Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears

Shigeki Nakagome,Masami Hasegawa,Shuhei Mano,Dennis O’Rourke

doi:10.1371/journal.pone.0078813

Shigeki Nakagome, Masami Hasegawa + Show 2 more

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https://doi.org/10.1371/journal.pone.0078813

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Abstract

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

Highlights

Genealogical discordance is highlighted in phylogenetic relationships between brown bears (Ursus arctos) and polar bears (U. maritimus)
Phylogenetic analyses based on mitochondrial DNA indicate that the root of polar bear lineage is within brown bear diversity, representing a paraphyletic relationship [1,2]
The authors concluded that discrepancies in phylogenies between autosomal DNA (aDNA) and mitochondrial DNA (mtDNA) were the result of mtDNA introgression from brown bears to polar bears due to hybridization

Summary

Introduction

Genealogical discordance is highlighted in phylogenetic relationships between brown bears (Ursus arctos) and polar bears (U. maritimus). Based on genome scale sequence data, Miller et al [4] suggested the ancient divergence of polar bears from brown bears with an estimated split time of 4 to 5 million years ago (MYA). To infer an ancestral allele at each segregating site among brown and polar bears, we used orthologous sequences from the giant panda for 14 aDNA loci [11] and the complete mtDNA sequences of one giant panda (the accession number: EF212882) and two American black bears (JX196366; NC003426).

Results

Conclusion