Alternative treatments of genetic distances for species delimitation in Callosciurinae and Sciurinae (Rodentia: Sciuridae)

Abstract

There are many DNA taxonomy methods available, but single-locus data coupled with distance-based analyses still dominate species identification in practice. Genetic distance thresholds are often used for assigning genetic diversity into entities corresponding to species but are criticized for non-universality or arbitrary. This study investigated an alternative approach for determining genetic thresholds that used iteratively sister-clade clustering for sister species boundary detection within a phylogenetic framework. This method was separately applied to two close subfamilies of Callosciurinae and Sciurinae in Rodentia using the cyt b gene. Our results showed that genetic thresholds for Callosciurinae and Sciurinae were 4.0% and 6.0%, respectively, indicating that the optimized thresholds could be lineage-specific. The use of these thresholds for taxa partitioning yielded a very similar putative species number as the prevailing ABGD method, and increased species diversity by 74.2% and 20.7% in Callosciurinae and Sciurinae, respectively. This suggested that additional cryptic species were present that warrant further investigation. We further tested the performance limitation of our method by simulating the impacts of tree construction and sampling limitation. The results showed that it preformed equally well for different trees but failed to work when inter- or intraspecific sampling is insufficient. These findings support the feasibility of this approach as an alternative tool for species delineation when only single-locus information is available for large datasets.