Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.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.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, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.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.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.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.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.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).DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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, 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.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genetic Variation: Genotypic differences observed among individuals in a population.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.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)RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.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).Mammals: Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.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.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.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)Gymnosperms: Gymnosperms are a group of vascular plants whose seeds are not enclosed by a ripened ovary (fruit), in contrast to ANGIOSPERMS whose seeds are surrounded by an ovary wall. The seeds of many gymnosperms (literally, "naked seed") are borne in cones and are not visible. Taxonomists now recognize four distinct divisions of extant gymnospermous plants (CONIFEROPHYTA; CYCADOPHYTA; GINKGOPHYTA; and GNETOPHYTA).Invertebrates: Animals that have no spinal column.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.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.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.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)PrimatesMultigene 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)Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Birds: Warm-blooded VERTEBRATES possessing FEATHERS and belonging to the class Aves.Vertebrates: Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.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.Extinction, Biological: The ceasing of existence of a species or taxonomic groups of 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.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.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.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.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.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.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.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.Anthocerotophyta: A plant division that includes hornworts, named for the horn-like appearance of the spore-producing plant (sporophyte).Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Strepsirhini: A suborder of PRIMATES consisting of the following five families: CHEIROGALEIDAE; Daubentoniidae; Indriidae; LEMURIDAE; and LORISIDAE.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.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)DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Peptide Elongation Factor 1: Peptide elongation factor 1 is a multisubunit protein that is responsible for the GTP-dependent binding of aminoacyl-tRNAs to eukaryotic ribosomes. The alpha subunit (EF-1alpha) binds aminoacyl-tRNA and transfers it to the ribosome in a process linked to GTP hydrolysis. The beta and delta subunits (EF-1beta, EF-1delta) are involved in exchanging GDP for GTP. The gamma subunit (EF-1gamma) is a structural component.Platyhelminths: A phylum of acoelomate, bilaterally symmetrical flatworms, without a definite anus. It includes three classes: Cestoda, Turbellaria, and Trematoda.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Gene Order: The sequential location of genes on a chromosome.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)Fishes: A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.Genes, Archaeal: The functional genetic units of ARCHAEA.LizardsRhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Ciliophora: A phylum of EUKARYOTES characterized by the presence of cilia at some time during the life cycle. It comprises three classes: KINETOFRAGMINOPHOREA; OLIGOHYMENOPHOREA; and POLYMENOPHOREA.Paleontology: The study of early forms of life through fossil remains.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.Insects: The class Insecta, in the phylum ARTHROPODA, whose members are characterized by division into three parts: head, thorax, and abdomen. They are the dominant group of animals on earth; several hundred thousand different kinds having been described. Three orders, HEMIPTERA; DIPTERA; and SIPHONAPTERA; are of medical interest in that they cause disease in humans and animals. (From Borror et al., An Introduction to the Study of Insects, 4th ed, p1)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).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.Genes, Chloroplast: Those nucleic acid sequences that function as units of heredity which are located within the CHLOROPLAST DNA.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.Gastropoda: A class in the phylum MOLLUSCA comprised of SNAILS and slugs. The former have coiled external shells and the latter usually lack shells.Madagascar: One of the Indian Ocean Islands off the southeast coast of Africa. Its capital is Antananarivo. It was formerly called the Malagasy Republic. Discovered by the Portuguese in 1500, its history has been tied predominantly to the French, becoming a French protectorate in 1882, a French colony in 1896, and a territory within the French union in 1946. The Malagasy Republic was established in the French Community in 1958 but it achieved independence in 1960. Its name was changed to Madagascar in 1975. (From Webster's New Geographical Dictionary, 1988, p714)Kinetoplastida: An order of flagellate protozoa. Characteristics include the presence of one or two flagella arising from a depression in the cell body and a single mitochondrion that extends the length of the body.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.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.Hylobates: A genus of the family HYLOBATIDAE consisting of six species. The members of this genus inhabit rain forests in southeast Asia. They are arboreal and differ from other anthropoids in the great length of their arms and very slender bodies and limbs. Their major means of locomotion is by swinging from branch to branch by their arms. Hylobates means dweller in the trees. Some authors refer to Symphalangus and Nomascus as Hylobates. The six genera include: H. concolor (crested or black gibbon), H. hoolock (Hoolock gibbon), H. klossii (Kloss's gibbon; dwarf siamang), H. lar (common gibbon), H. pileatus (pileated gibbon), and H. syndactylus (siamang). H. lar is also known as H. agilis (lar gibbon), H. moloch (agile gibbon), and H. muelleri (silvery gibbon).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.Geology: The science of the earth and other celestial bodies and their history as recorded in the rocks. It includes the study of geologic processes of an area such as rock formations, weathering and erosion, and sedimentation. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Insectivora: An order of insect eating MAMMALS including MOLES; SHREWS; HEDGEHOGS and tenrecs.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Liliaceae: A monocot family within the order Liliales. This family is divided by some botanists into other families such as Convallariaceae, Hyacinthaceae and Amaryllidaceae. Amaryllidaceae, which have inferior ovaries, includes CRINUM; GALANTHUS; LYCORIS; and NARCISSUS and are known for AMARYLLIDACEAE ALKALOIDS.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.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Asteraceae: A large plant family of the order Asterales, subclass Asteridae, class Magnoliopsida. The family is also known as Compositae. Flower petals are joined near the base and stamens alternate with the corolla lobes. The common name of "daisy" refers to several genera of this family including Aster; CHRYSANTHEMUM; RUDBECKIA; TANACETUM.South AmericaSequence 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.Cryptophyta: A class of EUKARYOTA (traditionally algae), characterized by biflagellated cells and found in both freshwater and marine environments. Pigmentation varies but only one CHLOROPLAST is present. Unique structures include a nucleomorph and ejectosomes.Ribosome Subunits, Small: The small ribonucleoprotein component of RIBOSOMES. It contains the MESSENGER RNA binding site and two TRANSFER RNA binding sites - one for the incoming AMINO ACYL TRNA (A site) and the other (P site) for the peptidyl tRNA carrying the elongating peptide chain.