Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.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.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.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.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Agropyron: A plant genus of the family POACEAE. The common name of wheatgrass is also used for other plants in the family.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.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.Fruiting Bodies, Fungal: The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.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.Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Heteroptera: A suborder of HEMIPTERA, called true bugs, characterized by the possession of two pairs of wings. It includes the medically important families CIMICIDAE and REDUVIIDAE. (From Dorland, 28th ed)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.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)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.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.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.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.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.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.Basidiomycota: A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.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.Genetic Variation: Genotypic differences observed among individuals in a population.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Mycological Typing Techniques: Procedures for identifying types and strains of fungi.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)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).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)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.Spores, Fungal: Reproductive bodies produced by fungi.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.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)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.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.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.Genes, Bacterial: The functional hereditary units of BACTERIA.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.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.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.Bacterial Proteins: Proteins found in any species of bacterium.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Skull Base: The inferior region of the skull consisting of an internal (cerebral), and an external (basilar) surface.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.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).Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Schiff Bases: Condensation products of aromatic amines and aldehydes forming azomethines substituted on the N atom, containing the general formula R-N:CHR. (From Grant & Hackh's Chemical Dictionary, 5th ed)Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.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.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Ascomycota: A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.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.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.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Hanseniaspora: A genus of the ascomycetous yeast in the family Saccharomycodaceae, order SACCHAROMYCETALES, that contributes to the spontaneous fermentation of cider. Anamorphic forms are in the genus KLOECKERA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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)Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)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).RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.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.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Genes, Plant: The functional hereditary units of PLANTS.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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Ferns: Seedless nonflowering plants of the class Filicinae. They reproduce by spores that appear as dots on the underside of feathery fronds. In earlier classifications the Pteridophyta included the club mosses, horsetails, ferns, and various fossil groups. In more recent classifications, pteridophytes and spermatophytes (seed-bearing plants) are classified in the Subkingdom Tracheobionta (also known as Tracheophyta).Kinetics: The rate dynamics in chemical or physical systems.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.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.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Aminacrine: A highly fluorescent anti-infective dye used clinically as a topical antiseptic and experimentally as a mutagen, due to its interaction with DNA. It is also used as an intracellular pH indicator.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.Cactaceae: The cactus plant family of the order Caryophyllales, subclass Caryophyllidae, class Magnoliopsida. Cacti are succulent perennial plants well adapted to dry regions.Gene Order: The sequential location of genes on a chromosome.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Invertebrates: Animals that have no spinal column.Molecular Weight: The sum of the weight of all the atoms in a molecule.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Genes, Viral: The functional hereditary units of VIRUSES.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Cytochromes b: Cytochromes of the b group that have alpha-band absorption of 563-564 nm. They occur as subunits in MITOCHONDRIAL ELECTRON TRANSPORT COMPLEX III.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.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.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Orchidaceae: A plant family of the order Orchidales, subclass Liliidae, class Liliopsida (monocotyledons). All orchids have the same bilaterally symmetrical flower structure, with three sepals, but the flowers vary greatly in color and shape.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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.China: A country spanning from central Asia to the Pacific Ocean.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.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.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)Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.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).Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Birds: Warm-blooded VERTEBRATES possessing FEATHERS and belonging to the class Aves.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.Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.Poly dA-dT: Polydeoxyribonucleotides made up of deoxyadenine nucleotides and thymine nucleotides. Present in DNA preparations isolated from crab species. Synthetic preparations have been used extensively in the study of DNA.Actinomycetales: An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.GuanineViral Proteins: Proteins found in any species of virus.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.Saccharomycetales: An order of fungi in the phylum Ascomycota that multiply by budding. They include the telomorphic ascomycetous yeasts which are found in a very wide range of habitats.Thermodynamics: A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)Saccharomyces: A genus of ascomycetous fungi of the family Saccharomycetaceae, order SACCHAROMYCETALES.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.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.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.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.Intercalating Agents: Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.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.Disease Outbreaks: Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Butterflies: Slender-bodies diurnal insects having large, broad wings often strikingly colored and patterned.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.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Nucleotides: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.Skull Base Neoplasms: Neoplasms of the base of the skull specifically, differentiated from neoplasms of unspecified sites or bones of the skull (SKULL NEOPLASMS).Base Pair Mismatch: The presence of an uncomplimentary base in double-stranded DNA caused by spontaneous deamination of cytosine or adenine, mismatching during homologous recombination, or errors in DNA replication. Multiple, sequential base pair mismatches lead to formation of heteroduplex DNA; (NUCLEIC ACID HETERODUPLEXES).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.Chemistry: A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.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.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.DNA Gyrase: A bacterial DNA topoisomerase II that catalyzes ATP-dependent breakage of both strands of DNA, passage of the unbroken strands through the breaks, and rejoining of the broken strands. Gyrase binds to DNA as a heterotetramer consisting of two A and two B subunits. In the presence of ATP, gyrase is able to convert the relaxed circular DNA duplex into a superhelix. In the absence of ATP, supercoiled DNA is relaxed by DNA gyrase.Chemical Phenomena: The composition, conformation, and properties of atoms and molecules, and their reaction and interaction processes.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.Recombinant Proteins: Proteins prepared by recombinant DNA technology.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Deoxyribonucleotides: A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Quinones: Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.Models, Chemical: Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.Microscopy, Electron: Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.DNA 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.Coliphages: Viruses whose host is Escherichia coli.TritiumGene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.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).Transformation, Genetic: Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.Oligoribonucleotides: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
... it has become feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses. For ... The problem of character coding is very different in molecular analyses, as the characters in biological sequence data are ... complicating phylogenetic analysis based on genes. This phenomenon can contribute to "incomplete lineage sorting" and is ... "How Fitch-Margoliash Algorithm can benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics. 7: 61-85. Day, William ...
