Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
Abstract Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low‐coverage whole‐genome sequenci...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-08-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.7878 |
| _version_ | 1818858824330641408 |
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| author | Timothy P. O’Donnell Timothy J. Sullivan |
| author_facet | Timothy P. O’Donnell Timothy J. Sullivan |
| author_sort | Timothy P. O’Donnell |
| collection | DOAJ |
| description | Abstract Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low‐coverage whole‐genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter‐spawning groups at specific regions of the genome. Guided regularized random forest and ranked FST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter‐spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments. |
| first_indexed | 2024-12-19T09:02:25Z |
| format | Article |
| id | doaj.art-c20f0b12da64494592a84728c221fd6c |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-19T09:02:25Z |
| publishDate | 2021-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-c20f0b12da64494592a84728c221fd6c2022-12-21T20:28:26ZengWileyEcology and Evolution2045-77582021-08-011115106591067110.1002/ece3.7878Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)Timothy P. O’Donnell0Timothy J. Sullivan1Gloucester Marine Genomics Institute Gloucester MA USAGloucester Marine Genomics Institute Gloucester MA USAAbstract Atlantic cod (Gadus morhua, Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low‐coverage whole‐genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter‐spawning groups at specific regions of the genome. Guided regularized random forest and ranked FST methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter‐spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.https://doi.org/10.1002/ece3.7878Atlantic codrandom forestsexSNPsspawning season |
| spellingShingle | Timothy P. O’Donnell Timothy J. Sullivan Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) Ecology and Evolution Atlantic cod random forest sex SNPs spawning season |
| title | Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) |
| title_full | Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) |
| title_fullStr | Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) |
| title_full_unstemmed | Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) |
| title_short | Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758) |
| title_sort | low coverage whole genome sequencing reveals molecular markers for spawning season and sex identification in gulf of maine atlantic cod gadus morhua linnaeus 1758 |
| topic | Atlantic cod random forest sex SNPs spawning season |
| url | https://doi.org/10.1002/ece3.7878 |
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