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Crustacea: A large subphylum of mostly marine ARTHROPODS containing over 42,000 species. They include familiar arthropods such as lobsters (NEPHROPIDAE), crabs (BRACHYURA), shrimp (PENAEIDAE), and barnacles (THORACICA).Ficus: A plant genus of the family MORACEAE. It is the source of the familiar fig fruit and the latex from this tree contains FICAIN.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.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.PanamaProteobacteria: A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.Genes, Bacterial: The functional hereditary units of BACTERIA.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.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Hepatophyta: A plant division. They are simple plants that lack vascular tissue and possess rudimentary rootlike organs (rhizoids). Like MOSSES, liverworts have alternation of generations between haploid gamete-bearing forms (gametophytes) and diploid spore-bearing forms (sporophytes).Genes, Plant: The functional hereditary units of PLANTS.DNA Barcoding, Taxonomic: Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.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.Asia: The largest of the continents. It was known to the Romans more specifically as what we know today as Asia Minor. The name comes from at least two possible sources: from the Assyrian asu (to rise) or from the Sanskrit usa (dawn), both with reference to its being the land of the rising sun, i.e., eastern as opposed to Europe, to the west. (From Webster's New Geographical Dictionary, 1988, p82 & Room, Brewer's Dictionary of Names, 1992, p34)Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Geological Phenomena: The inanimate matter of Earth, the structures and properties of this matter, and the processes that affect it.Solanaceae: A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.Echinodermata: A phylum of the most familiar marine invertebrates. Its class Stelleroidea contains two subclasses, the Asteroidea (the STARFISH or sea stars) and the Ophiuroidea (the brittle stars, also called basket stars and serpent stars). There are 1500 described species of STARFISH found throughout the world. The second class, Echinoidea, contains about 950 species of SEA URCHINS, heart urchins, and sand dollars. A third class, Holothuroidea, comprises about 900 echinoderms known as SEA CUCUMBERS. Echinoderms are used extensively in biological research. (From Barnes, Invertebrate Zoology, 5th ed, pp773-826)ArtiodactylaGenome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Dictyosteliida: An order of protozoa characterized by their ability to aggregate to form a multicellular pseudoplasmodium, which gives rise to a multispored fruiting body. A stalk tube is present.Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Rhizaria: A large supergroup of mostly amoeboid EUKARYOTES whose three main subgroups are CERCOZOA; FORAMINIFERA; and HAPLOSPORIDA. Nearly all of the species possess MITOCHONDRIA and historically many were considered ANIMALS.Body Size: The physical measurements of a body.Rodentia: A mammalian order which consists of 29 families and many genera.Xenarthra: An order of New World mammals characterized by the absence of incisors and canines from among their teeth, and comprising the ARMADILLOS, the SLOTHS, and the anteaters. The order is distinguished from all others by what are known as xenarthrous vertebrae (xenos, strange; arthron, joint): there are secondary, and sometimes even more, articulations between the vertebrae of the lumbar series. The order was formerly called Edentata. (From Random House Unabridged Dictionary, 2d ed; Walker's Mammals of the World, 5th ed, vol. I, p515)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.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.Hymenoptera: An extensive order of highly specialized insects including bees, wasps, and ants.Lagomorpha: An order of small mammals comprising two families, Ochotonidae (pikas) and Leporidae (RABBITS and HARES). Head and body length ranges from about 125 mm to 750 mm. Hares and rabbits have a short tail, and the pikas lack a tail. Rabbits are born furless and with both eyes and ears closed. HARES are born fully haired with eyes and ears open. All are vegetarians. (From Nowak, Walker's Mammals of the World, 5th ed, p539-41)Annelida: A phylum of metazoan invertebrates comprising the segmented worms, and including marine annelids (POLYCHAETA), freshwater annelids, earthworms (OLIGOCHAETA), and LEECHES. Only the leeches are of medical interest. (Dorland, 27th ed)Bacterial Proteins: Proteins found in any species of bacterium.Dinoflagellida: Flagellate EUKARYOTES, found mainly in the oceans. They are characterized by the presence of transverse and longitudinal flagella which propel the organisms in a rotating manner through the water. Dinoflagellida were formerly members of the class Phytomastigophorea under the old five kingdom paradigm.AfricaGenetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Porifera: The phylum of sponges which are sessile, suspension-feeding, multicellular animals that utilize flagellated cells called choanocytes to circulate water. Most are hermaphroditic. They are probably an early evolutionary side branch that gave rise to no other group of animals. Except for about 150 freshwater species, sponges are marine animals. They are a source of ALKALOIDS; STEROLS; and other complex molecules useful in medicine and biological research.North AmericaMarkov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.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.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)Viridiplantae: A monophyletic group of green plants that includes all land plants (EMBRYOPHYTA) and all green algae (CHLOROPHYTA and STREPTOPHYTA).Wasps: Any of numerous winged hymenopterous insects of social as well as solitary habits and having formidable stings.Americas: The general name for NORTH AMERICA; CENTRAL AMERICA; and SOUTH AMERICA unspecified or combined.Platyrrhini: An infraorder of New World monkeys, comprised of the families AOTIDAE; ATELIDAE; CEBIDAE; and PITHECIIDAE. They are found exclusively in the Americas.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Programming, Linear: A technique of operations research for solving certain kinds of problems involving many variables where a best value or set of best values is to be found. It is most likely to be feasible when the quantity to be optimized, sometimes called the objective function, can be stated as a mathematical expression in terms of the various activities within the system, and when this expression is simply proportional to the measure of the activities, i.e., is linear, and when all the restrictions are also linear. It is different from computer programming, although problems using linear programming techniques may be programmed on a computer.Moles: Any of numerous burrowing mammals found in temperate regions and having minute eyes often covered with skin.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.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Musaceae: A plant family of the order ZINGIBERALES, subclass Zingiberidae, class Liliopsida best known for banana (MUSA). The slender false trunk, formed by leaf sheaths of the spirally arranged leaves, may rise to 15 meters (50 feet). There is a crown of large leaves at the top.Dolphins: Mammals of the families Delphinidae (ocean dolphins), Iniidae, Lipotidae, Pontoporiidae, and Platanistidae (all river dolphins). Among the most well-known species are the BOTTLE-NOSED DOLPHIN and the KILLER WHALE (a dolphin). The common name dolphin is applied to small cetaceans having a beaklike snout and a slender, streamlined body, whereas PORPOISES are small cetaceans with a blunt snout and rather stocky body. (From Walker's Mammals of the World, 5th ed, pp978-9)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.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)