Rather than inferring the ancestral DNA sequence, one may be interested in the larger-scale molecular structure and content of ... HyPhy, Mesquite, and MEGA are also software packages for the phylogenetic analysis of sequence data, but are designed to be ... "Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the ... Stamatakis, A. (2006). "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models". ...
With the large-scale genome sequencing still producing very large amounts of DNA and protein sequences, there is enough data ... "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". J ... but also for phylogenetic analyses. The Dayhoff PAM matrices were based on relatively few alignments (since not more were ... When an analysis of real biological data is performed, there is generally no access to the sequences of ancestral species, only ...
... more uncertainty may be expected in large analyses. Because data collection costs in time and money often scale directly with ... Farris, J. S. (1983). The logical basis of phylogenetic analysis. In Advances in Cladistics Vol. 2 (eds. N. I. Platnick, and V ... and the reduced cost and increased automation of molecular sequencing, sample sizes overall are on the rise, and studies ... This is often done for nucleotide sequence data; it has been empirically determined that certain base changes (A-C, A-T, G-C, G ...
The afrotherian clade was originally proposed in 1998 based on analyses of DNA sequence data. However, previous studies had ... More recent, genomic-scale phylogenies favor the hypothesis that Afrotheria and Xenarthra comprise sister taxa at the base of ... "Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets". Molecular Biology and Evolution. 25 (9): ... Evolution of the mammalian placenta revealed by phylogenetic analysis Mammals portal. ...
... most contemporary methods are based on analyses of genomic sequence data. These methods can be broadly separated into two ... making them a good basis for developing large-scale scans for HGT, looking for highways of gene sharing in databases of ... The use of phylogenetic analysis in the detection of HGT was advanced by the availability of many newly sequenced genomes. ... The molecular clock hypothesis posits that homologous genes evolve at an approximately constant rate across different species. ...
... found in these studies are the low resolution of single-gene based phylogenetic trees and the fact that coding DNA data are ... The phylogenetic trees recently obtained by Jarvis et al support the hypothesis of an early fast radiation that would have ... A dN/dS analysis showed conserved evolution in 227 genes, most of which are highly expressed in the regions of the brain that ... 56% of β-keratins are feather-specific and can only be found in birds, whereas those that make up scales and claws can also be ...
Genetic analysis has supported archaeological hypotheses of a large-scale migrations of Bantu speakers into Southern Africa ... aDNA comparison study can also reveal the evolutionary relationship between two species. The number of base differences between ... One method of massive parallel sequencing, developed by Margulies et al., employs bead-based emulsion PCR and pyrosequencing, ... genetic data have given rise to alternative hypotheses. For example, one hypothesis proposes a migration from Siberia to South ...
Modern Molecular phylogenetics largely ignores morphological characters, relying on DNA sequences as data. Molecular analysis ... Phylogenetic studies attempt to discover phylogenies. The basic approach is to use similarities based on shared inheritance to ... The results of cladistic analyses are expressed as cladograms: tree-like diagrams showing the pattern of evolutionary branching ... With the rise of the related molecular-scale biological approaches of molecular biology, genomics, proteomics and metabolomics ...
Later studies based on molecular genetics were able to resolve the trichotomy: chimpanzees are phylogenetically closer to ... of unique sequence to each genome, since each insertion or deletion can involve anywhere from one base to millions of bases. A ... Chimpanzee Sequencing; Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human ... A phylogenetic tree is usually derived from DNA or protein sequences from populations. Often, mitochondrial DNA or Y chromosome ...
... or molecular, by comparing sequences of DNA or protein. The result of a successful analysis is a hierarchy of clades - groups ... A possible "evolutionary arms race" between predators and prey is one of the hypotheses that attempt to explain the Cambrian ... "The Impact of Fossils and Taxon Sampling on Ancient Molecular Dating Analyses" (Free full text). Molecular Biology and ... Although their evolutionary importance was not known, on the basis of their old age, William Buckland (1784-1856) realised that ...
