Phylogenetics

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right|thumb|One small clade of fish, showing how venom has evolved multiple times.

thumb|400px| Cladogram (a branching tree diagram) illustrating the relationships of organisms within groups of taxa known as clades. The vertical line (stem) at the base (bottom) represents the [[last common ancestor. The blue and red subgroups are clades, each defined by a common ancestor stem at the base of its respective subgroup (branch). The green subgroup alone, however, is not a clade; it is a paraphyletic group relative to the blue subgroup because it excludes the blue branch, which shares the same common ancestor. Together, the green and blue subgroups form a clade.]]

Cladistics ( ; from Ancient Greek 'branch') is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics (synapomorphies) that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitut

collaborative project intended to create an encyclopedia documenting all living species known to science

thumb|300px|In this phylogenetic tree, the green group is paraphyletic; it is composed of a common ancestor (the lowest green vertical stem) and some of its descendants, but it excludes the blue group (a monophyletic group) which diverged from the green group.

existence of shared ancestry between a pair of structures, or genes, in different taxa

thumb|300x300px|A phylogenetic tree: both blue and red groups are monophyletic. The green group is paraphyletic: it is missing a monophyletic subgroup – the blue group – that shares a common ancestor with itself. In this form, monophyletic means "no sideways stems leaving the group". thumb|300px|A cladogram of the primates, showing a monophyletic taxon: the [[simians (in yellow); a paraphyletic taxon: the prosimians (in cyan, including the red patch); and a polyphyletic group: the night-active primates, i.e., the lorises and the tarsiers (in red).]] thumbnail|300px|A cladogram of the vertebrat

A haplotype is a group of alleles in an organism that are inherited together from a single parent, and a haplogroup (haploid from the , haploûs, "onefold, simple" and ) is a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation. More specifically, a haplotype is a combination of alleles at different chromosomal regions that are closely linked and tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. Such as t

thumb|300px|In this phylogenetic tree, the blue and red groups (which are both monophyletic) do not share an immediate common ancestor. If they are grouped together because they share characteristics which appear to be similar, then their combination forms a polyphyletic group. thumb|300px|Cladogram of the [[primates, showing a monophyly (the simians, in yellow), a paraphyly (the prosimians, in cyan, including the red patch), and a polyphyly (the night-active primates, the lorises and the tarsiers, in red).]] thumbnail|300px|Phylogenetic groups: A monophyletic taxon (in yellow, the clade Sauro

branching diagram of evolutionary relationships between organisms

most recent common ancestor of all current life on Earth

online database of taxa

technique to deduce the time in prehistory when two or more life forms diverged

fossilized remains of a life form that exhibits traits common to both an ancestral group and its derived descendant group

closest relative(s) of another given taxon in a phylogenetic tree

most recent individual from which all organisms in a group are directly descended

thumb|250px|A horizontal cladogram, with the root to the left thumb|250px|Two vertical cladograms, the root at the bottom

branch of phylogeny that analyzes genetic, hereditary molecular differences

taxon that disappears for one or more periods from the fossil record, only to appear again later;likewise in conservation biology and ecology, it can refer to species or populations that were thought to be extinct, and are rediscovered

The Cetruminantia are a clade made up of the Cetancodontamorpha (or Whippomorpha) and their closest living relatives, the Ruminantia.

monophyletic closure of a set of living species

Neomura (from Ancient Greek neo- "new", and Latin -murus "wall") is a proposed clade of life composed of the two domains Archaea and Eukaryota, coined by Thomas Cavalier-Smith in 2002. Its name reflects the hypothesis that both archaea and eukaryotes evolved out of the domain Bacteria, and one of the major changes was the replacement of the bacterial peptidoglycan cell walls with other glycoproteins.

heritable trait shared by two or more taxa and thus thought to have evolved in their most recent common ancestor

measure between populations of divergence

thumb|right|260px|An example of cladogenesis today is the Hawaiian Islands|Hawaiian archipelago, to which stray organisms traveled across the ocean via ocean currents and winds. Most of the species on the islands are not found anywhere else on Earth due to evolutionary divergence.