*  PhD Funding in Phylogeny

Search Funded PhD Projects, Programs & Scholarships in Phylogeny. Search for PhD funding, scholarships & studentships in the UK ... Phylogeny PhD Projects, Programs & Scholarships. We have 7 Phylogeny PhD Projects, Programs & Scholarships. * Keywords:. ' ... EASTBIO* Massively Parallel Phylogeny Reconstruction for the Age of DNA Big Data University of Edinburgh School of Biological ...
https://findaphd.com/search/phd.aspx?Keywords=phylogeny

*  Context: Alumni

Phylogeny, taxonomy, biogeography and evolution of asexuality within the southeast Asian lizard genus Leiolepis Cuvier, (1829) ...
bibliography.library.villanova.edu/Collection/folder-114/HierarchyTree?recordID=11268

*  The Phylogeny of Little Red Riding Hood

Researchers have long been fascinated by the strong continuities evident in the oral traditions associated with different cultures. According to the 'historic-geographic' school, it is possible to classify similar tales into
journals.plos.org/plosone/article?id=10.1371/journal.pone.0078871

*  Xerinae

This page is a Tree of Life Branch Page.. Each ToL branch page provides a synopsis of the characteristics of a group of organisms representing a branch of the Tree of Life. The major distinction between a branch and a leaf of the Tree of Life is that each branch can be further subdivided into descendent branches, that is, subgroups representing distinct genetic lineages.. For a more detailed explanation of the different ToL page types, have a look at the Structure of the Tree of Life page.. close box ...
tolweb.org/Xerinae

*  Figure 1: Retroviral phylogeny illustrating how FVs and FLERVs relate to other retroviruses.

... From: Marine origin of ... The un-rooted phylogenies were estimated from a reverse transcriptase protein alignment. Since both Bayesian maximum clade ...
nature.com/articles/ncomms13954/figures/1?error=cookies_not_supported&code=718adf1f-2521-4da6-82c3-b7a9fe54d149

*  Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer | BMC Biology | Full Text

Whole genome SNP phylogenies are highly accurate in terms of defining both branching order and branch lengths, despite ... The inferred phylogenies are a meaningful approximation of descent, and not simply a depiction of the inevitable stochastic ... Li C, Orti G, Zhang G, Lu G: A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case ... Thus, we used B. pseudomallei isolate 668 as an outgroup for rooting our B. pseudomallei/B. mallei phylogeny, which was ...
https://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-7-78

