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)

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

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)

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

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)

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. (3/52004)

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)

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

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)

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

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)

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

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)

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

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)

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

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)

One visceral example of ancestral sequence reconstruction was done by the Matz group (currently residing at the University of Texas at Austin). Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have? Sequences for the common ancestor nodes were synthesized and tested for their activity. The ancestral sequences revealed an interesting evolutionary history. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. This evolution of this ancestor resolved into either a green or red peak, losing the emission bimodality and specializing. ...
One example of ancestral sequence reconstruction was done by the Matz group (currently residing at the University of Texas at Austin). Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red[3]. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have? Different models for reconstruction based on amino acids, codons and nucleotides resulted in reconstructed proteins differing in 4-8 amino acids out of 217. Gene synthesis utilized codons designed "to be degenerate in order to incorporate alternative predictions." [3] The reconstructed sequences included red, pre-red, Red/Green and ALL. The ancestral sequences revealed an interesting evolutionary history. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller ...
Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in almost all fields of applied molecular biology. This book starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a
Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high accuracy with excellent theoretical properties. However, RAxML, the current leading method for large-scale ML estimation, can require weeks or longer when used on datasets with thousands of molecular sequences. Faster methods for ML estimation, among them FastTree, have also been developed, but their relative performance to RAxML is not yet fully understood. In this study, we explore the performance with respect to ML score, running time, and topological accuracy, of FastTree and RAxML on thousands of alignments (based on both simulated and biological nucleotide datasets) with up to 27,634 sequences. We find that when RAxML and FastTree are constrained to the same running time, FastTree produces topologically much more accurate trees in almost all cases. We also find that when RAxML is allowed to run to completion, it provides an advantage over FastTree in terms of the ML score, but does not produce
Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch
Ancestral reconstruction (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the ...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic ...
Mitochondrial and nuclear DNA phylogenies reveal a complex evolutionary history in the Australasian robins (Passeriformes: Petroicidae)
We present a comprehensive molecular phylogeny of the lichen family Graphidaceae (subfamilies Graphidoideae and Fissurinoideae) based on partial sequences of the mtSSU, nuLSU rDNA, and RPB2 loci. The phylogeny includes all currently available sequences in Genbank plus 897 newly generated sequences, from a total of 908 ingroup OTUs representing 428 species. The phylogeny supports the synomymy of Graphidaceae and Thelotremataceae and confirms that rounded and lirellate ascomata evolved multiple times in unrelated clades within the family. The phylogenetic distinctiveness of Fissurinoideae versus Graphidoideae is also supported in our extended taxon sampling. The three-gene phylogeny suggest that in addition to the three tribes previously established for the major clades within subfamily Graphidoideae, several further clades exist that might represent additional tribes. Specifically, the Leptotrema clade is excluded from tribe Ocellularieae and the Carbacanthographis, Heiomasia, Topeliopsis, and
Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do
Phylogeny , Construct Phylogeny , Maximum Parsimony This command is used to construct phylogenetic trees under the maximum parsimony criterion. For a given topology, the sum of the minimum possible substitutions over all sites is known as the Tree Length. The topology with the minimum tree length is known as the Maximum Parsimony tree.. The phylogenetic tree(s) inferred using this criterion are unrooted trees, even though, for ease of inspection, they are often displayed in a manner similar to rooted trees. MEGA includes the Max-mini branch-and-bound search, which is guaranteed to find all the MP trees. However, it is often too time consuming for more than 15 sequences. In those cases, you should use the Close-Neighbor-Interchange (CNI) algorithm to find the MP tree. CNI is a branch swapping method that begins with a given initial tree. You can ask MEGA to automatically obtain a set of initial trees by using the Min-mini algorithm with a given search factor. Alternatively, you can produce the ...
A phylogeny of the fungal phylum Basidiomycota. is presented based on a survey of 160 taxa and five nuclear genes. Two genes, rpb2, and tef1, are presented in detail. The rpb2 gene is more variable than tef1 and recovers well-supported clades at shallow and deep taxonomic levels. The tef1 gene recovers some deep and ordinal-level relationships but with greater branch support from nucleotides compared to amino acids. Intron placement is dynamic in tef1, often lineage-specific, and diagnostic for many clades. Introns are fewer in rpb2 and tend to be highly conserved by position. When both protein-coding loci are combined with sequences of nuclear ribosomal RNA genes, 18 inclusive clades of Basidiomycota are strongly supported by Bayesian posterior probabilities and 16 by parsimony bootstrapping. These numbers are greater than produced by single genes and combined ribosomal RNA gene regions. Combination of nrDNA with amino acid sequences, or exons with third codon positions removed, produces strong ...
Life is extremely complex and amazingly diverse; it has taken billions of years of evolution to attain the level of complexity we observe in nature now and ranges from single-celled prokaryotes to multi-cellular human beings. With availability of molecular sequence data, algorithms inferring homology and gene families have emerged and similarity in gene content between two genes has been the major signal utilized for homology inference. Recently there has been a significant rise in number of species with fully sequenced genome, which provides an opportunity to investigate and infer homologs with greater accuracy and in a more informed way. Phylogeny analysis explains the relationship between member genes of a gene family in a simple, graphical and plausible way using a tree representation. Bayesian phylogenetic inference is a probabilistic method used to infer gene phylogenies and posteriors of other evolutionary parameters. Markov chain Monte Carlo (MCMC) algorithm, in particular using ...
A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision Stephen L. C
A phylogenetic tree, also known as a tree of life or simply a phylogeny, describes branching relationships among species, showing which species shares its most recent common ancestor with which other species.. A phylogeny implicitly has a time axis, and time usually goes up the page. Phylogenetic relations have to be inferred using homologies because the splitting events and common ancestors existed in the past and cannot be directly observed. There are two methods of phylogenetic inference:. 1. Parsimony. Species are arranged in a phylogeny such that the smallest number of evolutionary changes is required.. 2. Distance (or similarity.) Species are arranged in a phylogeny such that each species is grouped with the other species that it shares the most characters with.. Figure: a phylogenetic tree of the main vertebrate groups. Lizards and snakes share a more common ancestor than other species and so are grouped together.. ...
Citation. Basu, M. K., Selengut, J. D., Haft, D. H.. ProPhylo: Partial Phylogenetic Profiling to Guide Protein Family Construction and Assignment of Biological Process. BMC Bioinformatics. 2011 Dec 01; 12: 434.. PubMed Citation. Abstract. ABSTRACT: BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies. RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather ...
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PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...
Asiloidea are a group of 9 lower brachyceran fly families, considered to be the closest relative to the large Metazoan radiation Eremoneura (Cyclorrhapha + Empidoidea). The evidence for asiloid monophyly is limited, and few characters define the relationships between the families of Asiloidea and Eremoneura. Additionally, enigmatic genera, Hilarimorpha and Apystomyia, retain morphological characters of both asiloids and higher flies. We use the nuclear protein-coding gene CAD and 28S rDNA to test the monophyly of Asiloidea and to resolve its relationship to Eremoneura. We explore the effects of taxon sampling on support values and topological stability, the resolving power of additional genes, and hypothesis testing using four-cluster likelihood mapping. We find that: (1) the asiloid genus Apystomyia is sister to Cyclorrhapha, (2) the remaining asiloids are monophyletic at the exclusion of the family Bombyliidae, and (3) our best estimate of relationships places the asiloid flies excluding ...
This MATLAB function computes PhyloTree, a phylogenetic tree object, from Distances, pairwise distances between the species or products, using the neighbor-joining method.
