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. 2022 Aug 2;119(31):e2120307119.
doi: 10.1073/pnas.2120307119. Epub 2022 Jul 18.

Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear

Tiantian Zou  1 , Weimin Kuang  1 , Tingting Yin  2 , Laurent Frantz  3   4 , Chang Zhang  1 , Jianquan Liu  5   6 , Hong Wu  1 , Li Yu  1
Affiliations

Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear

Tiantian Zou et al. Proc Natl Acad Sci U S A. .

Abstract

Bears are fascinating mammals because of their complex pattern of speciation and rapid evolution of distinct phenotypes. Interspecific hybridization has been common and has shaped the complex evolutionary history of bears. In this study, based on the largest population-level genomic dataset to date involving all Ursinae species and recently developed methods for detecting hybrid speciation, we provide explicit evidence for the hybrid origin of Asiatic black bears, which arose through historical hybridization between the ancestor of polar bear/brown bear/American black bears and the ancestor of sun bear/sloth bears. This was inferred to have occurred soon after the divergence of the two parental lineages in Eurasia due to climate-driven population expansion and dispersal. In addition, we found that the intermediate body size of this hybrid species arose from its combination of relevant genes derived from two parental lineages of contrasting sizes. This and alternate fixation of numerous other loci that had diverged between parental lineages may have initiated the reproductive isolation of the Asiatic black bear from its two parents. Our study sheds further light on the evolutionary history of bears and documents the importance of hybridization in new species formation and phenotypic evolution in mammals.

Keywords: Asiatic black bear; Ursinae; hybridization; population genomics.

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Conflict of interest statement

The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
Geographic distribution and phylogenetic analyses of Ursinae. (A) Geographic distributions of six Ursinae species (IUCN, www.iucnredlist.org). PoB: polar bear; BrB: brown bear; AmB: American black bear; AsB: Asiatic black bear; SuB: sun bear; SlB: sloth bear. (B) Species trees of six Ursinae species constructed by MP-EST and SVDquartets. Both analyses produced the same topology, with strong support (100%) for all interspecific-level branches. Spectacled bear (SpB) was used as the outgroup. In the SVDquartets tree, the size of triangles for the species represents the number of individuals. (C) Distributions of phylogenetic trees based on three window sizes (50, 100, and 200 kb). Tree-1, Tree-2, and Tree-3 correspond to the three phylogenetic topologies described in the text. NG represents the North Group. SG represents the South Group. (D) Distributions of the phylogenetic tree topologies (Tree-1, Tree-2, Tree-3, and Others) across the Asiatic black bear genome based on 100-kb sliding window. (E) Phylogenetic network analysis with a threshold level of 30% showing the reticulate evolutionary history of the Asiatic black bear.
Fig. 2.
Fig. 2.
The hybrid origin of the Asiatic black bear based on HyDe, PCA, FST, and shared variations analyses. (A) HyDe analysis. AsB represents Asiatic black bear. The y axis indicates the proportion of genetic mixture for each individual; blue represents genetic contribution (γ) from the North Group and red represents genetic contribution (1 − γ) from the South Group. (B) HyDe scans with 100-kb sliding windows across the genome of the Asiatic black bear. (C) PCA results for 60 bears representing six Ursinae species. The inset bar plot shows the values of the 10 primary components, of which PC1 and PC2 explained the greatest proportions of the variance. (D) Distributions and comparisons of genomic 100-kb windowed FST for the three population pairs (SG vs. AsB, NG vs. AsB, and NG vs. SG). (E) Detection of hybrid speciation based on shared INDELs (S: South Group; H: Hybrid species Asiatic black bear; N: North Group; O: Outgroup spectacled bear). (Top) Percentages of shared INDELs in SH (South Group and Hybrid species Asiatic black bear: red bars), NH (North Group and Hybrid species Asiatic black bear: blue bars), and SN (South Group and North Group: yellow bars). A KKSC test supports the hybrid speciation model G(H)N. (Middle) Proportion of AVs. The values of SH, NH, and SN were calculated based on the numbers of shared INDELs in SHO/SH, NHO/NH, and SNO/SN, respectively. A Student’s t test of these data supported PSHOPSH<PSNOPSN and PNHOPNH<PSNOPSN. (Bottom) Percentages of shared phylogenetically informative variations in SH, NH, and SN.
Fig. 3.
Fig. 3.
Evolutionary scenario simulations of the hybrid origin of the Asiatic black bear. TDIV1 represents the divergence time of the ancestor of subfamily Ursinae; THybrid represents the time of the hybrid origin of the Asiatic black bear; TDIV2 represents the divergence time of the ancestor of the South Group; TDIV3 represents the divergence time of the ancestor of the North Group; TDIV4 represents the divergence time of the ancestor of polar bears and brown bears. Gray arrows represent introgressions between the Asiatic black bear and other bear species before and after species divergence. The thickness of each of these arrows is proportional to the corresponding intensity of gene flow.
Fig. 4.
Fig. 4.
Genetic basis of the intermediate body size of Asiatic black bears. (A) Genomic selective scans of HKA test and population-specific fixed mutation calculation for the merged populations of AsB and NG. Two candidate PSGs in the top 20 are shown. (B) Genomic selective scans of HKA test and population-specific fixed mutation calculation for the merged populations of AsB and SG. Two candidate PSGs in the top 20 are shown. (C) Haplotype clustering analysis of the four candidate PSGs. (D) Haplotype networks for the four candidate PSGs. (E) Schematic illustration of the genetic basis of the intermediate body size in the Asiatic black bear relative to its parental lineages.
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