Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico

Abstract

The fossil record indicates that the brown bear (Ursus arctos) colonized North America from Asia over 50 000 years ago. The species historically occupied the western United States and northern Mexico but has been extirpated from over 99% of this range in the last two centuries. To evaluate colonization hypotheses, subspecific classifications, and historical patterns and levels of genetic diversity in this region, we sequenced 229 nucleotides of the mitochondrial DNA control region in 108 museum specimens. The work was set in a global context by synthesizing all previous brown bear control region sequences from around the world. In mid-latitude North America a single moderately diverse clade is observed, represented by 23 haplotypes with up to 3.5% divergence. Only eight of 23 haplotypes (35%) are observed in the extensively sampled extant populations suggesting a substantial loss of genetic variability. The restriction of all haplotypes from mid-latitude North America to a single clade suggests that this region was founded by bears with a similar maternal ancestry. However, the levels and distributions of diversity also suggest that the colonizing population was not a small founder event, and that expansion occurred long enough ago for local mutations to accrue. Our data are consistent with recent genetic evidence that brown bears were south of the ice prior to the last glacial maximum. There is no support for previous subspecies designations, although bears of the southwestern United States may have had a distinctive, but recent, pattern of ancestry.

The use of museum specimens with high-throughput DNA sequencers

“…Improved laboratory methods led to the use of nuclear DNA (nDNA) sequences in the early 2000s (Li et al, 2000; Vallianatos et al, 2002; de la Herrán et al, 2004), and the number of studies using multiple loci has increased since then. Research using many museum samples (> 100) has also become more common (e.g., Godoy et al, 2004; Miller et al, 2006). Polymerase chain reaction-based studies of natural history collections, however, still almost always use fewer than 20 loci and commonly use just one, especially when working with relatively large sample sizes.…”

Evidence of a phylogeographic break in the Romanian brown bear (Ursus arctos) population from the Carpathians

“…Taberlet and Bouvet (1994) identified two highly divergent lineages which on average differed by more than 7%. The western lineage is found in Spain, the Pyrenees, Norway, southern Sweden, Italy (Alps and Apennines), Romania and the Balkans whereas the eastern lineage occurs in Slovakia, Estonia, Romania, Russia, Finland, northern Sweden and also in the Russian Far East, Japan and parts of northwestern North America (Taberlet and Bouvet 1994;Taberlet et al 1995;Miller et al 2006;Saarma et al 2007). The two lineages probably correspond to different glacial refugia during the earlier Quaternary (Taberlet and Bouvet 1994).…”

The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses

“…Secondly, the mitochondrial estimates for the MRCA of brown and polar bears may have been underestimated because several geographically isolated populations of U. arctos were not included in molecular dating analyses. Indeed, divergent mtDNA haplotypes have been detected in short D-loop or cytochrome b sequences of brown bears currently found in Iran, Pakistan, and Mongolia (Gobi Desert), as well as in extinct populations of North Africa [32][33][34][35].…”