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

  title={Comment on “Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage”},
  author={Shigeki Nakagome and Shuhei Mano and Masami Hasegawa},
  pages={1522 - 1522}
Based on nuclear and mitochondrial DNA, Hailer et al. (Reports, 20 April 2012, p. 344) suggested early divergence of polar bears from a common ancestor with brown bears and subsequent introgression. Our population genetic analysis that traces each of the genealogies in the independent nuclear loci does not support the evolutionary model proposed by the authors. 

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

It is asserted that the mitochondrial DNA–based scenario for polar bear evolution cannot be refuted and the sister-lineage model receives high support in a Bayesian model comparison.

Evolutionary History of Polar and Brown Bears

Taxonomists have long recognised polar and brown bears as separate species with distinct ecological niches and largely nonoverlapping ranges. Surprisingly, phylogenetic studies of maternally

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

Gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies, and highlights that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years.

The evolutionary history of bears is shaped by gene flow across species

A genome analysis of the bear family with representatives of all living species finds strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains numerous uncertainties in reconstructing the bear phylogeny.

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

The population demography of brown and polar bears is inferred and it is found that brown bears have 6 times or more than 14 times larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity.

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA

The estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands, and supports the new evolutionary hypothesis of theJapanese black bear.

Genetic relationships of North American bears (Ursus) inferred from amplified fragment length polymorphisms and mitochondrial DNA sequences

The data indicate that extant populations of brown bears and polar bears have separate nuclear and mitochondrial gene pools and are supported as species under the genetic species concept.

Molecular phylogeny and SNP variation of polar bears (Ursus maritimus), brown bears (U. arctos), and black bears (U. americanus) derived from genome sequences.

Genotypes for 162 SNP loci of 336 bears from Alaska and Montana showed that the species are genetically differentiated and there is geographic population structure of brown and black bears but not polar bears.

Implications of the Circumpolar Genetic Structure of Polar Bears for Their Conservation in a Rapidly Warming Arctic

An expansive analysis of polar bear (Ursus maritimus) circumpolar genetic variation during the last two decades of decline in their sea-ice habitat seeks to evaluate whether their genetic diversity and structure have changed, how their current genetic patterns compare with past patterns, and how genetic demography changed with ancient fluctuations in climate.



Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage

A high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears reveals polar bears as a sister lineage to all brown bears, and confirms previous suggestions that polar bears carry introgressed brown bear mitochondrial DNA due to past hybridization.

Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae.

The mtDNA data support some, but not all, of the currently designated subspecies of brown bears whose descriptions have been based essentially on morphology, and a weak correlation is suggested between types of mtDNA and habitat preference by brown bears in Alaska.

The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, a draft sequence of the giant panda genome is generated and assembled, indicating that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition.

Inference of human population history from individual whole-genome sequences.

A more detailed history of human population sizes between approximately ten thousand and a million years ago is presented, using the pairwise sequentially Markovian coalescent model applied to the complete diploid genome sequences of a Chinese male, a Korean male, three European individuals, and two Yoruba males.

Generating samples under a Wright-Fisher neutral model of genetic variation

A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model, and the samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.

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Curr. Biol

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