Population genetics of Ice Age brown bears

Abstract

The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.

Surprising migration and population size dynamics in ancient Iberian brown bears ( Ursus arctos )

“…Using the DNA sequences from 24 modern and 13 ancient Iberian brown bears, in combination with published sequences from seven ancient and one modern Iberian bears (see SI Fig. 3), we have been able to estimate the extent of genetic diversity change in the peninsula through time, from the Pleistocene until today. To test whether the changes in diversity show parallel developments in the rest of Europe, we conducted similar analyses for the non-Iberian European population samples, taking advantage of previously reported haplotypes (4,(18)(19)(20)23). It is noteworthy that the genetic diversity of the Spanish brown bear population continuously decreases from the Pleistocene to modern times (Table 1).…”

“…To include all of the data generated in the present study, we created two datasets, spanning 177 bp and 115 bp of the mitochondrial control region (referred below as the long and short datasets, respectively). In our analyses, we also included European brown bear haplotypes available from GenBank (4,(18)(19)(20)23). Together, the long and short datasets comprise 67 and 71 brown bear sequences, respectively (see SI Datasets 2 and 3).…”

“…If this is the case, the conservation of Iberian bears is of importance not only for Iberia but also for the whole of Europe, for which it has served as postglacial recolonization stock. However, several recent studies suggest that the extent of past gene flow, as inferred from contemporary material, may have been underestimated (18,19), and there is evidence that this also is true for Iberian bears (20).…”

“…These four samples (Ua1-Ua4) were extracted, amplified twice, and directly sequenced at Centro Mixto Universidad Complutense de MadridInstituto de Salud Carlos III de Evolució n y Comportamiento Humanos, Madrid, and replicated by using a solvent approach (18) at University College London. Both times the amplifications were performed according to Leonard et al (18) and directly sequenced.…”

Habitat selection and ecological speciation in Galápagos warbler finches ( Certhidea olivacea and Certhidea fusca )

“…An early set of reactions showing evidence of contamination in a blank control was discarded. No further evidence of contamination was detected after stricter procedures were implemented, including the use of a spatially isolated facility dedicated to low copy number DNA extraction (Leonard et al 2000). To facilitate the detection of contamination, individual birds from the same population were processed in different batches, and populations were intermingled within batches.…”