Loading…
Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards
Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controvers...
Saved in:
| Published in: | Molecular ecology 2015-11, Vol.24 (21), p.5364-5378 |
|---|---|
| Main Authors: | , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243 |
|---|---|
| cites | cdi_FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243 |
| container_end_page | 5378 |
| container_issue | 21 |
| container_start_page | 5364 |
| container_title | Molecular ecology |
| container_volume | 24 |
| creator | Lavretsky, Philip Dacosta, Jeffrey M Hernández‐Baños, Blanca E Engilis, Andrew, Jr Sorenson, Michael D Peters, Jeffrey L |
| description | Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to |
| doi_str_mv | 10.1111/mec.13402 |
| format | article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1761077336</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1735928416</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243</originalsourceid><addsrcrecordid>eNqNkU1v1DAQhiMEokvhwB8AS1zgkNbjjyR7REspSG057FatuFiOM966TeLFTujuv8dt2h6QkJjLSKNnHs3ozbK3QA8g1WGH5gC4oOxZNgNeyJzNxeXzbEbnBcuBVnwvexXjNaXAmZQvsz1WCBCCl7Nsu9ygcXpwvidr7H3nTCS6b4gmwbdIrA9kuELyk5ir4DsffYfE9fcz1KHdkTjoNUbiLWncbwxJYpDUONwi9uQUt87onjSjuZm8nW5bHZr4OnthdRvxzUPfz86_Hq0W3_KTH8ffF59PciNExXJZ0LqSHERdlFZaSaXmAirGK2BQALXQaCZ5wymzCI3VAmw9Z2kMrKyZ4PvZx8m7Cf7XiHFQnYsG0xE9-jEqKJOlLDkv_gPlcs4qAXfoh7_Qaz-GPj2SKJZ0IBhN1KeJMsHHGNCqTXCdDjsFVN0lp1Jy6j65xL57MI51h80T-RhVAg4n4Na1uPu3SZ0eLR6V-bTh4oDbpw0dblRR8lKqi7NjJb_I1dnlaqkuEv9-4q32Sq-Di-p8yShIShkDNi_5H11BuJ8</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1727731420</pqid></control><display><type>article</type><title>Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards</title><source>Wiley</source><creator>Lavretsky, Philip ; Dacosta, Jeffrey M ; Hernández‐Baños, Blanca E ; Engilis, Andrew, Jr ; Sorenson, Michael D ; Peters, Jeffrey L</creator><creatorcontrib>Lavretsky, Philip ; Dacosta, Jeffrey M ; Hernández‐Baños, Blanca E ; Engilis, Andrew, Jr ; Sorenson, Michael D ; Peters, Jeffrey L</creatorcontrib><description>Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.</description><identifier>ISSN: 0962-1083</identifier><identifier>EISSN: 1365-294X</identifier><identifier>DOI: 10.1111/mec.13402</identifier><identifier>PMID: 26414437</identifier><language>eng</language><publisher>England: Blackwell Scientific Publications</publisher><subject>Anas platyrhynchos ; Animals ; anseriformes ; Chromosomes ; DNA, Mitochondrial - genetics ; ducks ; Ducks - classification ; Ducks - genetics ; elevated Z divergence ; Evolution, Molecular ; Genetic diversity ; Genetic Speciation ; genetic variation ; Genetics, Population ; Genomics ; genotyping by sequencing ; hybridization ; loci ; marker discordance ; Mexico ; Mitochondrial DNA ; Models, Genetic ; Molecular Sequence Data ; phylogeography ; Population Density ; population size ; Sequence Analysis, DNA ; Sex Chromosomes - genetics ; speciation ; taxonomy ; United States ; Z chromosome</subject><ispartof>Molecular ecology, 2015-11, Vol.24 (21), p.5364-5378</ispartof><rights>2015 John Wiley & Sons Ltd</rights><rights>2015 John Wiley & Sons Ltd.