*  Myobatrachinae

Ford and Cannatella (1993) defined the node-based name Myobatrachinae to be the most recent common ancestor of Arenophryne, Assa, Crinia, Geocrinia, Myobatrachus, Paracrinia, Pseudophryne, Taudactylus, and Uperoleia, and all its descendants. Because the name is defined in terms of the ancestor and its descendants, it will remain stable regardless of whether Rheobatrachus or Sooglossidae is found to be nested within Myobatrachinae or not. Duellman and Trueb (1986) included the Eocene fossil †Indobatrachus in the Myobatrachinae; Ford and Cannatella (1993) did not use it in the definition because its relationships are uncertain. Rheobatrachus was not included in the definition, because it has been placed as closely related to Myobatrachinae, closely related to Limnodynastinae, or the sister-group of Limnodynastinae + Myobatrachinae.. Ford and Cannatella examined the literature on several character systems in myobatrachids (Heyer and Liem, 1976; Horton, 1982; Lynch, 1971) and found that in all ...
tolweb.org/Myobatrachinae/

*  Phylogenetic dendrogram of viral protein 4 (VP4) P[6] a | Open-i

Phylogenetic dendrogram of viral protein 4 (VP4) P[6] and P[8] rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) |65% are shown. The
https://openi.nlm.nih.gov/detailedresult.php?img=PMC2819891_09-0497-F2&req=4

*  Host Phylogeny Determines Viral Persistence and Replication in Novel Hosts

Author Summary Emerging infectious diseases such as SARS, HIV and swine-origin influenza have all been recently acquired by humans from other species. Understanding the reasons why parasites jump between different host species is essential to allow us to predict future threats and understand the causes of disease emergence. Here we ask how host-relatedness might determine when host-shifts can occur in the most important group of emerging diseases-RNA viruses. We show that the relationship between host species is the primary factor in determining a virus's ability to persist and replicate in a novel host following exposure. This can be broken down into two components. Firstly, species closely related to the virus's natural host are more susceptible than distantly related species. Secondly, independent of the distance effect, groups of closely related host species have similar levels of susceptibility. This has important implications for our understanding of disease-emergence, and until now the only large
journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1002260

*  HKU Scholars Hub: Molecular phylogeny of Dictyosporium and allied genera inferred from ribosomal DNA

Molecular phylogeny of Dictyosporium and allied genera inferred from ribosomal DNA. Authors. Tsui, CKMBerbee, MLJeewon, RHyde, ... Article: Molecular phylogeny of Dictyosporium and allied genera inferred from ribosomal DNA. *Show simple item record ...
hub.hku.hk/handle/10722/223525

*  Deep Green - Green Plant Phylogeny Research Coordination Group

... The green plants provide food, shelter, and medicines and ... An improved understanding of their phylogeny will not only allow the intellectual satisfaction of discovering the 'roots' of ... of the relationship between ontogeny and phylogeny, and modes of evolution at the molecular level. Addressing a phylogenetic ...
ucjeps.berkeley.edu/bryolab/GPphylo/

*  Lucy Ye - Bioinformatics2011

... experimental models of phylogeny have allowed us to test the accuracy and capabilities of several commonly used phylogeny ...
bioinformatics2011.wikidot.com/lucy-ye

*  The evolution of the Ecdysozoa | Philosophical Transactions of the Royal Society B: Biological Sciences

1995 rDNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature. 376, 165-167. doi:10.1038/ ... 2001 Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Dev. 3, ... 2004 Ecdysozoan phylogeny and bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the ... 2005 Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Soc. B. 272, ...
rstb.royalsocietypublishing.org/content/363/1496/1529

*  Taxonomic distribution of Mcm2-9 and a summarised phylo | Open-i

The Archaea were used as an outgroup for reconstructing MCM phylogeny. Mentions: BLAST algorithms were used to identify MCM ...
https://openi.nlm.nih.gov/detailedresult.php?img=PMC2667178_1471-2148-9-60-1&req=4

*  phylogeny

h yere eukaryoter , ==== EUKARYOTES ===, , (EUKARYA) , , ==== ARKEZOER (ARCHEZOA) =====, , , , , ===ERKEBAKTERIER (ARCHAEA)==, ==== Crenarchaeota-Eocytes , , , , , ===== Euryarchaeota ? =====, , , ===== Bl gr nnalger (Cyanobacteria) , ,==== Urgr nnalger (Chloroxybacteria) ===BAKTERIER (BACTERIA)=============,==== ,==== ,==== =============Str lesopp (Actinomycetes) ...
folk.uio.no/klaush/rot.htm

*  phylogeny programs

... Mary K.Kuhner mkkuhner at kingman.genetics.washington.edu Mon Aug 13 18:10:53 EST 2001 *Previous message: ... and the lecture by Paul Lewis on comparing different phylogeny methods. , In particular - is there a way to assess the 'error' ...
bio.net/bionet/mm/mol-evol/2001-August/007227.html

*  Angiosperm Phylogeny Website - Wikipedia

El Angiosperm Phylogeny Website (siglas APW o APWeb) es un sitio web dedicado a la filogenia y clasificación de las plantas ... Ver Anexo:Géneros de Rósidas Ver Anexo:Géneros de Astéridas Stevens, P. F. (2001 en adelante) Angiosperm Phylogeny Website ...
https://es.wikipedia.org/wiki/Angiosperm_Phylogeny_Website

*  Angiosperm Phylogeny Group - Wikipedia

L'Angiosperm Phylogeny Group (APG) est un groupe de botanistes qui travaillent sur la phylogénétique végétale, en utilisant les ... N.B. Ce groupe n'est pas responsable du site Angiosperm Phylogeny Website qui est géré uniquement par un de ses membres : le ...
https://fr.wikipedia.org/wiki/Angiosperm_Phylogeny_Group