But, as the debate over whale origins showed, I think an interdisciplinary approach can be useful to paleontologists. After all, any phylogeny is a hypothesis that is bound to shift as we learn more. (I cant even count all the phylogenies of theropod dinosaurs there have been...) Phylogenies are definitively provisional, and I think that molecular phylogenies can sometimes be useful in making predictions about relationships that can then be tested with data from the fossil record. If the origin of a particular group is unknown, for example, but a molecular phylogeny shows that two lineages are close together and shared a common ancestor, then paleontologists can examine the fossil evidence to see whether or not this relationship holds up. I dont really think about this debate in terms of which method is superior or inferior. Molecular phylogenies and anatomically-based phylogenies can be used as tools that test and complement each other, so I think a combined approach may continue to be ...
TY - JOUR. T1 - A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny. AU - Azani,Nasim. AU - Babineau,Marielle. AU - Bailey,C. Donovan. AU - Banks,Hannah. AU - Barbosa,Ariane R.. AU - Pinto,Rafael Barbosa. AU - Boatwright,James S.. AU - Borges,Leonardo M.. AU - Brown,Gillian K.. AU - Bruneau,Anne. AU - Candido,Elisa. AU - Cardoso,Domingos. AU - Chung,Kuo Fang. AU - Clark,Ruth P.. AU - Conceição,Adilva De S.. AU - Crisp,Michael. AU - Cubas,Paloma. AU - Delgado-Salinas,Alfonso. AU - Dexter,Kyle G.. AU - Doyle,Jeff J.. AU - Duminil,Jérôme. AU - Egan,Ashley N.. AU - De La Estrella,Manuel. AU - Falcão,Marcus J.. AU - Filatov,Dmitry A.. AU - Fortuna-Perez,Ana Paula. AU - Fortunato,Renée H.. AU - Gagnon,Edeline. AU - Gasson,Peter. AU - Rando,Juliana Gastaldello. AU - Tozzi,Ana Maria Goulart de Azevedo. AU - Gunn,Bee. AU - Harris,David. AU - Haston,Elspeth. AU - Hawkins,Julie A.. AU - Herendeen,Patrick S.. AU - Hughes,Colin E.. AU - Iganci,João ...
View Notes - Minerals-1 from GEOL 1610 at North Texas. Ontogeny Recapitulates Phylogeny Ontogeny Recapitulates Phylogeny y Phylogeny ¡ the evolutionary development of any plant or animal. y Ontogeny
An 1871-nucleotide region including the phoA gene (the structural gene encoding alkaline phosphatase, EC 3.1.3.1) was cloned and sequenced from eight naturally occurring strains of Escherichia coli. Alignment with the sequence from E. coli K-12 made apparent that there were 87 polymorphic nucleotide sites, of which 42 were informative for phylogenetic analysis. Maximum parsimony analysis revealed six equally parsimonious trees with a consistency index of 0.80. Of the 42 informative sites, 22 were inconsistent with each of the maximum parsimony trees. The spatial distribution of the inconsistent sites was highly nonrandom in a manner implying that intragenic recombination has played a major role in determining the evolutionary history of the nine alleles. The implication is that different segments of the phoA gene have different phylogenetic histories.. ...
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 recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.[7] Many kinds and subclasses of phylogenetic ...
Optional reference books: 1) Paul Lewiss unpublished text; 2) The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); 4) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 5) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference. Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...
Molecular phylogenetic is the branch of phylogeny that analyzes hereditary molecular diversity, mainly in DNA sequences, to increase data on an organisms evolutionary relationships. Due to the taxonomic levels of the study, various molecular markers are applied in molecular phylogeny. The selection of molecular instrument is of paramount matter to ensure that a proper level of variation is meliorated to respond the phylogenetic question. In this review, we have been trying to discuss about gene markers used in the plant phylogeny at various taxonomic levels. The current gene markers used in phylogeny include: the ribosomal nuclear genes, low copy nuclear genes and the extra-nuclear genome (mitochondrial and chloroplastic genomes). Conserved regions could be used at higher taxonomic levels in phylogenetics studies and regions with more changes could be applied between closely related taxa. One of the most common sequences for studying the phylogenetic relationships at the generic and infrageneric
The main focus of my project is to learn more about morphological character evolution in a phylogenetic context.. One of the goals is to erect homology hypotheses of morphological characters. The morphological characters are then used as a data base for reconstructing of a hypothesis of phylogenetic relationships (=tree) in combination with existing DNA sequences or are mapped on existing trees to study the character evolution.. The emphasis of my research is to unravel annelid character evolution.. Several anatomical structures are studied: body wall muscles, epidermis and cuticle, and genital ducts, using different methods such as transmission electron microscopy (TEM) and routin histology.. Another goal of the project is to study the morphology of homologous characters; characters that come out as derived from a common ancestor in both DNA and morphological analyses and that have long been recognized by morphologists to unite a certain group of organisms, e.g. the clitellum of Clitellata and ...
Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of
Defining units of diversity, disentangling the evolutionary history of a species, assessing the phylogenetic structure of communities are all pressing questions in ecology. Molecular phylogenies represent a pivotal help in unravelling them.. The two-day course will be devoted to: (1) providing a brief overview of the phylogenetic methods and software to obtain molecular phylogenies from DNA sequence data; (2) outlining the use the phylogenies as a base for DNA taxonomy.. During the course, students will be exposed to different ideas, rationale, methods, tools, and software that will widen their toolkit for their own research activities. Great emphasis will be placed on the use of the statistical software R to handle data and to perform specific statistical tests. All software used for the course is free and can be downloaded from the web.. Maximum number of participants: 10. Program. May 12th, overview of phylogenetic methods. morning, 2 hours lecture. ...
Pyroleae (Ericaceae) consist of four genera, all of which are distributed widely in temperate coniferous or sometimes deciduous forests of the Northern Hemisphere. To investigate the phylogenetic relationships among these genera and to explore the evolution of the characteristics of the subfamily, we conducted maximum parsimony and Bayesian analyses with nrDNA ITS and three cpDNA intergenic spacers (atpB-rbcL, trnS-trnG and trnL-trnF). The results from cpDNA and combined cpDNA + ITS data sets strongly support the monophyly of Pyroleae as well as a sister relationship between Pyrola and Moneses-Chimaphila, with Orthilia as the basal lineage. The sister-group relationship between Moneses and Chimaphila is supported by a set of synapomorphies, e.g., single flower, colpate pollen, five bundles in the style, straight fruiting pedicel orientation, complete capsule dehiscence, and the basic chromosome number, x = 13. The Moneses-Chimaphila-Pyrola clade is supported by at least one homologous character ...
View Notes - Phylogeny from BIOL 301 at Waterloo. Introduction to Phylogeny Required Reading: chapter 4 (Ignore Box 4.1) Objectives The basics of phylogenetic trees How phylogenetic trees are
The results of the molecular phylogenetic analysis show both similarities and differences with respect to the previous morphology-based hypothesis [22]. Previously well-supported clades were recovered with broadly similar relationships, but (somewhat surprisingly) the small A. alala group was recovered as sister to Limenitis, rendering Adelpha paraphyletic. Four morphological synapomorphies support the alala group as sister to all other Adelpha [22], so the position of the alala group clearly merits further study, with obvious potential implications for taxonomic revision. Most importantly for the present study, North American and Palaearctic Limenitis are robustly supported as the most closely related group to Adelpha. Whether Adelpha (sensu stricto) is monophyletic or not, the data clearly reveal the significant variation in diversification rates across the broader phylogeny, and that the variation arose from a dramatic increase in diversification rate within the lowland Adelpha clade.. In ...
Molecular phylogenetic tree of MAIR gene family. Phylogenetic analysis of the MAIR family genes was performed by using the UPGMA method of GENETYX-MAC software
The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent ...
Recombination plays an important role in shaping the genetic diversity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to
In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC) framework, an approach requiring computation times of hours or days when applied to large phylogenies. We demonstrate that a hill-climbing maximum a posteriori (MAP) adaptation of the MCMC scheme results in considerable gain in computational efficiency. We demonstrate also that a novel dynamic programming (DP) algorithm for branch length factorization, useful both in the hill-climbing and in the MCMC setting, further reduces
Phylogenomic approaches to the resolution of inter-species relationships have become well established in recent years. Often these involve concatenation of many orthologous genes found in the respective genomes followed by analysis using standard phylogenetic models. Genome-scale data promise increased resolution by minimising sampling error, yet are associated with well-known but often inappropriately addressed caveats arising through data heterogeneity and model violation. These can lead to the reconstruction of highly-supported but incorrect topologies. With the aim of obtaining a species tree for 18 species within the ascomycetous yeasts, we have investigated the use of appropriate evolutionary models to address inter-gene heterogeneities and the scalability and validity of supermatrix analysis as the phylogenetic problem becomes more difficult and the number of genes analysed approaches truly phylogenomic dimensions. We have extended a widely-known early phylogenomic study of yeasts by adding
