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

Cronin, Matthew A.; McDonough, Molly M.; Huynh, Howard M.; Baker, Robert J.

doi:10.1139/cjz-2013-0078

Cited by 14 publications

(12 citation statements)

References 57 publications

(85 reference statements)

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“…The timing of divergence between bear lineages in the genus Ursus has been a matter of much recent debate [17,18,24,[45][46][47]. This is due in part to the paucity of fossils representing the early divergence of this lineage [48] and to post-divergence hybridization, which may be common among bears [18,19,24,45].…”

Section: (B) Bears In the Genus Ursusmentioning

confidence: 99%

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Cahill

Soares

Green

et al. 2016

Phil. Trans. R. Soc. B

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Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus. Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

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Section: (B) Bears In the Genus Ursusmentioning

confidence: 99%

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Cahill

Soares

Green

et al. 2016

Phil. Trans. R. Soc. B

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“…The Y chromosome phylogeny of brown and polar bear lineages resembles the topology of species trees reconstructed from biparentally inherited autosomal markers (Hailer et al 2012;Miller et al 2012;Cronin et al 2013), where the species constitute distinct sister (or rather brother) lineages, with black bears clustering outside their variation ( fig. 2B).…”

Section: Speciation and Introgressionmentioning

confidence: 99%

Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages

Bidon

Janke

Fain

et al. 2014

Molecular Biology and Evolution

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Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.

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“…A number of additional studies utilizing multilocus data from the nuclear genome have recently been conducted, all recovering a sister species relationship (monophyly) of polar and brown bears. Intron sequences, autosomal microsatellites, amplified fragment length polymorphism (AFLP) and single nucleotide polymorphism (SNP) markers analyzed in samples from across the ranges of polar and brown bears support the conclusion that the two species are not hybridizing extensively at present, and that their genomes are largely differentiated from each other (Hailer et al 2012;Miller et al 2012;Cronin & MacNeil 2012;Cronin et al 2013Cronin et al , 2014Liu et al 2014). A notable exception are brown bears from the Alaskan ABC islands, in which prominent signals of introgression are found (see below).…”

Section: Discovery Of a Pleistocene Polar Bear Jawbone Stimulates Newmentioning

confidence: 81%

Evolutionary History of Polar and Brown Bears

Hailer

Welch

2016

Encyclopedia of Life Sciences

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Taxonomists have long recognised polar and brown bears as separate species with distinct ecological niches and largely nonoverlapping ranges. Surprisingly, phylogenetic studies of maternally inherited mitochondrial DNA (mtDNA) found polar bears nested within brown bears, with an estimated divergence time of <170 000 years. This indicated an unusually rapid speciation and adaptation of polar bears. However, several recent studies of autosomal and Y‐chromosomal DNA have revisited these findings, giving independent perspectives of bear evolutionary history. Results show that polar bears cluster separately from brown bears, and divergence time estimates are older than those based on mtDNA, ranging from >300 000 to 4–5 million years. These studies confirm uniqueness of the polar bear lineage, provide more time for speciation and adaptation, and have uncovered numerous candidate genes for evolutionary adaptations. Several instances of introgressive hybridisation between polar and brown bears have been inferred, revealing trans‐species transmission of mtDNA and some nuclear loci. Key Concepts DNA sequences in conjunction with a calibration of the mutation rate (e.g. inclusion of a previously estimated mutation rate, geological information or inclusion of a radiocarbon‐dated ancient sample) can be used to estimate the timing of speciation between species. Differentially inherited loci can reveal different aspects of evolutionary history. The genome of polar bears contains a wealth of alleles that are not found in brown bears, and vice versa. Polar bears have passed through bottlenecks during their evolutionary history, leaving them much less genetically variable than brown bears. When analysing DNA sequences that have passed through the species boundary due to introgressive hybridisation, studies will obtain information about the hybridisation event rather than the (earlier) speciation event. Brown bears have acted as vectors for polar bear alleles, transporting introgressed genetic material far beyond the species' contact zones. Incomplete lineage sorting (see ‘Glossary’) complicates phylogenetic inferences among rapidly and/or recently diverged taxa. Lineage sorting takes on average four N e generations, which for many taxa can span at least several hundred thousand years (N e being the effective population size). The time needed for lineages to be reciprocally monophyletic can therefore take very long, even under complete reproductive isolation. Molecular studies have found signals of positive selection in polar bear genes that are involved in fat metabolism, energy production and cardiovascular function. These genes are exciting candidates that may help us better understand the genetic basis of polar bear adaptations to Arctic conditions.

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

Cited by 14 publications

References 57 publications

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Inferring species divergence times using pairwise sequential Markovian coalescent modelling and low-coverage genomic data

Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages

Evolutionary History of Polar and Brown Bears

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