Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China
[Display omitted] •A potential new subgenus represented by the O. syrinx species complex.•Uncover three potential new species.•Mitochondrial introgression was observed from O. cansus to O. curzoniae. The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in...
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| Veröffentlicht in: | Molecular phylogenetics and evolution 2017-02, Vol.107, p.239-245 |
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| creator | Koju, Narayan Prasad He, Kai Chalise, Mukesh Kumar Ray, Chris Chen, Zhongzheng Zhang, Bin Wan, Tao Chen, Shunde Jiang, Xuelong |
| description | [Display omitted]
•A potential new subgenus represented by the O. syrinx species complex.•Uncover three potential new species.•Mitochondrial introgression was observed from O. cansus to O. curzoniae.
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the “sky-island” mountains of southwest China. |
| doi_str_mv | 10.1016/j.ympev.2016.11.005 |
| format | Article |
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•A potential new subgenus represented by the O. syrinx species complex.•Uncover three potential new species.•Mitochondrial introgression was observed from O. cansus to O. curzoniae.
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the “sky-island” mountains of southwest China.</description><identifier>ISSN: 1055-7903</identifier><identifier>EISSN: 1095-9513</identifier><identifier>DOI: 10.1016/j.ympev.2016.11.005</identifier><identifier>PMID: 27838310</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Animals ; Base Sequence ; Bayes Theorem ; China ; Cryptic species ; Gene Flow ; Genetic Loci ; Genetic Variation ; Geography ; Lagomorpha - classification ; Lagomorpha - genetics ; Mitochondrial introgression ; Multilocus species delimitation ; Ochotona ; Phylogeny ; Species Specificity</subject><ispartof>Molecular phylogenetics and evolution, 2017-02, Vol.107, p.239-245</ispartof><rights>2016 Elsevier Inc.</rights><rights>Copyright © 2016 Elsevier Inc. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c359t-a8658f436ae10b65a0edaa54db5a8c9e6d458e16a863fa635005ec9601bdd8783</citedby><cites>FETCH-LOGICAL-c359t-a8658f436ae10b65a0edaa54db5a8c9e6d458e16a863fa635005ec9601bdd8783</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S1055790316303293$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27838310$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Koju, Narayan Prasad</creatorcontrib><creatorcontrib>He, Kai</creatorcontrib><creatorcontrib>Chalise, Mukesh Kumar</creatorcontrib><creatorcontrib>Ray, Chris</creatorcontrib><creatorcontrib>Chen, Zhongzheng</creatorcontrib><creatorcontrib>Zhang, Bin</creatorcontrib><creatorcontrib>Wan, Tao</creatorcontrib><creatorcontrib>Chen, Shunde</creatorcontrib><creatorcontrib>Jiang, Xuelong</creatorcontrib><title>Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China</title><title>Molecular phylogenetics and evolution</title><addtitle>Mol Phylogenet Evol</addtitle><description>[Display omitted]
•A potential new subgenus represented by the O. syrinx species complex.•Uncover three potential new species.•Mitochondrial introgression was observed from O. cansus to O. curzoniae.