The evolutionary history of scleractinian corals is based on knowledge of skeletal characters and their 250 million yr fossil record. However, homologies of skeletal characters are not well-understood and fossil documentation of these characters is incomplete. As a result, relationships among families and suborders are poorly understood. We have analyzed a 225 bp segment of the nuclear 28S ribosomal RNA gene from 45 species of corals and a 566 bp segment of the mitochondrial 16S ribosomal RNA gene from 68 species. Unlike previous analyses of smaller numbers of taxa, the dataset presented here includes both reef-building and non-reef-building taxa from 20 of 24 families and all seven suborders. Nuclear sequences analyzed under maximum parsimony and minimum evolution criteria did not resolve relationships among families and suborders. Similar analyses of mitochondrial sequences resulted in a robust phylogenetic hypothesis. The mitochondrial hypothesis, like previous analyses of a subset of these ...
The issue of whether coelomates form a single clade, the Coelomata, or whether all animals that moult an exoskeleton (such as the coelomate arthropods and the pseudocoelomate nematodes) form a distinct clade, the Ecdysozoa, is the most puzzling issue in animal systematics and a major open-ended subject in evolutionary biology. Previous single-gene and genome-scale analyses designed to resolve the issue have produced contradictory results. Here we present the first genome-scale phylogenetic evidence that strongly supports the Ecdysozoa hypothesis. Through the most extensive phylogenetic analysis carried out to date, the complete genomes of 11 eukaryotic species have been analyzed in order to find homologous sequences derived from 18 human chromosomes. Phylogenetic analysis of datasets showing an increased adjustment to equal evolutionary rates between nematode and arthropod sequences produced a gradual change from support for Coelomata to support for Ecdysozoa. Transition between topologies occurred when
BACKGROUND:Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage sorting (deep coalescence), or horizontal gene transfer, that cause incongruence among gene trees. One such approach is gene tree parsimony, which, given a set of gene trees, seeks a species tree that requires the smallest number of evolutionary events to explain the incongruence of the gene trees. However, the only existing algorithms for gene tree parsimony under the duplication-loss or deep coalescence reconciliation cost are prohibitively slow for large datasets.RESULTS:We describe novel algorithms for SPR and TBR based local search heuristics under the duplication-loss cost, and we show how they can be adapted for the deep coalescence cost. These algorithms improve upon the best existing ...
The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago. To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. ...
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. ...
Authors: SERAP MUTUN, HÜLYA KARAGÖZOĞLU Abstract: Abstract: Genetic diversity and diversification of the Anatolian populations of Andricus lignicola (Hartig, 1840) (Hymenoptera: Cynipidae) were investigated using 433 base pairs of the mitochondrial cytochrome b gene. Eighteen distinct haplotypes from 15 populations were determined. Analyses indicated average haplotype and nucleotide diversity as 0.325 and 0.008, respectively. Phylogenetic analyses conducted through the application of maximum likelihood and maximum parsimony produced similar topologies with two major clade structures supported by high bootstrap values. Bayesian analysis produced more polytomies without major basal groupings of the haplotypes. Parsimony network analysis revealed four haplogroups, and the largest group comprised half of the haplotypes. Our preliminary ABGD analysis implied the presence of four hidden lineages with the possibility of a cryptic species complex within A. lignicola. Hierarchical F-statistics (AMOVA) ...
A recent paper in MBE presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces). The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole genomes). These authors are employing phylogenomics in the sense that multiple genes are used to reconstruct the phylogeny. This use is different from the J.Eisen/Sjölander sense which is to infer gene ...
The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches. We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on
This chapter explores the evolution and phylogeny of the molluscan class Scaphopoda. It describes the main features of scaphopods including their shell, mantle and mantle cavity, feeding habits, digestive tract, and nervous system. It provides a brief account of the history of classification and phylogeny of scaphopods and characterizes its two main clades, Dentaliida and Gadilida. It stresses the need to increase taxonomic sampling and to develop better repositories of material suitable for molecular analysis in order to understand better the scaphopod phylogeny. ...
Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be
Two forms of phylogenetic distortion are caused by recombination. The first affects the shape of the tree topology. Although this is a potentially serious difficulty, Jessica Hedge and I recently showed that phylogenies estimated from whole bacterial genomes are surprisingly robust to this problem. The second affects the lengths of the branches. When genetic material is replaced by a homologous but distantly related sequence, it gives the appearance of a cluster of substitutions in the genome, and this can exaggerate branch lengths. ClonalFrameML detects these clusters of substitutions, identifies them as recombination events, and corrects the branch lengths of the tree ...
The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all
Image phylogeny is the problem of reconstructing the structure that represents the history of generation of semantically similar images (e.g., near-duplicate images). Typical image phylogeny approaches break the problem into two steps: (1) estimating the dissimilarity between each pair of images and (2) reconstructing the phylogeny structure. In this article, the authors propose new approaches…
A proper understanding of the diversity, systematics, and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis - pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya) - has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools, and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analysis and computational methods. In this book, leading scientists from around the world explore current concepts in molecular phylogeny and their application with respect to microorganisms. The authors describe the
Harmon, L.J., Losos, J.B., Davies, T.J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B. et al. (2010) Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64, 2385-2396 ...
Module: Constructing phylogenetic tree. The uniqueness of DNA (RNA) from one lineage to another allows to reconstuct the evolutionary history through a phylogenetic tree and get information on the past evolutionary processes. A phylogenetic tree constructed from sequences of human influenza virus (an epidemic simulated accross a small community) seeded in a community by an individual named -1 in the transmission network (see following image). The phylogenetic tree is composed of branches (edges) and nodes, where branches connect nodes (node: points at which two or more branches diverge). It has internal and external branches and nodes (terminal), and internal node corresponds to the hypothetical last common ancestor (LCA) of everything arising from it. Terminal nodes correspond to the sequences (DNA/RNA) from which the tree was constructed. The lengths of the branches correspond to sequence difference between the two nodes they connect. The phylogenetic tree is constructed by considering the ...
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the
In mammals, the members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection. Viruses exert strong selective pressures on the defense system. Accordingly, antiviral TRIMs have diversified highly through gene expansion, positive selection and alternative splicing. Characterizing immune TRIMs in other vertebrates may enlighten their complex evolution. We describe here a large new subfamily of TRIMs in teleosts, called finTRIMs, identified in rainbow trout as virus-induced transcripts. FinTRIMs are formed of nearly identical RING/B-box regions and C-termini of variable length; the long variants include a B30.2 domain. The zebrafish genome harbors a striking diversity of finTRIMs, with 84 genes distributed in clusters on different chromosomes. A phylogenetic analysis revealed different subsets suggesting lineage-specific diversification events. Accordingly, the number of fintrim genes varies greatly among fish species.
Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively
TY - JOUR. T1 - Phylogenetic investigation of Dogiels pericellular nests and Cajals initial glomeruli in the dorsal root ganglion. AU - Matsuda, Seiji. AU - Kobayashi, Naoto. AU - Terashita, Takehiro. AU - Shimokawa, Tetsuya. AU - Shigemoto, Kazuhiro. AU - Mominoki, Katsumi. AU - Wakisaka, Hiroyuki. AU - Saito, Shouichiro. AU - Miyawaki, Kyoujy. AU - Saito, Kyoko. AU - Kushihata, Fumiki. AU - Chen, Jie. AU - Gao, Shuang Yan. AU - Li, Chun Yu. AU - Wang, Min. AU - Fujiwara, Takashi. PY - 2005/10/24. Y1 - 2005/10/24. N2 - Cajals initial glomeruli (IG) and Dogiels pericellular nests (PCNs) were first described from methylene blue preparations of healthy animal tissues around the beginning of the last century. Since that time, although many reports have been published concerning these structures, few have focused on their development and phylogeny in healthy animals. The aim of this study was to examine the phylogenetic development of the sensory neurons in Cajals IG (also called axonal ...
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What is amazing is the evolutionists high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is "no known mechanism or function that would account for this level of conservation at the observed evolutionary distances." Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are "astonishing ...
What is amazing is the evolutionists high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is "no known mechanism or function that would account for this level of conservation at the observed evolutionary distances." Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are "astonishing ...
