The relationships of groups of organisms as reflected by their genetic makeup.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
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.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
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.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A 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.
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
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 sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Genotypic differences observed among individuals in a population.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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)
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
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).
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
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 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.
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 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).
Animals that have no spinal column.
Deoxyribonucleic acid that makes up the genetic material of plants.
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.
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.
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)
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)
The variety of all native living organisms and their various forms and interrelationships.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
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.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The genetic complement of a BACTERIA as represented in its DNA.
Warm-blooded VERTEBRATES possessing FEATHERS and belonging to the class Aves.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
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.
The ceasing of existence of a species or taxonomic groups of organisms.
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.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The 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.
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.
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.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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.
A plant division that includes hornworts, named for the horn-like appearance of the spore-producing plant (sporophyte).
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A suborder of PRIMATES consisting of the following five families: CHEIROGALEIDAE; Daubentoniidae; Indriidae; LEMURIDAE; and LORISIDAE.
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.
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)
Deoxyribonucleic acid that makes up the genetic material of 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 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.
A phylum of acoelomate, bilaterally symmetrical flatworms, without a definite anus. It includes three classes: Cestoda, Turbellaria, and Trematoda.
Deoxyribonucleic acid that makes up the genetic material of fungi.
Sequential operating programs and data which instruct the functioning of a digital computer.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
The sequential location of genes on a chromosome.
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)
A group of cold-blooded, aquatic vertebrates having gills, fins, a cartilaginous or bony endoskeleton, and elongated bodies covered with scales.
The functional genetic units of ARCHAEA.
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).
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.
The study of early forms of life through fossil remains.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
The 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)
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).
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.
Those nucleic acid sequences that function as units of heredity which are located within the CHLOROPLAST DNA.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A class in the phylum MOLLUSCA comprised of SNAILS and slugs. The former have coiled external shells and the latter usually lack shells.
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)
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.
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.
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.
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).
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.
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)
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
Databases devoted to knowledge about specific genes and gene products.
An order of insect eating MAMMALS including MOLES; SHREWS; HEDGEHOGS and tenrecs.
A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.
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.
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.
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.
The genetic complement of a plant (PLANTS) as represented in its DNA.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
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.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
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).
A plant genus of the family MORACEAE. It is the source of the familiar fig fruit and the latex from this tree contains FICAIN.
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.
The genetic complement of PLASTIDS as represented in their DNA.
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.
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.
The functional hereditary units of BACTERIA.
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.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
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).
The functional hereditary units of PLANTS.
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-based representation of physical systems and phenomena such as chemical processes.
The family of Old World monkeys and baboons consisting of two subfamilies: CERCOPITHECINAE and COLOBINAE. They are found in Africa and part of 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)
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).
The inanimate matter of Earth, the structures and properties of this matter, and the processes that affect it.
A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.
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)
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
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.
A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.
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.
The physical measurements of a body.
A mammalian order which consists of 29 families and many genera.
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)
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.
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.
An extensive order of highly specialized insects including bees, wasps, and ants.
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)
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)
Proteins found in any species of bacterium.
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.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
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.
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.
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.
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)
A monophyletic group of green plants that includes all land plants (EMBRYOPHYTA) and all green algae (CHLOROPHYTA and STREPTOPHYTA).
Any of numerous winged hymenopterous insects of social as well as solitary habits and having formidable stings.
The general name for NORTH AMERICA; CENTRAL AMERICA; and SOUTH AMERICA unspecified or combined.
An infraorder of New World monkeys, comprised of the families AOTIDAE; ATELIDAE; CEBIDAE; and PITHECIIDAE. They are found exclusively in the Americas.
Deoxyribonucleic acid that makes up the genetic material of protozoa.
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.
Any of numerous burrowing mammals found in temperate regions and having minute eyes often covered with skin.
INSECTS of the order Coleoptera, containing over 350,000 species in 150 families. They possess hard bodies and their mouthparts are adapted for chewing.
The genetic complement of CHLOROPLASTS as represented in their DNA.
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.
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)
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.
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
Phylogenetic tree can be constructed from genetic sequences using distance-based methods or character-based methods. Distance-based methods, including unweighted pair group method with arithmetic means (UPGMA) and Neighbor-joining (NJ), are based on the matrix of pairwise genetic distances calculated between sequences. The character-based methods, including maximum parsimony (MP) (Fitch 1971), maximum likelihood (ML) (J. Felsenstein 1981), and Bayesian Markov Chain Monte Carlo (BMCMC) method (Rannala and Yang 1996), are based on mathematical model that describes the evolution of genetic characters and search for the best phylogenetic tree according to their own optimality criteria.. Maximum Parsimony (MP) method assumes that the evolutionary change is rare and minimizes the amount of character-state changes (e.g., number of DNA substitutions). The criterion is similar to Occams razor, that the simplest hypothesis that can explains the data is the best hypothesis. Unweighted parsimony assumes ...
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 (, 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)
Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share MLs desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BIs long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve
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
Maximum likelihood (ML) assumes the best tree is the tree that is most likely with the given data, under a certain model. ML will take into account all the data we have generated so far in order to construct our final tree. It is a commonly used tree-building algorithm that will give us a single tree as our output.. Making it pretty. When we have created our tree, then its time to make it publication ready.. If we need to change the taxa names, font, or size, use Adobe Illustrator or a similar image manipulation program. Make sure our taxa names can be clearly read and the bootstrap values are visible above each node.. Not all data will require such robust analysis. But we will not know for certain how much better or different a tree produced from a more robust analysis will be until this analysis is performed.. In general, the output tree of a phylogenetic analysis is an estimate of the characters phylogeny (a gene tree) and not the phylogeny of the taxa (species tree) though ideally, both ...
