Genetic Structure and Phylogeography of the Fox Squirrel, Sciurus niger, as Inferred From a Mitochondrial Gene

Abstract

Sciurus niger (Rodentia: Sciuridae) is a large tree squirrel which inhabits the southeastern portion of North America. Currently there are ten recognized subspecies which are distinguished based on differences in morphology and ecology. While molecular work has been undertaken for a few subspecies of S. niger, the patterns of genetic differentiation of the entire species have yet to be examined. This study attempts to characterize the genetic structure of S. niger in order to help determine the validity of current subspecies designations and offer insight into the post-glacial colonization patterns of the species. A 296 base pair fragment of the mitochondrial control region (dloop) was sequenced from 55 specimens of S. n. vulpinus, 13 samples of S. n. niger, and 13 samples of S. n. rufiventer. Fifteen previously reported haplotypes (Lance et al. 2003) representing S. n. cinereus, S. n. rufiventer, and S. n. vulpinus were incorporated into the analysis. Additionally, a data set of 89 sequences generated at the Van Den Bussche Laboratory of Molecular Systematics and Conservation Genetics were added to this data set. These sequences included representatives of the following 8 subspecies: S. n. bachmani, S. n. cinereus, S. n. limitis, S. n. ludovicianus, S. n. niger, S. n. rufiventer, S. n. subauratus, and S. n. vulpinus. The compiled data set of 258 individuals belonging to 8 subspecies yielded 125 unique haplotypes, indicating extremely high levels of diversity in the control region. Several tree-based methods recovered two distinct shallow clades which do not correspond to geographic regions or subspecies. A parsimony-based minimum spanning network revealed two haplotype clusters which correspond to the two clades found in the tree-based methods. The haplotypes are closely linked in a starshaped phylogenetic network; several of the most frequent haplotypes were internal, while the majority were unique to single populations and presented distal positions in the network. Overall there was a lack of genetic structure amongst populations with most of the variance explained by within population genetic diversity. Despite poor branch support, the congruent recovery of the two S. niger clades via both clustering-based and optimality criterion-based methods supports the separation of haplotypes into two major haplogroups. These results indicate that the currently recognized subspecies based on alpha taxonomic characters are not concordant with the mitochondrial history of S. niger. Instead, my findings suggest that the control region haplotype distribution in fox squirrels may be the result of repeated and rapid habitat expansions/retractions during glacial events in the Pleistocene. The shallow divergence between haplotypes across wide geographic distances suggest that the patterns of morphological and ecological differentiation the we observe within S. niger may have occurred much more recently than previously thought.