We studied the evolution of colour pattern in Malagasy poison frogs, genus Mantella, a group of diurnal and toxic frogs endemic to Madagascar. Based on a phylogeny reconstructed using 1130 bp of the mitochondrial 16S rRNA gene, the genus can be divided into five species groups. Within some of these groups, inter-specific genetic divergences were very low (1.2 - 2.8% sequence divergence) while colour patterns were markedly different. In contrast, Mantella madagascariensis and M. baroni, two species which show extremely similar dorsal coloration patterns, were not included in the same clade. This conclusion was supported by high bootstrap values and by significant rejection of alternative topologies using KH-tests. Analysis of colour patterns and tentative reconstruction of ancestral states yielded five character states shared by these two species but not by their respective sister species, M. aurantiaca and M. nigricans. Considering these detailed similarities as symplesiomorphic therefore ...
(A) Anomeric region analysis of strain MMHC82 spectrum for MM. (B) Anomeric region analysis of strain MMHC82 spectrum for CD medium. (C) Anomeric region analysi
In 2001 I initiated a project at the University of Vienna, aiming at the first molecular phylogeny of pholcid spiders. When I left Vienna, the work was taken over by Branka Bruvo who did an excellent job in finishing the project. It was obvious that these were preliminary results, as both the numbers of taxa and genes were small, but the study provided a useful basis for further research on the molecular phylogeny of pholcid spiders. Due primarily to the constraint of getting access to fresh DNA-ready material, it took seven years for the next step, with significant increases in taxa and genes, but still far from complete (published in 2013 in Cladistics ...
The objective of this study was to investigate the relationship between nucleotide substitutions and time in evolving HIV-1 populations, i.e., if a molecular clock exists or not, and if so how the clock should be described. With this aim we investigated a unique set of samples for which the evolutionary history is exactly known (8, 9), which allowed direct correlation between the genetic distances and the time that separated the samples. Two important conclusions could be drawn from the study. First, we show that the concept of a molecular clock fits HIV-1 evolution well. Second, we demonstrate that a significant genetic distance at zero divergence time exists, a finding we show depends on a pretransmission interval.. Evolving HIV-1 populations display very high nucleotide substitution rates. During the evolution some sites will fluctuate rapidly in their nucleotide state whereas other sites will display substitutions that are stable over longer time intervals. Under these circumstances fixation ...
The near-simultaneous appearance of most modern animal body plans (phyla) ~530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation, yet the exact speed and nature of this grand adaptive radiation remain debated [1-12]. Crucially, rates of morphological evolution in the past (i.e., in ancestral lineages) can be inferred from phenotypic differences among living organisms-just as molecular evolutionary rates in ancestral lineages can be inferred from genetic divergences [13]. We here employed Bayesian [14] and maximum likelihood [15] phylogenetic clock methods on an extensive anatomical[16]and genomic[17] data set for arthropods, the most diverse phylum in the Cambrian and today. Assuming an Ediacaran origin for arthropods, phenotypic evolution was ~4 times faster, and molecular evolution ~5.5 times faster, during the Cambrian explosion compared to all subsequent parts of the Phanerozoic. These rapid evolutionary rates ...
Temporal patterns in species occupancy and geographic range size are a major topic in evolutionary ecology research. Here we investigate these patterns in Pliocene to Recent large mammal species and genera in Western Eurasia. By using an extensively sampled fossil record including some 700 fossil localities, we found occupancy and range size trajectories over time to be predominantly peaked among both species and genera, meaning that occupancy and range size reached their maxima midway along taxon existence. These metrics are strongly correlated with each other and to body size, after phylogeny is accounted for by using two different phylogenetic topologies for both species and genera. Phylogenetic signal is strong in body size, and weaker but significant in both occupancy and range size mean values among genera, indicating that these variables are heritable. The intensity of phylogenetic signal is much weaker and often not significant at the species level. This suggests that within genera, ...
In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At ...
In the case of the partly homoplasious data, the median-joining network reconstructs a synapomorphy of the clade BC, because A is not placed on the node. This is because one character in our matrix is a methodologically undetectable parallelism - the same trait evolved in the sister taxa B and C, but only after both evolved from A. Clade BC is non-inclusive (paraphyletic), since A is the direct ancestor of both B and C and the clade BC lacks a real synapomorphy (if we go back to Hennigs concept). The reconstructed A would, however, be a stem taxon and clade BC would be inclusive (monophyletic) with one (inferred) synapomorphy. But this is a purely semantic problem of cladistics. In the real world, we will hardly have the data to discern whether A represents: the last common ancestor of B and C, a stem taxon of the ABC-lineage (a), a very early precursor of B or C (b/c), or an ancient sister lineage of A, B, and/or C (a*). For practicality, one would eventually include all fossil forms with ...
CCD is a Java software package for the selection of core collections of diverse taxa (e.g. from germplasm collections) that are intended to capture the genetic diversity of the input dataset.. The software takes as input a binary matrix which transcribes the different alleles (genetic forms) for each taxon. It then tries to find a most diverse collection of alleles under various constraints (e.g. sample size, geographic location of samples).. The software implements many of the most popular methods for determining core collection. In addition it includes novel greedy methods for selection based on polymorphism information content, Shannon entropy and phylogenetic trees/networks. In particular, for the latter approach we construct either a Neighbor-joining tree or Neighbor-net network from a distance matrix computed in PHYLIP distance matrix format by CCD. The resulting structure (tree or network) in tabbed text or NEXUS format and can then be loaded into CCD to determine the core collection. The ...
Animal phylogeny is undergoing a major revolution due to the availability of an exponentially increasing amount of molecular data and the application of novel methods of phylogentic reconstruction, as well as the many spectacular advances in palaeontology and molecular developmental biology. Traditional views of the relationships among major phyla have been shaken and new, often unexpected, relationships are now being considered.
Recent developments are providing exciting new insights into the evolutionary dynamics of species diversification and the importance of evolutionary radiations, or rapid episodes of lineage diversification. The aim of this meeting is to explore questions about where, when and why plant evolutionary radiations happen, and how they proceed. The meeting will bring together contributions spanning: (i) new models of species diversification, including paleodiversity and trait evolution, and the increasingly sophisticated and powerful tools available for testing hypotheses about diversification trajectories and their causes; (ii) the proliferation of new molecular phylogenetic data, for more and larger plant clades spanning broader taxonomic, geographical and temporal levels, as well as opportunities for unprecedented phylogenetic resolution of rapidly evolving clades coming from genome-scale DNA sequence data; (iii) assembly of more comprehensive species geographic distribution, functional and life ...
This post belongs in the write it down before you forget category. Edit - this approach is necessary for handling the trees produced by RAxML, but not those produced by IQ-TREE. Edit #2 - Ancestral state reconstruction in RAxML does not seem to work very well. Im trying IQ-TREE (v1.6) instead. I have a tree…
The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and concepts may be understood in systematics, which, in turn, provides data for a more general account ...
Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no ...
Registration open for this course, that will be held from September 11th-15th, 2017 in Barcelona (Spain).. Instructor: Dr. Chris Klingenberg (MAnchester University, UK).. This course provides an overview of the interface between geometric morphometrics and phylogenetics. It aims to give an overview of the different approaches and methods that link the two fields and to enable participants to apply them to their own research problems.. Lectures that introduce concepts and methods are integrated with demonstrations of software that put them into practice right away. The main emphasis is on mapping shape data on existing phylogenies to reconstruct the evolutionary history of shape diversification, as well as comparative methods that take phylogeny into account.. To enhance the practical approach of the course, participants are encouraged to bring their own data to conduct analyses and discuss results.. Software that will be used during the course: MorphoJ ...
First of all, Im a student in non-English-speaking country... Newbie in bioinformatics. My Question is about Phylogenetic tree and divergence time. (for training) For drawing Phylogenetic tree, I used MEGA 7 for windows 7 64bit, GUI.. I draw the tree with 16 species mtDNA .fasta data and new mtDNA data, and then I try to calculate the divergence time. But I dont know how to calculate this time. So... the first question is Is it possible to calculate divergence time with MEGA7? if possible, how? And if it is impossible or not recommendable, what tools can be used for it?. Anyway in this situation I did something with MEGA7. (maybe... pointless task?) I found "Compute Pairwise distance..." and get a matrix from it. But I dont know what these numbers mean. 0.05731, 1.012493, 1.42815, 1.197099 .... no unit. Surely this values looks like getting bigger if compared two species have distant evolutionary relationship. What is it? It is my second question. If you have an idea for at least one of ...
