Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum

Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral speci...
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Gespeichert in:

Autor*in:	Kenji Takata [verfasserIn] Fumihito Iwase [verfasserIn] Akira Iguchi [verfasserIn] Hideaki Yuasa [verfasserIn] Hiroki Taninaka [verfasserIn] Nozomu Iwasaki [verfasserIn] Kouji Uda [verfasserIn] Tomohiko Suzuki [verfasserIn] Masanori Nonaka [verfasserIn] Taisei Kikuchi [verfasserIn] Nina Yasuda [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral

Übergeordnetes Werk:	In: Frontiers in Marine Science - Frontiers Media S.A., 2015, 8(2021)
Übergeordnetes Werk:	volume:8 ; year:2021

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3389/fmars.2021.667481

Katalog-ID:	DOAJ057612900

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520			\|a Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.
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allfields	10.3389/fmars.2021.667481 doi (DE-627)DOAJ057612900 (DE-599)DOAJ3e63a62c8bda48dca1dd9f9a0eb23462 DE-627 ger DE-627 rakwb eng QH1-199.5 Kenji Takata verfasserin aut Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species. precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral Science Q General. Including nature conservation, geographical distribution Fumihito Iwase verfasserin aut Akira Iguchi verfasserin aut Hideaki Yuasa verfasserin aut Hiroki Taninaka verfasserin aut Nozomu Iwasaki verfasserin aut Kouji Uda verfasserin aut Tomohiko Suzuki verfasserin aut Masanori Nonaka verfasserin aut Taisei Kikuchi verfasserin aut Nina Yasuda verfasserin aut In Frontiers in Marine Science Frontiers Media S.A., 2015 8(2021) (DE-627)779393945 (DE-600)2757748-X 22967745 nnns volume:8 year:2021 https://doi.org/10.3389/fmars.2021.667481 kostenfrei https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 kostenfrei https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full kostenfrei https://doaj.org/toc/2296-7745 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2021
spelling	10.3389/fmars.2021.667481 doi (DE-627)DOAJ057612900 (DE-599)DOAJ3e63a62c8bda48dca1dd9f9a0eb23462 DE-627 ger DE-627 rakwb eng QH1-199.5 Kenji Takata verfasserin aut Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species. precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral Science Q General. Including nature conservation, geographical distribution Fumihito Iwase verfasserin aut Akira Iguchi verfasserin aut Hideaki Yuasa verfasserin aut Hiroki Taninaka verfasserin aut Nozomu Iwasaki verfasserin aut Kouji Uda verfasserin aut Tomohiko Suzuki verfasserin aut Masanori Nonaka verfasserin aut Taisei Kikuchi verfasserin aut Nina Yasuda verfasserin aut In Frontiers in Marine Science Frontiers Media S.A., 2015 8(2021) (DE-627)779393945 (DE-600)2757748-X 22967745 nnns volume:8 year:2021 https://doi.org/10.3389/fmars.2021.667481 kostenfrei https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 kostenfrei https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full kostenfrei https://doaj.org/toc/2296-7745 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2021
allfields_unstemmed	10.3389/fmars.2021.667481 doi (DE-627)DOAJ057612900 (DE-599)DOAJ3e63a62c8bda48dca1dd9f9a0eb23462 DE-627 ger DE-627 rakwb eng QH1-199.5 Kenji Takata verfasserin aut Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species. precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral Science Q General. Including nature conservation, geographical distribution Fumihito Iwase verfasserin aut Akira Iguchi verfasserin aut Hideaki Yuasa verfasserin aut Hiroki Taninaka verfasserin aut Nozomu Iwasaki verfasserin aut Kouji Uda verfasserin aut Tomohiko Suzuki verfasserin aut Masanori Nonaka verfasserin aut Taisei Kikuchi verfasserin aut Nina Yasuda verfasserin aut In Frontiers in Marine Science Frontiers Media S.A., 2015 8(2021) (DE-627)779393945 (DE-600)2757748-X 22967745 nnns volume:8 year:2021 https://doi.org/10.3389/fmars.2021.667481 kostenfrei https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 kostenfrei https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full kostenfrei https://doaj.org/toc/2296-7745 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2021
allfieldsGer	10.3389/fmars.2021.667481 doi (DE-627)DOAJ057612900 (DE-599)DOAJ3e63a62c8bda48dca1dd9f9a0eb23462 DE-627 ger DE-627 rakwb eng QH1-199.5 Kenji Takata verfasserin aut Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species. precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral Science Q General. Including nature conservation, geographical distribution Fumihito Iwase verfasserin aut Akira Iguchi verfasserin aut Hideaki Yuasa verfasserin aut Hiroki Taninaka verfasserin aut Nozomu Iwasaki verfasserin aut Kouji Uda verfasserin aut Tomohiko Suzuki verfasserin aut Masanori Nonaka verfasserin aut Taisei Kikuchi verfasserin aut Nina Yasuda verfasserin aut In Frontiers in Marine Science Frontiers Media S.A., 2015 8(2021) (DE-627)779393945 (DE-600)2757748-X 22967745 nnns volume:8 year:2021 https://doi.org/10.3389/fmars.2021.667481 kostenfrei https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 kostenfrei https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full kostenfrei https://doaj.org/toc/2296-7745 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2021
allfieldsSound	10.3389/fmars.2021.667481 doi (DE-627)DOAJ057612900 (DE-599)DOAJ3e63a62c8bda48dca1dd9f9a0eb23462 DE-627 ger DE-627 rakwb eng QH1-199.5 Kenji Takata verfasserin aut Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species. precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral Science Q General. Including nature conservation, geographical distribution Fumihito Iwase verfasserin aut Akira Iguchi verfasserin aut Hideaki Yuasa verfasserin aut Hiroki Taninaka verfasserin aut Nozomu Iwasaki verfasserin aut Kouji Uda verfasserin aut Tomohiko Suzuki verfasserin aut Masanori Nonaka verfasserin aut Taisei Kikuchi verfasserin aut Nina Yasuda verfasserin aut In Frontiers in Marine Science Frontiers Media S.A., 2015 8(2021) (DE-627)779393945 (DE-600)2757748-X 22967745 nnns volume:8 year:2021 https://doi.org/10.3389/fmars.2021.667481 kostenfrei https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 kostenfrei https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full kostenfrei https://doaj.org/toc/2296-7745 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2021
