Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened"...
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| creator | Pazmiño, Diana A Maes, Gregory E Green, Madeline E Simpfendorfer, Colin A Hoyos-Padilla, E Mauricio Duffy, Clinton J A Meyer, Carl G Kerwath, Sven E Salinas-de-León, Pelayo van Herwerden, Lynne |
| description | The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ
defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F
= 0.023-0.035), mtDNA exhibited more divergence (Φ
= 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales. |
| doi_str_mv | 10.1038/s41437-017-0025-2 |
| format | Article |
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defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F
= 0.023-0.035), mtDNA exhibited more divergence (Φ
= 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.</description><identifier>ISSN: 0018-067X</identifier><identifier>EISSN: 1365-2540</identifier><identifier>DOI: 10.1038/s41437-017-0025-2</identifier><identifier>PMID: 29321624</identifier><language>eng</language><publisher>England: Springer Nature B.V</publisher><subject>Animals ; Biodiversity ; Carcharhinus galapagensis ; Conservation ; Conservation of Natural Resources ; Data processing ; Demographics ; Demography ; Divergence ; DNA, Mitochondrial - genetics ; Ecuador ; Female ; Fish conservation ; Gene sequencing ; Genetic diversity ; Genetic Variation ; Genetics, Population ; Genomes ; Genotype ; Habitat utilization ; Male ; Mitochondria ; Mitochondrial DNA ; Pacific Ocean ; Phylogeny ; Polymorphism ; Polymorphism, Single Nucleotide - genetics ; Population ; Population genetics ; Population structure ; Populations ; Sharks - genetics ; Single-nucleotide polymorphism ; Wildlife conservation</subject><ispartof>Heredity, 2018-05, Vol.120 (5), p.407-421</ispartof><rights>Copyright Nature Publishing Group May 2018</rights><rights>The Genetics Society 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c427t-c1a9d524bf0a4aa9bffca909ec201850f17b0ed920005a93ffc55ada944b211a3</citedby><cites>FETCH-LOGICAL-c427t-c1a9d524bf0a4aa9bffca909ec201850f17b0ed920005a93ffc55ada944b211a3</cites><orcidid>0000-0001-7082-3254</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/PMC5889387/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889387/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29321624$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pazmiño, Diana A</creatorcontrib><creatorcontrib>Maes, Gregory E</creatorcontrib><creatorcontrib>Green, Madeline E</creatorcontrib><creatorcontrib>Simpfendorfer, Colin A</creatorcontrib><creatorcontrib>Hoyos-Padilla, E Mauricio</creatorcontrib><creatorcontrib>Duffy, Clinton J A</creatorcontrib><creatorcontrib>Meyer, Carl G</creatorcontrib><creatorcontrib>Kerwath, Sven E</creatorcontrib><creatorcontrib>Salinas-de-León, Pelayo</creatorcontrib><creatorcontrib>van Herwerden, Lynne</creatorcontrib><title>Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers</title><title>Heredity</title><addtitle>Heredity (Edinb)</addtitle><description>The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ
defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F
= 0.023-0.035), mtDNA exhibited more divergence (Φ
= 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.</description><subject>Animals</subject><subject>Biodiversity</subject><subject>Carcharhinus galapagensis</subject><subject>Conservation</subject><subject>Conservation of Natural Resources</subject><subject>Data processing</subject><subject>Demographics</subject><subject>Demography</subject><subject>Divergence</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Ecuador</subject><subject>Female</subject><subject>Fish conservation</subject><subject>Gene sequencing</subject><subject>Genetic diversity</subject><subject>Genetic Variation</subject><subject>Genetics, Population</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Habitat utilization</subject><subject>Male</subject><subject>Mitochondria</subject><subject>Mitochondrial DNA</subject><subject>Pacific Ocean</subject><subject>Phylogeny</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Population</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Populations</subject><subject>Sharks - genetics</subject><subject>Single-nucleotide