Abstract The ulvophytes are of particular evolutionary interest because they display a wide morphological and cytological diversity with unique features among green algae. In this review we describe this diversity in an evolutionary perspective, discuss recent progress made towards understanding the genetic underpinning of highly specialized cytomorphological types, such as siphonous cells, and describe the recent progresses made towards the understanding of the peculiar and highly diverse chloroplast genomes found among ulvophytes. We discuss the difficulties in resolving the ancient phylogenetic relationships among ulvophytes, and the core Chlorophyta lineages, even when applying chloroplast phylogenomic analyses. Furthermore, we highlight the advantages and opportunities in using phylotranscriptomics as an alternative tool to resolve difficult phylogenetic relationships and to unveil the evolution of major cyto-morphological innovations and molecular features associated to them. ...
There are three issues that you question in the above statements. First, the Nasonia gut microbiome recapitulates the hosts phylogeny. We demonstrated this pattern in our Evolution paper, this article, and a third set of experiments that we are currently working on. So we think your commentary here stems from a misinterpretation of what phylosymbiosis is, rather than its lack of evidence. Heres how we view it operationally. Phylosymbiosis is simply the reconstruction of the hosts phylogeny with a UniFrac inference method used to compare microbial community relationships. Like phylogenies, UniFrac trees are statistical inferences based on the weighted (Fig 2B) and unweighted abundances (Fig 2C) of OTUs. Remarkably, both the weighted and unweighted Unifrac trees are in complete agreement with a phylosymbiotic microbiome. We suspect you are laser focused on the pie charts, which create the illusion that G and V have very similar communities based on the single, dominant Providencia genus. The ...
U.S. Fish & Wildlife Service Candidate Conservation Agreements What Are Candidate Species? What the U.S. Fish and Wildlife Service (FWS) considers candidate species are those plants and animals that are candidates for listing under the Endangered Species Act (ESA). These are species for which the FWS has enough information regarding their biological status and threats to propose them as threatened or endangered, but listing is currently precluded by higher priority listing activities. Candidate species are not subject to the legal protections of the ESA. Proactive conservation efforts for these species can, in some cases, eliminate the need to list them under the ESA. What Are the Benefits of Conserving Candidate Species? Implementing conservation efforts before species are listed and their habitats become highly imperiled increases the likelihood that simpler, more cost-effective conservation options are available, and that conservation efforts will succeed. In addition, through early ...
This example of a molecular phylogenetic tree is an unrooted dendrogram. The length of the branches quantitatively represents the evolutionary distance separating gene sequences within these organisms.This particular tree is based on the analysis of small subunit ribosomal RNA sequences. In this tree, the tips of branches are modern organisms. Each node within the tree represents a common ancestor. The last common ancestor (the root) is here marked with the star. How this is determined will be described in a later lecture.. Notice that there is no explicit or implied ranking of above (superior) or below (inferior) in the tree. Evolutionary distance (divergence) is measured along the lengths of the branches connecting species. There are no axes in this graph.. One of the most exciting outcomes of this method early on was the discovery of a new type of organism - the Archaea (a.k.a. archaebacteria). Previously it was thought that all living things were either Bacteria (a.k.a. eubacteria) or ...
For example, our recent work includes the development of methods for reconstructing phylogenetic networks directly from molecular data such as the NeighborNet algorithm [1] (which is available as part of the software package Splitstree4 , and the QNet algorithm [2]. We have also developed methods [3] for computing consensus networks, phylogenetic networks used to summarise, for example, collections of gene trees. In case the collection of gene trees is built from patchy data, more sophisticated tools are needed to summarise them. One approach [4] developed by members of our group is implemented in the Q-imputation algorithm.. Another software package developed by our group, called PADRE, aims to provide tools for constructing an explicit representation of the evolutionary history of polyploid organisms such as plants . PADRE is based on our work on modelling reticulate evolution [5, 6], which includes recent theoretical results [7] concerning the complexity of computing multi-labelled trees. ...
Read "Rooting molecular trees: problems and strategies, Biological Journal of the Linnean Society" on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Three plant genera with South American-Australasian disjunctive distributions were studied: Eucryphia, Griselinia and Coriaria . The aims of the project were: a) to assess the utility of different chloroplast and nuclear DNA sequences for phylogenetic reconstruction and b) by means of molecular clocks to establish whether or not this distribution is due to vicariance (continental drift) or more recent dispersal events. DNA was extracted, and regions of interest were amplified and sequenced. These were rpoA, trnL-F and trnU-K from the chloroplast genome, and rDNA 5.8S and intergenic spacers 1 and 2, Adh and two loci of the G3pdh gene from the nuclear genome. In each of the three genera, a single trans-Antarctic disjunction was indicated. Molecular phylogenies were produced using parsimony. Individual base pair variation was analysed in detail, and graphs were drawn to highlight variable regions. Sequences providing the most resolution were trnL-F, ITS and the two loci of the G3pdh. Robust ...
Our work is largely done within the context of the software packages MrBayes and RevBayes. Among other things, we are interested in how evolutionary models can be formulated in a generic way, and we are trying to improve the numerical methods used in Bayesian phylogenetic inference. We also work with several different applications in evolutionary biology, for example, understanding how morphological characters change over time and how fossils can be used in dating past evolutionary events. ...
Ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantels test, computation of minimum spanning tree, the population parameter theta based on various approaches, nucleotide diversity, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using non-parametric rate smoothing, conversion of APE trees to and from hclust objects and for classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ and ML methods.
... Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.. ...
154 Hurley Hall. Phylogenetic Species Trees as Optimization Problems and Connections to Statistics and Geometry.. The fundamental problem in phylogenetics is to infer the evolutionary history of a group of species. This history is usually represented as a rooted tree whose leaves are the extant species from which data can be gathered. Molecular phylogenetics has led to some grand scientific challenges, driven by advances in genome sequencing technology: (1) data is gathered from long genomes for which evolutionary transformations must be modeled by myriad processes, (2) different regions of these genomes may have different evolutionary histories, and (3) there are intractable computational issues presented by the amount of "big data" used in the inference process. Fortunately for the interested mathematician, some of the most promising methods in phylogenetic inference use information about probabiity distributions of genes within large genomes. We will show this leads to interesting connections ...
The aquatic plant genus Ruppia (Ruppiaceae) comprises eight species mainly in coastal brackish areas of the world. While the known taxa of Ruppia thus far generally had either four- or eight-carpelled flowers, our recent Ruppia collection from Western Cape, South Africa showed flowers with only two carpels. This characteristic morphological evidence, together with elongated coiled peduncles, implied either: i) extensive morphological variation of the cosmopolitan R. cirrhosa; or ii) the occurrence of a new species in the genus. We tested these alternative hypotheses of the bicarpellate Ruppia taxon in a phylogenetic framework. Sequence data from four plastid DNA regions and nuclear phyB were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We obtained moderately to highly resolved phytogenies with both data sets. The collection from Western Cape showed unique DNA sequences which were, in both plastid and nuclear phylogenetic trees, placed as sister to the rest of the ...
The history of life unfolds within a phylogenetic context. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along phylogenetic trees. This task view describes R packages that implement a variety of different comparative phylogenetic methods. This is an active research area and much of the information is subject to change. One thing to note is that many important packages are not on CRAN: either they were formerly on CRAN and were later archived (for example, if they failed to incorporate necessary changes as R is updated) or they are developed elsewhere and have not been put on CRAN yet. Such packages may be found on GitHub, R-Forge, or authors websites. Getting trees into R : Trees in R are usually stored in the S3 phylo class (implemented in ape), though the S4 phylo4 class (implemented in phylobase) is also available. ape can read trees from external files in newick format (sometimes popularly known as phylip format) or NEXUS format. It can also ...