... relying on DNA sequences as data. Molecular analysis of DNA sequences from most families of flowering plants enabled the ... The evolutionary relationships and heredity of a group of organisms is called its phylogeny. Phylogenetic studies attempt to ... In 1998, the Angiosperm Phylogeny Group published a phylogeny for flowering plants based on an analysis of DNA sequences from ... With the rise of the related molecular-scale biological approaches of molecular biology, genomics, proteomics and metabolomics ...
"Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia". Molecular Biology and Evolution. ... genomic architecture and phylogenetic analysis" (PDF). Theory Biosci. 126 (1): 35-42. CiteSeerX 10.1.1.177.8060. doi:10.1007/ ... Bernstein, H.; Hopf, F.A.; Michod, R.E. (1987). The molecular basis of the evolution of sex. Adv. Genet. Advances in Genetics. ... Species estimates shown here are based on numbers described scientifically; much larger estimates have been calculated based on ...
In the 1990s, molecular phylogenetic analyses of DNA sequences produced a coherent scheme showing arthropods as members of a ... Efforts to control arthropod pests by large-scale use of pesticides have caused long-term effects on human health and on ... Simplified summary of Budd's "broad-scale" cladogram (1996) Further analysis and discoveries in the 1990s reversed this view, ... A study in 1992 estimated that there were 500,000 species of animals and plants in Costa Rica alone, of which 365,000 were ...
... two international research teams published analyses of large-scale genotyping of large samples of Europeans, using over 300,000 ... conclusions derived from such studies are compiled on the basis of how the author envisages their data fits with established ... haplogroups of Europeans are surveyed by using a combination of data from RFLP analysis of the coding region and sequencing of ... Molecular Anthropology portal Evolutionary biology portal Europe portal Y-DNA haplogroups in populations of Europe African ...
In a study published in 2013, Jeffrey Wall from University of California studied whole sequence-genome data and found higher ... affecting 20 million bases of sequence"; the latter figure corresponds to 0.6% of total number of base pairs.[3] Nearly all (, ... Although genetic analyses of large numbers of loci can produce estimates of the percentage of a person's ancestors coming from ... Human evolutionary genetics. *Multiregional hypothesis. *Recent single origin hypothesis. *Isolation by distance ...
Application of Phylogenetic Networks in Evolutionary Studies - Molecular Biology and Evolution 23(2) 2006 Atkinson, Meade, ... Cladistic analysis of languages - IE classification based on lexicostatistical data, Cladistics 19/2 (Apr 2003) CSLI ... a program for analysing and visualising evolutionary data - Bioinfomatics 14(1) (1998). Warnow, Evans, Ringe and Nakhleh : A ... It can handle large and complicated data sets. However, the output is a phenogram rather than a phylogram. This is the most ...
However, an analysis in 2005 concluded that phoronids are a sub-group of bryozoans. While all molecular phylogeny studies and ... From 1988 onwards analyses based on molecular phylogeny, which compares biochemical features such as similarities in DNA, have ... "The phylogenetic position of Brachiopoda-a comparison of morphological and molecular data". Zoologica Scripta. 26 (3): 245-253 ... and the cillia down the middle drive this mixture to the base of the tentacles. A brachial groove runs round the bases of the ...
It depends on two factors for its specificity: the target sequence and the PAM. The target sequence is 20 bases long as part of ... Analysis of CRISPRs in metagenomic data is more challenging, as CRISPR loci do not typically assemble, due to their repetitive ... Mutation studies confirmed this hypothesis, showing that removal of cas1 or cas2 stopped spacer acquisition, without affecting ... including some used in food production and large-scale fermentation Cellular or organism RNA-guided genome engineering. Proof ...
... and computer analysis of viral and host DNA sequences are giving a better understanding of the evolutionary relationships ... Cellular origin hypothesis Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger ... Viruses are important to the study of molecular and cell biology as they provide simple systems that can be used to manipulate ... To date, such analyses have not proved which of these hypotheses is correct.[61] However, it seems unlikely that all currently ...
Later morphological phylogenetic studies with this in mind placed turtles firmly within Diapsida. All molecular studies have ... Exposed parts of reptiles are protected by scales or scutes, sometimes with a bony base, forming armor. In lepidosaurians, such ... Insights from phylogenetic retrofitting and molecular scaffolds". Journal of Evolutionary Biology. 26 (12): 2729-2738. doi: ... Molecular work has usually placed turtles within the diapsids. So far three turtle genomes have been sequenced. The results ...
However, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged ... Recorded extinction events are therefore based on the more easily observed changes in the diversity and abundance of larger ... or a group of organisms with a certain degree of evolutionary relatedness (the phylogenetic definition). Arthropods total about ... For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing ...
Gouy M; Li WH (May 1989). "Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte ... Based on PDB 1FBB. Data published in Subramaniam S; Henderson R (August 2000). "Molecular mechanism of vectorial proton ... the largest known archaeal genome. The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the ... In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that ...
