Inferring the impact of past climate changes and hunting on the South American sea lion

Abstract

© 2021 The Authors. Diversity and Distributions published by John Wiley & Sons Ltd.Aim: Many pinniped species have experienced drastic demographic changes due to their interaction with humans. Most studies, however, have failed to detect recent bottlenecks in otariids from genetic data. The South American Sea Lion Otaria flavescens have a long history of population changes associated with interglacial expansion and hunting to almost extinction. This study aimed at investigating these different demographic fluctuations integrating population genetics and phylogeographic approaches. Location: Pacific coast of South America. Methods: Eighty-five samples from the Chilean coast were collected. Eight microsatellite loci were genotyped, and D-Loop mitochondrial DNA (mtDNA) sequenced. Genetic diversity was assessed, and tests of recent genetic bottlenecks were performed. Past demographic changes were inferred based on neutrality tests, adjustment of a sudden expansion model and Bayesian skyline plots. The magnitude and timing of the different population size changes were further investigated through approximate Bayesian computation (ABC) of coalescent inferences. Results: The mtDNA shows relatively high diversity (h = 0.98 and π = 0.01) compared to most otariids, corroborates the divergence between Pacific and Atlantic populations, around 80,000 years ago (ya), and revealed a secondary contact zone in the Magellan strait. Microsatellite data support a second genetic discontinuity at 40°S, associated with post-glacial colonization of Patagonia. ABC analyses confirmed that glaciation affected the effective population size (Ne) all along the Pacific Coast, between ~50,000 and 15,000 ya. A strong reduction of Ne was also inferred for the hunting period (73–66 ya from sampling). Main conclusions: O. flavescens shows clear signatures of susceptibility to climatic and anthropogenic disturbances and a spatial genetic structure that should be taken into account in the context of management and conservation policies. Yet, despite a recent history of demographic bottlenecks, the genetic diversity remains high, likely a consequence of the demographic dynamics in otariids, characterized by large and connected metapopulations.