Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal
, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of thi...
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Veröffentlicht in: | Genes 2023-02, Vol.14 (3), p.619 |
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creator | Yakupova, Aliya Tomarovsky, Andrey Totikov, Azamat Beklemisheva, Violetta Logacheva, Maria Perelman, Polina L Komissarov, Aleksey Dobrynin, Pavel Krasheninnikova, Ksenia Tamazian, Gaik Serdyukova, Natalia A Rayko, Mike Bulyonkova, Tatiana Cherkasov, Nikolay Pylev, Vladimir Peterfeld, Vladimir Penin, Aleksey Balanovska, Elena Lapidus, Alla Dna Zoo Consortium OBrien, Stephen J Graphodatsky, Alexander Koepfli, Klaus-Peter Kliver, Sergei |
description | , the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions. |
doi_str_mv | 10.3390/genes14030619 |
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The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes14030619</identifier><identifier>PMID: 36980891</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Analysis ; Animals ; Chromosome 6 ; Chromosomes ; Demography ; Environmental aspects ; Environmental conditions ; Females ; Fisheries ; Fishing ; Genetic diversity ; Genomes ; Genomics ; Heterozygosity ; Karyotype ; Karyotypes ; Lakes ; Marine mammals ; Mitochondrial DNA ; Phylogenetics ; Population ; Population decline ; Pusa sibirica ; Seals, Earless - genetics ; Single-nucleotide polymorphism ; Species</subject><ispartof>Genes, 2023-02, Vol.14 (3), p.619</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). 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The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.</description><subject>Analysis</subject><subject>Animals</subject><subject>Chromosome 6</subject><subject>Chromosomes</subject><subject>Demography</subject><subject>Environmental aspects</subject><subject>Environmental conditions</subject><subject>Females</subject><subject>Fisheries</subject><subject>Fishing</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Heterozygosity</subject><subject>Karyotype</subject><subject>Karyotypes</subject><subject>Lakes</subject><subject>Marine mammals</subject><subject>Mitochondrial DNA</subject><subject>Phylogenetics</subject><subject>Population</subject><subject>Population decline</subject><subject>Pusa sibirica</subject><subject>Seals, Earless - genetics</subject><subject>Single-nucleotide 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Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal</title><author>Yakupova, Aliya ; Tomarovsky, Andrey ; Totikov, Azamat ; Beklemisheva, Violetta ; Logacheva, Maria ; Perelman, Polina L ; Komissarov, Aleksey ; Dobrynin, Pavel ; Krasheninnikova, Ksenia ; Tamazian, Gaik ; Serdyukova, Natalia A ; Rayko, Mike ; Bulyonkova, Tatiana ; Cherkasov, Nikolay ; Pylev, Vladimir ; Peterfeld, Vladimir ; Penin, Aleksey ; Balanovska, Elena ; Lapidus, Alla ; Dna Zoo Consortium ; OBrien, Stephen J ; Graphodatsky, Alexander ; Koepfli, Klaus-Peter ; Kliver, Sergei</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c400t-62c8df5fecbb766267111ca0cc7a7cd35cd3a8a4b13b872013237e655941e3e83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Analysis</topic><topic>Animals</topic><topic>Chromosome 6</topic><topic>Chromosomes</topic><topic>Demography</topic><topic>Environmental aspects</topic><topic>Environmental conditions</topic><topic>Females</topic><topic>Fisheries</topic><topic>Fishing</topic><topic>Genetic diversity</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Heterozygosity</topic><topic>Karyotype</topic><topic>Karyotypes</topic><topic>Lakes</topic><topic>Marine mammals</topic><topic>Mitochondrial DNA</topic><topic>Phylogenetics</topic><topic>Population</topic><topic>Population decline</topic><topic>Pusa sibirica</topic><topic>Seals, Earless - genetics</topic><topic>Single-nucleotide polymorphism</topic><topic>Species</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yakupova, Aliya</creatorcontrib><creatorcontrib>Tomarovsky, Andrey</creatorcontrib><creatorcontrib>Totikov, Azamat</creatorcontrib><creatorcontrib>Beklemisheva, Violetta</creatorcontrib><creatorcontrib>Logacheva, 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Baikal</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2023-02-28</date><risdate>2023</risdate><volume>14</volume><issue>3</issue><spage>619</spage><pages>619-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>36980891</pmid><doi>10.3390/genes14030619</doi><orcidid>https://orcid.org/0000-0001-9541-8319</orcidid><orcidid>https://orcid.org/0000-0003-1236-631X</orcidid><orcidid>https://orcid.org/0000-0001-7281-0676</orcidid><orcidid>https://orcid.org/0000-0002-3882-8300</orcidid><orcidid>https://orcid.org/0000-0003-1486-0864</orcidid><orcidid>https://orcid.org/0000-0001-6981-7316</orcidid><orcidid>https://orcid.org/0000-0002-9122-4143</orcidid><orcidid>https://orcid.org/0000-0002-8282-1085</orcidid><orcidid>https://orcid.org/0000-0002-0982-5100</orcidid><orcidid>https://orcid.org/0000-0002-2931-1123</orcidid><orcidid>https://orcid.org/0000-0003-0427-8731</orcidid><oa>free_for_read</oa></addata></record> |
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source | MDPI - Multidisciplinary Digital Publishing Institute; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access |
subjects | Analysis Animals Chromosome 6 Chromosomes Demography Environmental aspects Environmental conditions Females Fisheries Fishing Genetic diversity Genomes Genomics Heterozygosity Karyotype Karyotypes Lakes Marine mammals Mitochondrial DNA Phylogenetics Population Population decline Pusa sibirica Seals, Earless - genetics Single-nucleotide polymorphism Species |
title | Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-19T15%3A45%3A21IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Chromosome-Length%20Assembly%20of%20the%20Baikal%20Seal%20(%20Pusa%20sibirica%20)%20Genome%20Reveals%20a%20Historically%20Large%20Population%20Prior%20to%20Isolation%20in%20Lake%20Baikal&rft.jtitle=Genes&rft.au=Yakupova,%20Aliya&rft.aucorp=DNA%20Zoo%20Consortium&rft.date=2023-02-28&rft.volume=14&rft.issue=3&rft.spage=619&rft.pages=619-&rft.issn=2073-4425&rft.eissn=2073-4425&rft_id=info:doi/10.3390/genes14030619&rft_dat=%3Cgale_pubme%3EA743765279%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2794653260&rft_id=info:pmid/36980891&rft_galeid=A743765279&rfr_iscdi=true |