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Encyclopedia > Phylogenetics
Phylogenetic groups, or taxa, can be monophyletic, paraphyletic, or polyphyletic.

In biology, phylogenetics (Greek: phyle = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Also known as phylogenetic systematics or cladistics, phylogenetics treats a species as a group of lineage-connected individuals over time.[citation needed] Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct.[1] Image File history File links No higher resolution available. ... Image File history File links No higher resolution available. ... A taxon (plural taxa), or taxonomic unit, is a grouping of organisms (named or unnamed). ... In phylogenetics, a group is monophyletic (Greek: of one race) if it consists of an inferred common ancestor and all its descendants. ... In phylogenetics, a grouping of organisms is said to be paraphyletic (Greek para = near and phyle = race) if all the members of the group have a common ancestor, but the group does not include all the descendants of the most recent common ancestor of all group members. ... In phylogenetics, a taxon is polyphyletic (Greek for of many races) if the trait its members have in common evolved separately in different places in the phylogenetic tree. ... For the song by Girls Aloud see Biology (song) Biology studies the variety of life (clockwise from top-left) E. coli, tree fern, gazelle, Goliath beetle Biology (from Greek: βίος, bio, life; and λόγος, logos, speech lit. ... This article is about evolution in biology. ... Domains and Kingdoms Nanobes Acytota Cytota Bacteria Neomura Archaea Eukaryota Bikonta Apusozoa Rhizaria Excavata Archaeplastida Rhodophyta Glaucophyta Plantae Heterokontophyta Haptophyta Cryptophyta Alveolata Unikonta Amoebozoa Opisthokonta Choanozoa Fungi Animalia An ericoid mycorrhizal fungus Life on Earth redirects here. ... For other uses, see Species (disambiguation). ... This cladogram shows the relationship among various insect groups. ... It has been suggested that Clade be merged into this article or section. ... For the science of classifying living things, see alpha taxonomy. ...


Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized as a multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.[2] This article is about a biological term. ... For other uses, see Extinction (disambiguation). ... A scientific visualization of an extremely large simulation of a Raleigh-Taylor instability caused by two mixing fluids. ... The technique is also used in marketing, see Multidimensional scaling in marketing Multidimensional scaling (MDS) are a set of related statistical techniques often used in data visualisation for exploring similarities or dissimilarities in a given data set. ... This article is about the general scientific term. ... For other uses, see Fossil (disambiguation). ...


Cladistics provides a simplified method of understanding phylogenetic trees. There are some terms that describe the nature of a grouping. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram) is called monophyletic. "Modern reptile" (cyan in the diagram) is a grouping that contains a common ancestor, but does not contain all descendents of that ancestor (birds are excluded). This is an example of a paraphyletic group. A grouping such as warm-blooded animals would include only mammals and birds (red/orange in the diagram) and is called polyphyletic because the members of this grouping do not include the most recent common ancestor. It has been suggested that Clade be merged into this article or section. ... In phylogenetics, a group is monophyletic (Greek: of one race) if it consists of an inferred common ancestor and all its descendants. ... Cyan (from Greek κυανοs, meaning blue) may be used as the name of any of a number of a range of colors in the blue/green part of the spectrum. ... In phylogenetics, a grouping of organisms is said to be paraphyletic (Greek para = near and phyle = race) if all the members of the group have a common ancestor, but the group does not include all the descendants of the most recent common ancestor of all group members. ... A warm-blooded (homeothermic) animal is one that can keep its core body temperature at a nearly constant level regardless of the temperature of the surrounding environment (that is, to maintain thermal homeostasis) . This can involve not only the ability to generate heat, but also the ability to cool down... In phylogenetics, a taxon is polyphyletic (Greek for of many races) if the trait its members have in common evolved separately in different places in the phylogenetic tree. ...


