Systematic comparison of organism characteristics for the sake of establishing evolutionary relationships.
Ideally those characteristics that are examined have a genetic basis, and phylogenetic analysis itself is an important facet of the science of systematics. Typically the result of such efforts will be a phylogeny, or evolutionary tree, which is then represented as a cladogram, i.e., a depiction of that tree.
The goal in phylogenetic analysis is determination of the positions of nodes, which represent points of divergence between separate lineages (i.e., most recent common ancestors). The position of these nodes is dependent on two criteria. One is the distance in units of relative or absolute time between the organisms in question and one or more of these nodes. The other is determination of what organisms a given node should be associated with.
The latter is another way of saying that the goal in taxonomy is to group together organisms in such as way that more similar and therefore more closely related organisms are more closely grouped. Evolutionary distance, on the other hand, which in part is a function of time, is assessed either as a function of divergence in organism characteristics (relative distance in terms of time, though an absolute distance in terms of actual measures of divergence) or instead is inferred from well-dated fossils (absolute distance in terms of time).
It often is preferable at a minimum to establish a qualitatively correct phylogeny, particularly when comparing more than two organisms, that is, correctly matching organisms with nodes. More quantitative determinations, that is, distance between nodes, may then be established.
With modern approaches to phylogenetic analysis, ones that are largely (though ideally not exclusively!) based upon sequence data – it is common practice to establish degrees of genetic distance first, with these estimations minimally determinations of relative time. One can then use those distances to infer the position of nodes. That is, two individuals which are more similar, here as quantitatively determined in terms of sequence divergence, should also share closer nodes than two organisms which are less similar.
Fortunately, computer programs, including numerous which are web based, are readily available for performing such analyses. For consideration of how phylogenetic analyses are actually performed, see phylogenetic comparative methods. Note as a caveat that horizontal gene transfer can greatly complicate phylogenetic analyses.
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