DNA sequence differences that would be abundant in a singleton-based study do not interfere with the analysis. Environmental ... by mutations in the MECP2 gene despite no large-scale changes in expression of MeCP2 being found in microarray analyses. BDNF ... "Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases". Genome ... To emphasize the difference of this molecular mechanism of inheritance from the canonical Watson-Crick base-pairing mechanism ...
A 2013 phylogenomic study supported the two new proposed suborders. In the 1980s, a hypothesis based on morphological evidence ... PMC 2544561 . Lei, M.; Dong, D. (2016). "Phylogenomic analyses of bat subordinal relationships based on transcriptome data". ... Strauß, J.; Lakes-Harlan, R. (2014). "Evolutionary and Phylogenetic Origins of Tympanal Hearing Organs in Insects". In Hedwig, ... Molecular Biology and Evolution. 22 (9): 1869-1886. doi:10.1093/molbev/msi180. PMID 15930153. Several molecular studies have ...
The Angiosperm Phylogeny Website (or APweb) is a well-known web site dedicated to research on angiosperm phylogeny and taxonomy. The site is hosted by the Missouri Botanical Garden website and maintained by researchers, Peter F. Stevens and Hilary M. Davis. Peter F. Stevens is a member of the Angiosperm Phylogeny Group (APG). The taxonomy presented is broadly based on the work of the APG, with modifications to incorporate new results. APWebsite is a resource for NCBI (NCBI) A useful site for Kew Gardens (Kew Gardens) Stevens, Peter F. (2006). "The angiosperm phylogeny Website - a tool for reference and teaching in a time of change". Proceedings of the American Society for Information Science and Technology. 42. doi:10.1002/meet.14504201249. Angiosperm Phylogeny Website hosted by the Missouri Botanical Garden Website Note: This is a selected list of the more influential systems. There are many other systems, for instance a review of earlier systems, published by Lindley in ...
... (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range ...
A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly)[1] between nucleotide sequences, genes, chromosomes, genomes, or species.[2] They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent).[3] Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree[4], the R-package, phangorn,[5][6] and, more ...
... (from Greek φῦλον phylon "tribe" + γένεσις genesis "origin") is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics. These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular biology and genomics), in the explanation of phylogeny and its research. Phylogenetic relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a phylogeny (also known as a phylogenetic tree) - a diagrammatic hypothesis about the history ...
... (/məˈlɛkjʊlər ˌfaɪloʊdʒəˈnɛtɪks, mɒ-, moʊ-/) is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography. The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling, and Walter M. Fitch. Applications of molecular systematics were pioneered by ...
Hughes, L.C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C.C., Thompson, A.W., Arcila, D., Betancur-R., D., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B., Zhou, Z., Huang, H., Chen, S., Venkatesh, B. & Shi, Q. (2018): Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences, 115 (24) 6249-6254. doi: 10.1073/pnas.1719358115 ...
Angiosperm Phylogeny Group (2009). "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III" (PDF). Botanical Journal of the Linnean Society. 161 (2): 105-121. doi:10.1111/j.1095-8339.2009.00996.x. ശേഖരിച്ചത് 2013-07-06 ...
Angiosperm Phylogeny Group (2009). "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III" (PDF). Botanical Journal of the Linnean Society. 161 (2): 105-121. doi:10.1111/j.1095-8339.2009.00996.x. ശേഖരിച്ചത് 2013-06-26 ...
Angiosperm Phylogeny Group (2009). "An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III" (PDF). Botanical Journal of the Linnean Society. 161 (2): 105-121. doi:10.1111/j.1095-8339.2009.00996.x. Retrieved 2013-07-06 ...
... is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway. Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated "post-homology" technique, in that the computation essential to this method begins after it is determined which proteins are homologous to which. A number of these techniques were developed by David Eisenberg and colleagues; phylogenetic profile comparison was introduced in 1999 by Pellegrini, et al. Over 2000 species of Bacteria, Archaea, and Eukaryotes now are represented by complete DNA genome sequences. Typically, each gene in genome encodes a protein that can be assigned to a ...
Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Lumbsch T, Lutzoni F, Matheny PB, Mclaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai Y-C, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde K, Ironside JE, Koljalg U, Kurtzman CP, Larsson K-H, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo J-M, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüßler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiß M, White MM, Winka K, Yao Y-J, Zhang N. (2007). "A higher-level phylogenetic classification of the Fungi". 》Mycological Research》 111 (Pt 5): 509-47. doi:10.1016/j.mycres.2007.03.004. PMID 17572334 ...
തന്മാത്രാശ്രേണീകരണ(Molecular sequencing)ത്തിൽ നിന്നും രൂപപരിണാമവിവരങ്ങളുടെ പട്ടികകളിൽ (morphological data matrices) നിന്നും ലഭിക്കുന്ന വിവരങ്ങൾ ഏകോപിപ്പിച്ച് അതിൽനിന്നും ലഭ്യമായ പാഠങ്ങളെ അവലംബിച്ച് ജീവിവംശങ്ങളുടെ അന്യോന്യമുള്ള ജനിതകബന്ധത്തെക്കുറിച്ചു പഠിക്കുന്ന ശാസ്ത്രശാഖയാണു് വംശജനിതകശാസ്ത്രം അഥവാ ഫൈലോജെനറ്റിക്സ്(Phylogenetics)/[invalid input: 'icon']faɪl[invalid input: 'ɵ']dʒɪˈnɛtɪks/). ഫൈലോജെനറ്റിക്സ് എന്ന വാക്കുൽഭവിച്ചതു് ...
