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Segawa T, Rey-Iglesia A, Lorenzen ED, Westbury MV. The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations. Proc Biol Sci 2024; 291:20232411. [PMID: 38264778 PMCID: PMC10806438 DOI: 10.1098/rspb.2023.2411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.
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Affiliation(s)
- Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi, Japan
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Utzeri VJ, Cilli E, Fontani F, Zoboli D, Orsini M, Ribani A, Latorre A, Lissovsky AA, Pillola GL, Bovo S, Gruppioni G, Luiselli D, Fontanesi L. Ancient DNA re-opens the question of the phylogenetic position of the Sardinian pika Prolagus sardus (Wagner, 1829), an extinct lagomorph. Sci Rep 2023; 13:13635. [PMID: 37604894 PMCID: PMC10442435 DOI: 10.1038/s41598-023-40746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Palaeogenomics is contributing to refine our understanding of many major evolutionary events at an unprecedented resolution, with relevant impacts in several fields, including phylogenetics of extinct species. Few extant and extinct animal species from Mediterranean regions have been characterised at the DNA level thus far. The Sardinian pika, Prolagus sardus (Wagner, 1829), was an iconic lagomorph species that populated Sardinia and Corsica and became extinct during the Holocene. There is a certain scientific debate on the phylogenetic assignment of the extinct genus Prolagus to the family Ochotonidae (one of the only two extant families of the order Lagomorpha) or to a separated family Prolagidae, or to the subfamily Prolaginae within the family Ochotonidae. In this study, we successfully reconstructed a portion of the mitogenome of a Sardinian pika dated to the Neolithic period and recovered from the Cabaddaris cave, an archaeological site in Sardinia. Our calibrated phylogeny may support the hypothesis that the genus Prolagus is an independent sister group to the family Ochotonidae that diverged from the Ochotona genus lineage about 30 million years ago. These results may contribute to refine the phylogenetic interpretation of the morphological peculiarities of the Prolagus genus already described by palaeontological studies.
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Affiliation(s)
- Valerio Joe Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy.
| | - Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Daniel Zoboli
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Massimiliano Orsini
- Laboratory of Microbial Ecology, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'università 10, 35120, Legnaro, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Adriana Latorre
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Andrey A Lissovsky
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Gian Luigi Pillola
- Department of Chemical and Geological Sciences, University of Cagliari, Cittadella Universitaria SS 554, 09042, Monserrato, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, 48121, Ravenna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127, Bologna, Italy.
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de Jong MJ, Niamir A, Wolf M, Kitchener AC, Lecomte N, Seryodkin IV, Fain SR, Hagen SB, Saarma U, Janke A. Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence. Commun Biol 2023; 6:153. [PMID: 36746982 PMCID: PMC9902616 DOI: 10.1038/s42003-023-04514-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.
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Affiliation(s)
- Menno J. de Jong
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany
| | - Aidin Niamir
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany
| | - Magnus Wolf
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany ,grid.7839.50000 0004 1936 9721Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany
| | - Andrew C. Kitchener
- grid.422302.50000 0001 0943 6159Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh, EH1 1JF UK ,grid.4305.20000 0004 1936 7988School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh, EH8 9XP UK
| | - Nicolas Lecomte
- grid.265686.90000 0001 2175 1792Canada Research Chair in Polar and Boreal Ecology, Department of Biology, University of Moncton, Moncton, New Brunswick E1H1R2 Canada
| | - Ivan V. Seryodkin
- grid.465394.90000 0004 0611 5319Pacific Geographical Institute of the Far Eastern Branch of the Russian Academy of Sciences, 7 Radio St., Vladivostok, 690041 Russia
| | - Steven R. Fain
- National Fish & Wildlife Forensic Laboratory, Ashland, OR USA
| | - Snorre B. Hagen
- grid.454322.60000 0004 4910 9859Norwegian Institute of Bioeconomy Research, Division of Environment and Natural Resources, Svanhovd, N-9925 Svanvik, Norway
| | - Urmas Saarma
- grid.10939.320000 0001 0943 7661Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409 Estonia
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, 60325 Germany ,grid.7839.50000 0004 1936 9721Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany ,grid.511284.b0000 0004 8004 5574LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany
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Boulygina E, Sharko F, Cheprasov M, Gladysheva-Azgari M, Slobodova N, Tsygankova S, Rastorguev S, Grigorieva L, Kopp M, Fernandes JMO, Novgorodov G, Boeskorov G, Protopopov A, Hwang WS, Tikhonov A, Nedoluzhko A. Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear ( Ursus arctos) Population during the Holocene. Genes (Basel) 2022; 13:1961. [PMID: 36360198 PMCID: PMC9689912 DOI: 10.3390/genes13111961] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 09/14/2023] Open
Abstract
Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.
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Affiliation(s)
- Eugenia Boulygina
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Fedor Sharko
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Maksim Cheprasov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Maria Gladysheva-Azgari
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Natalia Slobodova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Svetlana Tsygankova
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
| | - Sergey Rastorguev
- Kurchatov Center for Genomic Research, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia
- Limited Liability Company ELGENE, 109029 Moscow, Russia
| | - Lena Grigorieva
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Martina Kopp
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge M. O. Fernandes
- Genomics Division, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Gavril Novgorodov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
| | - Gennady Boeskorov
- Institute of Diamond and Precious Metals Geology, Siberian Branch of Russian 5 Academy of Sciences, 677007 Yakutsk, Russia
| | - Albert Protopopov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Academy of Sciences of Sakha (Yakutia), 677007 Yakutsk, Russia
| | - Woo-Suk Hwang
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- UAE Biotech Research Center, Abu Dhabi 30310, United Arab Emirates
| | - Alexei Tikhonov
- Laboratory of P.A. Lazarev Mammoth Museum of the Research Institute of Applied Ecology of the North, North-Eastern Federal University Named after M. K. Ammosov, 677000 Yakutsk, Russia
- Zoological Institute Russian Academy of Sciences, 190121 Saint-Petersburg, Russia
| | - Artem Nedoluzhko
- Limited Liability Company ELGENE, 109029 Moscow, Russia
- Paleogenomics Laboratory, European University at Saint Petersburg, 191187 Saint-Petersburg, Russia
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