The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses

Hassanin, Alexandre

doi:10.1016/j.crvi.2015.04.008

Cited by 53 publications

(11 citation statements)

References 44 publications

(98 reference statements)

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“…Genotype data at unlinked markers have been commonly used to assess hybridization, genomewide levels of admixture and introgression in conservation genomics studies (Bradbury et al, 2015;Hassanin, 2015;Hohenlohe et al, 2013;King, Stelkens, Webster, Smith, & Brockhurst, 2015;Lamaze, Sauvage, Marie, Garant, & Bernatchez, 2012; Le Moan, Gagnaire, & Bonhomme,, 2016;Rougemont et al, 2017). Nevertheless, the use of a linkage map enabling to explicitly consider the relative order and linkage disequilibrium among loci, and the increasing availability of references genome allow to access local ancestry information at the haplotype level, which has the potential to increase the sensitivity of admixture estimates even for low sample size studies (Allendorf et al, 2010;Duranton et al, 2018).…”

Section: Implications In Conservation Genomicsmentioning

confidence: 99%

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

et al. 2018

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Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.

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Section: Implications In Conservation Genomicsmentioning

confidence: 99%

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

et al. 2018

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“…The brown and polar bears show the most contrasting patterns despite they diverged less than a million years ago (Hassanin, ; Kumar et al, ). Within U. arctos , we found an extensive lineage differentiation resulting in complex groups with the widest distribution along the different regions of North America, Europe, Middle East and Asia, including a mixture of intercontinental regions.…”

Section: Discussionmentioning

confidence: 99%

“…We provided calibration points and error estimates and used a lognormal prior for the calibration dates. Six time‐calibration points were applied based on previous studies regarding the divergence time between U. maritimus and U. arctos of 0.88 million years ago (Ma) and between this clade and U. spelaeus (2.75 Ma) (Hassanin, ); between U. spelaeus and U. deningeri (0.75 Ma) (Puckett, Etter, Johnson, & Eggert, ); between U. thibetanus and U. americanus (3.9 Ma), the diversification of all Ursus (4.5 Ma), and between the Ursus clade and the outgroup (6.28 Ma) (Krause et al, ). These analyses estimated tree shape and divergence dates for all nodes and were sampled every 1,000th iteration for 100,000,000 generations, with a burn‐in of 10% of the initial samples discarded.…”

Section: Methodsmentioning

confidence: 99%

A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species

Luna‐Aranguré¹,

Soberón

Vázquez‐Domínguez

2019

Journal of Biogeography

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Aim Assessing the relevance of niche evolution in the diversification patterns and geographical distribution of species driven by climate remains a challenge. We apply an integrative approach to evaluate the role of the environment on the phylogeography of bear species, incorporating fossil data to characterize the changes in the ecological niche through time. We evaluate our approach with the four extant species of bears within Ursus, the best represented taxon in the fossil record of the family Ursidae. Location Eurasia and North America. Taxa Asian black bear, Ursus thibetanus; American black bear, U. americanus; Brown bear, U. arctos; and Polar bear, U. maritimus. Methods We built a genetic and a geographical database from all published mitochondrial DNA sequences and of species occurrence records. We defined the most significant climatic variables based on each species ecological realm using correlation matrices, and characterized the ecological niches and existing environmental conditions with ellipsoid models. We inferred their current and Last Glacial Maximum (LGM) ecological niche modellings (ENMs) and compared the results with the fossil record. We estimated the times of divergence (d‐loop sequences) of lineages and applied a phyloclimatespace approach to discern the phylogeographical patterns along each species’ ecological space. Results Ecological niche modelling showed wider niches for U. thibetanus and U. americanus encompassing higher temperature and precipitation, while U. arctos and U. maritimus showed an opposite pattern. LGM models were consistent with the fossil record, predicting 55%–89% of the fossil occurrences (within their suitability areas). The phyloclimatespace revealed different degrees of environmental signal in the lineages’ phylogeographical patterns and ecological trajectories associated with LGM climatic conditions. Results indicated habitat tracking and ecological expansion since the LGM towards more extreme precipitation and temperature conditions for three species, except U. maritimus that showed ecological niche reduction. Main Conclusions Incorporating fossil information from the LGM improved our characterization and interpretation of ecological models, by enabling definition of the limits of the climatic conditions explored by the species in the past. Our approach also provided insights about the existing set of environmental conditions shaping the ecological niche divergence of Ursus bears. We were able to depict key features of the lineages’ evolutionary history, ecology and distribution, revealing the dynamics of niche occupation and the environmental signal on the phylogeographical patterns of Ursus.

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“…However, numerous molecular studies have revealed that the mitochondrial tree may deviate from the species tree. Indeed, the maternal inheritance of the mtDNA genome can be misleading for species delimitation in mammals, because females and males have usually different dispersal behaviours (female philopatry versus male dispersal) [5,6], and because interspecific hybrid females are generally fertile, whereas hybrid males are often sterile (Haldane's rule), facilitating mitochondrial introgression between closely related species [7][8][9]. To overcome these limitations, most recent taxonomic studies dealing with the delimitation between cryptic mammal species have focused on multi-locus datasets [10][11][12], as the use of multiple independent DNA markers has been shown to provide a strong and reliable signal for deciphering relationships among closely related taxa [13,14].…”

Section: Introductionmentioning

confidence: 99%

A comparative approach for species delimitation based on multiple methods of multi-locus DNA sequence analysis: A case study of the genus Giraffa (Mammalia, Cetartiodactyla)

Petzold

Hassanin

2020

PLoS ONE

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Molecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described. In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping, haplowebs and conspecificity matrix) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genus Giraffa. Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizes G. camelopardalis sensu strico A, G. giraffa, and G. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51%) and mitochondrial sequences (3-4%), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such as G. peralta, G. reticulata, G. thornicrofti or G. tippelskirchi sensu stricto, do not exhibit any ES in the nuclear genes. A robust mito-nuclear conflict was found for the position and monophyly of G. giraffa and G. tippelskirchi, which is interpreted as the result of a mitochondrial introgression from Masai to southeastern giraffe during the Pleistocene and nuclear gene flow mediated by male dispersal between southern populations (subspecies G. g. giraffa and G. g. angolensis).

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The role of Pleistocene glaciations in shaping the evolution of polar and brown bears. Evidence from a critical review of mitochondrial and nuclear genome analyses

Cited by 53 publications

References 44 publications

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

Genomic consequences of a recent three‐way admixture in supplemented wild brown trout populations revealed by local ancestry tracts

A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species

A comparative approach for species delimitation based on multiple methods of multi-locus DNA sequence analysis: A case study of the genus Giraffa (Mammalia, Cetartiodactyla)

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