Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal
Pusa sibirica, 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 div...
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2023
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Online Access: | https://curis.ku.dk/portal/da/publications/chromosomelength-assembly-of-the-baikal-seal-pusa-sibirica-genome-reveals-a-historically-large-population-prior-to-isolation-in-lake-baikal(ba464d40-71d7-41ce-a0b2-944641d2ec6e).html https://doi.org/10.3390/genes14030619 https://curis.ku.dk/ws/files/341476320/genes_14_00619_v2.pdf |
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ftcopenhagenunip:oai:pure.atira.dk:publications/ba464d40-71d7-41ce-a0b2-944641d2ec6e 2024-06-09T07:44:12+00:00 Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal 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 OBrien, Stephen J. Graphodatsky, Alexander Koepfli, Klaus-Peter Kliver, Sergei 2023 application/pdf https://curis.ku.dk/portal/da/publications/chromosomelength-assembly-of-the-baikal-seal-pusa-sibirica-genome-reveals-a-historically-large-population-prior-to-isolation-in-lake-baikal(ba464d40-71d7-41ce-a0b2-944641d2ec6e).html https://doi.org/10.3390/genes14030619 https://curis.ku.dk/ws/files/341476320/genes_14_00619_v2.pdf eng eng info:eu-repo/semantics/openAccess Yakupova , A , Tomarovsky , A , Totikov , A , Beklemisheva , V , Logacheva , M , Perelman , P L , Komissarov , A , Dobrynin , P , Krasheninnikova , K , Tamazian , G , Serdyukova , N A , Rayko , M , Bulyonkova , T , Cherkasov , N , Pylev , V , Peterfeld , V , Penin , A , Balanovska , E , Lapidus , A , DNA Zoo Consortium , OBrien , S J , Graphodatsky , A , Koepfli , K-P & Kliver , S 2023 , ' Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal ' , Genes , vol. 14 , no. 3 , 619 . https://doi.org/10.3390/genes14030619 conservation demography heterozygosity pinnipeds Pusa sibirica article 2023 ftcopenhagenunip https://doi.org/10.3390/genes14030619 2024-05-16T11:29:28Z Pusa sibirica, 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. Article in Journal/Newspaper Arctic Arctic Ocean Sibirica University of Copenhagen: Research Arctic Arctic Ocean Genes 14 3 619 |
institution |
Open Polar |
collection |
University of Copenhagen: Research |
op_collection_id |
ftcopenhagenunip |
language |
English |
topic |
conservation demography heterozygosity pinnipeds Pusa sibirica |
spellingShingle |
conservation demography heterozygosity pinnipeds Pusa sibirica 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 OBrien, Stephen J. Graphodatsky, Alexander Koepfli, Klaus-Peter Kliver, Sergei Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
topic_facet |
conservation demography heterozygosity pinnipeds Pusa sibirica |
description |
Pusa sibirica, 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. |
format |
Article in Journal/Newspaper |
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 OBrien, Stephen J. Graphodatsky, Alexander Koepfli, Klaus-Peter Kliver, Sergei |
author_facet |
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 OBrien, Stephen J. Graphodatsky, Alexander Koepfli, Klaus-Peter Kliver, Sergei |
author_sort |
Yakupova, Aliya |
title |
Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
title_short |
Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
title_full |
Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
title_fullStr |
Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
title_full_unstemmed |
Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal |
title_sort |
chromosome-length assembly of the baikal seal ( pusa sibirica ) genome reveals a historically large population prior to isolation in lake baikal |
publishDate |
2023 |
url |
https://curis.ku.dk/portal/da/publications/chromosomelength-assembly-of-the-baikal-seal-pusa-sibirica-genome-reveals-a-historically-large-population-prior-to-isolation-in-lake-baikal(ba464d40-71d7-41ce-a0b2-944641d2ec6e).html https://doi.org/10.3390/genes14030619 https://curis.ku.dk/ws/files/341476320/genes_14_00619_v2.pdf |
geographic |
Arctic Arctic Ocean |
geographic_facet |
Arctic Arctic Ocean |
genre |
Arctic Arctic Ocean Sibirica |
genre_facet |
Arctic Arctic Ocean Sibirica |
op_source |
Yakupova , A , Tomarovsky , A , Totikov , A , Beklemisheva , V , Logacheva , M , Perelman , P L , Komissarov , A , Dobrynin , P , Krasheninnikova , K , Tamazian , G , Serdyukova , N A , Rayko , M , Bulyonkova , T , Cherkasov , N , Pylev , V , Peterfeld , V , Penin , A , Balanovska , E , Lapidus , A , DNA Zoo Consortium , OBrien , S J , Graphodatsky , A , Koepfli , K-P & Kliver , S 2023 , ' Chromosome-Length Assembly of the Baikal Seal ( Pusa sibirica ) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal ' , Genes , vol. 14 , no. 3 , 619 . https://doi.org/10.3390/genes14030619 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3390/genes14030619 |
container_title |
Genes |
container_volume |
14 |
container_issue |
3 |
container_start_page |
619 |
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1801372993661698048 |