Gene trees: A powerful tool for exploring the evolutionary biology of species and speciation

Evolutionary trees can be constructed from the haplotypes observed with molecular surveys of sequence or restriction site variation. Such gene trees can be constructed regardless of whether or not all of the individual specimens came from one or many species. Hence, these gene trees can straddle the species/population interface, thereby providing a powerful tool for studying the meaning of species and the process of speciation. We illustrate how historical approaches using gene trees can be used to separate the effects of population structure from population history, in order to rigorously test the species status of a group, and to test hypotheses about the process of speciation. A worked example of species status in the Piriqueta caroliniana complex is presented. Species status is evaluated under the cohesion species concept that defines a species as an evolutionary lineage with boundaries arising from the forces that create reproductive communities. Such forces are collectively called cohesion mechanisms and consist of two main subtypes: (i) genetic exchangeability, and (ii) ecological interchangeability. To make this definition operational, populations that behave as separate evolutionary lineages are first identified. A method is reviewed for inferring lineages using explicit statistical criteria from geographic overlays upon gene trees. Once lineages have been identified, the next step is to use the cohesion mechanisms to identify candidate traits that should contribute to genetic exchangeability and/or ecological interchangeability. The cohesion species are then identified by performing overlays upon gene trees in order to identify significant transitions in the candidate traits. Cohesion species are recognized only when statistically significant reproductive/ecological transitions occur that are concordant with the lineages defined earlier. This data-rich method of recognizing species automatically generates much information about the biogeography, population structure, historical events, and ecology and/or reproductive biology of the group under study. In turn, this information provides much insight into the process of speciation. It also makes the criteria, data, methods of analysis and degree of support for the species inference completely explicit, thereby avoiding confusion, inconsistency and artificial controversies that plague much of the literature on species concepts.