spinal column.Eukaryota: 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.Pseudogenes: 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.Pan troglodytes: 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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Reproduction: The total process by which organisms produce offspring. (Stedman, 25th ed)Recombination, Genetic: 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.Genetic Drift: The fluctuation of the ALLELE FREQUENCY from one generation to the next.Plants: 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.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Chordata, Nonvertebrate: 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.Genetic Fitness: 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.Evolution, Planetary: Creation and development of bodies within solar systems, includes study of early planetary geology.Introns: 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.Computational Biology: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Genes, Plant: The functional hereditary units of PLANTS.Fishes: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.Genetics, Population: 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 Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Bayes Theorem: 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.Genes, Duplicate: 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)Drosophila: 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, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Biogenesis: 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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Arthropods: 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.Codon: 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).Ecosystem: 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)Protein Structure, Tertiary: 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.Genes, Insect: The functional hereditary units of INSECTS.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Bacteria: 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.Chordata: 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).Time Factors: Elements of limited time intervals, contributing to particular results or situations.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Cloning, Molecular: 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.Retroelements: 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.Symbiosis: 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.Paleontology: The study of early forms of life through fossil remains.Sexual Behavior, Animal: Sexual activities of animals.Reptiles: Cold-blooded, air-breathing VERTEBRATES belonging to the class Reptilia, usually covered with external scales or bony plates.Amino Acid Substitution: 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.Proteins: 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.Environment: The external elements and conditions which surround, influence, and affect the life and development of an organism or population.Mutation Rate: 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.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Polymorphism, Genetic: 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.Ecology: 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)Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Game Theory: 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.LizardsDNA Transposable Elements: 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.Gene Order: The sequential location of genes on a chromosome.Cluster Analysis: 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.Geography: 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)Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Pigmentation: Coloration or discoloration of a part by a pigment.Sequence Homology: 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.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Dinosaurs: General name for two extinct orders of reptiles from the Mesozoic era: Saurischia and Ornithischia.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Flowers: The reproductive organs of plants.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Escherichia coli: 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.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Gorilla gorilla: 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.Exons: 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.Models, Theoretical: 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.Archaea: 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.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.DNA: 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).Sex Chromosomes: 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)Pongo pygmaeus: A species of orangutan, family HOMINIDAE, found in the forests on the island of Borneo.DNA Shuffling: 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.Platypus: A small aquatic oviparous mammal of the order Monotremata found in Australia and Tasmania.Bacterial Proteins: Proteins found in any species of bacterium.Open Reading Frames: 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).Population Dynamics: The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.Repetitive Sequences, Nucleic Acid: 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).Polymerase Chain Reaction: 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.Mating Preference, Animal: 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.DNA Primers: 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.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Anatomy, Comparative: The comparative study of animal structure with regard to homologous organs or parts. (Stedman, 25th ed)Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Host-Parasite Interactions: 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.DNA, Intergenic: 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.Gene Conversion: 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.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Smegmamorpha: 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 http://www.nanfa.org/articles/Elassoma/elassoma.htm, 8/4/2000)Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Nematoda: A class of unsegmented helminths with fundamental bilateral symmetry and secondary triradiate symmetry of the oral and esophageal structures. Many species are parasites.Genome, Human: 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.Genes, Bacterial: The functional hereditary units of BACTERIA.Brassicaceae: 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.Social Behavior: Any behavior caused by or affecting another individual, usually of the same species.History, 20th Century: Time period from 1901 through 2000 of the common era.Cercopithecidae: The family of Old World monkeys and baboons consisting of two subfamilies: CERCOPITHECINAE and COLOBINAE. They are found in Africa and part of Asia.Gene Library: 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.Predatory Behavior: Instinctual behavior pattern in which food is obtained by killing and consuming other species.Jaw: Bony structure of the mouth that holds the teeth. It consists of the MANDIBLE and the MAXILLA.Gene Expression Regulation, Developmental: 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.Cetacea: 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)Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Genes: 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.Rodentia: A mammalian order which consists of 29 families and many genera.Marsupialia: 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.Animal Communication: 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.Photosynthesis: 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)Butterflies: Slender-bodies diurnal insects having large, broad wings often strikingly colored and patterned.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Stochastic Processes: Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.Reproduction, Asexual: 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).Lampreys: 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.Altruism: Consideration and concern for others, as opposed to self-love or egoism, which can be a motivating influence.History, Ancient: The period of history before 500 of the common era.Extinction, Biological: The ceasing of existence of a species or taxonomic groups of organisms.Sex: The totality of characteristics of reproductive structure, functions, PHENOTYPE, and GENOTYPE, differentiating the MALE from the FEMALE organism.Cichlids: Common name for perch-like fish of the family Cichlidae, belonging to the suborder Labroidei, order PERCIFORMES.Sequence Analysis, Protein: 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.Cnidaria: 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.Genetic Code: 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).Insect Proteins: Proteins found in any species of insect.Fungi: 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.Ants: 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)History, 19th Century: Time period from 1801 through 1900 of the common era.ArtiodactylaCompetitive Behavior: The direct struggle between individuals for environmental necessities or for a common goal.Genes, Homeobox: 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.Plastids: 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.Population Density: Number of individuals in a population relative to space.Chlorophyta: 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.Drosophila Proteins: 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.Arabidopsis: 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, Mitochondrial: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Developmental Biology: The field of biology which deals with the process of the growth and differentiation of an organism.Parasites: 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.Saccharomyces cerevisiae: 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.Takifugu: A genus of pufferfish commonly used for research.Oryza sativa: 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.Phylogeography: 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)Hymenoptera: An extensive order of highly specialized insects including bees, wasps, and ants.Tetraodontiformes: 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.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Ciona intestinalis: The only species of a cosmopolitan ascidian.Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.Models, Statistical: 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.Beetles: INSECTS of the order Coleoptera, containing over 350,000 species in 150 families. They possess hard bodies and their mouthparts are adapted for chewing.Skull: The SKELETON of the HEAD including the FACIAL BONES and the bones enclosing the BRAIN.Protein Conformation: 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).INDEL Mutation: 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.History, 21st Century: Time period from 2001 through 2100 of the common era.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Sex Determination Processes: The mechanisms by which the SEX of an individual's GONADS are fixed.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Opsins: 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.Microsatellite Repeats: 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).DNA, Complementary: 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.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.X Chromosome: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

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 ...