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 ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under max-imum parsimony, maximum likelihood, and Bayesian techniques. The relative accuracy of species tree inference methods under simulation has received less study. The number of analytical techniques available for inferring species trees is in-creasing rapidly, and in this paper, we compare the performance of several species tree inference techniques at estimating recent species divergences using computer simulation. Simulating gene trees within species trees of different shapes and with varying tree lengths (T) and population sizes (θ), and evolving sequences on those gene trees, allows us to determine how phylogenetic accuracy changes in relation to different levels of deep coalescence and phylogenetic signal. When the probability of discordance between the gene trees and the species tree is high (i.e., T is small and/or
A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha ...
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 - Phylogeny and evolution of medical species of candida and related taxa. T2 - A multigenic analysis. AU - Diezmann, S.. AU - Cox, C. J.. AU - Schönian, G.. AU - Vilgalys, R. J.. AU - Mitchell, T. G.. PY - 2004/12/1. Y1 - 2004/12/1. N2 - Hemiascomycetes are species of yeasts within the order Saccharomycetales. The order encompasses disparate genera with a variety of life styles, including opportunistic human pathogens (e.g., Candida albicans), plant pathogens (e.g., Eremothecium gossypii), and cosmopolitan yeasts associated with water and decaying vegetation. To analyze the phylogeny of medically important species of yeasts, we selected 38 human pathogenic and related strains in the order Saccharomycetales. The DNA sequences of six nuclear genes were analyzed by maximum likelihood and Bayesian phylogenetic methods. The maximum likelihood analysis of the combined data for all six genes resolved three major lineages with significant support according to Bayesian posterior ...
UNLABELLED: Phylogenetic inference in bacterial genomics is fundamental to understanding problems such as population history, antimicrobial resistance, and transmission dynamics. The field has been plagued by an apparent state of contradiction since the distorting effects of recombination on phylogeny were discovered more than a decade ago. Researchers persist with detailed phylogenetic analyses while simultaneously acknowledging that recombination seriously misleads inference of population dynamics and selection. Here we resolve this paradox by showing that phylogenetic tree topologies based on whole genomes robustly reconstruct the clonal frame topology but that branch lengths are badly skewed. Surprisingly, removing recombining sites can exacerbate branch length distortion caused by recombination. IMPORTANCE: Phylogenetic tree reconstruction is a popular approach for understanding the relatedness of bacteria in a population from differences in their genome sequences. However, bacteria frequently
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 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 ...
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 ...
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 resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in ...
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
Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave
The Stomatopoda make up an order of crustaceans that have evolved for more than 400 million years since they emerged from their haplocarid ancestors. In previous phylogenetic studies based on morphological characters, seven superfamilies and 19 families were erected for more than 400 extant stomatopod species. Prior to this study, no effort was made to investigate the interrelationships among stomatopod superfamilies using molecular markers. In this study, 18s rDNA, 28s rDNA, and COI genes of 25 stomatopod species from 10 families and four superfamilies were sequenced to build a molecular phylogeny for these stomatopods. Whereas some interfamilial relationships are in congruence with previous studies, the deep structure of the fully resolved molecular phylogeny reconstructed in the present study is fundamentally different. Two previously proposed sister clades, the smashers and the spearers, were collapsed in the molecular tree. Hemisquilidae, other than closely related to other families from ...
INTRODUCTION. The genus Bacillus is a phenotypically large, diverse collection of Gram-positive or Gram-variable staining, endospore-forming, aerobic or facultatively anaerobic, rod-shaped bacteria that have undergone considerable reclassification as advances in molecular biology have revealed a high phylogenetic heterogeneity (5, 21). The genus Bacillus and related genera are distributed widely in nature and include thermophilic, psychrophilic, acidophilic, alkalophilic and halophilic bacteria that utilize a wide range of carbon sources for heterotrophic growth or grow autotrophically.. The investigations on phylogenetic divergence of the genus Bacillus and its mesophilic and thermophilic members indicated the need for further and extensive studies to place some of these bacilli in appropriate taxonomic levels (1, 23, 21). With the accumulation of further 16S rRNA gene sequence data, Bacillus has been divided into more manageable and better-defined groups (16). According to Ludwig et al. (2007) ...
The dictyostelids possess a complex life cycle including aggregative and multicellular stages. They also include one of the most widely studied protistan model organisms, Dictyostelium discoideum. The current molecular phylogeny of dictyostelids is based largely on SSU (18S) rDNA sequences and shows a deep taxon consisting of four major groups, none of which correspond to the three traditional morphologically-defined genera. However, due to the generally slowly evolving nature of SSU rDNA, these data fail to resolve the majority of branches within the four groups. Given the highly morphologically mixed nature of the dictyostelid groups, it is important to resolve relationships within them. We have determined sequences for the internal transcribed spacers (ITS) of rDNA for nearly all species in the original dictyostelid global phylogeny. Phylogenetic analyses of these data, in combination with the previously determined SSUr DNA sequences, confidently resolve nearly all branches in the tree. This ...
Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the ...
Phylogeny reconstruction at the species level, especially using organellar markers, is often complicated by problems such as incomplete lineage sorting and interspecific hybridization. Single-copy nuclear genes may be useful for these cases because they have higher mutation rates and are biparentally inherited. One plant group in which hybridization and incomplete lineage sorting have been proposed based on analyses of internal transcribed spacer (ITS) and plastid data is a clade of mints from the southeastern United States: Conradina and the related genera Dicerandra, Piloblephis, Stachydeoma, and Clinopodium (Lamiaceae). To clarify the phylogeny in this clade and investigate the possibility of incomplete lineage sorting and interspecific hybridization, we isolated three members of the nuclear GapC gene family and used two to reconstruct phylogeny. Separate phylogenetic analyses of the two GapC loci did not resolve species relationships. We then used two approaches to concatenate the two ...
Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. ...