polymorphism</subject><subject>Wildlife conservation</subject><issn>0018-067X</issn><issn>1365-2540</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNpdUcGKFDEQDaK44-oHeJGAl_XQWkl3pjsXYRl0FRYUVPAWqtPVM9nNJGPSPTI_4veaYdZFPRRV5L161Mtj7LmA1wLq7k1uRFO3FYhSIFUlH7CFqJdlUA08ZAsA0VWwbL-fsSc53wBA3Ur9mJ1JXUuxlM2C_foypRjWfEoYcvUZrRud5X0ivOUYBu6jRc9tDJnSHicXA5-DmzJ3gU8b4lfocYfrmHneYLrlFytMtkwbF-bM1yeUQnb5FU-0J_Q08P7Ay1vcUvXTDcTtYYphtp4w8W0RoZSfskcj-kzP7vo5-_b-3dfVh-r609XH1eV1ZRvZTpUVqAclm34EbBB1P44WNWiyslhXMIq2Bxq0LNYV6rrASuGAuml6KQTW5-ztSXc391saLIXyEd7skiuHHExEZ_5FgtuYddwb1XW67toicHEnkOKPmfJkti5b8h4DxTkboTutOoC2K9SX_1Fv4pxCsWckSKkk6O7IEieWTTHnROP9MQLMMXVzSt2U1M0xdSPLzou_Xdxv_Im5_g3o0qxb</recordid><startdate>20180501</startdate><enddate>20180501</enddate><creator>Pazmiño, Diana A</creator><creator>Maes, Gregory E</creator><creator>Green, Madeline E</creator><creator>Simpfendorfer, Colin A</creator><creator>Hoyos-Padilla, E Mauricio</creator><creator>Duffy, Clinton J A</creator><creator>Meyer, Carl G</creator><creator>Kerwath, Sven E</creator><creator>Salinas-de-León, Pelayo</creator><creator>van Herwerden, Lynne</creator><general>Springer Nature B.V</general><general>Springer International Publishing</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>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7TK</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-7082-3254</orcidid></search><sort><creationdate>20180501</creationdate><title>Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers</title><author>Pazmiño, Diana A ; Maes, Gregory E ; Green, Madeline E ; Simpfendorfer, Colin A ; Hoyos-Padilla, E Mauricio ; Duffy, Clinton J A ; Meyer, Carl G ; Kerwath, Sven E ; Salinas-de-León, Pelayo ; van Herwerden, Lynne</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c427t-c1a9d524bf0a4aa9bffca909ec201850f17b0ed920005a93ffc55ada944b211a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animals</topic><topic>Biodiversity</topic><topic>Carcharhinus galapagensis</topic><topic>Conservation</topic><topic>Conservation of Natural Resources</topic><topic>Data processing</topic><topic>Demographics</topic><topic>Demography</topic><topic>Divergence</topic><topic>DNA, Mitochondrial - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Heredity</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Pazmiño, Diana A</au><au>Maes, Gregory E</au><au>Green, Madeline E</au><au>Simpfendorfer, Colin A</au><au>Hoyos-Padilla, E Mauricio</au><au>Duffy, Clinton J A</au><au>Meyer, Carl G</au><au>Kerwath, Sven E</au><au>Salinas-de-León, Pelayo</au><au>van Herwerden, Lynne</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers</atitle><jtitle>Heredity</jtitle><addtitle>Heredity (Edinb)</addtitle><date>2018-05-01</date><risdate>2018</risdate><volume>120</volume><issue>5</issue><spage>407</spage><epage>421</epage><pages>407-421</pages><issn>0018-067X</issn><eissn>1365-2540</eissn><abstract>The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ
defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F
= 0.023-0.035), mtDNA exhibited more divergence (Φ
= 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and regional scales.</abstract><cop>England</cop><pub>Springer Nature B.V</pub><pmid>29321624</pmid><doi>10.1038/s41437-017-0025-2</doi><tpages>15</tpages><orcidid>https://orcid.org/0000-0001-7082-3254</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Heredity, 2018-05, Vol.120 (5), p.407-421 |
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| source | MEDLINE; Springer Nature - Complete Springer Journals; Nature Journals Online; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Animals Biodiversity Carcharhinus galapagensis Conservation Conservation of Natural Resources Data processing Demographics Demography Divergence DNA, Mitochondrial - genetics Ecuador Female Fish conservation Gene sequencing Genetic diversity Genetic Variation Genetics, Population Genomes Genotype Habitat utilization Male Mitochondria Mitochondrial DNA Pacific Ocean Phylogeny Polymorphism Polymorphism, Single Nucleotide - genetics Population Population genetics Population structure Populations Sharks - genetics Single-nucleotide polymorphism Wildlife conservation |
| title | Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers |
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