Comment on “Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage”

Hailer et al. (1) sequenced 14 independent nuclear loci across the genomes of polar (Ursus maritimus), brown (U. arctos), and American black bears (U. americanus). The Bayesian multilocus coalescent approach showed one species tree in which polar bears split from brown bears before the diversification of brown bear lineages. The divergence of polar bears was estimated to have occurred 603 thousand years ago (ka). These results conflict with the mitochondrial DNA phylogeny, which defines the root of the polar bear lineage within brown bear diversity (2, 3) (“standard model” in Fig. 1A). Additional phylogenetic analysis using the concatenated sequences supported the sister lineage of polar bears to all brown bears. Based on these observations, the authors proposed a new evolutionarymodel in which polar bears diverged from the common ancestor of all extant brown bears, whereas hybridization with female brown bears facilitated introgression (“newmodel” in Fig. 1A). Here, we focused on a unique genealogical history in each locus and applied population genetic analysis to the same data set evaluated in Hailer et al. (1), including 14 unlinked nuclear loci from brown bears (2N = 36) and polar bears (2N = 36). A crucial difference between the standard model and the new model is the time to the most recent common ancestor (MRCA) in brown bears (TMRCA-uar) (Fig. 1A). In the standard model, the TMRCA-uar is the same for all of the samples from brown and polar bears (TMRCA-all) (TMRCA-all = TMRCA-uar). The ratio of TMRCA-uar to TMRCA-all (TMRCA-uar/TMRCA-all) is expected to be 1.00 in this model. In contrast, the new model shows that the TMRCA-all is older than the TMRCA-uar. From the estimates ofTMRCA-all (603 ka) and TMRCA-uar (125 ka), Hailer et al. (1) estimated the ratio of 0.21. We used the TMRCA-uar/TMRCA-all as a test statistic to ask whether the observed genetic variation significantly deviates from the null hypothesis of the standard model. We estimated the TMRCA-all, TMRCA-uar, and TMRCA in polar bears (TMRCA-uma) for 13 loci using the GENETREE program (4) (Table 1). TECHNICALCOMMENT