Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China
Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and pa...
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| Veröffentlicht in: | Genes 2022-09, Vol.13 (10), p.1684 |
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| creator | Hou, Xindong Zhao, Jian Zhang, Hucai Preick, Michaela Hu, Jiaming Xiao, Bo Wang, Linying Deng, Miaoxuan Liu, Sizhao Chang, Fengqin Sheng, Guilian Lai, Xulong Hofreiter, Michael Yuan, Junxia |
| description | Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct. |
| doi_str_mv | 10.3390/genes13101684 |
| format | Article |
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Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes13101684</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>Analysis ; Bayesian analysis ; Bison ; Buffalo ; Endangered & extinct species ; Evolution ; Extinct animals ; Extinction ; Genetic aspects ; Genetic diversity ; Genetic structure ; Genomes ; Hybridization ; Laboratories ; Mitochondria ; Mitochondrial DNA ; Natural history ; Phylogenetics ; Pleistocene ; Population genetics ; Population structure ; Steppes</subject><ispartof>Genes, 2022-09, Vol.13 (10), p.1684</ispartof><rights>COPYRIGHT 2022 MDPI AG</rights><rights>2022 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/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 by the authors. 2022</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c459t-af232340ae931c8a4b02d67d4db6d883fd0db79e97d2169550fe8b7de259ede13</citedby><cites>FETCH-LOGICAL-c459t-af232340ae931c8a4b02d67d4db6d883fd0db79e97d2169550fe8b7de259ede13</cites><orcidid>0000-0003-2314-1650 ; 0000-0002-2640-923X ; 0000-0002-6932-587X ; 0000-0001-7733-2036 ; 0000-0003-0441-4705</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9602171/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9602171/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids></links><search><creatorcontrib>Hou, Xindong</creatorcontrib><creatorcontrib>Zhao, Jian</creatorcontrib><creatorcontrib>Zhang, Hucai</creatorcontrib><creatorcontrib>Preick, Michaela</creatorcontrib><creatorcontrib>Hu, Jiaming</creatorcontrib><creatorcontrib>Xiao, Bo</creatorcontrib><creatorcontrib>Wang, Linying</creatorcontrib><creatorcontrib>Deng, Miaoxuan</creatorcontrib><creatorcontrib>Liu, Sizhao</creatorcontrib><creatorcontrib>Chang, Fengqin</creatorcontrib><creatorcontrib>Sheng, Guilian</creatorcontrib><creatorcontrib>Lai, Xulong</creatorcontrib><creatorcontrib>Hofreiter, Michael</creatorcontrib><creatorcontrib>Yuan, Junxia</creatorcontrib><title>Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China</title><title>Genes</title><description>Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. 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Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.</description><subject>Analysis</subject><subject>Bayesian analysis</subject><subject>Bison</subject><subject>Buffalo</subject><subject>Endangered & extinct species</subject><subject>Evolution</subject><subject>Extinct animals</subject><subject>Extinction</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic structure</subject><subject>Genomes</subject><subject>Hybridization</subject><subject>Laboratories</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>Natural history</subject><subject>Phylogenetics</subject><subject>Pleistocene</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Steppes</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptkk1r3DAQhk1JoSHNMXdBL7k41adlXQrJkjSFpQ2lOQvZGu8qyNJGspf031dmQ9stlQ4zjJ55Z0ZMVV0QfMWYwh83ECATRjBpWv6mOqVYsppzKk7-8t9V5zk_4XI4phiL06p7MB5iSY4jZPQd9mA8MmgVx52HF3S7j36eXAwm_UT3Lk-x2DigtZkAPXhYIn2pjG5cjgG5gL7GNG3B5AlSQKutC-Z99XYwPsP5qz2rHu9uf6zu6_W3z19W1-u650JNtRkoo4xjA4qRvjW8w9Q20nLbNbZt2WCx7aQCJS0ljRICD9B20gIVCiwQdlZ9Ouju5m4EW9qakvF6l9xYutfROH38EtxWb-JeqwZTIheBy1eBFJ9nyJMeXe7BexMgzllTSZWgLRG4oB_-QZ_inEIZb6FaLhuJ-R9qUz5ZuzDEUrdfRPW15EJSdqCu_kOVa2F0fQwwuBI_SqgPCX2KOScYfs9IsF6WQR8tA_sFfWmoDQ</recordid><startdate>20220920</startdate><enddate>20220920</enddate><creator>Hou, Xindong</creator><creator>Zhao, Jian</creator><creator>Zhang, Hucai</creator><creator>Preick, Michaela</creator><creator>Hu, Jiaming</creator><creator>Xiao, Bo</creator><creator>Wang, Linying</creator><creator>Deng, Miaoxuan</creator><creator>Liu, Sizhao</creator><creator>Chang, Fengqin</creator><creator>Sheng, Guilian</creator><creator>Lai, Xulong</creator><creator>Hofreiter, Michael</creator><creator>Yuan, Junxia</creator><general>MDPI AG</general><general>MDPI</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-2314-1650</orcidid><orcidid>https://orcid.org/0000-0002-2640-923X</orcidid><orcidid>https://orcid.org/0000-0002-6932-587X</orcidid><orcidid>https://orcid.org/0000-0001-7733-2036</orcidid><orcidid>https://orcid.org/0000-0003-0441-4705</orcidid></search><sort><creationdate>20220920</creationdate><title>Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China</title><author>Hou, Xindong ; 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Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.</abstract><cop>Basel</cop><pub>MDPI AG</pub><doi>10.3390/genes13101684</doi><orcidid>https://orcid.org/0000-0003-2314-1650</orcidid><orcidid>https://orcid.org/0000-0002-2640-923X</orcidid><orcidid>https://orcid.org/0000-0002-6932-587X</orcidid><orcidid>https://orcid.org/0000-0001-7733-2036</orcidid><orcidid>https://orcid.org/0000-0003-0441-4705</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Bayesian analysis Bison Buffalo Endangered & extinct species Evolution Extinct animals Extinction Genetic aspects Genetic diversity Genetic structure Genomes Hybridization Laboratories Mitochondria Mitochondrial DNA Natural history Phylogenetics Pleistocene Population genetics Population structure Steppes |
| title | Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China |
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