*  Angiosperm Phylogeny Website - Wikipedia

O Commons possui imagens e outras mídias sobre Angiosperm Phylogeny Website O Angiosperm Phylogeny Website (ou APWeb) um sítio ... Ver Anexo:Lista de géneros de rosídeas Ver Anexo:Lista de géneros de asterídeas sítio do Angiosperm Phylogeny Website Sítio do ... membro do Angiosperm Phylogeny Group (APG). A taxonomia apresentada é grandemente baseada no trabalho do APG, com modificações ...
https://pt.wikipedia.org/wiki/Angiosperm_Phylogeny_Website

*  The Undirected Incomplete Perfect Phylogeny Problem

... problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of ... In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor ... The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with ... In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor ...
https://computer.org/csdl/trans/tb/2008/04/ttb2008040618-abs.html

*  The Phylogeny of Bread Clips - Neatorama

Main Blog , The Phylogeny of Bread Clips The Phylogeny of Bread Clips ... This isn't really a "phylogeny"... that would be evolutionary history. This is more just "taxonomy". ...
neatorama.com/2011/09/21/the-phylogeny-of-bread-clips/

*  User:Ilya/Yeast/Phylogeny - OpenWetWare

User:Ilya/Yeast/Phylogeny. From OpenWetWare. , User:Ilya‎ , Yeast. Revision as of 20:15, 30 August 2007 by Ilya. (talk , ... Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Ilya/Yeast/Phylogeny&oldid=146697" ...
https://openwetware.org/wiki/?title=User:Ilya/Yeast/Phylogeny&oldid=146697

*  Phytophthora infestans | Phylogeny

Phytophthora infestans , Phylogeny. The phylogenetic position of Phytophthora infestans relative to two other stramenopiles is ...
megasun.bch.umontreal.ca/People/lang/species/phyti/phylo.html

*  Drosera Phylogeny | ICPS

None of the bifurcating phylogeny trees, including NeighborNet, can actually represent the true nature of the Drosera phylogeny ... What is a problem for the phylogeny is multiple chloroplast lineages in a species. If populations of a species have been ... Rivadavia, Fernando, Katsuhiko Kondo, Masahiro Kato, and Mitsuyasu Hasebe (2003) Phylogeny of the sundews, Drosera (Droseraceae ... Rivadavia, Fernando, Katsuhiko Kondo, Masahiro Kato, and Mitsuyasu Hasebe (2003) Phylogeny of the sundews, Drosera (Droseraceae ...
carnivorousplants.org/cp/evolution/DroseraPhylogeny

Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Decoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.Coles PhillipsHaplogroup L0 (mtDNA)CS-BLASTHyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.Large ornamented Ediacaran microfossil: Large ornamented Ediacaran microfossils (LOEMs) are microscopic acritarchs, usually over 100 μm in diameter, which are common in sediments of the Ediacaran period, . They largely disappear from the Ediacaran fossil record before , roughly coeval with the origin of the Ediacara biota.Community Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.Genetic variation: right|thumbPhylogeography: Phylogeography is the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals. This is accomplished by considering the geographic distribution of individuals in light of the patterns associated with a gene genealogy.NADH-QSymmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Glossary of scientific names: A glossary of the meaning of scientific names of living things, viruses and prions .Horizontal gene transfer in evolutionAmborellaHealth geography: Health geography is the application of geographical information, perspectives, and methods to the study of health, disease, and health care.Bennettites: Bennettites refers to an extinct genus of the order Bennettitales.BrachiopodStromule: A stromule is a microscopic structure found in plant cells. Stromules (stroma-filled tubules) are highly dynamic structures extending from the surface of all plastid types, including proplastids, chloroplasts, etioplasts, leucoplasts, amyloplasts, and chromoplasts.Chelicerata: Late Ordovician (but see text) – RecentMT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.Gene duplication: Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene.Oxymonad: The Oxymonads are a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Along with the similar parabasalid flagellates, they harbor the symbiotic bacteria that are responsible for breaking down cellulose.List of sequenced eukaryotic genomesGlobal microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Bird trapping: Bird trapping techniques to capture wild birds include a wide range of techniques that have their origins in the hunting of birds for food. While hunting for food does not require birds to be caught alive, some trapping techniques capture birds without harming them and are of use in ornithology research.Cambrian–Ordovician extinction eventProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Symbiosis Center of Health Care: Symbiosis Center of Health Care (SCHC) is an organization under Symbiosis Society which takes care of health of symbiosis family be it student or staff.http://www.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Lasiodiplodia: Lasiodiplodia is a genus of fungi in the family Botryosphaeriaceae. There are 21 species.Anthoceros: Anthoceros is a genus of hornworts in the family Anthocerotaceae. The genus is global in its distribution.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Domain (biology): In biological taxonomy, a domain (also superregnum, superkingdom, empire, or regio) is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains: Archaea (a term which Woese created), Bacteria, and Eukaryota.EcosystemExogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Eukaryotic elongation factors: Eukaryotic elongation factors are very similar to those in prokaryotes.Microcotyle: Microcotyle is a genus which belongs to the phylum Platyhelminthes and class Monogenea. It is an ectoparasite that affects its host by attaching itself as a larva on the gills of the fish and grows into adult stage.Mac OS X Server 1.0AmbulocetidaeBaltic sculpin: The Baltic sculpinBaltic sculpin (Cottus microstomus) at EOL (Cottus microstomus) is a species of sculpin, a European freshwater fish in the Cottidae family. It is widespread in the Dniester drainage (Black Sea basin), Odra and Vistula drainages (southern Baltic basin), most likely extending further east to Gulf of Finland.Tokay gecko: The tokay gecko (Gekko gecko) is a nocturnal arboreal gecko, ranging from northeast India, Bhutan, Nepal, Bangladesh, throughout Southeast Asia, Philippines to Indonesia and western New Guinea. Its native habitat is rainforest trees and cliffs, and it also frequently adapts to rural human habitations, roaming walls and ceilings at night in search of insect prey.Cyanidioschyzon merolae: C. merolae is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments (pH 1.Blepharisma japonicum: Blepharisma japonicum is a species of protozoans, that can be found either in water or soilHabitat of Japan.Caninia (genus)Intergenic region: An Intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of Noncoding DNA.Rakiura (genus): Rakiura is a genus of Trichoptera (caddisfly). The genus contains only one species, R.Nippleus Erectus: Nippleus Erectus was a drummer of GWAR (played by former White Cross member Rob Mosby), who did all the drumming for Hell-O. He is also credited for the drums on Scumdogs of the Universe, though it was Jizmak Da Gusha who played them.Marine fungi: Marine fungi are species of fungi that live in marine or estuarine environments. They are not a taxonomic group but share a common habitat.MoniliellaRespiratory system of gastropods: The respiratory system of gastropods varies greatly in form. These variations were once used as a basis for dividing the group into subclasses.Transport in Madagascar: == Railways ==Bodo people: (Assam)Haematococcus pluvialis: Haematococcus pluvialis is a freshwater species of Chlorophyta from the family Haematococcaceae. This species is well known for its high content of the strong antioxidant astaxanthin, which is important in aquaculture, and cosmetics.Thermal cyclerPlasmodium eylesi: Plasmodium eylesi is a parasite of the genus Plasmodium subgenus Plasmodium.Puccinia striiformis var. striiformis: Puccinia striiformis var. striiformis is a plant pathogen.Index of geology articles: This is a list of all articles related to geology that cannot be readily placed on the following subtopic pages:HEPN domain: In molecular biology, the HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding domain) is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains:Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Confusion (New Order song): "Confusion" is a single released by British group New Order in August 1983 with the catalogue number FAC 93.New Order - Confusion at discogs.Alkalimonas: Alkalimonas is a genus in the phylum Proteobacteria (Bacteria).Erythronium japonicum: Katakuri (Erythronium japonicum; ) is a pink-flowered species trout lily, belonging to the Lily family and native to Japan, Korea, the Russian Far East (Sakhalin Island, Kuril Islands) and northeastern China (Jilin and Liaoning).Flora of China v 24 p 126Kew World Checklist of Selected Plant Families It is a spring ephemeral, blooming April–June in woodlands.Tithonia diversifoliaUtiaritichthys: Utiaritichthys is a genus of serrasalmid found in the Amazon and Orinoco basins in tropical South America.Nucleomorph: Nucleomorphs are small, vestigial eukaryotic nuclei found between the inner and outer pairs of membranes in certain plastids. They are thought to be vestiges of primitive red and green algal nuclei that engulfed a prokaryote (plastid).

(1/52004) A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing.

The assembly pathway of spliceosomal snRNPs in yeast is poorly understood. We devised a screen to identify mutations blocking the assembly of newly synthesized U4 snRNA into a functional snRNP. Fifteen mutant strains failing either to accumulate the newly synthesized U4 snRNA or to assemble a U4/U6 particle were identified and categorized into 13 complementation groups. Thirteen previously identified splicing-defective prp mutants were also assayed for U4 snRNP assembly defects. Mutations in the U4/U6 snRNP components Prp3p, Prp4p, and Prp24p led to disassembly of the U4/U6 snRNP particle and degradation of the U6 snRNA, while prp17-1 and prp19-1 strains accumulated free U4 and U6 snRNA. A detailed analysis of a newly identified mutant, the sad1-1 mutant, is presented. In addition to having the snRNP assembly defect, the sad1-1 mutant is severely impaired in splicing at the restrictive temperature: the RP29 pre-mRNA strongly accumulates and splicing-dependent production of beta-galactosidase from reporter constructs is abolished, while extracts prepared from sad1-1 strains fail to splice pre-mRNA substrates in vitro. The sad1-1 mutant is the only splicing-defective mutant analyzed whose mutation preferentially affects assembly of newly synthesized U4 snRNA into the U4/U6 particle. SAD1 encodes a novel protein of 52 kDa which is essential for cell viability. Sad1p localizes to the nucleus and is not stably associated with any of the U snRNAs. Sad1p contains a putative zinc finger and is phylogenetically highly conserved, with homologues identified in human, Caenorhabditis elegans, Arabidospis, and Drosophila.  (+info)

(2/52004) The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes.

