How much is enough? Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae)
Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, an endangered annual plant endemic to the California Channel Islands which was presumed extinct for nearly 50 years, is currently known from only a few small patches on San Clemente Island (SCl) and Santa Catalina Island (SCa). In additi...
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description | Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, an endangered annual plant endemic to the California Channel Islands which was presumed extinct for nearly 50 years, is currently known from only a few small patches on San Clemente Island (SCl) and Santa Catalina Island (SCa). In addition to protecting extant populations, recovery efforts have included ex situ seed collections to hedge against stochastic population losses. We examined genetic diversity and population structure in the wild and the effect of sampling intensity on the genetic diversity of ex situ seed collections using 13 species-specific microsatellite loci. Much of the genetic variation on each island consisted of rare alleles; 33 % (SCl) or 56 % (SCa) of the non-fixed alleles occurred at frequencies ≤0.05. Patches on SCl were genetically depauperate (mean HO = 0.002) compared to patches on SCa (mean HO = 0.344). One patch on SCl was genetically distinct, while the remaining four patches were genetically indistinguishable. The three patches on SCa were genetically distinct from those on SCl, but not from one another. Simulated sampling for the ex situ seed collections found that 10 individuals was sufficient to capture 90 % of the diversity for normalized measures (NE, HO, and HE) in a depauperate (SCl) population, while 30 individuals was necessary in a diverse (SCa) population. However, sampling 125 (SCl) or 60 (SCa) individuals was necessary to capture 90 % of all the alleles present. These findings indicate that theoretical guidelines for ex situ seed collections that recommend targeting 50 individuals per population overestimate the sampling effort required to adequately preserve common alleles, but may underestimate the effort necessary to capture most alleles in wild populations. |
doi_str_mv | 10.1007/s10592-014-0655-3 |
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Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae)</title><source>SpringerLink_现刊</source><creator>McGlaughlin, Mitchell E ; Riley, Lynn ; Brandsrud, Michelle ; Arcibal, Erica ; Helenurm, Mark K ; Helenurm, Kaius</creator><creatorcontrib>McGlaughlin, Mitchell E ; Riley, Lynn ; Brandsrud, Michelle ; Arcibal, Erica ; Helenurm, Mark K ; Helenurm, Kaius</creatorcontrib><description>Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, an endangered annual plant endemic to the California Channel Islands which was presumed extinct for nearly 50 years, is currently known from only a few small patches on San Clemente Island (SCl) and Santa Catalina Island (SCa). In addition to protecting extant populations, recovery efforts have included ex situ seed collections to hedge against stochastic population losses. We examined genetic diversity and population structure in the wild and the effect of sampling intensity on the genetic diversity of ex situ seed collections using 13 species-specific microsatellite loci. Much of the genetic variation on each island consisted of rare alleles; 33 % (SCl) or 56 % (SCa) of the non-fixed alleles occurred at frequencies ≤0.05. Patches on SCl were genetically depauperate (mean HO = 0.002) compared to patches on SCa (mean HO = 0.344). One patch on SCl was genetically distinct, while the remaining four patches were genetically indistinguishable. The three patches on SCa were genetically distinct from those on SCl, but not from one another. Simulated sampling for the ex situ seed collections found that 10 individuals was sufficient to capture 90 % of the diversity for normalized measures (NE, HO, and HE) in a depauperate (SCl) population, while 30 individuals was necessary in a diverse (SCa) population. However, sampling 125 (SCl) or 60 (SCa) individuals was necessary to capture 90 % of all the alleles present. These findings indicate that theoretical guidelines for ex situ seed collections that recommend targeting 50 individuals per population overestimate the sampling effort required to adequately preserve common alleles, but may underestimate the effort necessary to capture most alleles in wild populations.