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 ...
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
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.
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 ...
TheInfoList.com - (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.
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: http://dx.doi.org/10.1101/020958 Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the…
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 ...
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.. ...
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 ...
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 ...
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 ...
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The nucleotide diversity (pi) in humans is studied by using published cDNA and genomic sequences that have been carefully checked for sequencing accuracy. This measure of genetic variability is defined as the number of nucleotide differences per site between two randomly chosen sequences from a population. A total of more than 75,000 base pairs from 49 loci are compared. The DNA regions studied are the 5 and 3 untranslated regions and the amino acid coding regions. The coding regions are divided into nondegenerate sites (i.e., sites at which all possible changes are nonsynonymous), twofold degenerate sites (i.e., sites at each of which one of the three possible changes is synonymous) and fourfold degenerate sites (i.e., sites at which all three possible changes are synonymous). The pi values estimated are, respectively, 0.03 and 0.04% for the 5 and 3 UT regions, and 0.03, 0.06 and 0.11% for nondegenerate, twofold degenerate and fourfold degenerate sites. Since the highest pi value is only ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Convergent and Divergent Evolution Different geographical areas sometimes exhibit groups of plants and animals of strikingly similar appearance, even though the organisms may be only distantly related. It is difficult to explain so many similarities as the result of coincidence. Instead, natural selection appears to have favored parallel evolutionary adaptations in similar environments. Because selection in these instances has tended to favor changes that made the two groups more alike, their phenotypes have converged. This form of evolutionary change is referred to as convergent evolution, or sometimes, parallel evolution.. The Marsupial-Placental Convergence. In the best known case of convergent evolution, two major groups of mammals, marsupials and placentals, have evolved in a very similar way, even though the two lineages have been living independently on separate continents. Australia separated from the other continents more than 50 million years ago, after marsupials had evolved but ...
There are just two questions to be asked in evolution: how are things related, and what makes them differ? Lamarck was the first biologist-he invented the word-to address both. In his Philosophie Zoologique (1809) he suggested that the relationships among species are better described by branching trees than by a simple ladder, that new species arise gradually by descent with modification and that they adapt to changing environments through the inheritance of acquired characteristics. Much that Lamarck imagined has since been superseded. Following Wallace and Darwin, we now envision that species belong to a single highly branched tree and that natural selection is the mechanism of adaptation. Nonetheless, to Lamarck we owe the insight that pattern is produced by process and that both need mechanistic explanation.. Questions of pattern, process and mechanism pervade the modern discipline of molecular evolution. The field was established when Zuckerkandl & Pauling (1965) noted that haemoglobins ...
Information for MOLECULAR-EVOLUTION/bionet.molbio.evolution (moderated) USENET newsgroup name: bionet.molbio.evolution Status: Moderated One line Description: Discussions about research in molecular evolution. Moderation address: mol-evol-moderator at net.bio.net (mol-evol-moderator at net.bio.net is an alias for mol-evol-moderator at net.bio.net) Moderators: Jerry Learn James McInerney Mailing list name: MOLECULAR-EVOLUTION E-mail addresses: mol-evol at net.bio.net Newsgroup charter: Bionet.molbio.evolution is a forum for scientific discussions and a source of information for the community of scientists interested in the study of the processes of how DNA, RNA, proteins and organisms have evolved at a molecular level. Functions of the newsgroup: The newsgroup will facilitate rapid communication among research scientists, educators and other individuals interested in the study of molecular evolution. This includes, but is not limited to discussions of molecular phylogenies, methods of analysis, ...
CiteWeb id: 19800000002. CiteWeb score: 26507. SummarySome simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = - (1/2) ln {(1 - 2P - Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are ...
We examined patterns of genetic variation and divergence in 20 immune-related genes and 17 control genes. We found that, on average, immune genes have elevated rates of amino acid divergence compared to nonimmune genes, and this was particularly true for genes involved in the Imd pathway. Our findings are consistent with studies of other insects, which show that, as a group, immune genes are rapidly evolving (Schlenke and Begun 2003; Sackton et al. 2007; Viljakainen et al. 2009). The rapid divergence of immune system genes is often hypothesized to be the result of positive selection driving adaptive evolution of the immune system in response to pathogen pressure (Sackton et al. 2007). However, when we examined patterns of nucleotide diversity in the genes in our dataset, we found no evidence of recent positive selection driving the evolution of most of the immune genes. For example, although genes in the Imd pathway exhibit elevated amino acid divergence, they also tended to have higher levels ...
America is fatter than it compliments entirely enjoyed, and maturing fatter every download molecular, because we are noted placed, here ablaze, by a surprising determination of how and why the branch 1980s right. We undergo found on potent wounds and Other years. The antiquarian recipes of this download molecular evolution need daily flavored.