The Geneco course "Making Phylogenetic Trees" run by Prof Niklas Wahlberg will be at Lund University from the 2nd to 4th of October . This 3 day course will provide an introduction to the fundamental principles of building phylogenies using molecular data, as well as the latest techniques and programmes in this field.. The aims of this course are to introduce the theory and practice of phylogenetic inference from molecular data and to provide an introduction to some of the most used methods and computer programs. The emphasis will be on model-based methods using maximum likelihood and Bayesian inference, with a focus on DNA sequences as data. We will introduce programs such as RAxML, MrBayes, as well as BEAST for timing of divergence analyses. The course will consist of lectures, demonstrations of computer programs, and independent projects on fully analysing an example dataset (either your own or given by the lecturer).. The course is available to everyone and there is no charge for attendance. ...
This is a common problem I have when trying to construct a phylogeny for a set of taxa when all taxa do not have sequence data associated. 1. read your tree into R as a phylo object 2a. label all the nodes tree|-makeNodeLabel(tree) 2b. your tree may not have branch lengths and thus no branching…
Darwin / Wallace Tree of Life = branching with a single common ancestor. vs. Lamarck Chain of Being = not branching, multiple common ancestors. Phylogenetics. Phylogeny = genealogy of a group of taxa; a kind of family tree. The goal of cladistics is to provide a phylogeny that reflects evolutionary history. Essentially we seek to make hierarchical groups.. Minimum Essential Terms (also see pg 437). 1) Monophyletic Group = a group that contains all descendants of a common ancestor. The motivation for creating these can be kind of confusing. Youre probably familiar with taxonomy (Kingdom, Phylum, Class, etc.) though. Imagine we have a bunch of squid-like things that Frank wants to put into the same genus and Curt does not. We can do a phylogenetic analysis to reveal the evolutionary relationships among these squid-like things. If they indeed form a monophyletic group, Frank has support for placing them in the same taxonomic group. If not, then these squid-like things are not closely related ...
3. Overview of Friday (Corey and Doug). 4. Back to the modules- break into 3 groups to discuss new module themes.. A) Chris, Tracy, Eileen, Tania: locomotion-related. B) Corey, Scott, Scott: limbs, trait evolution; cryptic diversity; evol @ molecular level and adaptation; evolution of sensory abilities; gene duplication and adaptation; evolution of domestication (Russian foxes, dogs, mustard plants); ring species; evolution of gliding ability. C) Kayce, Rob, Julie: molecules to ecosystems in space and time; glaciation effects, across landscapes; infectious disease. D) Doug, Pam, Ana: plant diversity, phylogeny, biogeography, climate change. E) Mark, Kurt, Joe: genomics-related concepts; pop gen to species level: phylogeography, processes that structure genetic variation within species, gene trees vs species trees, macroevolution, reconstruction of ancestral states; community assembly: history of populations in space and time; glaciation; parasites/emerging disease; stress gene trees vs species ...
HIV-1 CRF07_BC and CRF08_BC are closely related circulating recombinant forms (CRFs) with serious public health consequences in China. The temporal and spatial dynamics of these CRFs were determined by estimating their times of divergence, using phylogenetic and Bayesian coalescent methods. Studies of the timelines of CRF07_BC and CRF08_BC trace the expansion of these strains back their origins to Yunnan province. The present study highlights the relevance of incorporating evolutionary and molecular epidemiological analyses into an in-depth understanding of the genesis of HIV epidemic, providing information for determining regional and global public health policies, including future vaccine strategies.
When two clusters are merged, their mass distributions are combined according to a weighted average. The edges of the reference tree in this figure are thickened in proportion to the mass distribution (for simplicity, just a subtree of the reference tree is shown here). In this example, the lower mass distribution is an equal-proportion average of the upper two mass distributions. Similarities between mass distributions, such as the similarity seen between the two clusters for the G. vaginalis clade shown here, are what cause clusters to be merged. Such similarities between internal nodes can be visualized for the squash clustering algorithm; the software implementation produces such a visualization for every internal node of the clustering tree. Note that in this figure only the number of reads placed on each edge is shown, although each placement has an associated location on each edge when performing computation ...
Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our
A novel ikarugamycin-producing actinomycete, designated strain NEAU-Da3T, was isolated from soybean root [Glycine max (L.) Merr.] and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-Da3T belonged to the genus Streptomyces , and was most closely related to Streptomyces carpaticus NRRL B-16359T (99.5 %), Streptomyces cheonanensis VC-A46T (99.3 %) and Streptomyces xiamenensis MCCC 1A01550T (97.2 %); similarities to other type strains of species of the genus Streptomyces were lower than 97.1 %. The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with S. carpaticus NRRL B-16359T, S. cheonanensis VC-A46T and S. xiamenensis MCCC 1A01550T. This branching pattern was also supported by the tree reconstructed with the neighbour-joining method. A comparative study between strain NEAU-Da3T and the type strains of the closest related species of the genus Streptomyces
Obtaining full-length 16S rRNA gene sequences is important for generating accurate taxonomy assignments of bacteria, which normally is realized via clone library construction. However, the application of clone library has been hindered due to its limitations in sample throughput and in capturing minor populations (<1 % of total microorganisms). To overcome these limitations, a new strategy, two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE can compare microbial communities based on its first-round DGGE profiles and generate partial 16S rRNA gene sequences (8-534 bp, Escherichia coli numbering). Then, strain-specific primers can be designed based on sequence information of bacteria of interest to PCR amplify their remaining 16S rRNA gene sequences (515-1541 bps, E. coli numbering). The second-round DGGE can confirm DNA sequence purity of these PCR products. Finally, the full-length 16S rRNA gene sequences can be ...
A Gram-stain-negative, non-motile, non-spore-forming and short rod- or rod-shaped bacterial strain, designated 22-5T, was isolated from a bluespotted cornetfish, Fistularia commersonii, and subjected to taxonomic study. Strain 22-5T grew optimally at 30 °C and in the presence of 2-5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 22-5T belonged to the genus Paracoccus and joined the cluster comprising Paracoccus homiensis DD-R11T and Paracoccus zeaxanthinifaciens ATCC 21588T, with which strain 22-5T exhibited 97.4 and 96.9 % 16S rRNA gene sequence similarity, respectively. Strain 22-5T exhibited 94.0-96.6 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Paracoccus. Strain 22-5T contained Q-10 as the predominant menaquinone and C18 : 1 ω7c as the predominant fatty acid. In this study, P. zeaxanthinifaciens KCTC 22688T also contained Q-10 as the predominant isoprenoid quinone. The DNA G+C content of strain 22-5T was 63.6
5S rRNA sequences were determined for the myxobacteria Cystobacter fuscus, Myxococcus coralloides, Sorangium cellulosum, and Nannocystis exedens and for the radioresistant bacteria Deinococcus radiodurans and Deinococcus radiophilus. A dendrogram was constructed by using weighted pairwise grouping based on these and all other previously known eubacterial 5S rRNA sequences, and this dendrogram showed differences as well as similarities compared with results derived from 16S rRNA analyses. In the dendrogram, Deinococcus 5S rRNA sequences clustered with 5S rRNA sequences of the genus Thermus, as suggested by the results of 16S rRNA analyses. However, in contrast to the 16S rRNA results, the Deinococcus-Thermus cluster divided the 5S rRNA sequences of the alpha subdivision of the class Proteobacteria from the 5S rRNA sequences of the beta and gamma subgroups of the Proteobacteria. The myxobacterial 5S rRNA sequence data failed to confirm the existence of a delta subgroup of the class Proteobacteria, which
A Gram-stain-positive, aerobic, non-spore-forming, atrichous and short rod-shaped endophytic actinomycete, designated strain BGMRC 2075 , was isolated from the leaves of Kandelia candel, and was subjected to polyphasic characterization to unravel its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BGMRC 2075 belongs to the genus Nocardioides ,showing the highest 16S rRNA gene sequence similarity to Nocardioides aestuarii JC2056 (96.1 %), Nocardioides agariphilus MSL-28 (95.1 %) andNocardioides islandiensis MSL-26 (95.1 %). The predominant cellular fatty acids of strain BGMRC 2075 were iso-C16 : 0, C17 : 1ω8c and C17 : 0. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of ribose and glucose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, ...
TY - JOUR. T1 - Evolution of the LINE-like I element in the Drosophila melanogaster species subgroup. AU - Sezutsu, Hideki. AU - Nitasaka, Eiji. AU - Yamazaki, Tsuneyuki. PY - 1995/3/1. Y1 - 1995/3/1. N2 - LINE-like retrotransposons, the so-called I elements, control the system of I-R (inducer-reactive) hybrid dysgenesis in Drosophila melanogaster. I elements are present in many Drosophila species. It has been suggested that active, complete I elements, located at different sites on the chromosomes, invaded natural populations of D. melanogaster recently (1920-1970). But old strains lacking active I elements have only defective I elements located in the chromocenter. We have cloned I elements from D. melanogaster and the melanogaster subgroup. In D. melanogaster, the nucleotide sequences of chromocentral I elements differed from those on chromosome arms by as much as 7%. All the I elements of D. mauritiana and D. sechellia are more closely related to the chromosomal I elements of D. melanogaster ...
Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of V. nakaiana and the related species V. persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica and Veronicastrum sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51 and 53 in V. nakaiana, V. persica and Veronicastrum sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating
Publisher: Frontiers Media S.A.. Date Issued: 4/14/16. Abstract: An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37 ...
Fossil history and phylogeny. Cephalopods have existed for 500 million years and octopus ancestors were in the Carboniferous ... Two possible extant cephalopod phylogenies, based on genetics studies by Strugnell et al. 2007, are shown in the possible ... Strugnell, J.; Nishiguchi, M. K. (2007). "Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from ...
Phylogeny. The whales are part of the largely terrestrial mammalian clade Laurasiatheria. Whales do not form a clade or order; ...
Geographical range and body size predominantly explains diet composition of Neotropical parrots rather than phylogeny.[55] ... from the Green River Formation and a Combined Phylogeny of Pan-Psittaciformes". Journal of Paleontology. 85 (5): 835-852. doi: ... from the Green River Formation and a Combined Phylogeny of Pan-Psittaciformes". Journal of Paleontology. 85 (5): 835-852. doi: ... "Diet of Neotropical parrots is independent of phylogeny but correlates with body size and geographical range". Ibis. 160 (4): ...
Phylogeny[edit]. Below is a cladogram showing the phylogenetic relationships of osteostracans from Sansom (2009):[3] ... Sansom, R. S. (2009). "Phylogeny, classification and character polarity of the Osteostraci (Vertebrata)". Journal of Systematic ...
Phylogeny[edit]. Below is a simplified phylogeny of Telluraves which is the clade where the birds of prey belong to along with ... Griffiths, C. S.; Barrowclough, G. F.; Groth, J. G.; Mertz, L. A. (2007). "Phylogeny, diversity, and classification of the ... Joseph, L.; Lessa, E. P.; Christidis, L. (1999). "Phylogeny and biogeography in the evolution of migration: shorebirds of the ... The phylogeny of Accipitriformes is complex and difficult to unravel. Widespread paraphylies were observed in many phylogenetic ...
Senter, P. (2007). "A new look at the phylogeny of Coelurosauria (Dinosauria: Theropoda)." Journal of Systematic Palaeontology ...
Taxonomy and phylogeny[edit]. The giant anteater got its binomial name from Carl Linnaeus in 1758. Its generic name, ... Gaudin, T. J.; Branham, D. G. (1998). "The phylogeny of the Myrmecophagidae (Mammalia, Xenarthra, Vermilingua) and the ...
"Mikko's Phylogeny Archive. Retrieved 30 December 2015.. *^ "Taxonomic lists- Aves". Paleofile.com (net, info). Archived from ... Species, Phylogeny and Evolution. 1: 59-64. ISSN 1098-660X. Retrieved 12 August 2009.. ... Phylogeny[edit]. Living Podicipediformes based on the work by John Boyd.[29] ... "Systematics and evolution of the Gruiformes (class Aves). 3, Phylogeny of the suborder Grues". Bulletin of the American Museum ...
Phylogeny[edit]. Despite being classified in Caranx based on anatomical features, the generic affinities of the false scad have ... been questioned after a molecular phylogeny of the Carangidae was published. Using mitochondrial cytochrome b sequences, the ...
Taxonomy and phylogeny[edit]. American zoologist Samuel Garman published the original description of the longtail stingray in ...
a b Witmer, L.M. (2005). "The Debate on Avian Ancestry; Phylogeny, Function and Fossils", "Mesozoic Birds: Above the Heads of ... Phylogeny[edit]. The 2007 cladistic analysis of Turner and colleagues recovered the Oviraptorosauria as a maniraptoran clade ( ...
Phylogeny[edit]. Below is a cladogram modified from Brochu (2011).[4] Alligatoridae Alligatorinae ...
2005). "A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)". Biol Rev Camb Philos Soc ... Phylogeny. The traditional view has been that Mysticeti (baleen whales) and Odontoceti (toothed whales) arose from more ... 2008). "The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of ... Heyning, J. (23 August 2006). "Sperm Whale Phylogeny Revisited: Analysis of the Morphological Evidence". Marine Mammal Science ...
Phylogeny[edit]. The Sahul Shelf and the Sunda Shelf during the past 12,000 years: Tasmania separated from the mainland 12,000 ... "26-Phylogeny and the tree of life". Campbell Biology Australian and New Zealand version (10 ed.). Pierson Australia. pp. 561- ...
Phylogeny[edit]. There are six classes within the phylum Chloroflexi: Chloroflexi, Anaerolinea, Caldilinea, Dehalococcoidia ( ...
Phylogeny[edit]. Adephagans diverged from their sister group in the late Permian, the most recent common ancestor of living ... The phylogeny of adephagans is disputed. The group is usually divided into two main groups: *The Geadephaga comprise the two ...
Phylogeny[edit]. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN ... 4] and National Center for Biotechnology Information (NCBI)[5] and the phylogeny is based on 16S rRNA-based LTP release 111 by ...
"Evolution and phylogeny of Old world deer" (PDF). Molecular Phylogenetics and Evolution. 33 (3): 880-95. doi:10.1016/j.ympev. ...
Taxonomy and phylogeny[edit]. Garman's illustration of the frilled shark, accompanying his 1884 species description ...
Phylogeny[edit]. Below is the phylogeny of the Pinophyta based on cladistic analysis of molecular data. It shows the position ... "Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae". Telopea. 7 (3): 275-290 ...
Phylogeny[edit]. A phylogenetic tree showing the position of the hemichordates is: .mw-parser-output table.clade{border-spacing ... Ken Halanych "Phylogeny and Evolution of Hemichordates". *Dr. Chris Lowe "Genomics and Development of Saccoglossus kowalevskii" ... Cameron, C.B. (2005). "A phylogeny of the hemichordates based on morphological characters". Canadian Journal of Zoology. 83 (1 ...
Phylogeny[edit]. The genus Wollemia shares morphological characteristics with the genera Araucaria and Agathis. Wollemia and ... Below is the phylogeny of the Araucariaceae based on the consensus from the most recent cladistic analysis of molecular data. ... "Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae" (PDF). Telopea. 7: 275-91 ...
Phylogeny[edit]. Molecular studies of phylogeny indicate that hutias nest within the Neotropical spiny rats (Echimyidae).[4] ... Upham, Nathan S.; Patterson, Bruce D. (2015). "Evolution of Caviomorph rodents: a complete phylogeny and timetree for living ... "Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats". Molecular Biology and Evolution. 34 (3 ...
Phylogeny[edit]. Reisz (1972) tentatively classified Echinerpeton as an ophiacodontid in its initial description, but later ( ...
Phylogeny[edit]. Based on recent DNA-analysis, the red-headed quelea forms a clade with the cardinal quelea (Q. cardinalis), ... A first robust phylogeny based on mitochondrial and nuclear markers". Molecular Phylogenetics and Evolution. 109: 21-32. doi: ...
Phylogeny[edit]. Wuerhosaurus is one of the most derived stegosaurians, being closely related to either Dacentrurus and ... Maidment, Susannah C.R.; Norman, David B.; Barrett, Paul M.; Upchurch, Paul (2008). "Systematics and phylogeny of Stegosauria ( ... "A new phylogeny of Stegosauria (Dinosauria, Ornithischia)" (PDF). Palaeontology. 2017 (3): 1-8. doi:10.1111/pala.12291. hdl: ...
Core genome phylogeny analysis. To investigate genetic relatedness of the CRAb isolates evaluated in this study with those ... described in the literature, core genome phylogeny was performed with Harvest Suite version v1.1.2 [23]. In addition to the ...
Angiosperm Phylogeny Group IV (2016). "An update of the Angiosperm Phylogeny Group classification for the orders and families ... Angiosperm Phylogeny Group. System (1998-2009). *An ordinal classification for the families of flowering plants (APG I) ... Spears, Priscilla (2006), A tour of the flowering plants based on the classification system of the Angiosperm phylogeny group, ... An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II ...
Gonzalo Giribet s (USA) study of the evolution and phylogeny of the Bivalvia again raised the question of the monophyly of the ... One of the centerpieces of the Perth Congress was the symposium on the Phylogeny of Molluscs organized by Winston F. Ponder ( ... The current state of knowledge regarding caenogastropod phylogeny was summarized by Winston Ponder (Australia). Opisthobranch ... asked what we really know about pulmonate phylogeny. ... phylogeny was explored by Heike W egel and Annette Klussmann- ...
... tinuing interest in the phylogeny of immune reactivities and structure. First is the fundamental concern of biologists with the ... There are two now classic reasons for the widespread and con- tinuing interest in the phylogeny of immune reactivities and ...
I recently posted about the work by Pagel and colleagues regarding ancient lexicons. That work, recently revived in the press for whatever reasons such things happen, is the same project reported a while back in Nature. And, as I recall, I read that paper and promised to blog about it but did not get to it. Yet. So here we go. The tail does not wag the dog The primary finding of the Pagel et al. study is this: When comparing lexicons from different languages, meanings that shared a common word in an ancestral language change over time more slowly if the word in question is used more… ...
... phylogeny and ontogeny, physiology, and pharmacology as well as clinical areas including immunopathology, cancer, infectious ...
Phylogeny. A phylogenetic tree, also known as a tree of life or simply a phylogeny, describes branching relationships among ... A phylogeny implicitly has a time axis, and time usually goes up the page. Phylogenetic relations have to be inferred using ... 2. Distance (or similarity.) Species are arranged in a phylogeny such that each species is grouped with the other species that ... Species are arranged in a phylogeny such that the smallest number of evolutionary changes is required. ...
... Michel Laurin and Jacques A. Gauthier Even though diapsid phylogeny has been intensively studied, relatively ... Page: Tree of Life Diapsid Phylogeny Authored by Michel Laurin and Jacques A. Gauthier. The TEXT of this page is licensed under ... This phylogeny suggests that turtles are actually diapsids that have lost their temporal fenestrae. While this conclusion ... More recently, phylogenies based on data matrices incorporating several diapsid terminal taxa (more than 20) were presented. ...