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the “sky-island” mountains of southwest China.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Bayes Theorem</subject><subject>China</subject><subject>Cryptic species</subject><subject>Gene Flow</subject><subject>Genetic Loci</subject><subject>Genetic Variation</subject><subject>Geography</subject><subject>Lagomorpha - classification</subject><subject>Lagomorpha - genetics</subject><subject>Mitochondrial introgression</subject><subject>Multilocus species delimitation</subject><subject>Ochotona</subject><subject>Phylogeny</subject><subject>Species Specificity</subject><issn>1055-7903</issn><issn>1095-9513</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UcFu1DAUtBAVLYUvQEI-lkNSv_U6TQ4c0KpQpKJeytl6a7-wXhI72M5W-wN8d73dliMn25p5bzwzjH0AUYOA5nJb78eJdvWiPGqAWgj1ip2B6FTVKZCvD3elqqtOyFP2NqWtEACqU2_Y6eKqla0Eccb-_piH7IZg5sRxmmJAs6HEI-0IBz57S5FSdiNmsjxNZFxBrdtRTC7vOXrLnc8Uqyesd4b_Ik-8H8JDAfjkfmPiF3dmE3Lw-In3MYw8hTlvHspeip6vNs7jO3bS45Do_fN5zn5-vb5f3VS3d9--r77cVkaqLlfYNqrtl7JBArFuFAqyiGpp1wpb01Fjl6olaApP9thIVTIh0zUC1ta2xfQ5uzjuLU7_zOUHenTJ0DCgpzAnDa3sSkiwWBSqPFJNDClF6vUUSw5xr0HoQwF6q58K0IcCNIAuYmXq47PAvB7J_pt5SbwQPh8JVGzuHEWdSqbekHWRTNY2uP8KPAJ3bJt0</recordid><startdate>201702</startdate><enddate>201702</enddate><creator>Koju, Narayan Prasad</creator><creator>He, Kai</creator><creator>Chalise, Mukesh Kumar</creator><creator>Ray, Chris</creator><creator>Chen, Zhongzheng</creator><creator>Zhang, Bin</creator><creator>Wan, Tao</creator><creator>Chen, Shunde</creator><creator>Jiang, Xuelong</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201702</creationdate><title>Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China</title><author>Koju, Narayan Prasad ; He, Kai ; Chalise, Mukesh Kumar ; Ray, Chris ; Chen, Zhongzheng ; Zhang, Bin ; Wan, Tao ; Chen, Shunde ; Jiang, Xuelong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c359t-a8658f436ae10b65a0edaa54db5a8c9e6d458e16a863fa635005ec9601bdd8783</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Bayes Theorem</topic><topic>China</topic><topic>Cryptic species</topic><topic>Gene Flow</topic><topic>Genetic Loci</topic><topic>Genetic Variation</topic><topic>Geography</topic><topic>Lagomorpha - classification</topic><topic>Lagomorpha - genetics</topic><topic>Mitochondrial introgression</topic><topic>Multilocus species delimitation</topic><topic>Ochotona</topic><topic>Phylogeny</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Koju, Narayan Prasad</creatorcontrib><creatorcontrib>He, Kai</creatorcontrib><creatorcontrib>Chalise, Mukesh Kumar</creatorcontrib><creatorcontrib>Ray, Chris</creatorcontrib><creatorcontrib>Chen, Zhongzheng</creatorcontrib><creatorcontrib>Zhang, Bin</creatorcontrib><creatorcontrib>Wan, Tao</creatorcontrib><creatorcontrib>Chen, Shunde</creatorcontrib><creatorcontrib>Jiang, Xuelong</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular phylogenetics and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Koju, Narayan Prasad</au><au>He, Kai</au><au>Chalise, Mukesh Kumar</au><au>Ray, Chris</au><au>Chen, Zhongzheng</au><au>Zhang, Bin</au><au>Wan, Tao</au><au>Chen, Shunde</au><au>Jiang, Xuelong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China</atitle><jtitle>Molecular phylogenetics and evolution</jtitle><addtitle>Mol Phylogenet Evol</addtitle><date>2017-02</date><risdate>2017</risdate><volume>107</volume><spage>239</spage><epage>245</epage><pages>239-245</pages><issn>1055-7903</issn><eissn>1095-9513</eissn><abstract>[Display omitted]
•A potential new subgenus represented by the O. syrinx species complex.•Uncover three potential new species.•Mitochondrial introgression was observed from O. cansus to O. curzoniae.
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the “sky-island” mountains of southwest China.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>27838310</pmid><doi>10.1016/j.ympev.2016.11.005</doi><tpages>7</tpages></addata></record> |
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| subjects | Animals Base Sequence Bayes Theorem China Cryptic species Gene Flow Genetic Loci Genetic Variation Geography Lagomorpha - classification Lagomorpha - genetics Mitochondrial introgression Multilocus species delimitation Ochotona Phylogeny Species Specificity |
| title | Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China |
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