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Phylogenetic inference relies heavily on statistical models that have been extended and refined over the past years into complex hierarchical models to capture the intricacies of evolutionary processes. The wealth of information in the form of fully sequenced genomes has led to the development of methods that are used to reconstruct the gene and species evolutionary histories in greater and more accurate detail. However, genes are composed of evolutionary conserved sequence segments called domains, and domains can also be affected by duplications, losses, and bifurcations implied by gene or species evolution. This thesis proposes an extension of evolutionary models, such as duplication-loss, rate, and substitution, that have previously been used to model gene evolution, to model the domain evolution.. In this thesis, I am proposing DomainDLRS: a comprehensive, hierarchical Bayesian method, based on the DLRS model by Åkerborg et al., 2009, that models domain evolution as occurring inside the ...
Has the Earnest Student in the following conversation chosen a false Guru? How are the two failing to understand each other? ******* Guru: The vast majority of evolution is probably not due to natural selection (unless you define evolution as natural selection - but nobody does that these days). Earnest Student: You have defined evolution as change in allele frequency, but you have said that allele frequency is defined as the histogram made by counting the various allelles in the population for each gene. So, your definition of evolution would exclude a *redistribution* of alleles that leaves the histogram unchanged. A quantitative definition of evolution or rate of evolution should take account of changes in the *distribution* of alleles, not just the histogram of allele frequencies. Guru: The current definition of evolution is change in allele frequency. Are you claiming that the last generation of biologists were so stupid that they made up a useless definition? ******* Earnest Student: I ...
Our research is integrative and focussed on the interface between evolution and ecology of phenotypes in natural populations. One major goal of our research is to connect microevolutionary processes on short time scales with macroevolutionary diversification on longer time scales. Together we explore various central topics in ecology and evolution, including natural and sexual selection in the wild, the evolutionary dynamics discrete visual phenotypic polymorphisms (e. g. colour polymorphisms), frequency-dependent evolutionary dynamics, the evolution of reproductive isolation, quantitative genetics of trait evolution, canalization and phenotypic plasticity. Another rapidly emerging research theme in our laboratory is the evolution of thermal adaptation and thermal plasticity.. ...
Life is life is life. Life is gene, and gene is gene is gene. There is no primitive early-stage life versus evolved modern life. Complexity in life is what physics calls Broken Symmetry, which is what biology calls Evolution. And lifes evolution is simply a cosmic mass evolution, life being just one of the many cosmic mass formats. And, like in cosmic mass evolutions, lifes (Darwinian) evolution is based on and consists of the genes replicating with or without change, depending on whether its suggested-by-feed-back progenys expression gains or does not gain more constrained energy. Plain and simple. All cosmic and life evolutions are initiated and proceed and accumulate in answer to this one single question. All evolutionary complexities, of all degrees of complexity, evolve and develop in response to and in the direction of this one single question ...
Hsa (Homo sapiens (NM_003286); Mmu (Mus musculus, Dl0061); Rno (Rattus norvegicus, NM_02261S). , 2001. Zebrafish sequence from Smith et at, 2001 and ESTs fdlStu7 (AI666877, topIb) and ZF-ESTl24 (AI204804, topIa). An important feature of the topi tree is the relative branch lengths. Assuming that evolution occurred at equal rates in the mammalian and fish lineages, then the duplication event in the fish lineage occurred long before the divergence of rodent and primate lineages 112 million years ago (Kumar and Hedges 1998). Zebrafish sequence from Smith et at, 2001 and ESTs fdlStu7 (AI666877, topIb) and ZF-ESTl24 (AI204804, topIa). An important feature of the topi tree is the relative branch lengths. Assuming that evolution occurred at equal rates in the mammalian and fish lineages, then the duplication event in the fish lineage occurred long before the divergence of rodent and primate lineages 112 million years ago (Kumar and Hedges 1998). And assuming that evolution rates have been about the ...
Information from Wikipedia on the emergence of this field of study following the rise of molecular biology and the advent of protein sequencing. The differences between homologous sequences can be used as a molecular clock to estimate the time since...
Biological and artificial evolutionary systems exhibit varying degrees of evolvability and different rates of evolution. Such quantities can be affected by various factors. Here, we review some evolutionary mechanisms and discuss new developments in biology that can potentially improve evolvability or accelerate evolution in artificial systems. Biological notions are discussed to the degree they correspond to notions in Evolutionary Computation. We hope that the findings put forward here can be used to design computational models of evolution that produce significant gains in evolvability and evolutionary speed.. ...
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. The increasing availability of large genomic data sets requires powerful statistical methods to analyze and interpret them, generating both computational and conceptual challenges for the field.
Says lead researcher Dr Ian Wood of the Universitys Faculty of Biological Sciences: "This is the first study of the human genome to look at REST in such detail and compare the specific genes it regulates in different species. Weve found that it works by binding to specific genetic sequences and repressing or enhancing the expression of genes associated with these sequences. "Scientists have believed for many years that differences in the way genes are expressed into functional proteins is what differentiates one species from another and drives evolutionary change - but no-one has been able to prove it until now." The Leeds team, in collaboration with scientists in Singapore, examined the repertoire of genes that REST regulates, in particular those which are expressed in the central nervous system. The team compared 16 whole genome sequences in fish, primates and humans to see where and how REST binds to them. Until now, the nature and extent of such variation has been unknown but the present ...
In this video Dr. Jude Fitzgibbon, Barts Cancer Institute, Queen Mary University of London discusses his work investigating the molecular evolution of familial Acute Myeloid Leukemia (AML). He explains how his laboratory has investigated clinical heterogeneity between families involving at least three inherited gene mutations that can result in familial leukemia. Jude tells SelectScience how this work has implications for the clinical management of these families and how exome sequencing will enable more personalized treatment of familial AML by identifying additional co-operating mutations.
Page 7 of 7 - Why Evolution Is Clear To Me - posted in Best all time threads.: Hi Percy,I agree that is what evolution believes. But that is not what is being discussed. How does that fit within either of the 2 scenarios below?Pick one that best fits your view of evolution:So let me ask you a question: Pick one that best fits your view:1. Evolution is predestination. Given a similar environment evolution is predestined to produce nearly exactly the same organisms.2. Evolution i...