</rights><rights>Copyright © 2015 John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243</citedby><cites>FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,783,787,27936,27937</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26414437$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lavretsky, Philip</creatorcontrib><creatorcontrib>Dacosta, Jeffrey M</creatorcontrib><creatorcontrib>Hernández‐Baños, Blanca E</creatorcontrib><creatorcontrib>Engilis, Andrew, Jr</creatorcontrib><creatorcontrib>Sorenson, Michael D</creatorcontrib><creatorcontrib>Peters, Jeffrey L</creatorcontrib><title>Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards</title><title>Molecular ecology</title><addtitle>Mol Ecol</addtitle><description>Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.</description><subject>Anas platyrhynchos</subject><subject>Animals</subject><subject>anseriformes</subject><subject>Chromosomes</subject><subject>DNA, Mitochondrial - genetics</subject><subject>ducks</subject><subject>Ducks - classification</subject><subject>Ducks - genetics</subject><subject>elevated Z divergence</subject><subject>Evolution, Molecular</subject><subject>Genetic diversity</subject><subject>Genetic Speciation</subject><subject>genetic variation</subject><subject>Genetics, Population</subject><subject>Genomics</subject><subject>genotyping by sequencing</subject><subject>hybridization</subject><subject>loci</subject><subject>marker discordance</subject><subject>Mexico</subject><subject>Mitochondrial DNA</subject><subject>Models, Genetic</subject><subject>Molecular Sequence Data</subject><subject>phylogeography</subject><subject>Population Density</subject><subject>population size</subject><subject>Sequence Analysis, DNA</subject><subject>Sex Chromosomes - genetics</subject><subject>speciation</subject><subject>taxonomy</subject><subject>United States</subject><subject>Z chromosome</subject><issn>0962-1083</issn><issn>1365-294X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqNkU1v1DAQhiMEokvhwB8AS1zgkNbjjyR7REspSG057FatuFiOM966TeLFTujuv8dt2h6QkJjLSKNnHs3ozbK3QA8g1WGH5gC4oOxZNgNeyJzNxeXzbEbnBcuBVnwvexXjNaXAmZQvsz1WCBCCl7Nsu9ygcXpwvidr7H3nTCS6b4gmwbdIrA9kuELyk5ir4DsffYfE9fcz1KHdkTjoNUbiLWncbwxJYpDUONwi9uQUt87onjSjuZm8nW5bHZr4OnthdRvxzUPfz86_Hq0W3_KTH8ffF59PciNExXJZ0LqSHERdlFZaSaXmAirGK2BQALXQaCZ5wymzCI3VAmw9Z2kMrKyZ4PvZx8m7Cf7XiHFQnYsG0xE9-jEqKJOlLDkv_gPlcs4qAXfoh7_Qaz-GPj2SKJZ0IBhN1KeJMsHHGNCqTXCdDjsFVN0lp1Jy6j65xL57MI51h80T-RhVAg4n4Na1uPu3SZ0eLR6V-bTh4oDbpw0dblRR8lKqi7NjJb_I1dnlaqkuEv9-4q32Sq-Di-p8yShIShkDNi_5H11BuJ8</recordid><startdate>201511</startdate><enddate>201511</enddate><creator>Lavretsky, Philip</creator><creator>Dacosta, Jeffrey M</creator><creator>Hernández‐Baños, Blanca E</creator><creator>Engilis, Andrew, Jr</creator><creator>Sorenson, Michael D</creator><creator>Peters, Jeffrey L</creator><general>Blackwell Scientific Publications</general><general>Blackwell Publishing Ltd</general><scope>FBQ</scope><scope>BSCLL</scope><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>7SN</scope><scope>7SS</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201511</creationdate><title>Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards</title><author>Lavretsky, Philip ; Dacosta, Jeffrey M ; Hernández‐Baños, Blanca E ; Engilis, Andrew, Jr ; Sorenson, Michael D ; Peters, Jeffrey L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Anas platyrhynchos</topic><topic>Animals</topic><topic>anseriformes</topic><topic>Chromosomes</topic><topic>DNA, Mitochondrial - genetics</topic><topic>ducks</topic><topic>Ducks - classification</topic><topic>Ducks - genetics</topic><topic>elevated Z