Different Microsatellite Mutation Models May Lead to Contrasting Demographic Inferences through Genealogy-Based Approaches: A Case Study of the Finless Porpoise off the East Asian Coast

Abstract

Understanding the population history of wide-ranging species, especially those ranging over varying landscapes, helps in deciphering the evolutionary force (s) that shaped the present genetic diversity/structure of regional fauna. In the shelf region, evolution of coastal morphology through glacial oscillations played an important role in shaping the contemporary genetic structure of coastal marine organisms, although the type and extent of such influence may differ between ecologically dissimilar species, such as marine mammals vs. other marine vertebrates. We reconstructed the demographic trajectories of four populations of the finless porpoise (Neophocaena spp.), covering a wide latitudinal range in the western Pacific and using coalescent-based techniques. Subsequently, we compare the findings with the evolution of suitable ecological niche by reconstructing historic sea level fluctuations with a maximum entropy method. Our results indicate that the finless porpoise was distributed along the continental slope during the low stand of sea level, while the post-glacial marine transgression enabled the porpoise to re-colonize a vast region of the shelf, leading to the most recent expansion of the genus in east Asia. We underscore that inferences of past demographic events are sensitive to the evolutionary model of microsatellite loci and the proportion of multi-step mutation. For coastal cetaceans inhabiting complex coastal habitats, caution has to be exercised when examining demographic parameters to prevent biased inferences due to historic gene flow during marine transgression. Systematic sampling scheme should be encouraged for rigorous quantification of demographic parameters, which may be further applied to more adaptable methods such as approximate Bayesian computation.