Read "Functional Systems and Modular Evolution: The Relationship between Fixation of New Domain Copies and the Present Structure of the Connections in the Functional System, Russian Journal of Genetics" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Purchase Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 - 1st Edition. Print Book & E-Book. ISBN 9780121820848, 9780080883007
Sapporo, Japan (SPX) Jul 26, 2016 - Scientists at Hokkaido University have revealed temperature-dependent energy-state conversion of molecular hydrogen on ice surfaces, suggesting the need for a reconsideration of molecular evolution
It is sometimes claimed that the pace of human evolution should have slowed as cultural adaptation supplanted genetic adaptation. The high empirical number of recent adaptive variants would seem sufficient to refute this claim. It is important to note that the peak ages of new selected variants in our data do not reflect the highest intensity of selection, but merely our ability to detect selection. Due to the recent acceleration, many more new adaptive mutations should exist than have yet been ascertained, occurring at a faster and faster rate during historic times. Adaptive alleles with frequencies under 22% should then greatly outnumber those at higher frequencies. To the extent that new adaptive alleles continued to reflect demographic growth, the Neolithic and later periods would have experienced a rate of adaptive evolution more than 100 times higher than characterized most of human evolution. Cultural changes have reduced mortality rates, but variance in reproduction has continued to fuel ...
The Genome Evolution Laboratory, directed by Prof. Nicole T. Perna, performs research into rates and patterns of adaptive genome evolution in animal and plant associated microbes. Our research involves experimental characterization of pathogens and computational modeling of genome evolution.
The protein kinase family is large and important, but it is only one family in a larger superfamily of homologous kinases that phosphorylate a variety of substrates and play important roles in all three superkingdoms of life. We used a carefully constructed structural alignment of selected kinases as the basis for a study of the structural evolution of the protein kinase–like superfamily. The comparison of structures revealed a “universal core” domain consisting only of regions required for ATP binding and the phosphotransfer reaction.
Our model results strongly suggest that "plasticity" or mutational stability of a sequence is correlated with its thermodynamic stability. We believe that this general conclusion follows directly from a fundamental principle of sequence design-that it is important to both design in the target structure and design out nontarget structures (32). Thus native states of better designed sequences are energetically more separated from their nonnative conformations, implying that they have higher thermodynamic stabilities (14, 22). Some threshold native stability may also be needed to avoid misfolding on multimerization and aggregation (33). Insofar as stability of a given native structure varies relatively smoothly in sequence space, a superfunnel-like organization is likely. In evolutionary terms, this means that in most cases the wild-type sequence may be identified with the prototype sequence, and that most if not all single-point mutations on the wild-type sequence would be thermodynamically ...
Abstract: In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and ...
2.3: Eukaryotic Evolution and Diversity pg. 67 For about 1.5 billion years Prokaryotes were on the only living organism on Earth. 3.5 to 2 billion years ago Prokaryotes thrive in many different environments.
Nothing new to readers of this weblog, but Wade does a good job surveying the various angles. Anyone with a model of evolution in their head shouldnt be surprised, the range of human variation is to be expected; we are a species which spans Arctic and tropical biomes, evolutionary pressures generally reshape populations into localized ecotypes. Dogs are similar except their selection pressure was our species, and our preferences (as opposed to environmental conditions) served as evolutions sculpting tool. Note that Wade mentions that selection seems notable on both disease and metabolically salient genomic regions. This illustrates the dynamic and multi-layered texture of evolutionary processes, pathogen resistance is always something which all complex species are always tinkering with as we attempt to stay ahead of the race. In regards to the changes in metabolism Wade alludes to the shift between hunter-gather and farming lifestyles. In most of the world this transition occurred between 5 to ...
Natural Selection refers to Darwins ideas about the forces that drive evolutionary change and it forms part of the theory of Evolution. Natural Selection suggests that the sole force driving evolution is competition for food, space and mates, i.e. survival. The theory of natural selection proposes that all variations that exist amongst organisms are generated randomly; and organisms compete to increase the representation of their own genes in next generations. Any cooperation that exists amongst organisms is an incidental result of individuals seeking their own advantage.Evolution according to Darwin has no direction. It does not inevitably lead to higher things; organisms just become better adapted to their environment. Darwin described a process that relies on chance mutations and natural selection to account for the adaptive complexity of the biological world. Individuals with successful traits are more fit than their competitors; thus they reproduce and pass on their genes to offspring at a ...
Bi/Ge/ESE 105. Evolution. 12 units (3-4-5): second term. The theory of evolution is arguably biologys greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as ...
A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.. The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.. The researchers -- Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon -- made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.. "The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution ...
This WebQuest was designed to help you locate evidence for evolution from different areas of science. New evidence for evolution is being discovered every day. No evidence has been found which cannot be explained by evolution. If the future continues as in the past, we can look forward to more information about the genomes of earths creatures, new discoveries in the fossil record, and the finding of new species in places like the ocean depths and the tropical rainforests. One thing is certain, more evidence will be added to support the theory of evolution. ...
Crisp et al. Genome Biology (2015) 16:50 DOI /s RESEARCH Open Access Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes
There is an interesting article on evolvability which I wrote a bit more about here. It is by Massimo Pigliucci and titled, Is Evolvability Evolvable, for which the whole PDF is available online. Pigliucci discusses definitions of evolvability as well as different ideas about the origins of evolvability. Here is the abstract: In recent years,…
The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation
The field of molecular evolution, which includes genome evolution, is devoted to finding variation within and between groups of organisms and explaining the processes responsible for generating this variation
Biologists, on the other hand, can confidently claim the equivalent "cinematic" sequence of fossils for a very large number of evolutionary transitions. Not all, but very many, including our own descent from the bipedal ape Australopithecus. And - far more telling - not a single authentic fossil has ever been found in the "wrong" place in the evolutionary sequence. Such an anachronistic fossil, if one were ever unearthed, would blow evolution out of the water ...
