Population and diet of the New Zealand fur seal (Arctocephalus forsteri): molecular approaches

Abstract

The recent increase in the New Zealand fur seal (Arctocephalus forsteri) population has given rise to socio-economic concerns regarding the potential conflicts with human interests. Elaboration of a comprehensive management strategy has been hindered by the paucity of solid information concerning New Zealand fur seal ecology. Recent developments in massive parallel DNA sequencing and computational infrastructures were used to address some of the major areas of conflict with human commercial interests. The first focus of the current study was to test a series of non-destructive methods for collecting biological samples for high- throughput DNA analysis. A second focus of the study was application of whole mitochondrial genomes in conjunction with Y chromosome Zinc fingers (ZFY) from New Zealand fur seals throughout the whole range of the species distribution in an Approximate Bayesian Computation framework to reconstruct the recent demographic history of the species. The pristine population size (pre-human colonisation), historical population size after human first arrival and the bottleneck population size were estimated. There was enough variability left in the mitochondrial genomes to detect the 18th -19th- century’s population bottleneck in the species. The pattern observed in ZFY data set was more complicated indicating more subtle population genetics dynamics. Mitochondrial DNA were uniform in its distribution with few distant haplotypes that could represents the presence of old lineages or potential introgression from other sympatric species. The intriguing pattern observed in ZFY data also resulted in the discovery of a rare genomic event called ‘’ectopic gene conversion” between non- recombining parts of Y and X chromosomes in the New Zealand fur seal genome The third focus of the study is on the fine scale population structure of NZ fur seals at a local scale around Banks Peninsula, -South Island, and New Zealand. No evidence of local population structure was found in the area suggesting the presence of substantial gene flow among colonies at a local scale. Moreover, the “spill over“ colony expansion dynamics, suggested previously as a pattern for recolonizing new habitat, was supported at the local scale using genetic data. Most of the newly-established colonies in the area showed the highest degree of genetic structure similarities with older colonies in their vicinity emphasizing the important role of “spill over” dynamics of older colonies in formation of new colonies. The data significantly support multi recolonization events with occasional local recruitment of immigrating individuals. There is a short mitogenomic announcement in chapter five where I used the complete mitogenomes of New Zealand fur seals in addition to three mustelid species (all de novo sequenced in the current research) to re-examine the origin of pinnipeds in the light of new available mitogenomes. The final focus of the study used molecular-based methods to identify the prey and parasite items of the New Zealand fur seal from massive parallel sequencing of faeces and regurgitates. The overlap between the diet of the seals and commercial fisheries were also estimated. Data supported a generalist pattern of feeding behaviour of the New Zealand fur seal. As many as 64 prey species were identified from faecal samples and/or regurgitates in a single colony. Surprisingly, only 10% of species in fur seals diet were species of commercial interest. The population and diet data will provide marine ecosystem managers with an increased knowledge necessary for elaborating any long-term conservation plan for the New Zealand fur seal.