The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences. Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... Look up parsimony in Wiktionary, the free dictionary. ... Maximum likelihood estimation (MLE) is a popular statistical method used to make inferences about parameters of the underlying probability distribution from a given data set. ... Markov chain Monte Carlo (MCMC) methods (which include random walk Monte Carlo methods) are a class of algorithms for sampling from probability distributions based on constructing a Markov chain that has the desired distribution as its stationary distribution. ... Bayesian inference is statistical inference in which evidence or observations are used to update or to newly infer the probability that a hypothesis may be true. ... In biology, phenetics, also known as numerical taxonomy, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation. ... A mathematical model is an abstract model that uses mathematical language to describe the behaviour of a system. ... Molecular phylogeny is the use of the structure of molecules to gain information on an organisms evolutionary relationships. ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... This article is about the class of chemicals. ...

Contents

Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or biogenetic law, was widely accepted. This theory was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of an organism exactly mirrors the evolutionary development of the species. Haeckel's early version of this hypothesis (that the embryo mirrors adult evolutionary ancestors) has since been rejected, and the hypothesis amended as the embryo's development mirroring embryos of its evolutionary ancestors. Most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory, or view them as supporting evidence for that theory. Donald Williamson suggested that larvae and embryos represented adults in other taxa that have been transferred by hybridization (the larval transfer theory)[3] [4] Alternative meaning: Nineteenth Century (periodical) (18th century — 19th century — 20th century — more centuries) As a means of recording the passage of time, the 19th century was that century which lasted from 1801-1900 in the sense of the Gregorian calendar. ... Ernst Haeckel. ... The theory of recapitulation, also called the biogenetic law or ontogeny recapitulates phylogeny, is a theory in biology which attempts to explain apparent similarities between humans and other animals. ... Ontogeny (also ontogenesis or morphogenesis) describes the origin and the development of an organism from the fertilized egg to its mature form. ... Evolutionary developmental biology (evolution of development or informally, evo-devo) is a field of biology that compares the developmental processes of different animals in an attempt to determine the ancestral relationship between organisms and how developmental processes evolved. ... Donald J. Williamson is the mayor of Flint, Michigan. ...


Gene transfer

Organisms can generally inherit genes in two ways: from parent to offspring (vertical gene transfer), or by horizontal or lateral gene transfer, in which genes jump between unrelated organisms, a common phenomenon in prokaryotes. Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. ... Prokaryotic bacteria cell structure Prokaryotes (IPA: //) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. ...


Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen.


Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.


This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.


Taxon sampling and phylogenetic signal

Owing to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting phylogeny. This is partly due to the breaking up of long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Using simulations, Derrick Zwickl and Hillis[5] found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses. Molecular biology is the study of biology at a molecular level. ... Long branch attraction (LBA) is a phenomenon in phylogenetic analyses (most commonly those employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships. ... Dr. Derrick Zwickl is a researcher in the field of phylogenetics. ...


Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain useful phylogenetic signal, a term that is used generally to denote whether related organisms tend to resemble each other with respect to their genetic material or phenotypic traits.[6]


See also

It has been suggested that this article or section be merged into body plan. ... Map of the human X chromosome (from the NCBI website). ... Mathematical biology or biomathematics is an interdisciplinary field of academic study which models natural, biological processes using mathematical techniques. ... It has been suggested that Clade be merged into this article or section. ... In genetics, coalescent theory is a retrospective model of population genetics that traces all alleles of a gene in a sample from a population to a single ancestral copy shared by all members of the population, known as the most recent common ancestor (MRCA; sometimes also termed the coancestor to... The EDGE of Existence programme is a research and conservation initiative that focuses on species deemed to be the world’s most Evolutionarily Distinct and Globally Endangered (EDGE). ... The evolutionary tree of living things is currently supposed to run something along the lines of that listed below. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... A language family is a group of languages related by descent from a common proto-language. ... Maximum parsimony, often simply referred to as parsimony, is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. ... Molecular phylogeny is the use of the structure of molecules to gain information on an organisms evolutionary relationships. ... Types of Clade (Note: Stem-based is now branch-based, to avoid confusion with the term stem group which means total clade minus crown clade.) The PhyloCode is a developing draft for a formal set of rules governing phylogenetic nomenclature. ... Fig. ... A phylogenetic network is any graph used to visualize evolutionary relationships between species or organisms. ... This list of phylogenetics software is a compilation of computational phylogenetics software used to produce phylogenetic trees. ... Phylogeography is the attempt to take into account the geographic distribution of species in establishing their phylogeny, and to understand the geographic patterns that may result from divergence, ultimately leading to speciation. ... // When applied to comparative data, conventional statistical methods assume, in effect, that all species are completely unrelated, as if they descended from a big bang of special creation. ... Biological systematics is the study of the diversity of life on the planet earth, both past and present, and the relationships among living things through time. ...