The main aim of my research is the understanding of how novel functions and biological complexity emerge in nature. In particular, we are interested in identifying the evolutionary trajectories, at the genome and regulatory levels, to biological innovations. This aim is relevant not only to the understanding of species diversification and the emergence of complexity but also to provide key knowledge for biotechnological and biomedical developments. Many biological innovations are simply off-limits for evolution because they involve dramatic changes to organisms that are often not tolerated by natural selection. However, under certain conditions, some molecular mechanisms can minimize the effects of innovative mutations allowing them to survive in the genome and become eventually fixed, potentially emerging as adaptive features when the environment changes. Our focus is on the characterization and use of buffering molecular mechanisms that provide robustness to mutations allowing the exploration ...
An interdisciplinary team of scientists at the Centre for Genomic Regulation in Barcelona, Spain, deepens understanding of tumor genome evolution and suggests negative selection acting on cancer-essential genes plays a more important role than previously anticipated.
We need to observe what humans have in common with their closer relatives, the apes and old world monkeys. We have one opsin that adapted to dim light and three for color vision. Most mammals only have two for color and this is why they are colorblind. The reason humans, apes and monkeys have three for color is due to the fact that our common ancestor experienced a duplication in the DNA sequences thus resulting in one extra copy for that particularly opsin ...
minimizing evolution-shifts: Each evolutionary sub-theory (as described in Section 2) is supported by different evidence, and should have different plausibility. We need conceptual clarity; the sub-theories of evolution should be precisely defined and their relationships should be carefully analyzed, because if there is only "evolution" it is easy to assume that evidence for some aspects of evolution necessarily provides strong support for other aspects. When we estimate the plausibility of an extrapolation from micro-E to Total Macro-E, there should be a rigorous evaluation for each step connecting the intermediate levels. This evaluation should be based on tight logic, not loose language that allows a transfer of support from one level to another. { Perhaps advocates of evolution can make a strong case for moving from lower levels of E to Total Macro-E, but the process of extrapolating between levels should be explicitly recognized ...
When speaking here of Darwinism, I shall speak always of todays theory - that is Darwins own theory of natural selection supported by the Mendelian theory of heredity, by the theory of the mutation and recombination of genes in a gene pool, and by the decoded genetic code. This is an immensely impressive and powerful theory. The claim that it completely explains evolution is of course a bold claim, and very far from being established. All scientific theories are conjectures, even those that have successfully passed many severe and varied tests. The Mendelian underpinning of modern Darwinism has been well tested, and so has the theory of evolution which says that all terrestrial life has evolved from a few primitive unicellular organisms, possibly even from one single organism. However, Darwins own most important contribution to the theory of evolution, his theory of natural selection, is difficult to test. There are some tests, even some experimental tests; and in some cases, such as the ...
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
Commonly, apologists for evolution put up a bold front and try to deny that the tree of evolution is full of holes (or, more accurately, is mostly holes with just twigs at the end). It is therefore instructive whenever an article appears that is written by evolutionists who candidly acknowledged the major discontinuities in (alleged) evolutionary sequences.. ...
The new review published recently in Royal Society Philosophical Transactions B highlights that the same genes are used throughout the animal kingdom for generating neural stem cells and other precursor cells of the nervous system. If the same genes are used, how then did the different shapes and behaviours evolve? Using the hugely diverse arthropods as an example, the review shows that neural genes can have many different functions in early nervous system development in the different species and morphological contexts.. The review suggests that this flexibility of the neural genes has facilitated the evolution of the neuronal networks and the adaptation to different shapes and environments. The paper came out following a Royal Society discussion meeting on the Origin and evolution of the nervous system in March 2015.. Author of the review and Reader in Evolutionary Development Biology at SBCS Angelika Stollewerk explains:. "The data clearly show that in order to understand the evolution of ...
The theory of evolution offers an explanation for the existence of 2 The theory of evolution offers an explanation for the existence of all living organisms on the Earth today and in the past It supposes that present day organisms have all been derived from organisms that lived in the past By a series of very small changes over millions of years new species have developed from previous species* Over a period of about 3000 million years, many new species have been produced and many have become extinct. * In some cases it appears that evolution proceeded by periods of rapid change, interspersed with periods of little or no change, We know a great deal about the organisms that lived millions of years ago from studying their fossilised remains. Theory of evolution
Woese believes that along the way biologists were seduced by their own success into thinking they had found the final truth about all evolution. "Biology built up a facade of mathematics around the juxtaposition of Mendelian genetics with Darwinism," he says. "And as a result it neglected to study the most important problem in science - the nature of the evolutionary process.". In particular, he argues, nothing in the modern synthesis explains the most fundamental steps in early life: how evolution could have produced the genetic code and the basic genetic machinery used by all organisms, especially the enzymes and structures involved in translating genetic information into proteins. Most biologists, following Francis Crick, simply supposed that these were uninformative "accidents of history". That was a big mistake, says Woese, who has made his academic reputation proving the point.. In 1977, Woese stunned biologists when his analysis of the genetic machinery involved in gene expression ...