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)

(3/52004) Isolation of zebrafish gdf7 and comparative genetic mapping of genes belonging to the growth/differentiation factor 5, 6, 7 subgroup of the TGF-beta superfamily.

The Growth/differentiation factor (Gdf) 5, 6, 7 genes form a closely related subgroup belonging to the TGF-beta superfamily. In zebrafish, there are three genes that belong to the Gdf5, 6, 7 subgroup that have been named radar, dynamo, and contact. The genes radar and dynamo both encode proteins most similar to mouse GDF6. The orthologous identity of these genes on the basis of amino acid similarities has not been clear. We have identified gdf7, a fourth zebrafish gene belonging to the Gdf5, 6, 7 subgroup. To assign correct orthologies and to investigate the evolutionary relationships of the human, mouse, and zebrafish Gdf5, 6, 7 subgroup, we have compared genetic map positions of the zebrafish and mammalian genes. We have mapped zebrafish gdf7 to linkage group (LG) 17, contact to LG9, GDF6 to human chromosome (Hsa) 8 and GDF7 to Hsa2p. The radar and dynamo genes have been localized previously to LG16 and LG19, respectively. A comparison of syntenies shared among human, mouse, and zebrafish genomes indicates that gdf7 is the ortholog of mammalian GDF7/Gdf7. LG16 shares syntenic relationships with mouse chromosome (Mmu) 4, including Gdf6. Portions of LG16 and LG19 appear to be duplicate chromosomes, thus suggesting that radar and dynamo are both orthologs of Gdf6. Finally, the mapping data is consistent with contact being the zebrafish ortholog of mammalian GDF5/Gdf5.  (+info)

(4/52004) Novel endotheliotropic herpesviruses fatal for Asian and African elephants.

A highly fatal hemorrhagic disease has been identified in 10 young Asian and African elephants at North American zoos. In the affected animals there was ultrastructural evidence for herpesvirus-like particles in endothelial cells of the heart, liver, and tongue. Consensus primer polymerase chain reaction combined with sequencing yielded molecular evidence that confirmed the presence of two novel but related herpesviruses associated with the disease, one in Asian elephants and another in African elephants. Otherwise healthy African elephants with external herpetic lesions yielded herpesvirus sequences identical to that found in Asian elephants with endothelial disease. This finding suggests that the Asian elephant deaths were caused by cross-species infection with a herpesvirus that is naturally latent in, but normally not lethal to, African elephants. A reciprocal relationship may exist for the African elephant disease.  (+info)

(5/52004) Evolutionary relationships of pathogenic clones of Vibrio cholerae by sequence analysis of four housekeeping genes.

Studies of the Vibrio cholerae population, using molecular typing techniques, have shown the existence of several pathogenic clones, mainly sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones. However, the relationship of the pathogenic clones to environmental V. cholerae isolates remains unclear. A previous study to determine the phylogeny of V. cholerae by sequencing the asd (aspartate semialdehyde dehydrogenase) gene of V. cholerae showed that the sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones had very different asd sequences which fell into separate lineages in the V. cholerae population. As gene trees drawn from a single gene may not reflect the true topology of the population, we sequenced the mdh (malate dehydrogenase) and hlyA (hemolysin A) genes from representatives of environmental and clinical isolates of V. cholerae and found that the mdh and hlyA sequences from the three pathogenic clones were identical, except for the previously reported 11-bp deletion in hlyA in the sixth-pandemic clone. Identical sequences were obtained, despite average nucleotide differences in the mdh and hlyA genes of 1.52 and 3.25%, respectively, among all the isolates, suggesting that the three pathogenic clones are closely related. To extend these observations, segments of the recA and dnaE genes were sequenced from a selection of the pathogenic isolates, where the sequences were either identical or substantially different between the clones. The results show that the three pathogenic clones are very closely related and that there has been a high level of recombination in their evolution.  (+info)

(6/52004) Three receptor genes for plasminogen related growth factors in the genome of the puffer fish Fugu rubripes.

Plasminogen related growth factors (PRGFs) and their receptors play major roles in embryogenesis, tissue regeneration and neoplasia. In order to investigate the complexity and evolution of the PRGF receptor family we have cloned and sequenced three receptors for PRGFs in the teleost fish Fugu rubripes, a model vertebrate with a compact genome. One of the receptor genes isolated encodes the orthologue of mammalian MET, whilst the other two may represent Fugu rubripes orthologues of RON and SEA. This is the first time three PRGF receptors have been identified in a single species.  (+info)

(7/52004) Cloning, molecular analysis and differential cell localisation of the p36 RACK analogue antigen from the parasite protozoon Crithidia fasciculata.