thumb|right|250px|Phylogenetic divergence (phyletic gradualism) (above) shows relatively slow changes during geologic epoch: the broken balance (below) illustrates morphological stability and (rarely) the relatively rapid evolutionary change.

root of a phylogenetic tree

Toxicofera (Latin for "toxin-bearers") is a clade of scaled reptiles (squamates) that includes the Serpentes (snakes), Anguimorpha (monitor lizards, beaded lizards, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). Toxicofera contains about 4,600 species (nearly 60%) of extant Squamata. It encompasses all venomous reptile species, as well as numerous related non-venomous species. There is little morphological evidence to support this grouping; however, it has been recovered by all molecular analyses as of 2012.

Homoplasy, in biology and phylogenetics, is the term used to describe a feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the term used to characterize the similarity of features that can be parsimoniously explained by common ancestry. Homoplasy can arise from both similar selection pressures acting on adapting species, and the effects of genetic drift. thumb|Homoplasy is the similarity in a feature that is not parsimoniously explained by descent from a common ancestor.

set of several similar genes

sequence of species that form a line of descent

Artiofabula is a clade made up of the Suina and the Cetruminantia. The clade was found in molecular phylogenetic analyses and contradicted traditional relationships based on morphological analyses.

Cetancodontamorpha is a total clade of artiodactyls defined, according to Spaulding et al., as Whippomorpha "plus all extinct taxa more closely related to extant members of Whippomorpha than to any other living species".

phylogenetic method in taxonomy

branch of biological classification

thumb|279px|Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait states (such as the evolution of a [[flatfish).]] In phylogenetics, an autapomorphy is a distinctive feature, known as a derived trait, that is unique to a given taxon. That is, it is found only in one taxon, but not found in any others or outgroup taxa, not even those most closely related to the focal taxon (which may be a species, family or in general any clade). It can therefore be considered as an apomorphy in relation to a single taxon. The word autapomorphy, int

ancestral character or trait state (plesiomorphy) shared by two or more taxa

thumb|In palaeontology, the evidence for [[species and evolution comes mainly from the comparative anatomy of fossils. A chronospecies is defined in a single lineage (solid line) whose morphology changes with time. At some point, palaeontologists judge that enough change has occurred that two forms (A and B), separated in time and anatomy, once existed. If only sporadic examples of each survive in the fossil record, the forms will appear sharply distinct.]] A chronospecies is a species derived from a sequential development pattern that involves continual and uniform changes from an extinct anc

biological homology between protein or DNA sequences resulting from shared evolutionary ancestry

provides information about biodiversity, the characteristics of different groups of organisms, and their evolutionary history

Alloenzymes (or also called allozymes) are variant forms of an enzyme which differ structurally but not functionally from other allozymes coded for by different alleles at the same locus. These are opposed to isozymes, which are enzymes that perform the same function, but which are coded by genes located at different loci.

a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study

Hypothesis in evolutionary biology

clustering method in bioinformatics

form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related

UPGMA (unweighted pair group method with arithmetic mean) is a simple agglomerative (bottom-up) hierarchical clustering method. It also has a weighted variant, WPGMA, and they are generally attributed to Sokal and Michener.

scientific journal

Merriam-Webster defines chemotaxonomy as the method of biological classification based on similarities and dissimilarity in the structure of certain compounds among the organisms being classified. Advocates argue that, as proteins are more closely controlled by genes and less subjected to natural selection than the anatomical features, they are more reliable indicators of genetic relationships. The compounds studied most are proteins, amino acids, nucleic acids, peptides etc.

the grouping in a higher taxon of animals with segmented bodies, consisting of Annelida and Panarthropoda – this theory states that these groups are descended from a common segmented ancestor

optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred; under this criterion, the shortest possible tree that explains the data is considered best

possible earliest ancestor of the LUCA ancestral cell

type of fossil

phylogenetic lineage that is inferred to exist but has no fossil record

inferred statistical population

method used for categorizing species using logical choices

control of growth and differentiation by deeply conserved genetic mechanisms

taxon that seems to resemble another taxon that has disappeared from the fossil record

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Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Four major areas fall under phylogenomics: Prediction of gene function Establishment a