Parallel-connected modules have been widely used in battery packs for electric vehicles nowadays. Unlike series-connected modules, the direct state inconsistency caused by parameter inconsistency in parallel modules is current and temperature non-uniformity, thus resulting in the inconsistency in th
Evolution can be considered to either have a direction or to be merely the result of the meandering of a complex system underpinned by random mutation. Convergent evolution would suggest, instead, ... More. Evolution can be considered to either have a direction or to be merely the result of the meandering of a complex system underpinned by random mutation. Convergent evolution would suggest, instead, that there are directions in the evolutionary process or that similar environmental contingencies generate similar solutions. A brief digression into human history and development would suggest that there is a direction, although often temporarily obscured. That direction is towards the construction of a suitable human niche in terms of satisfaction of basic life-long needs for food, water, and freedom from disease. The plant niche is often not referenced in the literature, but is constructed from a two-way flow of information between environment and organism. The environment and plant are to be ...
M uscale. A. E. Cell Evolution Analysis. Cell Evolution Analysis Software Automated Cell Migration and Proliferation Analysis. C. ELL. E. VOLUTION. A. NALYSIS. C. USTOMIZABLE. E. ASY TO USE. A. UTOMATED. Dish Area. Extraction of Cell Clustering Area (Region of Interest). Slideshow 5054157 by kyria
Whether a locus evolves neutrally or under the influence of natural selection is of great interest in molecular evolutionary study
Many of the fascinating examples resulting from millions of years of evolution are known from the vertebrate lineage of chordate animals. Because of the vast range of body plan diversifications that have arisen, knowing vertebrate evolutionary morphology is crucial for exploring the structural basis reflecting processes of adaptive (but also neutral) evolution. As such, especially functional systems that form the core of the survival of vertebrate organisms can be expected to best reflect the processes of variation, natural selection and adaptation. Two systems that have been subjected to intense selective pressures, but still show a tremendous variation and specialization towards an increased performance, are the feeding and the locomotory systems. The research within the group focuses on several aspects underlying the morphological evolution of these two systems in several representative lineages of vertebrates. Particularly animal groups with extreme specializations and/or performance are the ...
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Zinc atom in PDB 3gjn: Following Evolutionary Paths to High Affinity And Selectivity Protein-Protein Interactions Using COLICIN7 and Immunity Proteins
In organisms like humans, or even mice, it can be difficult to study the effects of evolution because evolutionary changes take many generations to appear, and for us humans, a new generation takes over a decade, often longer. Furthermore, in complex organisms, many changes can be difficult to spot and follow over time. Enter the lowly bacteria, Escherichia coli, which reproduces very quickly, and has a small genome in which to watch for mutations. Since February of 1988, Richard Lenski and his colleagues have kept up a long term evolution experiment (LTEE), which has propagated a bacterial culture every day for over 50,000 generations. Every 500 generations (75 days), samples are taken and frozen so that researchers in the future can go back in time to determine when a particular trait may have arisen, changed, or disappeared.. In todays paper, Leiby and Marx used samples from the Lenski LTEE to investigate the mechanism by which evolutionary adaptation arises. In particular, they wanted to ...
Next up was Madison, who is 4 months younger than Luca. The two of them have a blast together, though it seems they are going through the mine! stage at the same time, which can be interesting. Madisons mom sometimes watches Luca for me for a few hours at a time, and Luca is mildly obsessed with her, in a good way. When she sees pictures of her, she says her name and sometimes when were out places shell see something that makes her think of Madison and shell talk about her. Its really, really cute. We hung out with Madison for a few hours so her mom and dad could go watch the Cardinals win the game that got them into the Super Bowl ...
Details work exploring the evolution of novel ribozymes (deoxyribo and ribonucleic acid catalysts) from populations of random sequences, attempting to shed light on the origins of biological catalysis.
Remember, normal text is copied from Evolution 101 by the Understanding Evolution team! (And yes, it really says that on their web site) http://evolution.berkeley.edu/BOLD font is me, Rent A Friend 2000, being Bold.The family treeThe process of evolution produces a pattern of relationships between species. .Its cute how they use the word
Background The ferlin gene family possesses a rare and identifying feature consisting of multiple tandem C2 domains and a C-terminal transmembrane domain. Much currently remains unknown about the...
Biological complexity is a feature that increases during evolution, distinguishing us from more primitive forms of life. Whereas it has no straightforward definition, it is generally accepted that it can be measured by the number of different cell types in an organism ranging from 1 (bacteria) to about 200 (humans) [1-4]. As complexity is apparently related to the amount of information an organism needs to function properly, and such information is contained in our genes, it was generally expected that the number of genes correlates with biological complexity. This was called into doubt and referred to as the G-value paradox [5]. There have been numerous attempts to resolve the paradox, citing multifunctionality of proteins [6], microRNAs [7], non-protein-coding DNA [8] or alternative splicing [9]. In this paper we set out to revisit this problem as the genomes of many more eukaryotes have been sequenced and new information has accumulated about their alternative splicing. In addition, we have ...
Big One Runners is a specific product used to keep the protein reserves in muscles intact. It allows all athletes to face the necessary and constantly increasing work loads, with optimal recovery rates.
The Problem: "Evolutionists gloss over this evo-foundation issue.". Evo-Sith Lady of evolution Eugenie Scott is executive director of the National Center for Science Education, Inc - basically an anti-creationist hate-group (see their website if you dont believe me, at www.ncseweb.org ). When John Gibson of FOX News (5/6/2005) asked her if evolution can answer how life got started, she replied, "No. But thats not what evolution is all about. Evolution is the inference that living things had common ancestors. The origin of life is a completely separate problem … creationists like to confuse the two, because they look at the origin of life as the soft underbelly of evolution." Eugenies got it wrong here, at least about me anyway. I do not see the origin of life as the "soft underbelly of evolution." I see the whole evo-theory as just one big gigantic soft spot! But lets look close at this in particular which she called a "soft underbelly" of evolution, shall we? This looking-close exercise, ...
