The roles of selection and drift in the maintenance of MHC and neutral genetic variation in natural populations

In the first chapter I investigated the relative roles of drift and natural selection on the maintenance of diversity at the major histocompatibility complex (MHC) for the Channel Island fox (Urocyon littoralis). I observed an elevated level of heterozygosity for the San Nicolas Island fox (U. l. dickeyi) for a number of class 11 MHC loci (DRB, and three linked microsatellites). Simulations were preformed that indicate that the observed levels of variation at the MHC, coupled with a lack of variation at 18 microsatellite loci, were due to short and intense selection period/population bottleneck.; In the second chapter, I studied an introduced population of northern pike (Esox lucius) in Lake Davis, California. The pike had been introduced in the early 1990's, and eradication was attempted by rotenone treatment in 1997. The pike re-appeared in 1999, and questions rose about the origin of these fish. I was able to determine, against a panel of putative source populations, that the post-treatment individuals were survivors of the initial treatment in 1997. The Lake Davis population showed signatures of a recent population bottleneck, most likely from their initial introduction. Using temporal samples from Lake Davis, I was able to determine the effective size of the rotenone induced bottleneck was large (Ne--b ∼37 individuals).; In the third and fourth chapters I present a PCR based methodology to isolate an MHC gene from the little greenbul (Andropadus virens), analyzed this gene phylogenetically, and conducted a survey of population variation. Anvi-DAB1 had lower non-synonymous to synonymous substitution rates than 'classical' MHC genes and an allele with a frame-shift mutation, strongly suggesting that this gene is non-functional. Phylogenetically, the Anvi-DAB1 sequences were distinct from other A. virens and songbird MHC sequences, suggesting that Anvi-DAB1 is ancient and has not been subject to the forces of concerted evolution. Genetic variation and measures of population differentiation at Anvi-DAB1 were correlated with similar measures at six microsatellite loci. This result suggests, assuming neutrality at the microsatellite loci, that variation at the Anvi-DAB1 pseudogene is subject to the forces of drift and contemporary gene flow.