Paraphyly, Polyphyly, and the Nature of Species Boundaries in Pocket Gophers (Genus Thomomys)

Abstract

Species definitions are commonly based on documentation either of genetic or ecologic cohesion (biological species models) or of phylogenetic relationship (phylogenetic spe? cies concept). However, these philosophical positions are often incompatible with data on ge? nealogical relationship of and genetic/reproductive interactions among member populations. The difficulty in defining species in nature based on either viewpoint is exacerbated when times between divergence events are short, when differentiation among populations prior to speciation is extensive, and when reticulation events persist subsequent to speciation. We illustrate this set of problems with data on mitochondrial DNA sequences and both nuclear sequences and allozyme electromorphs for sets of populations of two currently recognized species of pocket gophers, Thomomys bottae and T. townsendii in the western United States. These molecular per? spectives give somewhat conflicting views of polyphyly, paraphyly, and monophyly at the population and species level due, in part, to probable differences in times to monophyly, dif? ferential lineage sorting, retention of ancestral polymorphisms, and/or episodes of asymmetrical introgressive hybridization. As a consequence, strict adherence to any species concept in the objective recognition of evolutionary units within this complex is difficult at best. (Species concepts; paraphyly; polyphyly; allozymes; mtDNA sequence; 0-globin sequence; pocket go? phers; Thomomys.)