A couple of weeks ago, if you randomly woke me in the middle of the night and demanded to know the fundamental difference between evolution and learning as adaptive processes, I would probably respond: how did you get into my house? and umm... I guess they are mostly the same, it is just a matter…
The versatility of the E220evolution Focused-ultrasonicator makes it possible to bring the advantages of AFA to numerous biological and chemical applications including: DNA and chromatin shearing, tissue homogenization, cell lysis, compound dissolution, and particle micronization. The E220evolution enables multi-sample, batch preparation, capable of processing a wide range of sample types and volumes and may be programed to process from 1 to 8 samples in a single batch. And, when workload increases, the E220evolution can be upgraded to an E220 capable of processing 1-96 samples/run or to an LE220 for high throughput processing without purchasing a new instrument.. ...
The Geologic Timeline and the Evolution of Life - The Origin of Life and the Evolution of Cells - THE ORIGIN AND CLASSIFICATION OF LIFE - CONCEPTS IN BIOLOGY - Lectures on biology. The study of biology.
Ongoing since 1999, the lab has worked to develop infrared probes of protein dynamics, specifically the carbon-deuterium (C-D) bond. Weve used C-D bonds to characterize stability, folding, and function of a variety of proteins, and compared their use to other common IR probes of proteins. A second biophysical project focuses on protein evolution, specifically evolution of antibodies and the role of somatic mutations in altering antibody structure and dynamics. Weve characterized antibodies raised against several chromophoric antigens, which have allowed us to measure the rigidity of the antibody-antigen complex using nonlinear optical spectroscopy.. ...
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 1.1.1.1) 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 ...
TY - JOUR. T1 - Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura. AU - Jensen, Jeffrey. AU - Bachtrog, Doris. PY - 2010. Y1 - 2010. N2 - Characterizing the distribution of selection coefficients in natural populations remains a central challenge in evolutionary biology. We resequenced a subset of 19 fast-evolving protein-coding genes in the sister species Drosophila miranda and D. pseudoobscura and their flanking regions to characterize the spatial footprint left by recurrent and recent selection. Consistent with previous findings, fast-evolving genes and their flanking regions show reduced levels of neutral diversity compared with randomly chosen genes, as expected under recurrent selection models. Applying a variety of statistical tests designed for the detection of selection at different evolutionary timescales, we attempt to characterize parameters of adaptive evolution. In D. miranda, fast-evolving genes generally show ...
Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these extra fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication ...
Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions
Transdermal delivery is an attractive option for drug delivery. Nevertheless, the skin is a tough barrier and only a limited number of drugs can be delivered through it. The most difficult to deliver are hydrophilic drugs. The stinging mechanism of the cnidarians is a sophisticated injection system consisting of microcapsular nematocysts, which utilize built-in high osmotic pressures to inject a submicron tubule that penetrates and delivers their contents to the prey. Here we show, for the first time, that the nematocysts of the starlet sea anemone Nematostella vectensis can be isolated and incorporated into a topical formulation for continuous drug delivery. We demonstrate quantitative delivery of nicotinamide and lidocaine hydrochloride as a function of microcapsular dose or drug exposure. We also show how the released submicron tubules can be exploited as a skin penetration enhancer prior to and independently of drug application. The microcapsules are non-irritant and may offer an attractive
Background: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which ...
Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ~900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human
Read "The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements, Plant Molecular Biology" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
A common feature of chemosensory systems is the involvement of G protein-coupled receptors (GPCRs) in the detection of environmental stimuli. Several lineages of GPCRs are involved in vertebrate olfaction, including trace amine-associated receptors, type 1 and 2 vomeronasal receptors and odorant receptors (ORs). Gene duplication and gene loss in different vertebrate lineages have lead to an enormous amount of variation in OR gene repertoire among species; some fish have fewer than 100 OR genes, while some mammals possess more than 1000. Fascinating features of the vertebrate olfactory system include allelic exclusion, where each olfactory neuron expresses only a single OR gene, and axonal guidance where neurons expressing the same receptor project axons to common glomerulae. By identifying homologous ORs in vertebrate and in non-vertebrate chordates, we hope to expose ancestral features of the chordate olfactory system that will help us to better understand the evolution of the receptors themselves and
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... 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. [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 ...
... temporary account for courses tmp16 at nuscc.nus.sg Mon Jul 6 03:01:39 EST 1992 *Previous message: ...
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. ...
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: orcid.org/0000-0002-4028 ...
Other journals dedicated to molecular evolution include Journal of Molecular Evolution and Molecular Phylogenetics and ... Genome evolution Heterotachy History of molecular evolution Horizontal gene transfer Human evolution Molecular clock Molecular ... The Society for Molecular Biology and Evolution publishes the journals "Molecular Biology and Evolution" and "Genome Biology ... Nei, M. (2005). "Selectionism and Neutralism in Molecular Evolution". Molecular Biology and Evolution. 22 (12): 2318-2342. doi: ...
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 ...
Previous message: [Molecular-evolution] [Microbiology] eight PhD fellowships * Messages sorted by: [ date ] [ thread ] [ ... Previous message: [Molecular-evolution] [Microbiology] eight PhD fellowships * Messages sorted by: [ date ] [ thread ] [ ... Molecular-evolution] [Microbiology] eight PhD fellowships. Isabell Witt via mol-evol%40net.bio.net (by isabell.witt from uni- ... We do research in molecular genetics, functional genomics, cell biology, developmental biology, biotechnology and biochemistry ...
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. ...