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authorswithroles_txt_mv	Kenji Takata @@aut@@ Fumihito Iwase @@aut@@ Akira Iguchi @@aut@@ Hideaki Yuasa @@aut@@ Hiroki Taninaka @@aut@@ Nozomu Iwasaki @@aut@@ Kouji Uda @@aut@@ Tomohiko Suzuki @@aut@@ Masanori Nonaka @@aut@@ Taisei Kikuchi @@aut@@ Nina Yasuda @@aut@@
publishDateDaySort_date	2021-01-01T00:00:00Z
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callnumber-first	Q - Science
author	Kenji Takata
spellingShingle	Kenji Takata misc QH1-199.5 misc precious coral misc spatial genetic structure misc spatial autocorrelation misc conservation misc larval dispersal misc deep-sea coral misc Science misc Q misc General. Including nature conservation, geographical distribution Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum
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topic_title	QH1-199.5 Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum precious coral spatial genetic structure spatial autocorrelation conservation larval dispersal deep-sea coral
topic	misc QH1-199.5 misc precious coral misc spatial genetic structure misc spatial autocorrelation misc conservation misc larval dispersal misc deep-sea coral misc Science misc Q misc General. Including nature conservation, geographical distribution
topic_unstemmed	misc QH1-199.5 misc precious coral misc spatial genetic structure misc spatial autocorrelation misc conservation misc larval dispersal misc deep-sea coral misc Science misc Q misc General. Including nature conservation, geographical distribution
topic_browse	misc QH1-199.5 misc precious coral misc spatial genetic structure misc spatial autocorrelation misc conservation misc larval dispersal misc deep-sea coral misc Science misc Q misc General. Including nature conservation, geographical distribution
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title	Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum
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title_full	Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum
author_sort	Kenji Takata
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author_browse	Kenji Takata Fumihito Iwase Akira Iguchi Hideaki Yuasa Hiroki Taninaka Nozomu Iwasaki Kouji Uda Tomohiko Suzuki Masanori Nonaka Taisei Kikuchi Nina Yasuda
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title_sort	genome-wide snp data revealed notable spatial genetic structure in the deep-sea precious coral corallium japonicum
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title_auth	Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum
abstract	Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.
abstractGer	Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.
abstract_unstemmed	Estimating the spatial extent of gamete and larval dispersal of deep-sea coral species, is challenging yet important for their conservation. Spatial autocorrelation analysis is useful for estimating the spatial range of dispersal of corals; however, it has not been performed for deep-sea coral species using genome-wide single nucleotide polymorphisms (SNPs). In this study, we examined the spatial genetic structure of a deep-sea coral species—the Japanese red coral, Corallium japonicum, sampled off the coast of Kochi, which lies to the southwest of the Shikoku Island in Japan; the Kochi region suffers from over-harvesting because of its high commercial value. We also examined the power of detecting significant spatial genetic structure by changing the number of loci and the proportion of missing data using both de novo analysis and mapping analysis. Similar results were obtained for both de novo and mapping analysis, although a higher number of loci were obtained by the mapping method. In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.
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title_short	Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum
url	https://doi.org/10.3389/fmars.2021.667481 https://doaj.org/article/3e63a62c8bda48dca1dd9f9a0eb23462 https://www.frontiersin.org/articles/10.3389/fmars.2021.667481/full https://doaj.org/toc/2296-7745
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In addition, “many SNPs with a lot of missing data” was generally more useful than “a small number of SNPs with a small amount of missing data” to detect significant fine-scale spatial genetic structure. Our data suggested that more than 700 neutral SNPs were needed to detect significant fine-scale spatial genetic structure. The maximum first distance class that can detect significant spatial genetic structure within Kochi for the C. japonicum population was less than 11 km, suggesting that the over-harvesting of C. japonicum within a diameter of approximately 11 km in the Kochi area should be avoided, because this can cause the local extinction of this species.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">precious coral</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">spatial genetic structure</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">spatial autocorrelation</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">conservation</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">larval dispersal</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">deep-sea coral</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Science</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Q</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">General. 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Genome-Wide SNP Data Revealed Notable Spatial Genetic Structure in the Deep-Sea Precious Coral Corallium japonicum

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