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). Also known as phylogenetic systematics, phylogenetics treats a species as a group of lineage-connected individuals over time. 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. Biology is the branch of science dealing with the study of life. ... In biology and ecology, an organism (in Greek organon = instrument) is a living complex adaptive system of organs that influence each other in such a way that they function as a more or less stable whole. ... In biology, a species is one of the basic units of biodiversity. ... Taxonomy (from Greek verb tassein = to classify and nomos = law, science, cf economy) may refer to: the science of classifying living things (see alpha taxonomy) a system of classification in some other field Taxonomy was once only the science of classifying living organisms, but later the word was applied in...

Phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually a set of species. A major task of systematics is to determine the ancestral relationships among known species (both living and extinct). 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. A hypothetical phylogenetic tree of all extant organisms, based on 16S rRNA gene sequence data, showing the evolutionary history of the three domains of life, bacteria, archaea and eukaryotes. ... In biology, systematics is the study of the diversity of organism characteristics, and especially how they relate evolutionarily. ... In biology and ecology, extinction is the ceasing of existence of a species or group of species. ... Parsimony, in the general sense, means taking extreme care at arriving at a course of action; or unusual or excessive frugality, extreme economy or stinginess. ... Maximum likelihood estimation (MLE) is a popular statistical method used to make inferences about parameters of the underlying probability distribution of a given data set. ... Markov chain Monte Carlo (MCMC) methods, sometimes called 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 a heterocyclic base, a sugar, and one or more phosphate groups. ... An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ...

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. The early version of this hypothesis has since been rejected as being oversimplified. However, most modern biologists recognize numerous connections between ontogeny and phylogeny, explain them using evolutionary theory, or view them as supporting evidence for that theory. 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. ... This article or section is in need of attention from an expert on the subject. ... 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. ...

Gene transfer

Organisms can generally inherit genes in two ways: by speciation (vertical gene transfer), from parent to offspring, 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 (i. ... Domain Archaea - Archaebacteria Bacteria - Eubacteria Prokaryotes (from Old Greek pro- before + karyon nut or kernel, referring to the cell nucleus, + suffix -otos, pl. ...

Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistences 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 rDNA 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

Due 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. Molecular biology is the study of biology at a molecular level. ... 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. ... 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. ...

Using simulations, Zwickl and Hillis (2002) found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.

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). ... This cladogram shows the relationship among various insect groups. ... 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. ... Current distribution of Human Language Families Most languages are known to belong to language families. ... Molecular phylogeny is the use of the structure of molecules to gain information on an organisms evolutionary relationships. ... Types of clade PhyloCode is a draft for a formal set of rules governing phylogenetic nomenclature. ... It has been suggested that Evolutionary tree be merged into this article or section. ... A phylogenetic network is any graph used to visualize evolutionary relationships between species or organisms. ... 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. ...

References

• Zwickl, D. J. and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology 51:588-598.

External links

• The Tree of Life
• PhyloCode
• UCMP Exhibit Halls: Phylogeny Wing