References

  1. ^ A.W.F. Edwards & L.L. Cavalli-Sforza (1964). in Systematics Assoc. Publ. No. 6: Phenetic and Phylogenetic Classification: Reconstruction of evolutionary trees, 67-76. 
  2. ^ L.L. Cavalli-Sforza and A.W.F. Edwards (Sep., 1967). "Phylogenetic analysis: Models and estimation procedures". Evol. 21 (3): 550-570.
  3. ^ Williamson, D. I. (2003) The Origins of Larvae. Kluwer. Dordrecht. xviii + 261 pp.
  4. ^ Williamson, D. I. (2006) Hybridization in the evolution of animal form and life-cycle. Zoological Journal of the Linnean Society 148: 585-602.
  5. ^ Zwickl DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology 51: 588-598.
  6. ^ Blomberg SP, Garland T Jr, Ives AR (2003). "Testing for phylogenetic signal in comparative data: behavioral traits are more labile". Evolution 57: 717-745.

Professor Anthony William Fairbank Edwards (born 1935) is a British statistician, geneticist and evolutionary biologist. ... Professor Anthony William Fairbank Edwards (born 1935) is a British statistician, geneticist and evolutionary biologist. ...

External links

While on board HMS Beagle, Charles Darwin collected numerous specimens, many new to science, which supported his later theory of evolution by natural selection. ... For other uses, see Adaptation (disambiguation). ... Macroevolution refers to evolution that occurs at or above the level of species, in contrast with microevolution, which refers to smaller evolutionary changes (typically described as changes in allele frequencies) within a species or population. ... Microevolution is the occurrence of small-scale changes in allele frequencies in a population, over a few generations, also known as change at or below the species level. ... Charles Darwins first sketch of an evolutionary tree from his First Notebook on Transmutation of Species (1837) Speciation is the evolutionary process by which new biological species arise. ... Population genetics is the study of the distribution of and change in allele frequencies under the influence of the four evolutionary forces: natural selection, genetic drift, mutation, and migration. ... For other uses, see Natural selection (disambiguation). ... In population genetics, genetic drift is the statistical effect that results from the influence that chance has on the success of alleles (variants of a gene). ... In population genetics, gene flow (also known as gene migration) is the transfer of alleles of genes from one population to another. ... For linguistic mutation, see Apophony. ... Evolutionary developmental biology (evolution of development or informally, evo-devo) is a field of biology that compares the developmental processes of different animals in an attempt to determine the ancestral relationship between organisms and how developmental processes evolved. ... We dont have an article called Phenotypic plasticity Start this article Search for Phenotypic plasticity in. ... Norms of reaction for two genotypes. ... Many organisms consist of modules, both anatomically and in their metabolism. ... The evolution of sex is a major puzzle in modern evolutionary biology. ... Why do almost all living things weaken and die with age? There is not yet agreement in the academic community on a single answer. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Diagram of major stages in the eyes evolution. ... For the history of humans on Earth, see History of the world. ... Anagenesis is the progressive evolution of species involving a change in gene frequency in an entire population rather than a cladogenetic branching event. ... Catagenesis is an archaic term from evolutionary biology referring to evolutionary directions that were considered retrogressive. ... Cladogenesis is an evolutionary splitting event in which each branch and its smaller branches is a clade; an evolutionary mechanism and a process of adaptive evolution that leads to the development of a greater variety of animals or plants. ... Evolutionary thought has roots in antiquity as philosophical ideas conceived during the Ancient Greek and Roman eras, but until the 18th century, biological thought was dominated by essentialism, the idea that living forms are static and unchanging in time. ... For other people of the same surname, and places and things named after Charles Darwin, see Darwin. ... The 1859 edition of On the Origin of Species First published in 1859, The Origin of Species (full title