Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

Abstract Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated...

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Autores principales:	Kyung Seok Kim, Kevin J. Roe
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/528be14ff6574bbea0999018ec4bb2c3
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spelling	oai:doaj.org-article:528be14ff6574bbea0999018ec4bb2c32021-12-02T14:47:31ZGenome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America10.1038/s41598-021-90325-02045-2322https://doaj.org/article/528be14ff6574bbea0999018ec4bb2c32021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-90325-0https://doaj.org/toc/2045-2322Abstract Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected F ST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.Kyung Seok KimKevin J. RoeNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kyung Seok Kim Kevin J. Roe Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
description	Abstract Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected F ST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
format	article
author	Kyung Seok Kim Kevin J. Roe
author_facet	Kyung Seok Kim Kevin J. Roe
author_sort	Kyung Seok Kim
title	Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
title_short	Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
title_full	Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
title_fullStr	Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
title_full_unstemmed	Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America
title_sort	genome-wide snps redefines species boundaries and conservation units in the freshwater mussel genus cyprogenia of north america
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/528be14ff6574bbea0999018ec4bb2c3
work_keys_str_mv	AT kyungseokkim genomewidesnpsredefinesspeciesboundariesandconservationunitsinthefreshwatermusselgenuscyprogeniaofnorthamerica AT kevinjroe genomewidesnpsredefinesspeciesboundariesandconservationunitsinthefreshwatermusselgenuscyprogeniaofnorthamerica
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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America

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