The family of the RACK molecules (receptors for activated C kinases) are present in all the species studied so far. In the genus Leishmania, these molecules also induce a strong immune reaction against the infection. We have cloned and characterised the gene that encodes the RACK analogue from the parasite trypanosomatid Crithidia fasciculata (CACK). The molecule seems to be encoded by two genes. The sequence analysis of the cloned open reading frame indicates the existence of a high degree of conservation not only with other members of the Trypanosomatidae but also with mammalians. The study of the protein kinase C phosphorylation sites shows the presence of three of them, shared with the mammalian species, additional to those present in the other protozoa suggesting a certain phylogenetic distance between the protozoon Crithidia fasciculata and the rest of the Trypanosomatidae. The CACK-encoded polypeptide shows an additional sequence of four amino acids at the carboxy-terminal end, which produces a different folding of the fragment with the presence of an alpha-helix instead of the beta-sheet usual in all the other species studied. A similar result is elicited at the amino-terminal end by the change of three amino acid residues. The immunolocalisation experiments show that the CACK displays a pattern with a distribution mainly at the plasma membrane, different from that of the related Leishmania species used as control, that displays a distribution close to the nucleus. Altogether, the data suggest that the existence of the structural differences found may have functional consequences.  (+info)

(8/52004) Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium.

Lindane-degrading activity under aerobic conditions has been observed in two bacterial strains: UT26, phenotypically identified as Sphingomonas paucimobilis, and a new single unidentified isolate named RP5557T. The rrs (16S rDNA) sequences for both strains and the phenotypic characteristics for the unidentified isolate RP5557T were determined. RP5557T does not have high identity (less than 90% in all cases) with any sequence in the GenBank or RDP databases. A phylogenetic analysis based on rrs sequences indicated that RP5557T belongs to the gamma-Proteobacteria in a coherent phylum that includes the genera Xanthomonas and Xylella (100% bootstrap), whereas UT26 is clearly separate from the Xanthomonas cluster. Based on the phylogenetic analyses and on the phenotypic characteristics, a new genus, Rhodanobacter, containing a single species, Rhodanobacter lindaniclasticus, is proposed for strain RP5557T (= LMG 18385T), which becomes the type strain.  (+info)



Angiosperm Phylogeny Website


  • El Angiosperm Phylogeny Website (siglas APW o APWeb) es un sitio web dedicado a la filogenia y clasificación de las plantas angiospermas. (wikipedia.org)
  • N.B. Ce groupe n'est pas responsable du site Angiosperm Phylogeny Website qui est géré uniquement par un de ses membres : le professeur Peter F. Stevens. (wikipedia.org)
  • O Commons possui imagens e outras mídias sobre Angiosperm Phylogeny Website O Angiosperm Phylogeny Website (ou APWeb) um sítio de internet conhecido, dedicado à pesquisa de taxonomia e filogenia das angiospérmicas. (wikipedia.org)

Ontogeny and Phylo


  • Turning to modern concepts, Gould demonstrates that, even though the whole subject of parallels between ontogeny and phylogeny fell into disrepute, it is still one of the great themes of evolutionary biology. (google.com.au)
  • Heterochrony--changes in developmental timing, producing parallels between ontogeny and phylogeny--is shown to be crucial to an understanding of gene regulation, the key to any rapprochement between molecular and evolutionary biology. (google.com.au)
  • Gould also made significant contributions to the field of evolutionary developmental biology, most notably in his work, Ontogeny and Phylogeny. (google.com.au)
  • A well-supported and detailed phylogenetic framework is critical to the solution of major open questions such as the evolutionary origin of multicellularity, diversification of life-history strategies, the conquest of land, the nature of the relationship between ontogeny and phylogeny, and modes of evolution at the molecular level. (berkeley.edu)

estimation


  • PhyloPars: estimation of missing parameter values using phylogeny. (nih.gov)

species


  • books.google.com.au - 'Ontogeny recapitulates phylogeny' was Haeckel's answer--the wrong one--to the most vexing question of nineteenth-century biology: what is the relationship between individual development (ontogeny) and the evolution of species and lineages (phylogeny)? (google.com.au)
  • Phylogeny-based information can complement direct empirical evidence, and is particularly valuable if experiments on the species of interest are not feasible. (nih.gov)
  • The PhyloPars web server provides a statistically consistent method that combines an incomplete set of empirical observations with the species phylogeny to produce a complete set of parameter estimates for all species. (nih.gov)
  • Here we show that resource partitioning and phylogeny determine community structure and outweigh the positive effects of Müllerian mimicry in a species-rich group of neotropical catfishes. (nature.com)

incomplete


  • The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of haplotypes or genotypes with missing entries. (computer.org)
  • Uploading a phylogeny and incomplete feature matrix suffices to obtain estimates of all missing values, along with a measure of certainty. (nih.gov)

methods


  • For your particular questions, try the lecture by Joseph Felsenstein on bootstraps and other means of assessing tree reliabilities, and the lecture by Paul Lewis on comparing different phylogeny methods. (bio.net)

evolution


  • Thus, we report the first evidence, to our knowledge, that competition for trophic resources and phylogeny are pivotal factors in the stable evolution of Müllerian mimicry rings. (nature.com)

Group


  • L'Angiosperm Phylogeny Group (APG) est un groupe de botanistes qui travaillent sur la phylogénétique végétale, en utilisant les techniques moléculaires et l'analyse cladistique. (wikipedia.org)
  • É alojado pelo sítio de internet do Missouri Botanical Garden e mantido pelo pesquisador Peter F. Stevens, membro do Angiosperm Phylogeny Group (APG). (wikipedia.org)

available


  • In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor trivially recoverable from the data. (computer.org)