Phylogenetic reconstructions of bacterial species from DNA sequences are hampered by the existence of horizontal gene transfer. One possible way to overcome the confounding influence of such movement of genes is to identify and remove sequences which are responsible for significant character incongruence when compared to a reference dataset free of horizontal transfer (e.g., multilocus enzyme electrophoresis, restriction fragment length polymorphism, or random amplified polymorphic DNA) using the incongruence length difference (ILD) test of Farris et al. {[}Cladistics 10 (1995) 315]. As obtaining this whole genome dataset prior to the reconstruction of a phylogeny is clearly troublesome, we have tested alternative approaches allowing the release from such reference dataset, designed for a species with modest level of horizontal gene transfer, i.e., Escherichia coli. Eleven different genes available or sequenced in this work were studied in a set of 30 E. coli reference (ECOR) strains. Either ...
Phylogenetic analyses of the family Trypanosomatidae have been conducted using both 18S rRNA gene sequences and a variety of protein sequences. Using a variety of phylogenetic methods, 18S rRNA phylogenies indicate that the genus Trypanosoma is not monophyletic. Rather, they suggest that the American and African trypanosomes constitute distinct clades. By contrast, phylogenetic analyses of available sequences in 42 protein families gene generally supported monophyly of the genus Trypanosoma. One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae.
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Molecular Phylogenetics and Evolution - in press. Abstract. The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the ...
Background In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. selection due to functional constraint. Vertical transmission of Juan and a few cases of phylogenetic incongruence Comparison of host phylogeny with TE phylogeny is one method used to address the question of vertical vs. horizontal transmission. A detailed mosquito phylogeny has been previously constructed using Vg-C [30]. We have only included Vg-C sequences from species for which Juan sequences were obtained in this study (Figure ?(Figure2A).2A). In addition, we have also obtained sequence for Vg-C from Ae. simpsoni, which was not available from the previous dataset [30]. We used nt sequences for phylogenetic inference as in the previous study, and our phylogeny is consistent with the phylogeny based on the larger Vg-C dataset [30]. Phylogenetic inference ...
TY - JOUR. T1 - Ontogeny discombobulates phylogeny. T2 - Paedomorphosis and higher-level salamander relationships. AU - Wiens, John J. AU - Bonett, Ronald M.. AU - Chippindale, Paul T.. PY - 2005/2. Y1 - 2005/2. N2 - Evolutionary developmental biology (evo-devo) has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of ...
Citation. Harasewych, M. G., Adamkewicz, S. L., Blake, J. A., Saudek, D., Spriggs, T., Bult, C. J.. Phylogeny and Relationships of Pleurotomariid Gastropods (Mollusca: Gastropoda): an Assessment Based on Partial 18S RDNA and Cytochrome C Oxidase I Sequences. Mol Mar Biol Biotechnol. 1997 Mar 01; 6(1): 1-20.. PubMed Citation. Abstract. The phylogenetic position of the ancient family Pleurotomariidae within the Molluscan class Gastropoda, as well as the relationships of its Recent genera and species, were assessed using an iterative, two-gene (18S rDNA and cytochrome c oxidase I) approach to phylogeny reconstruction. In order to orient the Pleurotomariidae within Gastropoda, partial 18S rDNA sequences were determined for 7 pleurotomariid and 22 other gastropods that span the major groups within the class as well as for one cephalopod and two polyplacophorans, which serve as outgroups. Cladistic analyses of a sequence of approximately 450 base pairs (bp) near the 5 end of the 18S rDNA support the ...
This research presents an analysis of two data sets, one consisting of mt16S rRNA sequences from 134 samples and the second a combination of four genes (12S rRNA, 16S rRNA, COI, GAPDH) from a subset of these samples to test species boundaries and establish phylogenetic hypotheses for New Guinean and selected northern Australian species. These data supports the recognition of 25 Cherax species, including three recently described species and five new species discovered in this study from Papua, Indonesia. Two main clades were identified based on phylogenetic analyses. The New Guinean crayfish does not form a monophyletic group but share relationships with northern Australian species at different evolutionary depths, which is consistent with the geological history of the region. The diverse highland Cherax fauna of the Wissel Lakes form a well support monophyletic lineage but show minimal molecular divergence, which is at odds with their high morphological diversity. The results of this study fill ...
The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10,000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been ...
The use of molecular clocks to estimate divergence times is controversially debated, due to conflicting results from different studies and disparities with paleontological or archaeological data [73-76]. Criticism focuses on the major problems such as faulty calibration, impact of rate heterogeneity among lineages, and time dependency of molecular rates [73, 75-77]. Some of the problems could be solved by the relaxed clock approach [78], and despite all pitfalls and criticism, molecular clock approaches have helped considerably to reveal the evolutionary history of life, especially when it comes to divergence times of groups with poor or no fossil record [75, 76, 79]. Thus, we consider it a valuable methodology to roughly estimate divergence times for tiny, sluggish gastropods for which there is no fossil record. Molecular clock dating stands and falls with the accuracy with which genetic distances can be estimated [80]; thus we consider the removal of ambiguous (i.e. potentially ...
Limosella is a small aquatic genus of Scrophulariaceae of twelve species, of which one is distributed in northern circumpolar regions, two in southern circumpolar regions, two in the Americas, one endemic to Australia, and six in tropical or southern Africa or both. The Australasian L. curdieana has always been considered distinct but its close phylogenetic relationships have never been inferred. Here, we investigated the following alternative phylogenetic hypotheses based on comparative leaf morphology and habitat preferences or floral morphology: (1) L. curdieana is sister to the African L. grandiflora; or (2) it is closely related to a group of other African species and the northern circumpolar L. aquatica. We tested these hypotheses in a phylogenetic framework using DNA sequence data from four plastid DNA regions and the nuclear ITS region. These were analyzed using maximum parsimony and Bayesian inference. We obtained moderately resolved, partially conflicting phylogenies, supporting that ...
