Factors shaping the population structure and historical abundance of pinnipeds and penguins

Abstract

The idea that there is a causal chain between ecological pressures, demographic trends, and the distribution of genetic variation in a population underlies the use of genetic markers to model biogeographic history and conservation priorities. Ecological traits are increasingly being linked to genetic loci in studies of natural selection, but are often only gestured at in studies using neutral markers to study population structure and demographic history. In this thesis, I investigate the modern population structure of the South American sea lion (Otaria flavescens) using SNPs derived from reduced-representation genome sequencing (RADseq) and mitochondrial loci, finding no evidence for nuclear structure, but confirming the existence of matrilineal (mitochondrial) structure and suggesting that it may have developed relatively recently. I then show that the populations of O. flavescens and a sympatric and ecologically similar penguin species, Spheniscus magellanicus, expanded at different times in the mid-to-late Holocene, paralleling recent dietary shifts indicated by analysis of stable isotopes (δ15N and δ13C), possibly towards more benthic prey.

To help identify populations with especially similar demographic histories and try to understand what ecological factors explain their similarity, I developed a program called ‘align_stairwayplot.py’, which quantitatively compares demographic histories based on a metric combining the magnitude of, and level of model support for, their growth or decline trajectories at aligned time points. With the support of this tool, I found that populations of pinniped and penguin species shared common patterns in their demographic histories that allowed them to be clustered with reasonable accuracy, even with low sample sizes. Antarctic and sub-Antarctic penguins had highly similar demographic responses to the last glacial maximum (LGM), but that the response was weaker in the most ice-tolerant species, the emperor penguin. Globally distributed pinniped species fell into clusters based on the similarity of their demographic histories; their relationships were best explained by differences in latitude from among the factors considered, but conclusions were limited by lack of diet information and small sample sizes with respect to some factors.