</description><identifier>ISSN: 1566-0621</identifier><identifier>EISSN: 1572-9737</identifier><identifier>DOI: 10.1007/s10592-014-0655-3</identifier><language>eng</language><publisher>Dordrecht: Springer-Verlag</publisher><subject>alleles ; Animal Genetics and Genomics ; annuals ; Biodiversity ; Biomedical and Life Sciences ; Brassicaceae ; Conservation ; Conservation Biology/Ecology ; Ecology ; Endangered & extinct species ; Endangered plants ; Endemic plants ; Evolutionary Biology ; Flowers & plants ; Genetic diversity ; genetic variation ; guidelines ; indigenous species ; Life Sciences ; microsatellite repeats ; Plant Genetics and Genomics ; Population structure ; Research Article ; Seeds ; Sibara filifolia</subject><ispartof>Conservation genetics, 2015-04, Vol.16 (2), p.253-266</ispartof><rights>Springer Science+Business Media Dordrecht 2014</rights><rights>Springer Science+Business Media Dordrecht 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c373t-8a5928af9e207ba3809edd8471765393a7308d4071a1c28f13fa0208e1632d513</citedby><cites>FETCH-LOGICAL-c373t-8a5928af9e207ba3809edd8471765393a7308d4071a1c28f13fa0208e1632d513</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10592-014-0655-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10592-014-0655-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>McGlaughlin, Mitchell E</creatorcontrib><creatorcontrib>Riley, Lynn</creatorcontrib><creatorcontrib>Brandsrud, Michelle</creatorcontrib><creatorcontrib>Arcibal, Erica</creatorcontrib><creatorcontrib>Helenurm, Mark K</creatorcontrib><creatorcontrib>Helenurm, Kaius</creatorcontrib><title>How much is enough? Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae)</title><title>Conservation genetics</title><addtitle>Conserv Genet</addtitle><description>Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, an endangered annual plant endemic to the California Channel Islands which was presumed extinct for nearly 50 years, is currently known from only a few small patches on San Clemente Island (SCl) and Santa Catalina Island (SCa). In addition to protecting extant populations, recovery efforts have included ex situ seed collections to hedge against stochastic population losses. We examined genetic diversity and population structure in the wild and the effect of sampling intensity on the genetic diversity of ex situ seed collections using 13 species-specific microsatellite loci. Much of the genetic variation on each island consisted of rare alleles; 33 % (SCl) or 56 % (SCa) of the non-fixed alleles occurred at frequencies ≤0.05. Patches on SCl were genetically depauperate (mean HO = 0.002) compared to patches on SCa (mean HO = 0.344). One patch on SCl was genetically distinct, while the remaining four patches were genetically indistinguishable. The three patches on SCa were genetically distinct from those on SCl, but not from one another. Simulated sampling for the ex situ seed collections found that 10 individuals was sufficient to capture 90 % of the diversity for normalized measures (NE, HO, and HE) in a depauperate (SCl) population, while 30 individuals was necessary in a diverse (SCa) population. However, sampling 125 (SCl) or 60 (SCa) individuals was necessary to capture 90 % of all the alleles present. These findings indicate that theoretical guidelines for ex situ seed collections that recommend targeting 50 individuals per population overestimate the sampling effort required to adequately preserve common alleles, but may underestimate the effort necessary to capture most alleles in wild populations.</description><subject>alleles</subject><subject>Animal Genetics and Genomics</subject><subject>annuals</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Brassicaceae</subject><subject>Conservation</subject><subject>Conservation Biology/Ecology</subject><subject>Ecology</subject><subject>Endangered & extinct species</subject><subject>Endangered plants</subject><subject>Endemic plants</subject><subject>Evolutionary Biology</subject><subject>Flowers & plants</subject><subject>Genetic diversity</subject><subject>genetic variation</subject><subject>guidelines</subject><subject>indigenous species</subject><subject>Life Sciences</subject><subject>microsatellite repeats</subject><subject>Plant Genetics and Genomics</subject><subject>Population structure</subject><subject>Research Article</subject><subject>Seeds</subject><subject>Sibara filifolia</subject><issn>1566-0621</issn><issn>1572-9737</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</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>eNp9kc1u1zAQxCMEEqXwAJywxKUcAv5I4oQLKhVQpCIOpWdr62zy3yqxU9sB-my8HE7DAXHgtCvNb0arnaJ4Lvhrwbl-EwWvO1lyUZW8qetSPSiORK1l2WmlH25702RFisfFkxhvOBeN1OKo-HXuf7B5tQdGkaHz63h4x76Qo3mdWYR5mciNjFxCFyndsYC3KwXsWfLMwpLWgAx_JnCJjegwkWU9fcdwD5PLGsvryiJmj_XThDaRd_FtVrZ0jGwIfmbpkHNcD27ELX2ZtsRLuoYAbKCJBj8RsJP3AWIkCxYBXz0tHg0wRXz2Zx4XVx8_fDs7Ly--fvp8dnpRWqVVKlvIn2lh6FByfQ2q5R32fVtpoZtadQq04m1fcS1AWNkOQg3AJW9RNEr2tVDHxcmeuwR_u2JMZqZocco3ol-jEY1WqpO10Bl9-Q9649fg8nWZapSqZFe3mRI7ZYOPMeBglkAzhDsjuNnqNHudJtdptjqNyh65e2Jmty_9lfwf04vdNIA3MAaK5upSclHf919VXP0G_M6uHg</recordid><startdate>20150401</startdate><enddate>20150401</enddate><creator>McGlaughlin, Mitchell E</creator><creator>Riley, Lynn</creator><creator>Brandsrud, Michelle</creator><creator>Arcibal, Erica</creator><creator>Helenurm, Mark K</creator><creator>Helenurm, Kaius</creator><general>Springer-Verlag</general><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>FBQ</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</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>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope></search><sort><creationdate>20150401</creationdate><title>How much is enough? Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae)</title><author>McGlaughlin, Mitchell E ; Riley, Lynn ; Brandsrud, Michelle ; Arcibal, Erica ; Helenurm, Mark K ; Helenurm, Kaius</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c373t-8a5928af9e207ba3809edd8471765393a7308d4071a1c28f13fa0208e1632d513</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>alleles</topic><topic>Animal Genetics and Genomics</topic><topic>annuals</topic><topic>Biodiversity</topic><topic>Biomedical and Life Sciences</topic><topic>Brassicaceae</topic><topic>Conservation</topic><topic>Conservation Biology/Ecology</topic><topic>Ecology</topic><topic>Endangered & extinct species</topic><topic>Endangered plants</topic><topic>Endemic plants</topic><topic>Evolutionary Biology</topic><topic>Flowers & plants</topic><topic>Genetic diversity</topic><topic>genetic variation</topic><topic>guidelines</topic><topic>indigenous species</topic><topic>Life Sciences</topic><topic>microsatellite repeats</topic><topic>Plant Genetics and Genomics</topic><topic>Population structure</topic><topic>Research Article</topic><topic>Seeds</topic><topic>Sibara filifolia</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>McGlaughlin, Mitchell E</creatorcontrib><creatorcontrib>Riley, Lynn</creatorcontrib><creatorcontrib>Brandsrud, Michelle</creatorcontrib><creatorcontrib>Arcibal, Erica</creatorcontrib><creatorcontrib>Helenurm, Mark K</creatorcontrib><creatorcontrib>Helenurm, Kaius</creatorcontrib><collection>AGRIS</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>ProQuest_Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><jtitle>Conservation genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>McGlaughlin, Mitchell E</au><au>Riley, Lynn</au><au>Brandsrud, Michelle</au><au>Arcibal, Erica</au><au>Helenurm, Mark K</au><au>Helenurm, Kaius</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>How much is enough? Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae)</atitle><jtitle>Conservation genetics</jtitle><stitle>Conserv Genet</stitle><date>2015-04-01</date><risdate>2015</risdate><volume>16</volume><issue>2</issue><spage>253</spage><epage>266</epage><pages>253-266</pages><issn>1566-0621</issn><eissn>1572-9737</eissn><abstract>Sibara filifolia (Brassicaceae), Santa Cruz Island Rock Cress, an endangered annual plant endemic to the California Channel Islands which was presumed extinct for nearly 50 years, is currently known from only a few small patches on San Clemente Island (SCl) and Santa Catalina Island (SCa). In addition to protecting extant populations, recovery efforts have included ex situ seed collections to hedge against stochastic population losses. We examined genetic diversity and population structure in the wild and the effect of sampling intensity on the genetic diversity of ex situ seed collections using 13 species-specific microsatellite loci. Much of the genetic variation on each island consisted of rare alleles; 33 % (SCl) or 56 % (SCa) of the non-fixed alleles occurred at frequencies ≤0.05. Patches on SCl were genetically depauperate (mean HO = 0.002) compared to patches on SCa (mean HO = 0.344). One patch on SCl was genetically distinct, while the remaining four patches were genetically indistinguishable. The three patches on SCa were genetically distinct from those on SCl, but not from one another. Simulated sampling for the ex situ seed collections found that 10 individuals was sufficient to capture 90 % of the diversity for normalized measures (NE, HO, and HE) in a depauperate (SCl) population, while 30 individuals was necessary in a diverse (SCa) population. However, sampling 125 (SCl) or 60 (SCa) individuals was necessary to capture 90 % of all the alleles present. These findings indicate that theoretical guidelines for ex situ seed collections that recommend targeting 50 individuals per population overestimate the sampling effort required to adequately preserve common alleles, but may underestimate the effort necessary to capture most alleles in wild populations.</abstract><cop>Dordrecht</cop><pub>Springer-Verlag</pub><doi>10.1007/s10592-014-0655-3</doi><tpages>14</tpages></addata></record> |
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subjects | alleles Animal Genetics and Genomics annuals Biodiversity Biomedical and Life Sciences Brassicaceae Conservation Conservation Biology/Ecology Ecology Endangered & extinct species Endangered plants Endemic plants Evolutionary Biology Flowers & plants Genetic diversity genetic variation guidelines indigenous species Life Sciences microsatellite repeats Plant Genetics and Genomics Population structure Research Article Seeds Sibara filifolia |
title | How much is enough? Minimum sampling intensity required to capture extant genetic diversity in ex situ seed collections: examples from the endangered plant Sibara filifolia (Brassicaceae) |
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