The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences. We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms
Identifying the organisms behind novel environmental lineages has been one of several major targets in microbial biodiversity research (9, 23, 38, 41). This is especially important in the case of evolutionarily interesting lineages at higher taxonomic levels and in the case of lineages that occur frequently in different environmental systems and whose morphological diversity and ecological function are unknown. The uncultured MAST clades identified recently (23, 44) meet all of these criteria and therefore deserve further study. Due to the information obtained as a result of the research that we conducted, we were able to determine the morphotype for the 18S rRNA gene sequence that branches within the MAST-12 clade which we retrieved from a Norwegian estuarine microbial mat sample.. Our phylogenetic reconstruction of stramenopiles using 18S rRNA gene signatures is consistent with previous analyses. The previous analyses confirmed the monophyly of phototrophic stramenopiles, resulting in ...
Morphological and molecular data were analyzed using parsimony to trace character evolution within Anagallis s.l., including Anagallis, Asterolinon, Pelletiera, Lysimachia nemorum, and L. serpyllifolia, which are distributed among two sister clades. The first clade, comprising Anagallis arvensis, A. foemina, A monelli, Asterolinon, Pelletiera, Lysimachia nemorum, and L. serpyllifolia is supported by synapomorphies such as an annual, repeatedly branching habit, sessile leaves, flowers in almost all leaf axils, and membraneous slightly dentate calyx margins, of which all but the last are homoplasious within Anagallis s.l. The second clade, comprising Anagallis species only, is supported by a large number of synapomorphies, of which the majority are floral features. Placement of then taxa, for which no DNA was available, is porposed based on morphological characters evaluated in the ligth of the result of the phylogentis analysis of sequenced taxa.. ...
1. Hedges SB. The origin and evolution of model organism. Nature Reviews Genetics. 2003 ;3:838-849 2. Winchell CJ, Sullivan J, Cameron CB. et al. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Mol Biol Evol. 2002 ;19:762-776 3. Brusca RC, Brusca GJ. Invertebrates. Sunderland, Massachusetts: Sinauer. 1990 4. Abouheif E, Zardoya R, Meyer A. Limitations of metazoans 18S rRNA sequence data: implications for reconstructiong a phylogeny the animal kingdom and inferring the reality of the Cambrian explosion. J Mol Evol. 1998 ;47:394-405 5. Takezaki N, Figueroa F, Zaleska-Rutczynska Z. et al. Molecular phylogeny of early vertebrates: Monophyly of the Agnathans as revealed by sequences of 35 genes. Mol Biol Evol. 2003 ;20:287-292 6. Jollie MJ. The origin of chordates. Acta Zool. 1973 ;54:81-100 7. Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and ...
TY - JOUR. T1 - Synonymous substitution rates in Drosophila. T2 - Mitochondrial versus nuclear genes. AU - Moriyama, Etsuko N.. AU - Powell, Jeffrey R.. PY - 1997. Y1 - 1997. N2 - Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 ...
Find the fascicles article Taxonomic rearrangement of |I|Anthostomella|/I| (Xylariaceae) based on a multigene phylogeny and morphology on the website of Scientific Publications of the Muséum national dHistoire naturelle, Paris
Refs - -. Agnarsson, I., Kuntner, M. & May-Collado, L. J. 2010. Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora. Molecular Phylogenetics and Evolution 54, 726-745.. Baskin, J. A. 1998. Mustelidae. In Janis, C. M., Scott, K. M. & Jacobs, L. L. (eds) Evolution of Tertiary Mammals of North America. Volume 1: Terrestrial Carnivores, Ungulates, and Ungulatelike Mammals. Cambridge University Press, pp. 152-173.. Bininda, Emonds, O. R. P., Gittleman, J. L. & Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74, 143-175.. Bryant, H. N., Russell, A. P. & Fitch, W. D. 1993. Phylogenetic relationships within the extant Mustelidae (Carnivora): appraisal of the cladistic status of the Simpsonian subfamilies. Zoological Journal of the Linnean Society 108, 301-334.. Dragoo, J. W. & Honeycutt, R. L. 1997. Systematics of mustelid-like carnivores. Journal of Mammalogy 78, 426-443.. Eizirik, ...
The chaetognaths are an extraordinarily homogeneous phylum of animals at the morphological level, with a bauplan that can be traced back to the Cambrian. Despite the attention of zoologists for over two centuries, there is little agreement on classification within the phylum. We have used a molecular biological approach to investigate the phylogeny of extant chaetognaths. A rapidly evolving expansion segment toward the 5 end of 28S ribosomal DNA (rDNA) was amplified using the polymerase chain reaction (PCR), cloned, and sequenced from 26 chaetognath samples representing 18 species. An unusual finding was the presence of two distinct classes of 28S rDNA gene in chaetognaths; our analyses suggest these arose by a gene (or gene cluster) duplication in a common ancestor of extant chaetognaths. The two classes of chaetognath 28S rDNA have been subject to different rates of molecular evolution; we present evidence that both are expressed and functional. In phylogenetic reconstructions, the two classes of 28S
Amphioxus, as the closest living animal of the last common ancestor of all vertebrates, occupies an extremely important phylogenetic position in the evolution of vertebrates and has attracted the interest of scientists from various research fields in recent years. However, despite their importance for the life sciences, taxonomic studies of amphioxus are relatively limited. In present review, we summarize current progress in both field investigations and taxonomic research of Chinese amphioxus. Based on the investigation data, we assume that amphioxus is distributed in all habitable sandy beaches along the Chinese coast from south to north. According to the rule of priority and recent taxonomic studies on amphioxus, we also propose that the original subspecies Brnachiostoma belcheri tsingtauense together with the population in most Japanese waters is an independent species and its name should be revised to B. japonicus. Consequently, there are at least two species of genus Brnachiostoma and 1-3 ...