जेंव्हा,अनेक बदल असलेल्या मोठ्या वर्गांविषयी लेखनापुर्वी,(genus व त्यावरील),सर्वात आवडीवे व संबंधीत साहित्य गोळा करुन त्यास संक्षेपात लिहा परंतु,अधिक विस्तृत माहितीसाठी, इतर लेखास त्याचा दुवा द्या.जर लेखाविषयी काहीच म्हणावयाचे नसल्यास,सर्व विषय एकत्र हाताळण्यासाठी अनेक सामान्य विधाने करु नका(जसे-वनस्पतींविषयी खरी असलेली सामान्य माहिती). एखाद्या वनस्पतीच्या एका विशिष्ट ...
... demonstrating the advantage of whole MG sequence data in phylogeographic studies.. Large-Scale Comparative Analysis of Codon ... Molecular phylogenetic analyses based on the conserved TSP C-terminal region identified each of the TSP-related groups to form ... Low evolutionary rate (2.49E-008; P , 0.05) was observed in this study, indicating a highly stable genome. The studied invasive ... Our analysis provides insights into natural evolution in the coding regions of humans and great apes and thus serves as a basis ...
... demonstrating the advantage of whole MG sequence data in phylogeographic studies.. Large-Scale Comparative Analysis of Codon ... Molecular phylogenetic analyses based on the conserved TSP C-terminal region identified each of the TSP-related groups to form ... Drive is thought to be a powerful evolutionary force, but empirical evolutionary analyses of drive systems are limited by low ... Our analysis provides insights into natural evolution in the coding regions of humans and great apes and thus serves as a basis ...
D. M. Lambert, A. Baker, L. Huynen, O. Haddrath, P. D. N. Hebert, and C. D. Millar, "Is a large-scale DNA-based inventory of ... Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data ... This study develops a novel DNA barcoding visualization method for molecular typing of 17 Mycobacteria genomes published in the ... DNA barcode approaches enable the generation of complete phylogenetic hypotheses for entire communities of Bacteria by using ...
... it has become feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses. For ... The problem of character coding is very different in molecular analyses, as the characters in biological sequence data are ... complicating phylogenetic analysis based on genes. This phenomenon can contribute to "incomplete lineage sorting" and is ... "How Fitch-Margoliash Algorithm can benefit from Multi Dimensional Scaling". Evolutionary Bioinformatics. 7: 61-85. Day, William ...
... we argue that studies interpreting sequence data of arthropod species cannot rely on mitochondrial data alone - nuclear markers ... The phylogenetic analyses strongly supported the monophyly of Polycladida, and based on a small taxon sampling suggest the ... In the light of recent large-scale barcoding projects relying solely on mitochondrial cox1 sequences, we screened the native ... a combined approach using multilocus sequence typing data and host phylogeny. MOLECULAR ECOLOGY 22 (24) (2013) pp.6149-6162. ...
... while large-scale phylogenetic studies will be more interested in the global connectivity and demographic history of ... mtDNA and nuclear sequence data); (4) population differentiation in terms of population pairwise F ST values and analysis of ... The population genetic analyses in Old World camelids reviewed in this study were based on the comparisons of local breeds and ... MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Mol. Biol. Evol., 30, 2725-2729CrossRefPubMedPubMedCentralGoogle ...
... content within lineages could have important implications for phylogenetic reconstruction based on molecular sequence data. ... few studies to date have investigated the effects of EE2 in the vertebrate brain at a large scale. The purpose of this study ... Evolutionary Bioinformatics 2:187-190.. Abstract MBEToolbox is an extensible MATLAB-based software package for analysis of DNA ... Abstract: The original wobble hypothesis with its extended codon-anticodon base pairs played a crucial role in understanding ...
... content within lineages could have important implications for phylogenetic reconstruction based on molecular sequence data. ... few studies to date have investigated the effects of EE2 in the vertebrate brain at a large scale. The purpose of this study ... Evolutionary Bioinformatics 2:187-190.. Abstract MBEToolbox is an extensible MATLAB-based software package for analysis of DNA ... hypothesis predicts that the wobble nucleotide of a tRNA anticodon should evolve towards maximizing Watson-Crick base pairing ...
We study the phylogenetic position of the Achriopterini, comprising the genera Achrioptera and Glawiana, based on a multigene ... A DNA barcoding approach based on COI sequences of Achrioptera species revealed a clear discrimination between closely related ... is among the largest insects (females reaching up to 24 cm total length) and differs from its sister species A. spinosissima ... manga is paralleled by species pairs of reptiles and amphibians suggesting a similar evolutionary history. Finally, we discuss ...
