Fig 1.
Divergence times of the family Ursidae.
Nodal numbers indicate the estimated divergence time (Ma). Horizontal gray bars spanning the nodes mark the 95% confidence interval for the divergence time. The phylogenetic positions of extinct lineages, which are indicated by the dashed lines, follow [18]. Horizontal black bars indicate temporal range based on fossil evidence. The temporal range of the common ancestor of Ursidae based on fossil evidence is indicated by the shading. Extinct species are marked by a dagger (†).
Fig 2.
Coalescent times of the Asian black bear.
Nodal numbers indicate the estimated coalescent time (Ma). Horizontal gray bars show the 95% confidence interval for the coalescent times. (a-c) Geographical distribution of fossils of Asian black bear in (a) the Calabrian (Early Pleistocene) [58], (b) the lonian (Middle Pleistocene) [58, Kohno, unpublished] and (c) the Tarantian (Late Pleistocene) [58, 60]. The illustration is of a Japanese black bear (Ursus thibetanus japonicus), kindly provided by Utako Kikutani. Circles on maps indicate the fossil record of Asian black bears (Blue circles indicate the fossil records reported by previous studies and red circle indicates the fossil records newly reported by this study.).
Fig 3.
Genealogy of eight Asian black bears as inferred from the 3rd codon positions of the complete mitochondrial protein genes using the GENETREE program.
Since the program did not work on the whole data set, probably due to excessive numbers of mutation sites, the whole data set was separated into six fragments. The dots on the branches indicate the number of mutation sites. The values of ρML (= 2×Nef×μ; μ is the mutation rate per sequence per generation) and tMRCAs were also estimated by GENETREE. The substitution rate of the 3rd codon positions of mitochondrial protein genes of Asian black bear was estimated to be 3.03×10−8/site/year (data not shown), and the average mutation rate of each of the six fragments is 5.99×10−5/sequence/generation.
Fig 4.
Phylogenetic relationships among Asian black bears.
(a) The ML tree as inferred from the D-loop sequence. Nodal numbers indicate bootstrap probabilities (rapid bootstrap method with 1000 replications). The binary backbone structure was given a priori on the basis of the mitochondrial genome data (the phylogenetic relationships on the basis of the mitochondrial genome data are shown in Fig 2). Branch lengths are proportional to the number of nucleotide substitutions. (b) The median joining network. The circles indicate individual haplotypes, and their sizes are proportional to the frequency of the haplotypes. The short thick bars on the branches indicate unobserved ancestral haplotypes. In both (a) and (b), individuals from the Japanese population, the southern continental population (including Taiwan) and the northern continental population are colored yellow, red and light blue, respectively (branches are colored in (a), and haplotypes in (b)). Since the geographical information of FM177759 is unknown, it is colored black.
Fig 5.
Dynamics of the population sizes and tMRCAs of all Asian black bears, the Japanese population and the continental population.
(a) Dynamics of the population sizes estimated by Bayesian Skyline Plot analysis. The y-axes indicates the effective population size × generation intervals, and the x-axes indicate the time in years before present. (b) Posterior distributions of the tMRCAs. The times of formation of land bridges before the oldest record of the Japanese black bear (337–330 Kilo annum) are indicated by shaded bars, following Dobson and Kawamura [60] and Rohling et al. [63] with recalibrations by Lisiecki and Raymo [67]. The shading around the lines indicates 95% confidence interval of effective population size for each time point.
Table 1.
Summary Statistics for the demography.
Fig 6.
Middle Pleistocene black bear from Japan with a comparison of the left upper second molars (M2) among bears.
1, Middle Pleistocene (ca. 337–330 Kilo annum, MIS 9 [68]) black bear, Ursus thibetanus subsp. indet., from Aomori Prefecture, northern Japan (NMNS-PV 22666). 2, Extant Japanese black bear, Ursus thibetanus japonicus, from Nagano Prefecture, central Japan (NMNS-PO 52). 3, Extant Tibetan black bear, Ursus thibetanus thibetanus, from Thailand (NMNS-PO 207). 4, Extant Hokkaido brown bear, Ursus arctos yesoensis, from Hokkaido, northern Japan (NMNS-PO 208). The black bears share a combination of M2 characters such as a relatively large metacone (as large as the paracone), a distinct constriction between the paracone and the metacone, and a less developed posterior talon. In contrast, the brown bear has a smaller metacone relative to the paracone, a less distinct constriction between the two cusps, and a well developed posterior talon in M2. These comparisons suggest that the tooth of Middle Pleistocene Japanese black bear is closer in size and shape to the teeth of continental black bears than it is to extant Japanese black bears, but it is far from the brown bears.