Domain combinations containing the Bcl-2 inhibitors of programmed cell death superfamily in Amphimedon queenslandica. Domain architectures illustrate each occurrence of the Bcl-2 inhibitors of programmed cell death superfamily.
p,Hemichordates have occupied a central role in hypotheses of deuterostome and early chordate evolution. However, surprisingly little is understood about evolution within hemichordates, including hemichordate ancestral characters that may relate to other deuterostome taxa. Previous phylogenetic studies suggested that enteropneust worms are either monophyletic (based on 28S rDNA) or paraphyletic (based on 18S rDNA). Here, we expand the number of hemichordate taxa used in phylogenetic analyses for 18S rDNA data and employ more quickly evolving mitochondrial gene sequences. Novel data from an undescribed deep-sea enteropneust species similar to Torquarator bullocki and a Gulf Stream tornaria larva suggest that these taxa are closely allied to or possibly within Ptychoderidae. Saxipendium coronatum, another deep-sea species commonly called the spaghetti worm, is shown to be a member of Harrimaniidae. Recognition of these deep-sea lineages as distinct families calls into question features used in ...
Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within ...
In evolutionary biology, convergent evolution describes the process whereby organisms not closely related, independently evolve similar traits as they both adapt to similar environments or Ecological niche. On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see Long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats. All four serve the same function and are similar in structure, but each evolved independently. Some aspects of the lens of eyes also evolved independently in various animals. Convergent evolution is similar to, but distinguishable from, the phenomena of evolutionary relay and parallel evolution. Evolutionary relay refers to independent species acquiring similar ...
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular ...
Background: Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. The total-evidence analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole. Results: Phylogenetic relationships within Annelida were analysed on the basis of 93 morphological characters and sequences of six genes (18S, 28S, and 16S rRNA, EF1 alpha, H3, COI), altogether, 87 terminals of all annelid families and 3,903 informative characters, by Bayesian and maximum-parsimony methods. The analysis of the combined dataset yields the following scheme of relationships: Phyllodocida and Eunicida are monophyletic groups, together probably ...
Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny. We use hierarchical Bayesian models coupled with nonlinear dynamical models of disease dynamics to incorporate the hierarchical nature of host phylogeny. Our analysis suggests an important role for both host phylogeny and species mass in determining factors important for viral spread such as the basic reproductive number, WNV production rate, peak viraemia in blood and competency of a host to infect mosquitoes. Our model is based on a ...
Jonathan F. Wendel wrote: , = , A paper was recently published in which it was demonstrated that in , phylogenetic analysis, a potentially misleading resolution could be , obtained in cases where the sampled genes varied greatly in their GC , content. The conclusion was, as I recall, that high-GC genes were , spuriously linked by virtue of this compositional bias by itself. Im , going crazy trying to recall what this reference was..... can anyone , help? , = , Thanks, Jonathan Wendel There are a number of references for this kind of work as it is thought to be a major problem in phylogeny reconstruction. Methods that seek to circumvent the problem: Galtier, N. and Gouy, M. (1995). =93Inferring phylogenies from DNA sequences of unequal base compositions.=94 Proc. Natl. Acad. Sci. USA 92:= 11317-11321. Lake, J. A. (1994). =93Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances.=94 Proc. Natl. Acad. Sci. USA 91= : 1455-1459. Lockhart, P. J., Steel, M. A., Hendy, ...
The present study provides the first phylogenomic evidence to support the monophyletic origin of four major orders of copepods and the group of podopleans. The monophyletic status of Copepoda has been broadly accepted by both morphological [5, 14] and large-scale phylogenomic analyses [28-30]. Although this study does not include all copepod orders, there can be no doubt of the monophyly of copepods. The subclass Copepoda consists of two infraclasses, Progymnoplea and Neocopepoda, suggested by Huys and Boxshall [5]. The infraclass Neocopepoda can be further divided into two superorder groups, Gymnoplea and Podoplea (Fig. 1). The concept of this classification was proposed by Giesbrecht [67] and became generally accepted [5, 12, 68]. However, the naupliar musculature and the molecular phylogeny using partial nuclear 28S rRNA gene (a total aligned sequence length of 484 bp from the D9/D10 region) (Fig. 2A) showed conflicting results and suggested a possible paraphyletic origin of podopleans [15, ...
A molecular phylogeny of the salamandrid genus Neurergus was reconstructed based on two sections of the 12S and 16S mitochondrial ribosomal genes (810 bp), 19 allozyme and three plasma protein loci. When representative species of all closely related salamandrid groups were included, mitochondrial data provided evidence for monophyly of Neurergus within the Salamandridae. Mitochondrial and allozyme data showed homogenous intrageneric tree topologies, but different estimates of times of separation. We calibrated the evolutionary rate to 0.46% pairwise sequence divergence per million years. Accordingly Neurergus diverged 18 million years ago (mya) from a lineage that comprised Euproctus asper and large bodied newts of the genus Triturus. A split around 11 mya produced two major clades within Neurergus. Further separation within the southern 'N. crocatus-clade' (comprising N. crocatus, N. microspilotus and N. kaiseri) occurred ca. 5 mya. The northern 'N. strauchii-clade' separated into N
Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock, 1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876 and ...
abstract) Ericson, P.G.P., I. Envall, M. Irestedt, and J.A. Norman (2003), Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data, BMC Evol. Biol. 3, 16. DOI: 10.1186/1471-2148-3-16. (pdf) Fain, M.G., and P. Houde (2007), Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes, BMC Evol. Biol. 7, 35. DOI: 10.1186/1471-2148-7-35. (pdf) Gibson, R. and A. Baker (2012), Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes), Mol. Phylogenet. Evol. 64, 66-72. DOI: 10.1016/j.ympev.2012.03.008. (abstract) Hu, C. C. Zhang, l. Sun, Y. Zhang, W. Xie, B. Zhang, and Q. Chang (2017), The mitochondrial genome of the pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes, PloS ONE 12(4), e0175244. DOI: 10.1371/journal.pone.0175244. (pdf) Jackson, D.G, S.D. Emslie, and M. van Tuinen (2012), Genome skimming identifies polymorphism in ...
