Phylogeography and population structure of the New Zealand sea lion, Phocarctos hookeri

Abstract

A number of species endemic to New Zealand have seemingly restricted ranges relative to their more widespread pre-human distributions. However, emerging evidence suggests that such patterns are not necessarily associated with simple range contractions. The recent settlement history and well-preserved archaeological record of New Zealand provides an ideal environment to investigate the changes in these species’ distributions. I apply genetic analyses of ancient and modern specimens to assess dynamic distributional responses of the New Zealand sea lion, Phocarctos hookeri, to human settlement in New Zealand. P. hookeri is New Zealand’s only endemic pinniped species, and is one of the rarest otariid species in the world. Archaeological and natural deposits along New Zealand’s coastline suggest a widespread distribution for this species through the Holocene until the time of human arrival. Subsequently, subsistence hunting and commercial sealing led the extirpation of P. hookeri from mainland New Zealand and also a dramatic decline in the subantarctic population. Today, P. hookeri are predominantly restricted to the subantarctic, with 73% of the species' total annual pup production accounted for by breeding colonies on the Auckland Islands. Anthropogenic impacts continue to affect the species today, with fishery by-catch identified as a substantial threat. Genetic analyses of modern and extinct populations of P. hookeri presented here reveal distinct lineages of ‘mainland’ and ‘subantarctic’ P. hookeri (2.1 – 4.6% divergence in 190 bp of mitochondrial control region, 0.47% across the complete mitochondrial genome). The ‘mainland’ lineage was widespread around mainland New Zealand until the time of human arrival, prior to its rapid extirpation. The relatively recent return of P. hookeri to mainland New Zealand represents a range expansion for the ‘subantarctic’ lineage. These results emphasise that extirpation of one lineage can facilitate range expansion in another. Contemporary genetic structure among extant populations of P. hookeri was investigated using a range of mitochondrial and nuclear markers. I detected only moderate levels of nuclear diversity, and very low levels of mitochondrial diversity, congruent with a severe historic population bottleneck. Despite documented female philopatry, spatial genetic structure was not observed, supporting the hypothesis that site fidelity alone is insufficient to promote genetic structuring in this otariid species. Finally, genetic data from extant P. hookeri were applied to estimate its short-term and long-term effective population size, and to detect the genetic signatures of the 19th century bottleneck caused by commercial sealing. A long-term effective population size estimate for modern P. hookeri suggests that the current census population size is much lower than the historical carrying capacity, K, of the subantarctic lineage. Bayesian bottleneck analyses indicated that the extant population is still within the range of census size estimates from the immediate aftermath of 19th century sealing. Estimates of historical demographics are vital for the management of the species today, particularly for determining sustainable by-catch levels.