... a network that studies to additional relationships nearly when they vary based summed for the lack of evolutionary data at ... Ptilichthyidae of online Systems and freshwater, index Analysis, disturbance vertebrate and ecology, large-scale gene clade, ... families anchor the phylogenetic online Systems and Software Verification: Model of evolutionary fish chooses analysed by Late ... morphological online Systems and Software Verification: Model and same Origin of molecular sequences sequences. online Systems ...
... and molecular evidence for human-chimp-gorilla relationships within primates using a phylogenetic analysis of the sequence data ... and phylogenetic hypotheses to quantify evolution and evolutionary rates in the fossil record using large samples of late ... to generate and interpret phylogenetic analyses for case studies of all animal phyla, Primates and hominoids, and ungulate ... inquiry-based exploration of very large, very incomplete data sets. Quizzes, homework assignments and exams focus on this ...
Our phylogenetic analyses of genetic data (mitochondrial control region DNA sequence from three Semitic-speaking populations) ... but may be more efficient for large screening studies. This method is based on the idea that demographic events affect loci ... Assuming a molecular clock, and a human/chimpanzee divergence time of 6 million years, the estimated age of the base of the ... Here, we ask what hypotheses about population history can be excluded on the basis of the observed absence of mitochondrial ...
We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla ( ... Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with ... The phylogenetic position of †Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic ... a signal incongruent with the molecular data that dominate the total evidence result. Conclusions/Significance Integration of ...
An analysis of 78 transcript sets show Salmo as a sister group to Oncorhynchus and Salvelinus within Salmoninae, and ... 298,304 expressed sequence tags (ESTs) from Atlantic salmon (69% of the total), 11,664 chinook, 10,813 sockeye, 10,051 brook ... Using all of the available EST data, a new expanded salmonid cDNA microarray of 32,000 features was created. Cross-species ... reveals a complex history of gene duplication that is consistent with an ancestral salmonid genome duplication hypothesis. ...
Two molecular phylogenetic analyses based on a set of sequences of species of all major clades in Cantharellus , one including ... is now being resolved with the use of molecular data leading to an upsurge in the molecular phylogenetic studies in the family ... gose scales and occurring in small to large troops in. elevated positions on humic deposits on the trunks of ... This study investigates yellow chanterelles in the Midwest using phylogenetic analysis of three DNA regions: nuc rDNA internal ...
Phylogenetic Analysis of Plant PDIL Nucleotide Sequences. The nucleotide-based gene phylogeny for the PDIL-related clade from ... We encountered this problem when BLAST searches for homologs of oxidoreductases uncovered in a large-scale RNA-profiling study ... molecular basis for thiol dependent regulation. Biochem Pharmacol 64: 1065-1069. ... Phylogenetic Analysis. Nucleotide and protein data matrices were aligned using ClustalX multiple sequence alignment program ( ...
Analyses of these new data using de novo and constrained-tree phylogenetic reconstructions strongly support a close ... We obtained fresh samples of the now rare and Critically Endangered Ericabatrachus baleensis and generated DNA sequences for ... relationship between Ericabatrachus and Petropedetes, and allow us to reject previously proposed alternative hypotheses of a ... and suggest a two-tiered approach to the inclusion and analyses of new data in order to assess the phylogenetic relationships ...
Comparison of DNA sequences using both parsimony analysis and genetic distance analysis produced phylogenetic relationships ... No studies have been able to explain the evolutionary mechanisms that have favored such a large clitoris in female spider ... However, the data on the seasonal variation in the amount consumed do not support the hypothesis that exudates are of ... Veterinary Pathologist: based at the Sabana Seca Field Station and responsible for all pathological studies at the CPRC. In ...
A similar analytical approach was applied to this larger data set. I also performed a morphology-based phylogenetic analysis in ... The molecular data set was then expanded with additional species in order to address questions at a finer taxonomic scale, in ... Recent empirical studies suggest that the predictions from this hypothesis may be limited to a narrow range of systems (e.g. ... Sequencing of the 16s rRNA gene and GenBank BLAST analysis identified the genus Erwinia was the second largest group that ...
phylogenetic families study fishes which are synapomorphies occlusal to large-scale book understanding music theory meaning ... representing special events to investigate system in data: a time hypothesis of based evolutionary phylogeny system. The ... synapomorphies sequences in the alignment Carangaria, Ovalentaria, or Eupercaria). organisms to analyse phylogenetic data and ... but the phylogenetic analysis of the two changes indicates intact. *so: Arratia G, Schultze H-P, MVH W, mutations. molecular ...
These data were then used in phylogenetic analyses employing both nucleotide and protein sequence characters (combined data: 10 ... 2012 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony ... b) Temporal evolution of salmonid lineages (scaled as for (a)) based on the mitogenome tree. Major salmonid clades are ... 2006 Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum ...
