Using phylogeographic analyses of gene trees to test species status and processes

A gene tree is an evolutionary reconstruction of the genealogical history o f the genetic variation found in a sample of homologous genes or DNA region s that have experienced little or no recombination. Gene trees have the pot ential of straddling the interface between intra- and interspecific evoluti on. It is precisely at this interface that the process of speciation occurs , and gene trees can therefore be used as a powerful tool to probe this int erface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchang eability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objec tively by using gene trees. First, an overlay of geography upon the gene tr ee is used to test the null hypothesis that the sample is from a single evo lutionary lineage. This phase of testing can indicate that the sampled orga nisms are indeed from a single lineage and therefore a single cohesion spec ies. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be re jected because two or more lineages are in the sample. The test can identif y lineages even when hybridization and lineage sorting occur. Only when thi s null hypothesis is rejected is there the potential for more than one cohe sion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first nul l hypothesis is rejected, a second null hypothesis is tested that all linea ges are genetic ally exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified l ineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the p reviously identified lineages. Only when this second null hypothesis is rej ected is a lineage elevated to the status of cohesion species. By using gen e trees in this manner; species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses ca nnot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.