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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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-90325-0 |
| _version_ | 1818571066718552064 |
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| author | Kyung Seok Kim Kevin J. Roe |
| author_facet | Kyung Seok Kim Kevin J. Roe |
| author_sort | Kyung Seok Kim |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T13:50:36Z |
| format | Article |
| id | doaj.art-528be14ff6574bbea0999018ec4bb2c3 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-14T13:50:36Z |
| publishDate | 2021-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-528be14ff6574bbea0999018ec4bb2c32022-12-21T22:59:05ZengNature PortfolioScientific Reports2045-23222021-05-0111111610.1038/s41598-021-90325-0Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North AmericaKyung Seok Kim0Kevin J. Roe1Department of Natural Resource Ecology and Management, Iowa State UniversityDepartment of Natural Resource Ecology and Management, Iowa State UniversityAbstract 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.https://doi.org/10.1038/s41598-021-90325-0 |
| spellingShingle | Kyung Seok Kim Kevin J. Roe Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-021-90325-0 |
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