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 ...
Phylogeny[edit]. The squirrel glider's closest relatives come from the same genus, Petaurus, and they include the sugar glider ...
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". (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 following phylogenetic tree has been suggested in 2012 for the relationship of the gharial:[28] .mw-parser ... "True and false gharials: a nuclear gene phylogeny of Crocodylia" (PDF). Systematic Biology. 52 (3): 386-402. doi:10.1080/ ...
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]. The relationships among Maratus and related genera are unclear, and many species await description. Otto and ...
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 ...
Taxonomy and phylogeny[edit]. Taxonomy[edit]. The redhead is in the family Anatidae (ducks, swans, geese) and genus Aythya ( ... Phylogeny[edit]. The redhead and the common pochard form a sister group which itself is sister to the canvasback.[5] This group ...
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]. Amaryllidinae are placed within Amaryllideae as follow: These are phylogenetically related as follows: .mw- ...
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: ...
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- ...
... 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. ...
One such example is that of Incomplete Directed Perfect Phylogeny. This concept involves utilizing perfect phylogenies with ... Character state matrices An example of a character matrix that can be depicted as a perfect phylogeny Perfect phylogeny is a ... "Clonality Inference in Tumors Using Phylogeny" (CITUP) Github for "Exact inference under the perfect phylogeny model" (EXACT) ... Inferring a phylogeny from noisy VAF data under the PPM is a hard problem. Most inference tools include some heuristic step to ...
Research on harvestman phylogeny (that is, the phylogenetic tree) is in a state of flux. While some families are clearly ... There is not yet a proposed phylogeny for the whole group of Laniatores, although some families have been researched in this ... Garwood, Russell J.; Dunlop, Jason A.; Knecht, Brian J.; Hegna, Thomas A. (2017). "The phylogeny of fossil whip spiders". BMC ... The Dyspnoi are probably the best studied harvestman group regarding phylogeny. They are clearly monophyletic, and divided into ...
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 ...
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 ...
Algae Alveolata Amoebozoa Archaeplastida Biodiversity Discoba Eukaryote Metamonada Obazoa Opisthokonta Phylogeny Protist ... Simpson A.G.B., Slamovits C.H., Archibald J.M. (2017) Protist Diversity and Eukaryote Phylogeny. In: Archibald J. et al. (eds) ... Baldauf, S. L., Roger, A. J., Wenk-Siefert, I., & Doolittle, W. F. (2000). A kingdom-level phylogeny of eukaryotes based on ... Leliaert, F., Smith, D. R., Moreau, H., Herron, M. D., Verbruggen, H., Delwiche, C. F., & De Clerck, O. (2012). Phylogeny and ...
Flora Piperales Polle botanical research development evolution phylogeny plant synthesis the origin wood wood anatomy ... Thorne Chapter Molecular Phylogenies and the Diversification of the Angiosperms 314 Kenneth J. Sytsma and David A. Baum 341 ...
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 Fri Dec 16 14:00:45 EST 1994 *Previous message: HSP phylogeny? ...
Phylogeny is a pseudo-scientific concept that describes the alleged relationships between groups of animals as understood by ... Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy ... Evolutionist Ernst Haeckel is well known for his claim that "ontogeny recapitulates phylogeny," meaning that organisms pass ... Evolutionists often argue that not only is phylogeny important for understanding paleontology, however, many Evolutionist ...
... Hans Sluiman h.sluiman at 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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... Xuhua Xia xia at Thu Apr 7 21:21:34 EST 1994 *Previous message: archaebacteria and the ... I am only popularizing the idea about ontogeny and phylogeny that may be interesting to some netters. The idea is not found in ...
Evolution and phylogeny of fungi: Fungi have ancient origins, with evidence indicating they likely first appeared about one ... Evolution and phylogeny of fungi. Fungi have ancient origins, with evidence indicating they likely first appeared about one ... also known as their phylogeny. The genes possessed by organisms in the present day have come to them through the lineage of ...
Researchers are beginning to realize that when it comes to the different ways bacteria and archaea evolve, what we dont know vastly outweighs what we do know. However, with the advent of metagenomics and increasingly sophisticated methods of study, scientists are starting to learn more about how these organisms came to be.
Phylogeny. the evolutionary history of a species or group of related species ...
This book is composed of 13 chapters that describe the methods of deducing phylogenies of protists from biochemical data. ... These chapters also provide a summary of numerous research studies biochemical phylogeny.This book will prove useful to ... A Biochemical Phylogeny of the Protists covers a wide variety of biochemical characters and their usefulness in phylogenetics. ... A biochemical phylogeny of the protists. Mark A. Ragan,David J. Chapman. Snippet view - 1978. ...
Data sharing is important-it helps scientists to reproduce others results, add data to previous analyses, and otherwise maximize the impact of an individual publication. This isnt really news, of course. But, now that we ...
ClustalW2 Phylogeny generates phylogenetic trees from multiple sequence alignment data. Users can choose between two methods of ... calculating phylogeny; neighbor joining or UPGMA (Unweighted Pair Group Method with Arithmetic Mean). The ClustalW2 Phylogeny ...
... Xuhua Xia xia at Mon Apr 11 18:12:11 EST 1994 *Previous message: Archaebacteria and ... Ontogeny and Phylogeny II: The Length of the Ontogenic Chain and its Evolutionary Implications In a previous posting I have ...
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Make research projects and school reports about Phylogeny easy with credible articles from our FREE, online encyclopedia and ... Phylogeny Plant Sciences COPYRIGHT 2001 The Gale Group Inc.. Phylogeny. Before the mid-1800s, classification of organisms into ... Phylogeny. Phylogeny is the inferred evolutionary history of a group of organisms (including microorganisms ). Paleontologists ... phylogeny A Dictionary of Earth Sciences © A Dictionary of Earth Sciences 1999, originally published by Oxford University Press ...
