Molecular Systematic and Population Genetic Studies of Pinnipeds: a Phylogeny of Our Fin-Footed Friends and Their S-Something "Species" Structures

Abstract

This thesis demonstrates the application of mitochondrial DNA sequence analysis to the genetic characterization of pinnipeds. This is theoretically and practically important because: l) Genetic studies of pinnipeds are not abundant, and have never been conducted on Southern hemisphere otariid species, eg— the New Zealand fur seal and Hooker's sea lion. 2) Pinnipeds have been exploited by sealing and these two species face continued pressure from fisheries operations. Some pinnipeds, including the Hooker's sea lion, exhibit compromised population recovery patterns and remain threatened by extinction. Population structure studies can be used to affect conservation and management of these species. 3) Field observations of philopatry suggest that population sub-structure may exist despite the fact that pinnipeds have considerable dispersal capabilities. In the absence of surveyable non-molecular traits, genetic characterization is necessary to reveal this underlying population structure. 4) Considerable debate on the evolutionary origin of the pinnipeds based on non-molecular techniques has reached an impasse. To address these issues, mitochondrial DNA sequences from three gene regions, cytochrome b , l25 rRNA, and the control region, were surveyed in over 120 individuals spanning all levels of the pinniped taxonomic hierarchy using PCR and direct DNA sequencing. The phylogenetic examination of the pinnipeds within the arctoid carnivore radiation is noteworthy in that it was conducted using spectral analysis, a new phylogenetic reconstruction method. This exercise represents the first detailed practical application of this method to real biological data. A simple but thorough methodological protocol for phylogenetic reconstruction was developed. This phylogenetic examination supports a monophyletic origin for the three pinniped families, the eared seals (Otariidae), the true seals (Phocidae), and the walrus (Odobenidae). However, the relationship of the walrus lineage among them remains partially unresolved. Further, the closest arctoid carnivore sister group to the pinnipeds remains unidentified. Surveys of intraspecific variation in the cytochrome b gene were conducted among four Southern Hemisphere otariid species. Comparative analysis reveals three distinct phylogeographic patterns of mitochondrial haplotypes among them. These results have implications for defining both "evolutionarily significant units" and "genetic management units" among Southern hemisphere fur seals. Finally, the most rapidly evolving mitochondrial gene region, the control region, is evaluated for its utility in addressing aspects of both macro- and micro-evolutionary questions among pinniped species. Intraspecific comparisons of Hooker's sea lions and New Zealand fur seals are examined for l) support for the phylogeographic relationships revealed in the mitochondrial cytochrome b gene of these species,and 2) diagnostic polymorphisms. Interspecific, intergeneric, and inter-sub-family comparisons are examined for a level of sequence variability and structural motifs that may be useful for phylogenetic analyses. The-work presented in this thesis and the DNA/tissue sample bank collected during its course culminate in a compelling case for establishing a national center for the continued study of molecular genetics in pinnipeds.