So far we have met two principles of phylogenetic inference:. • The parsimony principle. • The distance principle. In easy cases like that of humans, chimps, and amoebas, the distance and parsimony principles give the same result, and it might seem that it does not matter which is used. But in other cases they differ. The parsimony principle is then more reliable, because it has a better theoretical justification. However, distance statistics are an important method in phylogenetic inference, because there are circumstances in which they are almost as reliable as parsimony - and they can often be collected more rapidly. In order to know when any given method can be relied on, it is necessary to understand the underlying principle of phylogenetic inference. ...
Phylogeny of living Amniota. Major lineages are distinguished by the number and placement of temporal openings. The ancestral ...
... The Class Reptilia is a grade comprising the scaly tetrapod descendants of Carboniferous Cotylosaurs. It ...
Glycine Phylogeny. This is the evolutionary relationship determined from the analysis of the microsatellite amplification ...
Phylogeny is a potentially powerful tool for conserving biodiversity. This book explores how it can be used to tackle questions ... Phylogeny and Conservation. Series: Conservation Biology (No. 10). Edited by Andrew Purvis Imperial College of Science, ... 1. Phylogeny and conservation Andy Purvis, John L. Gittleman and Thomas M. Brooks; Part I. Units and Currencies: 2. Molecular ... Using case studies from many different taxa and regions of the world, the volume evaluates how useful phylogeny is in ...
Holectypoida: phylogeny and classification. The group is split into two suborders, Holectypina and Pygasterina, on the basis of ...
The Angiosperm Phylogeny Group. An update of the Angiosperm Phylogeny Group classification for the orders and families of ... Angiosperm Phylogeny Group (2009). An update of the Angiosperm Phylogeny Group classification for the orders and families of ... Angiosperm Phylogeny Group. 1998. An ordinal classification for the families of flowering plants. Annals of the Missouri ... Angiosperm Phylogeny Group (APG) - międzynarodowa grupa systematyków roślin (taksonomów) stworzona w celu ustalenia wspólnego ...
... David Baum and Susan Offner. The American Biology Teacher, April 2008, pp. 222-229 ... There are several lessons on the ENSI site that involve the use of phylogenies and the proper construction of cladograms. Go to ... Another value is to show how phylogenies are predictive, leading to new discoveries, as paleontologist Neil Shubin describes in ... An interesting and useful application for phylogenies is to show your class where a particular physiological or anatomical ...
... S. LaBonne labonnes at csc.albany.edu Fri Dec 16 14:00:45 EST 1994 *Previous message: HSP phylogeny? ...
... George Gutman ggutman at MEDED.MED.UCI.EDU Thu Sep 18 11:46:05 EST 1997 *Previous message: Molecular ... phylogeny.arizona.edu/tree/phylogeny.html Cheers, George ***************************************************************** * ...
... rodgers at onramp.net rodgers at onramp.net Mon Aug 13 15:51:25 EST 2001 *Previous message: inherited gene ...
... Hans Sluiman h.sluiman at rbge.org.uk Mon Aug 20 10:21:47 EST 2001 *Previous message: The bushy hominid ... phylogeny methods. , , , In particular - is there a way to assess the error or confidence , ,level in a tree? I understand ...
Bioinformatics: Sequences, Structures, Phylogeny Herausgeber. * Asheesh Shanker Copyright. 2018. Verlag. Springer Singapore. ...
It is probably worth mentioning that the phylogeny of Outlaw and Ricklef (1) is only as good as the data on which it is based ... Robust phylogenies allow us to test hypotheses about how parasites have moved from one species to another, and knowing how this ... Verifying these losses will not only provide a test of the phylogeny of Outlaw and Ricklef (1) but will yield invaluable ... 2002) A molecular phylogeny of malarial parasites recovered from cytochrome b gene sequences. J Parasitol 88:972-978. ...
Phylogeny Confounds Ontogeny. Recapitulate. Jukka. military-industrial complex. The Theory of Evolution is a valid theory. ... The statement "ontogeny recapitulates phylogeny" is credited to Ernst Haeckel, and was the credo and motivation for much ... The prevailing theory now holds that a correlation between ontogeny and phylogeny still holds true, but in the reverse ... phylogeny. "Those suckers are alive!". The Triple Helix. ... In fact, the modern credo is instead "phylogeny recapitulates ...
... Michel Laurin and Jean-Sébastien Steyer ,== Zatrachydidae. ,==10,. , `== ... Page: Tree of Life Phylogeny and Apomorphies of Temnospondyls Authored by Michel Laurin and Jean-S bastien Steyer. The TEXT of ... The phylogeny of the higher temnospondyls (Vertebrata: Choanata) and its implications for the monophyly and origins of the ... Ontogeny and phylogeny of temnospondyl amphibians, a new method of analysis. Zoological Journal of the Linnean Society 130: 449 ...
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  • Perfect phylogeny is a term used in computational phylogenetics to denote a phylogenetic tree in which all internal nodes may be labeled such that all characters evolve down the tree without homoplasy. (wikipedia.org)
  • A Biochemical Phylogeny of the Protists covers a wide variety of biochemical characters and their usefulness in phylogenetics. (google.com)
  • A fourth, phenetics , is little used nowadays but contributed to the statistical and philosophical (such as the distinction between hypothesis and phylogeny) approach of modern phylogenetics. (palaeos.com)
  • One of several programs available for analysis and creation of phylogenetic trees Another such program for phylogenetic tree analysis Additional program for tree analysis A paper detailing an example of how perfect phylogeny can be utilized outside of the field of genetics, as in language association Fernandez-Baca, David. (wikipedia.org)
  • Gardiner's (1982) and LØvtrup's (1985) study of amniote phylogeny exemplifies this differential treatment, and we focused on that group of organisms to test the proposition that fossils cannot overturn a theory of relationships based only on the Recent biota. (umich.edu)
  • The ClustalW2 Phylogeny API, provided by the European Bioinformatics Institute, makes these functions available over SOAP and REST protocols. (programmableweb.com)
  • For the deep metazoan phylogeny project, data sets of hitherto unmatched quality and quantity were compiled and analysed with innovative bioinformatics tools. (degruyter.com)
  • Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. (royalsocietypublishing.org)
  • Recent molecular analyses have suggested a phylogeny that differs dramatically from morphological hypotheses, especially in placing iguanians with snakes and anguimorphans [ 3 - 5 ]. (royalsocietypublishing.org)
  • All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum . (hindawi.com)
  • the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. (nih.gov)
  • Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. (pnas.org)
  • For decades, parasitologists had hypothesized that Plasmodium falciparum was so pathogenic because it had only been acquired recently as a human pathogen from a bird origin, and one the first 18S rDNA phylogenies seemed to confirm this hypothesis ( 10 ). (pnas.org)
  • In fact, the modern credo is instead "phylogeny recapitulates ontogeny", the reverse of Haeckel's idea and in fact the hypothesis originally put forth by Karl Ernst von Baer, Haeckel's predecessor . (everything2.com)
  • Kosakovsky Pond SL, Frost SD and Muse SV (2005) HyPhy: hypothesis testing using phylogenies. (els.net)
  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. (els.net)
  • It's a multi-locus molecular phylogeny of the ant genus Linepithema , a group of mostly obscure Neotropical ants that would be overlooked if they didn't happen to contain the infamous Argentine Ant . (myrmecos.net)
  • To address this, we are estimating the phylogeny of the genus using a diverse array of data sets, including mtDNA, ncDNA. (uidaho.edu)
  • Alfonso Delgado-Salinas , Ryan Bibler , and Matt Lavin "Phylogeny of the Genus Phaseolus (Leguminosae): A Recent Diversification in an Ancient Landscape," Systematic Botany 31(4), 779-791, (1 October 2006). (bioone.org)
  • As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. (nih.gov)
  • Nature 1997) as well as on the spectacular tree of life phylogeny created by David M. Hillis, Derrick Zwickl, and Robin Gutell, University of Texas. (prezi.com)
  • Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor. (pnas.org)
  • The phylogeny of the holometabolous insect orders inferred from transcriptomic, genomic, and morphological data. (zfmk.de)
  • Beyond providing a "backbone" phylogeny, the project is designed to catalyze a world-wide community effort to further resolve the lepidopteran tree, incorporating more traditional evidence from anatomy and behavior in addition to DNA. (umd.edu)
  • Parameter inference, whether performed within the maximum likelihood (ML) or Bayesian inference paradigms, relies on explicit definition of the substitution process, which may vary in spatial manner (across the alignment sites) and in temporal manner (branches of the phylogeny). (nature.com)
  • The evidence for phylogeny comes from palaeontology , comparative anatomy , and DNA sequence analysis . (wikipedia.org)
  • Yet as phylogeny has come increasingly into use, it's shown that perhaps the roots of the tree of life are somewhat atypical. (howstuffworks.com)
  • Brief History of Phylogeny A. Tree of Life III. (coursehero.com)
  • Phylogeny.fr offers three main modes. (nih.gov)
  • phylogeny methods. (bio.net)
  • Character state matrices An example of a character matrix that can be depicted as a perfect phylogeny Perfect phylogeny is a theoretical framework that can also be used in more practical methods. (wikipedia.org)
  • If you do not know what that means, the important point is it is a different DNA sequence from the Drosera phylogeny. (carnivorousplants.org)
  • The second is Cladistics , itself divided into several types, such as the older single tree parsimony-based approach and the newer computational statistical-based methodologies, and Molecular phylogeny . (palaeos.com)
  • Hello, I am wondering if anyone here can help me to find a clear up to date phylogeny and tree of early diverging/basal monocots? (pacificbulbsociety.org)