Thesis (Ph.D.) University of Alaska Fairbanks, 2006Complete nucleotide sequences of the mitochondrial cytochrome b, tRNAproline and tRNA threonine genes of the eight extant species of ursids, as well as 166 brown bears (Ursus arctos L.) from 10 geographic regions of Alaska and elsewhere, are used to generate hypotheses about phylogenetic relationships among ursids and phylogeographic relationships among brown bears. Additional data were obtained from mitochondrial DNA control region from over 200 brown bears among 14 populations in Alaska, to assess structuring among brown bears. Phylogenetic analyses indicate the giant panda (Ailuropoda melanoleuca) and spectacled bear (Tremarctos ornata) represent basal extant taxa. Ursines, including the sun bear (Helarctos malayanus), sloth bear (Melursus ursinus), Asiatic and American black bears (Ursus thibetanus and U. americanus), brown bear, and polar bear (U. maritimus) apparently experienced rapid radiation during the mid-Pliocene to early Pleistocene. The two black bears appear to be sister taxa; brown and polar bear are the most recently derived of the ursines. Polar bears apparently arose during the Pleistocene from within a clade of brown bears ancestral to populations currently inhabiting islands of the Alexander Archipelago of southeastern Alaska. Thus, brown bears are paraphyletic with respect to polar bears. Parsimony and distance analyses suggest two distinct clades of mtDNA: one (Clade I) composed only of Alexander Archipelago bears, and the other clade comprised of bears inhabiting all other regions of Alaska (Clade II). This latter clade represents bears inhabiting eastern (Clade IIa) and western (Clade IIb) Alaska. Mismatch analysis uncovered a pattern suggestive of recent expansion among some populations comprising Clade IIb. Over 90% of populations in Alaska were significantly differentiated as measured by variance in haplotype frequencies, suggesting limited contemporary female-mediated gene flow and/or shifts in gene frequency through genetic drift. The degree of population genetic differentiation revealed using mtDNA, as well as limited information from comparisons of multilocus microsatellite genotypes from bears representing four Alaska populations, suggests many Alaskan populations are evolving independently. Analyses of molecular variance gave little support for currently accepted subspecies hypotheses. This research has provided new perspectives on processes that drive population structure of brown bears of Alaska and worldwide