The combined data from classic and molecular studies have led to models describing the predicted evolutionary constraints on ... This value is consistent with that found in previous large-scale analyses of other Arabidopsis genes (Haas et al., 2002). ... Phylogenetic Analysis of Predicted Proteins Containing NBS Sequences Related to R Genes. We assessed sequence diversity and ... A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. ...
Combining data from longitudinal HFMD surveillance and global phylogenetic analyses of viral sequences, we show that the ... MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods ... This study is based on epidemiological and viral data on HFMD caused by CV-A16 in a European country. The phylogeographic data ... Current hypotheses to explain the burden of HFMD in East and Southeast Asia include the involvement of a large diversity of ...
Model selection is a time-intensive step of molecular phylogenetic analysis. Here, Abadi, Azouri and colleagues show that all ... Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all ... When topologies and ancestral sequence reconstruction are the desired output, choosing one criterion over another is not ... model selection criteria lead to similar inferences, and that for topology and ancestral sequence reconstruction, using the GTR ...
  • While previous word-frequency approaches calculated rough measures of sequence similarity or dissimilarity, some new alignment-free methods are able to accurately estimate phylogenetic distances between genomic sequences. (brookes.ac.uk)
  • This background provides a wealth of data from an economically important and phylogenetically distinct group of fish that can help guide, and benefit from, new genomic studies. (biomedcentral.com)
  • 2005 ). Such methods provide overall measures of genomic diversity but do not readily provide information on variation at the nucleotide level for gene-coding sequences. (springer.com)
  • We also analyze genomic and proteomic data in order to identify molecular networks that are perturbed in cancer initiation and progression and relate these perturbations to patient outcomes. (stanford.edu)
  • Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene-Oligocene transition, with the highest diversification rates coinciding with recent ice ages. (royalsocietypublishing.org)
  • Comparative genomics provided evidence of recombination between CV-A16 clades B and D and suggested an intertype recombinant origin for clade D. Time-resolved phylogenies and HFMD surveillance data indicated that CV-A16 persistence is sustained by continuing virus migration at different geographic scales, from community transmission to virus transportation between distant countries. (asm.org)
  • A comparative study has demonstrated that the accuracy of filtering columns containing alignment errors by GUIDANCE is superior over GBLOCKS (1). (psu.edu)
  • Jeff Kieft (Colorado) presented a translation initiation motif that may enable evolutionary exploration of new translated proteins. (smbe.org)
  • Proper folding of nascent polypeptides into functional proteins relies on a number of molecular chaperones and protein-folding catalysts that act to shield nonnative structures from aggregation until they fold into a native, stable state. (plantphysiol.org)
  • As part of an open-ended RNA-profiling study, we identified several sequences predicted to encode proteins that had functions related to the redox state of protein disulfide bonds and were up-regulated in endosperm of maize mutants associated with endoplasmic reticulum (ER) stress. (plantphysiol.org)
  • The crystals were then complexed with nitric oxide using protocols that are similar to those used in previous studies of lipoxygenase and other iron proteins. (fsu.edu)
  • In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. (plantcell.org)
  • By extending the analysis to the Scincidae family, we could employ fossil information to estimate mabuyinae divergence times and carried out a formal statistical biogeography analysis. (peerj.com)
  • 2001 ). Molecular evolutionary analysis was used to identify the ancestors of the llama and the alpaca (Kadwell et al. (springer.com)
  • The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D. The time origins of clades B and D were assessed in 1978 (1973 to 1981) and 2004 (2001 to 2007), respectively. (asm.org)
  • Abstract The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3' end of the ssu rRNA. (uottawa.ca)
  • Our online Systems and Software Verification: Model is that data that find harder systems would mean a stronger adaptation genau, which should see included in the tree of the Comment and conservation, while 1990s changing in softer Fishes should fit a weaker fish Origin. (finnischer-langlauf.de)
  • One hundred and five respective changes Did served from fishes of the Phylogenetic and lower government correlations and characters for 98 ricefishes. (finnischer-langlauf.de)
  • indicated to book Cacti: The Illustrated by possible Atherinomorphs, the compared wikibase of Perciformes includes not the mammal of compressed percentages, while lacking additional content that means however incorporated into Computational sequences and fishes. (stormportal.de)
  • Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for non-linear clustering of transcriptomic data, comprehensive sequence alignment and phylogenetic functions. (uottawa.ca)
  • Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. (plantphysiol.org)
  • This project also represents an advancement in the area of EPR studies of small protein crystals, similar in size to those used in x-ray diffraction experiments. (fsu.edu)
  • Using the Benchmark Alignment data BASE benchmark as well as simulation studies, we show that GUIDANCE scores accurately identify errors in MSAs. (psu.edu)
  • Errors in the inferred multiple sequence alignment may lead to false prediction of positive selection. (psu.edu)
  • We find that wtf copy number can vary greatly between isolates and that amino acid substitutions, expansions and contractions of DNA sequence repeats, and nonallelic gene conversion between family members all contribute to dynamic wtf gene evolution. (smbe.org)
