Editing Molecular evolution (section)

==Molecular phylogenetics==
{{Main|Molecular systematics|Phylogenetics}}

[[File:Site pattern frequencies models.jpg|thumb|440x440px|[[Multiple sequence alignment]] (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. The data in this alignment (in this case a toy example with 18 sites) is converted to a set of site patterns. The site patterns are shown along with the number of times they occur in alignment. These site patterns are used to calculate the [[Likelihood function|likelihood]] given the substitution model and a [[phylogenetic tree]] (in this case an unrooted four-taxon tree). It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). The evolutionary distance equation (''d''<sub>12</sub>) is based on the simple model proposed by [[Thomas H. Jukes|Jukes]] and [[Charles Cantor|Cantor]] in 1969. The equation transforms the proportion of nucleotide differences between taxa 1 and 2 (''p''<sub>12</sub> = 4/18; the four site patterns that differ between taxa 1 and 2 are indicated with asterisks) into an evolutionary distance (in this case ''d''<sub>12</sub>=0.2635 substitutions per site). ]]

Molecular phylogenetics uses [[DNA]], [[RNA]], or [[protein]] sequences to resolve questions in [[systematics]], i.e. about their correct [[Taxonomy (biology)|scientific classification]] from the point of view of [[History of life|evolutionary history]]. The result of a molecular [[phylogenetics|phylogenetic]] analysis is expressed in a [[phylogenetic tree]]. Phylogenetic inference is conducted using data from [[DNA sequencing]]. This is [[Multiple sequence alignment|aligned]] to identify which sites are [[Homology (biology)|homologous]]. A [[substitution model]] describes what patterns are expected to be common or rare. Sophisticated [[Computational phylogenetics|computational inference]] is then used to generate one or more plausible trees.

Some phylogenetic methods account for variation among sites and [[Heterotachy|among tree branches]]. Different genes, e.g. [[hemoglobin]] vs. [[cytochrome c]], generally evolve at different [[Rate of evolution|rates]].<ref name="Fay">{{cite journal | vauthors = Fay JC, Wu CI | title = Sequence divergence, functional constraint, and selection in protein evolution | journal = Annual Review of Genomics and Human Genetics | volume = 4 | pages = 213–235 | date = 2003 | pmid = 14527302 | doi = 10.1146/annurev.genom.4.020303.162528 | s2cid = 6360375 | doi-access = free }}</ref> These rates are relatively constant over time (e.g., hemoglobin does not evolve at the same rate as cytochrome c, but hemoglobins from humans, mice, etc. do have comparable rates of evolution), although rapid evolution along one branch can indicate increased [[directional selection]] on that branch.<ref>{{cite journal |last1=Álvarez-Carretero |first1=Sandra |last2=Kapli |first2=Paschalia |last3=Yang |first3=Ziheng |title=Beginner's Guide on the Use of PAML to Detect Positive Selection |journal=Molecular Biology and Evolution |date=4 April 2023 |volume=40 |issue=4 |doi=10.1093/molbev/msad041|pmid=37096789 |pmc=10127084 }}</ref> [[Purifying selection]] causes functionally important regions to evolve more slowly, and amino acid substitutions involving [[Conservative replacement|similar amino acids]] occurs more often than dissimilar substitutions.<ref name="Fay" />

[[File:Five Stages of Molecular Phylogenetic Analysis.png|800x80px|center|thumb|Five Stages of Molecular Phylogenetic Analysis]]