Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors
Abstract Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in a...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-06-01
|
| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.7531 |
| _version_ | 1818873229866958848 |
|---|---|
| author | Clare J. Venney Ben J. G. Sutherland Terry D. Beacham Daniel D. Heath |
| author_facet | Clare J. Venney Ben J. G. Sutherland Terry D. Beacham Daniel D. Heath |
| author_sort | Clare J. Venney |
| collection | DOAJ |
| description | Abstract Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene‐targeted PCR‐based assay for next‐generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise FST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single‐gene Mantel tests comparing methylation and pairwise FST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience. |
| first_indexed | 2024-12-19T12:51:24Z |
| format | Article |
| id | doaj.art-04445999962945ceb2d1f71c42f2ceba |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-12-19T12:51:24Z |
| publishDate | 2021-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-04445999962945ceb2d1f71c42f2ceba2022-12-21T20:20:32ZengWileyEcology and Evolution2045-77582021-06-0111116846686110.1002/ece3.7531Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factorsClare J. Venney0Ben J. G. Sutherland1Terry D. Beacham2Daniel D. Heath3Great Lakes Institute for Environmental Research University of Windsor Windsor ON CanadaFisheries and Oceans Canada Pacific Biological Station Nanaimo BC CanadaFisheries and Oceans Canada Pacific Biological Station Nanaimo BC CanadaGreat Lakes Institute for Environmental Research University of Windsor Windsor ON CanadaAbstract Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations of Chinook salmon (Oncorhynchus tshawytscha) and assayed DNA methylation at 23 genes involved in development, immune function, stress response, and metabolism using a gene‐targeted PCR‐based assay for next‐generation sequencing. Evidence for population differences in methylation was found at eight out of 23 gene loci after controlling for developmental timing in each individual. However, we found no correlation between freshwater environmental parameters and methylation variation among populations at those eight genes. A weak correlation was identified between pairwise DNA methylation dissimilarity among populations and pairwise FST based on 15 microsatellite loci, indicating weak effects of genetic drift or geographic distance on methylation. The weak correlation was primarily driven by two genes, GTIIBS and Nkef. However, single‐gene Mantel tests comparing methylation and pairwise FST were not significant after Bonferroni correction. Thus, population differences in DNA methylation are more likely related to unmeasured oceanic environmental conditions, local adaptation, and/or genetic drift. DNA methylation is an additional mechanism that contributes to among population variation, with potential influences on organism phenotype, adaptive potential, and population resilience.https://doi.org/10.1002/ece3.7531adaptive potentialDNA methylationepigeneticsgenetic driftpopulation geneticspopulation variation |
| spellingShingle | Clare J. Venney Ben J. G. Sutherland Terry D. Beacham Daniel D. Heath Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors Ecology and Evolution adaptive potential DNA methylation epigenetics genetic drift population genetics population variation |
| title | Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors |
| title_full | Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors |
| title_fullStr | Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors |
| title_full_unstemmed | Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors |
| title_short | Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: Genetic drift and environmental factors |
| title_sort | population differences in chinook salmon oncorhynchus tshawytscha dna methylation genetic drift and environmental factors |
| topic | adaptive potential DNA methylation epigenetics genetic drift population genetics population variation |
| url | https://doi.org/10.1002/ece3.7531 |
| work_keys_str_mv | AT clarejvenney populationdifferencesinchinooksalmononcorhynchustshawytschadnamethylationgeneticdriftandenvironmentalfactors AT benjgsutherland populationdifferencesinchinooksalmononcorhynchustshawytschadnamethylationgeneticdriftandenvironmentalfactors AT terrydbeacham populationdifferencesinchinooksalmononcorhynchustshawytschadnamethylationgeneticdriftandenvironmentalfactors AT danieldheath populationdifferencesinchinooksalmononcorhynchustshawytschadnamethylationgeneticdriftandenvironmentalfactors |