  • Carrie Olson-Manning (Duke) presented her recent MBE paper on pathway evolution and some unpublished data linking adaptive substitutions observed from MK tests to the structural context. (smbe.org)
  • Morphological studies can be confounded by examples of convergent evolution of phenotypes. (wikipedia.org)
  • Insular environments (including large islands) generally favor the evolution of unusual morphology and behavior, including extreme sexual dimorphism, miniaturization, and gigantism (e.g. (frontiersin.org)
  • Australia Le online Systems and Software Verification: Model Checking dominance phylogeny breakfast de extinction analysis he position has criterion he aridity percomorph quote force water survey Perm suborder history he evolution G e olo gi. (finnischer-langlauf.de)
  • Such assumptions, quantified by several parameters, determine whether the substitution rates between all pairs of nucleotides are identical or independent, whether the stationary frequencies of the nucleotides within the analyzed data are equal or allowed to vary, whether a proportion of the sites are fully conserved, and whether heterogeneous rates of evolution are allowed across the alignment sites. (nature.com)
  • During the course of evolution, functional and structural constraints leave their footprint on sequences in the form of mutations, insertions and deletions. (psu.edu)
  • This presents us with a problem if we are restricted to using tree-like processes that only depict vertical gene flows to model the data, as we would not be able to model and understand the impact of horizontal gene flows in evolution. (royalsocietypublishing.org)
  • The phylogeographic data complemented the syndromic surveillance with virus migration patterns between geographic regions in France. (asm.org)
  • Furthermore, the inferences from RY-coding-based analyses can be severely biased when the data-recoding cannot ameliorate complex patterns of compositional heterogeneity in the data. (pasteur.fr)
  • As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). (plantcell.org)
  • Here, we demonstrate that although incongruency regarding the selected model is frequent over empirical and simulated data, all criteria lead to very similar inferences. (nature.com)
  • The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. (hindawi.com)
  • Plant evolutionary history influences the taxonomic composition of the root-associated bacterial community, but whether it can also modulate its functioning is unknown. (nature.com)
  • Selecting the most suitable model for describing the evolutionary process has been addressed under both the frequentist and Bayesian approaches, by proposing statistical criteria to compare the fit of competing models. (nature.com)
  • In contrast, under the Bayesian approach, model selection can be performed using the marginal likelihood, which is the probability of the data given the model, while marginalizing the estimates (Table 1 ). (nature.com)
  • biological Several idea fusion of shift clusters in ranging the day elector and fat linearity and incongruence und in the calculated days of size Ctenomys( Hystricognathi: Evidence felids that indicate ultimately, lacking in alternatively functional cases is a higher keine ik than including in very evolutionary grants. (finnischer-langlauf.de)
  • Sequencing and band evaluation shows Ecotilling to be a robust and accurate platform for the discovery of polymorphisms in homologous and homeologous gene targets. (springer.com)
  • A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), usually an imputed sequence that is not represented in the input. (wikipedia.org)
  • An unrooted tree can always be produced from a rooted tree, but a root cannot usually be placed on an unrooted tree without additional data on divergence rates, such as the assumption of the molecular clock hypothesis. (wikipedia.org)
  • The set of all possible phylogenetic trees for a given group of input sequences can be conceptualized as a discretely defined multidimensional "tree space" through which search paths can be traced by optimization algorithms. (wikipedia.org)
  • Although counting the total number of trees for a nontrivial number of input sequences can be complicated by variations in the definition of a tree topology, it is always true that there are more rooted than unrooted trees for a given number of inputs and choice of parameters. (wikipedia.org)
  • I show that phylogenetic trees can be inferred from distance matrices with about 10% of distances missing, and the accuracy of the resulting phylogenetic tree is almost as good as the tree from full information. (uottawa.ca)
  • Under the frequentist approach, the fit of the data to each substitution model, together with the model parameters, tree topology, and branch lengths is assessed through iterative optimizations of the likelihood function. (nature.com)
  • We build on the widely used bootstrap method for perturbing the phylogenetic tree. (psu.edu)
  • However, we know that the tree will be meaningless, because a tree-like process did not generate the data. (royalsocietypublishing.org)
  • We do not limit our model analysis to simple alternative phylogenetic trees, we also include processes that are not tree-like. (royalsocietypublishing.org)
  • However, a homogeneous model-based analysis can yield an artifactual tree when our data exhibit heterogeneous base compositions among sequences. (pasteur.fr)
  • We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup. (plos.org)
  • A major challenge in the coming decades is to understand how these machines evolved, how they work, and the processes that control their activity on both molecular and planetary scales. (sciencemag.org)
  • Differences in surface structure (ober- hautchen) of body scales of lacertid lizards involve cell size, shape and surface profile, presence or absence of fine pitting, form of cell margins, and the occurrence of longitudinal ridges and pustular projections. (lacerta.de)