Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

Species are a fundamental unit of biodiversity that are delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use of coalescent-based species delimitation, we do not fully understand the sensitivity of these methods to potential sources of bias and violations of their underlying assumptions. One implicit assumption of coalescent-based species delimitation is that geographic sampling is adequate and representative of genetic variation among populations within the lineage of interest. Yet exhaustive geographic sampling is logistically difficult, if not impossible, for many taxa that span large geographic expanses or occupy remote regions. Here, we examine the impact of geographic sampling on the output of Bayes-factor delimitation with SNAPP, a popular coalescent-based species delimitation pipeline. First, we demonstrate the problematic nature of sparse geographic sampling and isolation by distance for species delimitation using simulate...