  • Phylogenetics, the science of phylogeny, is one part of the larger field of systematics , which also includes taxonomy . (
  • The molecular phylogeny and systematics of the actinomycetes. (
  • This phylogeny- part of Gunther Jansen 's Ph.D. thesis- finally sets the systematics of Myrmica on a firm evolutionary footing. (
  • Systematics is concerned both with Taxonomy , the naming and classification of life, and Phylogeny , the science and study of understanding the family tree of all life on Earth . (
  • Each methodology and sub-branch thereof claims to be the true one , either accepting the others as subordinates (e.g. many phylogenetic workers consider morphology-based cladistics secondary to molecular phylogeny) or rejecting them as outmoded (e.g. cladistics rejects evolutionary systematics). (
  • In fact, each has a different methodology and deals with different aspects of phylogeny and systematics, so it is not a matter of contradiction but complementarity. (
  • The Green Plant Phylogeny Research Coordination Group (GPPRCG) was formed in 1994 in order to remedy these shortcomings by facilitating or initiating interactions between distinct research groups that have independent foci yet entail some aspect of green plant phylogeny or systematics. (
  • Acquisition and loss of photosynthesis in Euglenophyceae, Structure and evolution of nuclear, mitochondrial and chloroplast genomes, Origin and evolution of introns in Euglenophyceae, Character evolution in Euglenophyceae, Phylogeny and Systematics of Euglenophyceae. (
  • Therefore, rather than naming all the individual contributors a decision was made to adopt the name Angiosperm Phylogeny Group classification, or APG for short. (
  • Bernhard A. Huber "Phylogeny and classification of Pholcidae (Araneae): an update," The Journal of Arachnology 39(2), 211-222, (1 August 2011). (
  • Cavalier‐Smith T and Chao EEY (2003) Phylogeny and classification of phylum Cercozoa (Protozoa). (
  • Mathematics of Evolution and Phylogeny ( 2003 and 2005 ). (
  • The Angiosperm Phylogeny Group , or APG , is an informal international group of systematic botanists who collaborate to establish a consensus on the taxonomy of flowering plants (angiosperms) that reflects new knowledge about plant relationships discovered through phylogenetic studies. (
  • the trees represent the phylogeny of some some kind of sequence feature, protein or nucleotide, or actual organism taxonomy trees. (
  • Phylogeny has yielded more precise taxonomy of animals, like the turtle. (
  • The reconstruction of phylogeny - How do we infer phylogeny? (
  • Phylogenetic trees and Reconstructing Phylogeny uses Java applets that can create random phylogenies to illustrate and teach some of the basic principles behind phylogeny reconstruction. (
  • Determining the most suitable model for phylogeny reconstruction constitutes a fundamental step in numerous evolutionary studies. (
  • 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 phylogenetic reconstruction, as well as the many spectacular advances in palaeontology and molecular developmental biology. (
  • 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. (
  • Species are arranged in a phylogeny such that the smallest number of evolutionary changes is required. (
  • Species are arranged in a phylogeny such that each species is grouped with the other species that it shares the most characters with. (
  • A phylogeny is usually represented as a phylogenetic tree or cladogram, which are like genealogies of species. (
  • Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. (
  • A broad-scale "family tree" (phylogeny, genealogy) will be estimated using DNA sequences from approximately 250 species, representing all 126 families into which Lepidoptera are currently divided. (
  • Jansen used genetic data from several loci and 106 specimens to infer the history of the genus, recovering a well-supported phylogeny spanning roughly half of the extant species. (
  • Ribosomal phylogenies are useful for inferring relationships within protistan phyla and for species identification. (
  • Sax, 1922) provided information on genome constitution, phylogeny and the evolution of Triticum and Aegilops species (summarized in Lilienfield, 1951). (
  • Specific details of the phylogeny could change with additional species or analysis with a different program. (
  • The most basal species of the Nepenthes phylogeny is Nepenthes distillatoria . (
  • - 'Ontogeny recapitulates phylogeny' was Haeckel's answer--the wrong one--to the most vexing question of nineteenth-century biology: what is the relationship between individual development (ontogeny) and the evolution of species and lineages (phylogeny)? (
  • Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom. (
  • Evolutionist Ernst Haeckel is well known for his claim that " ontogeny recapitulates phylogeny," meaning that organisms pass through stages in development that mirror their evolutionary history. (
  • Phylogeny refers to evolutionary history behind the development of a taxon or trait. (
  • A phylogeny is a proposal of how organisms are related by their evolutionary history. (
  • 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. (
  • The statement " ontogeny recapitulates phylogeny " is credited to Ernst Haeckel , and was the credo and motivation for much embrological research in the 19th and early 20th century. (
  • This book covers the major aspects of phylogeny and reproductive biology of frogs in chapters written by major authorities. (
  • Gauthier (1994) reviewed amniote phylogeny. (
  • Consensus phylogeny of temnospondyls, from Milner and Sequeira (1994, 1998), Yates and Warren (2000) and Steyer (2000), and Laurin and Soler-Gijón (2006). (
  • A Biochemical Phylogeny of the Protists covers a wide variety of biochemical characters and their usefulness in phylogenetics. (
  • 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. (
  • 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. (
  • Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. (
  • A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. (
  • 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. (
  • As an introduction to the Handbook of the Protists, Second Edition, we provide a brief account of the diversity of protistan eukaryotes, set within the context of eukaryote phylogeny as currently understood. (
  • The beginning of this century brought spectacular changes in our understanding of eukaryote phylogeny, especially the early evolution of microeukaryotic lineages commonly called protists. (
  • 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 ). (
  • 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 . (
  • Kosakovsky Pond SL, Frost SD and Muse SV (2005) HyPhy: hypothesis testing using phylogenies. (
  • Molecular phylogenetic inferences have been not only supportive of traditional phylogenies, but also instrumental in resolving some difficult questions regarding branching orders within many evolutionary lineages. (