Stevens, J.R., Noyes, H.A., Schofield, C.J. & Gibson, W. (2001) The Molecular Evolution of Trypanosomatidae. Advances in ... Molecular Phylogenetics and Evolution, 44 (1): 15-25. [PDF available on request] ... Molecular Phylogenetics and Evolution, 63: 521-526. [View PDF]. Stevens J.R. (2014) Free-living bodonids and derived parasitic ... Infection, Genetics and Evolution 1: 143-150. [View PDF] Hamilton, P.B., J.R. Stevens, M.W. Gaunt, J. Gidley & W.C. Gibson ( ...
  • 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. (hawaii.edu)
  • 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. (wiley.com)
  • Many excellent reviews describing the genetics and biochemistry of the origins, evolution, and mechanisms of antibiotic resistance have appeared over the last 60 years. (asm.org)
  • In both biochemistry and molecular evolution, the important role of information asymmetry remains largely unaddressed. (royalsocietypublishing.org)
  • When we see convergent evolution provide the same solution to a complex problem, we have a better understanding of its importance. (asbmb.org)
  • Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. (pnas.org)
  • previous descriptions of L. infantum and " L. archibaldi " from this region are a consequence of convergent evolution in the isoenzyme data. (springer.com)
  • 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. (grc.org)
  • Tom Whittam's pioneering research into the structure of Escherichia coli populations not only advanced the field of microbial evolution and genetics, but it also provided a contextual framework for investigating variation in the epidemiology and virulence of bacterial populations. (asmscience.org)
  • Thus, the characterization of PPL length and pseudogene profiling may be useful to understand the molecular evolution of SG and the epidemiology of FT. (medworm.com)
  • Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. (springer.com)
  • Computational Molecular Evolution provides an up-to-date and comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. (oup.com)
  • The new study begins to answer fundamental questions about changes at the molecular level that eventually shape the destinies of all organisms, Johnson said. (medindia.net)
  • UCLA molecular biologist James A. Lake reports important new insights about prokaryotes and the evolution of life in the Aug. 20 advance online edition of the journal Nature . (nsf.gov)
  • 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. (cambridge.org)
  • 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. (asbmb.org)
  • I have often neglected to consider evolution when trying to understand the molecular basis of a given cellular process. (asbmb.org)
  • 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. (icr.org)
  • Another major problem is that many complex molecular and cellular features unique among eukaryotes are not found in any prokaryotes. (icr.org)
  • 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. (icr.org)
  • Viewing molecular and cellular processes within their evolutionary contexts can reveal key mechanistic information. (grc.org)
  • Irreducibly complex parts at the molecular level are actually cobbled together by simpler parts and put together as a whole. (hubpages.com)
  • Evolution works at the DNA level. (hubpages.com)
  • Fay JC (2011) Weighing the evidence for adaptation at the molecular level. (els.net)
  • Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. (genetics.org)
  • Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. (nature.com)
  • This information will prove invaluable as we proceed to dissect, at a molecular level, events associated with Q fever pathogenesis. (infectioncontroltoday.com)
  • I need to be careful what I say here - one ticking off I got was from a biologist who was unhappy that I had over-stressed natural selection at the molecular level, which I freely confess was a slight failure of nerve - I have found that saying such things can induce apoplexy in folks who see the shadows of creationism everywhere. (blogspot.com)
  • In the research towards holistic preventative health, anti-aging hallmarks such as stem cell exhaustion, mitochondrial dysfunction, senescent cells accumulation and telomere attrition are being researched with the latest advances in molecular biology at the DNA sequencing level. (worldhealth.net)
  • I can understand how evolution occurs on the grander scale of things very easily, but take a moment and look at a diagram showing this whole process at the molecular level. (biology-online.org)
  • People begin to wonder if Darwin's evolution holds after going through what happens at the micro level at tremendous detail. (biology-online.org)
  • This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level. (unboundmedicine.com)
  • 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. (le.ac.uk)
  • This leads naturally to hypotheses on the evolution of development, that can be explored in the lab. (phys.org)
  • 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. (elsevier.com)
  • 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. (go.jp)
  • Evolution is a gradual process in which a biological organism changes into a different and usually more complex form. (hubpages.com)
  • This shows that an "irreducibly complex" mechanism in the final stage of development, was actually built up in parts.It evolved and this shows that evolution is still the best explanation for biological change. (hubpages.com)
  • Molecular biological approaches have become critical to understanding evolution. (grc.org)
  • The problem is that there are not really leading figures that can come down with what might be called The Standard Model of Biological Evolution. (blogspot.com)
  • Molecular biology will bring the mechanistic understanding of biological phenomena while evolutionary biology supplies understanding of the natural and historical contexts of the evolution of biological systems. (plos.org)
  • Biological macromolecules encode information: some of it to endow the molecule with structural flexibility, some of it to enable molecular actions as a catalyst or a substrate, but a residual part can be used to communicate with other macromolecules. (royalsocietypublishing.org)
  • 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. (innovations-report.com)
  • In the study, the researchers developed a special system that could detect the ortho/para ratio of molecular hydrogen on artificial ice particles. (space-travel.com)
  • Most researchers in the fields of molecular biology and medicine are unacquainted with evolutionary theory, and hence overlook the critical role of evolutionary processes in the phenomena they are studying. (plos.org)
  • This relationship resulted in a totally different type of life on Earth," said Lake, a UCLA distinguished professor of molecular, cell and developmental biology and of human genetics. (scienceblog.com)
  • Nucleic acids are attractive materials for creating functional molecules that have applications as catalysts, specific binders, and molecular switches. (mdpi.com)
  • 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. (mdpi.com)
  • This review focuses on the effectiveness of chemical modifications on the evolution of nucleic acids as functional molecules and the outlook for related technologies. (mdpi.com)
  • P.S. If your answer is that a high rate of evolution in archaebacteria explains the result then you would fail unless you have evidence that I'm unaware of. (blogspot.com)