On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life) by British naturalist Charles Darwin is one of the pivotal... The modern evolutionary synthesis refers to a set of ideas from several biological specialities that were brought together to form a unified theory of evolution accepted by the great majority of working biologists. ... The gene-centered view of evolution, gene selection theory or selfish gene theory holds that natural selection acts through differential survival of competing genes, increasing the frequency of those alleles whose phenotypic effects successfully promote their own propagation. ... The evolutionary history of life and the origin of life are fields of ongoing geological and biological research. ... This article is about life in general. ... Ecological genetics is the study of genetics (itself a field of biology) from an ecological perspective. ... For the history of humans on Earth, see History of the world. ... Molecular evolution is the process of the genetic material in populations of organisms changing over time. ... Biological systematics is the study of the diversity of life on the planet earth, both past and present, and the relationships among living things through time. ... This is a list of topics in evolutionary biology and evolution. ... Life on Earth  â€¢  â€¢  | Axis scale: millions of years ago. ... Computational phylogenetics is the study of computational algorithms, methods and computer programs for use in phylogenetic analyses. ... Molecular phylogeny is the use of the structure of molecules to gain information on an organisms evolutionary relationships. ... It has been suggested that Clade be merged into this article or section. ... Shared characteristics that define a cladistic grouping. ... Fig. ... A phylogenetic network is any graph used to visualize evolutionary relationships between species or organisms. ... Long branch attraction (LBA) is a phenomenon in phylogenetic analyses (most commonly those employing maximum parsimony) when rapidly evolving lineages are inferred to be closely related, regardless of their true evolutionary relationships. ... Maximum parsimony, often simply referred to as parsimony, is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. ... Maximum likelihood estimation (MLE) is a popular statistical method used to make inferences about parameters of the underlying probability distribution from a given data set. ... In bioinformatics, neighbor-joining is a bottom-up clustering method used for the creation of phylogenetic trees. ... UPGMA (Unweighted Pair Group Method with Arithmetic mean) is a simple bottom-up data clustering method used in bioinformatics for the creation of phylogenetic trees. ... Bayesian inference in phylogeny generates a posterior distribution for a parameter (composed of a phylogenetic tree (its branch lengths and topology) and a model of evolution) based on the prior for that parameter and the likelihood of the data (generated by a multiple alignment). ... Least squares inference in phylogeny generates a phylogenetic tree based on an observed matrix of pairwise genetic distances and optionally a weight matrix. ... Types of Clade (Note: Stem-based is now branch-based, to avoid confusion with the term stem group which means total clade minus crown clade.) The PhyloCode is a developing draft for a formal set of rules governing phylogenetic nomenclature. ... DNA barcoding is a taxonomic method which uses a short genetic marker in an organisms mitochondrial DNA to identify it as belonging to a particular species. ... This is a list of topics in evolutionary biology and evolution. ...

  Results from FactBites:
 
CLC bio: Phylogenetics (1390 words)
Phylogenetics is therefore an integral part of the science of systematics that aims to establish the phylogeny of organisms based on their characteristics.
Furthermore, phylogenetics is central to evolutionary biology as a whole as it is the condensation of the overall paradigm of how life arose and developed on earth.
The phylogenetic tree in figure 2.1 is rooted at the most recent common ancestor of all Hominidae species, and therefore represents a hypothesis of the direction of evolution e.g.
Britain.tv Wikipedia - Phylogenetics (617 words)
In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations).
Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.
All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.
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