  • The phylogeny of the Phocinae suggests that the ancestors of Cystophora (hooded seal) and the Phocini (e.g. harp seal, ringed seal) adapted to Arctic conditions and ice-breeding before 12 MYA (million years ago) as supported by the white natal coat of these lineages. (
  • Felsenstein J (1993) PHYLIP (phylogeny inference package). (
  • The ClustalW2 Phylogeny API, provided by the European Bioinformatics Institute, makes these functions available over SOAP and REST protocols. (
  • Previous phylogenies based on molecular data indicated that segregate genera from both the Northern and Southern Hemispheres ( Hepatica , Pulsatilla , Knowltonia, Oreithales, and Barneoudia ) are embedded within Anemone and should be subsumed within the genus. (
  • However, less commonly found genera have not been sampled in recent molecular phylogenies and their phylogenetic affiliation remains unclear. (
  • Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. (
  • Recent molecular analyses have suggested a phylogeny that differs dramatically from morphological hypotheses, especially in placing iguanians with snakes and anguimorphans [ 3 - 5 ]. (
  • All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum . (
  • 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. (
  • 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 . (
  • To address this, we are estimating the phylogeny of the genus using a diverse array of data sets, including mtDNA, ncDNA. (
  • By utilizing algorithms derived from perfect phylogeny data we are able to attempt to reconstruct a phylogenetic tree in spite of these limitations. (
  • Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. (
  • Huelsenbeck JP, Ronquist F, Nielsen R and Bollback J (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. (
  • 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). (
  • Based on various phylogeny research I've come across and some inference of mine. (
  • Multiple alignment was done with the Phylogeny Inference Package (PHYLIP version 3. (
  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. (
  • More recently, phylogenies based on data matrices incorporating several diapsid terminal taxa (more than 20) were presented. (
  • Using case studies from many different taxa and regions of the world, the volume evaluates how useful phylogeny is in understanding the processes that have generated today's diversity and the processes that now threaten it. (
  • Here, we analyse squamate phylogeny using extensive sampling of taxa (161) and characters (44 loci), the largest dataset yet assembled. (
  • This volume correlates available data and ideas concerning the development, reproductive morphology, function, and phylogeny of chondrichthyan fishes. (
  • The phylogeny, genetic divergence estimates, and morphology indicate that P. xanthopygus rupestris is polyphyletic, and that populations from the Pacific slope of the Andes currently assigned to that taxon are specifically distinct from P. xanthopygus . (
  • This hybrid field is called phylogeny , where the interrelatedness of organisms is established based on their shared DNA. (
  • Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. (
  • Phylogeny is a potentially powerful tool for conserving biodiversity. (
  • As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. (
  • 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. (
  • 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. (
  • The phylogeny of the holometabolous insect orders inferred from transcriptomic, genomic, and morphological data. (
  • A kingdom-level phylogeny of eukaryotes based on combined protein data. (
  • This book is composed of 13 chapters that describe the methods of deducing phylogenies of protists from biochemical data. (
  • ClustalW2 Phylogeny generates phylogenetic trees from multiple sequence alignment data. (
  • It is rare that actual data adheres to the concept of perfect phylogeny. (
  • By utilizing the concepts and algorithms described in perfect phylogeny one can determine information regarding missing and unavailable haplotype data. (
  • By assuming that the set of haplotypes that result from genotype mapping corresponds and adheres to the concept of perfect phylogeny (as well as other assumptions such as perfect Mendelian inheritance and the fact that there is only one mutation per SNP), one is able to infer missing haplotype data. (
  • Inferring a phylogeny from noisy VAF data under the PPM is a hard problem. (
  • A central project feature, also borrowed from modern genomics, will be an interactive website allowing the project team plus any other researcher to contribute and download data, methods, analysis and commentary on lepidopteran phylogeny at any level. (
  • Baldauf SL, Roger AJ, Wenk‐Siefert I and Doolittle WF (2000) A kingdom‐level phylogeny of eukaryotes based on combined protein data. (
  • All the data sets and findings of these symposia will be reflected on the GPPRCG web site, several series of papers in specialized professional journals, a review paper commissioned by Science, as well as in a planned book on the Phylogeny of Green Plants. (
  • 2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. (
  • Molecular phylogenies drastically changed our understanding of eukaryotes evolution. (
  • Deschamps P and Moreira D (2009) Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes. (
  • These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets. (
  • The statistical components of a perfect phylogenetic tree can best be described as follows: A perfect phylogeny for an n x m character state matrix M is a rooted tree T with n leaves satisfying: i. (
  • Research on harvestman phylogeny (that is, the phylogenetic tree) is in a state of flux. (
  • 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. (
  • Return this tree, a PhyloXML-compatible Phylogeny object. (
  • Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree). (
  • 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 . (
  • This is the most pervasive element in the phylogeny module, cataloging the "phylonodes" of tree graphs. (
  • Yet as phylogeny has come increasingly into use, it's shown that perhaps the roots of the tree of life are somewhat atypical. (
  • Typically, phylogeny is represented by a tree. (
  • Deep Phylogeny-How a Tree Can Help Characterize Early Life on Earth. (
  • The evidence for phylogeny comes from palaeontology , comparative anatomy , and DNA sequence analysis . (
  • Another value is to show how phylogenies are predictive , leading to new discoveries, as paleontologist Neil Shubin describes in his excellent book Your Inner Fish (Pantheon 2008). (
  • offers three main modes. (
  • phylogeny methods. (
  • 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. (
  • Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. (
  • If you do not know what that means, the important point is it is a different DNA sequence from the Drosera phylogeny. (
  • Phylogeny of novel naked filose and reticulose Cercozoa: Granofilosea cl. (
  • This concept involves utilizing perfect phylogenies with real, and therefore incomplete and imperfect, datasets. (