divergence</topic><topic>Evolution, Molecular</topic><topic>Genetic diversity</topic><topic>Genetic Speciation</topic><topic>genetic variation</topic><topic>Genetics, Population</topic><topic>Genomics</topic><topic>genotyping by sequencing</topic><topic>hybridization</topic><topic>loci</topic><topic>marker discordance</topic><topic>Mexico</topic><topic>Mitochondrial DNA</topic><topic>Models, Genetic</topic><topic>Molecular Sequence Data</topic><topic>phylogeography</topic><topic>Population Density</topic><topic>population size</topic><topic>Sequence Analysis, DNA</topic><topic>Sex Chromosomes - genetics</topic><topic>speciation</topic><topic>taxonomy</topic><topic>United States</topic><topic>Z chromosome</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lavretsky, Philip</creatorcontrib><creatorcontrib>Dacosta, Jeffrey M</creatorcontrib><creatorcontrib>Hernández‐Baños, Blanca E</creatorcontrib><creatorcontrib>Engilis, Andrew, Jr</creatorcontrib><creatorcontrib>Sorenson, Michael D</creatorcontrib><creatorcontrib>Peters, Jeffrey L</creatorcontrib><collection>AGRIS</collection><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular ecology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lavretsky, Philip</au><au>Dacosta, Jeffrey M</au><au>Hernández‐Baños, Blanca E</au><au>Engilis, Andrew, Jr</au><au>Sorenson, Michael D</au><au>Peters, Jeffrey L</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards</atitle><jtitle>Molecular ecology</jtitle><addtitle>Mol Ecol</addtitle><date>2015-11</date><risdate>2015</risdate><volume>24</volume><issue>21</issue><spage>5364</spage><epage>5378</epage><pages>5364-5378</pages><issn>0962-1083</issn><eissn>1365-294X</eissn><abstract>Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.</abstract><cop>England</cop><pub>Blackwell Scientific Publications</pub><pmid>26414437</pmid><doi>10.1111/mec.13402</doi><tpages>15</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0962-1083 |
| ispartof | Molecular ecology, 2015-11, Vol.24 (21), p.5364-5378 |
| issn | 0962-1083 1365-294X |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1761077336 |
| source | Wiley |
| subjects | Anas platyrhynchos Animals anseriformes Chromosomes DNA, Mitochondrial - genetics ducks Ducks - classification Ducks - genetics elevated Z divergence Evolution, Molecular Genetic diversity Genetic Speciation genetic variation Genetics, Population Genomics genotyping by sequencing hybridization loci marker discordance Mexico Mitochondrial DNA Models, Genetic Molecular Sequence Data phylogeography Population Density population size Sequence Analysis, DNA Sex Chromosomes - genetics speciation taxonomy United States Z chromosome |
| title | Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-11-13T18%3A02%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Speciation%20genomics%20and%20a%20role%20for%20the%20Z%20chromosome%20in%20the%20early%20stages%20of%20divergence%20between%20Mexican%20ducks%20and%20mallards&rft.jtitle=Molecular%20ecology&rft.au=Lavretsky,%20Philip&rft.date=2015-11&rft.volume=24&rft.issue=21&rft.spage=5364&rft.epage=5378&rft.pages=5364-5378&rft.issn=0962-1083&rft.eissn=1365-294X&rft_id=info:doi/10.1111/mec.13402&rft_dat=%3Cproquest_cross%3E1735928416%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c4482-560b85314b67f5f505a3418238121610f1da253d302fe1dfa41fb92f1d127b243%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1727731420&rft_id=info:pmid/26414437&rfr_iscdi=true |