Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra
Genetic diversity plays a vital role in the adaptability of salmon to changing environmental conditions that can introduce new selective pressures on populations. Variability among local subpopulations may increase the chance that certain advantageous genes are passed down to future generations to m...
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ftmdpi:oai:mdpi.com:/2076-2615/13/4/593/ 2023-08-20T04:09:02+02:00 Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra Evan J. Wilson Andrew M. Shedlock agris 2023-02-08 application/pdf https://doi.org/10.3390/ani13040593 EN eng Multidisciplinary Digital Publishing Institute Animal Genetics and Genomics https://dx.doi.org/10.3390/ani13040593 https://creativecommons.org/licenses/by/4.0/ Animals; Volume 13; Issue 4; Pages: 593 Oncorhynchus Chinook salmon Alaska Susitna River MHC Class I and II loci population genomics heterozygosity selection non-synonymous substitution peptide binding region Text 2023 ftmdpi https://doi.org/10.3390/ani13040593 2023-08-01T08:42:20Z Genetic diversity plays a vital role in the adaptability of salmon to changing environmental conditions that can introduce new selective pressures on populations. Variability among local subpopulations may increase the chance that certain advantageous genes are passed down to future generations to mitigate susceptibility to novel diseases, warming oceans, loss of genetic stocks, and ocean acidification. Class I and II genes of the major histocompatibility complex (MHC) are crucial for the fitness of Chinook salmon due to the role they play in disease and pathogen resistance. The objective of this study was to assess the DNA sequence variability among wild and hatchery populations of Alaskan Chinook salmon at the class I α1 and class II β1 exons of the MHC. We hypothesized that the 96 wild samples taken from the Deshka River would display greater levels of observed heterozygosity (Ho) relative to expected heterozygosity (He) in suggesting that individuals with similar phenotypes mate with one another more frequently than would be expected under random mating patterns. Conversely, since no mate selection occurs in the William Jack Hernandez Sport Fish hatchery, we would not expect to see this discrepancy (He = Ho) in the 96 hatchery fish tested in this study. Alternatively, we hypothesized that post-mating selection is driving higher levels of observed heterozygosity as opposed to mate selection. If this is the case, we will observe higher than expected levels of heterozygosity among hatchery salmon. Both populations displayed higher levels of observed heterozygosity than expected heterozygosity at the Class I and II loci but genetic differentiation between the spatially distinct communities was minimal. Class I sequences showed evidence of balancing selection, despite high rates of non-synonymous substitutions observed, specifically at the peptide binding regions of both MHC genes. Text Ocean acidification Alaska MDPI Open Access Publishing Hernandez ENVELOPE(-62.167,-62.167,-74.500,-74.500) Animals 13 4 593 |
institution |
Open Polar |
collection |
MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
Oncorhynchus Chinook salmon Alaska Susitna River MHC Class I and II loci population genomics heterozygosity selection non-synonymous substitution peptide binding region |
spellingShingle |
Oncorhynchus Chinook salmon Alaska Susitna River MHC Class I and II loci population genomics heterozygosity selection non-synonymous substitution peptide binding region Evan J. Wilson Andrew M. Shedlock Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
topic_facet |
Oncorhynchus Chinook salmon Alaska Susitna River MHC Class I and II loci population genomics heterozygosity selection non-synonymous substitution peptide binding region |
description |
Genetic diversity plays a vital role in the adaptability of salmon to changing environmental conditions that can introduce new selective pressures on populations. Variability among local subpopulations may increase the chance that certain advantageous genes are passed down to future generations to mitigate susceptibility to novel diseases, warming oceans, loss of genetic stocks, and ocean acidification. Class I and II genes of the major histocompatibility complex (MHC) are crucial for the fitness of Chinook salmon due to the role they play in disease and pathogen resistance. The objective of this study was to assess the DNA sequence variability among wild and hatchery populations of Alaskan Chinook salmon at the class I α1 and class II β1 exons of the MHC. We hypothesized that the 96 wild samples taken from the Deshka River would display greater levels of observed heterozygosity (Ho) relative to expected heterozygosity (He) in suggesting that individuals with similar phenotypes mate with one another more frequently than would be expected under random mating patterns. Conversely, since no mate selection occurs in the William Jack Hernandez Sport Fish hatchery, we would not expect to see this discrepancy (He = Ho) in the 96 hatchery fish tested in this study. Alternatively, we hypothesized that post-mating selection is driving higher levels of observed heterozygosity as opposed to mate selection. If this is the case, we will observe higher than expected levels of heterozygosity among hatchery salmon. Both populations displayed higher levels of observed heterozygosity than expected heterozygosity at the Class I and II loci but genetic differentiation between the spatially distinct communities was minimal. Class I sequences showed evidence of balancing selection, despite high rates of non-synonymous substitutions observed, specifically at the peptide binding regions of both MHC genes. |
format |
Text |
author |
Evan J. Wilson Andrew M. Shedlock |
author_facet |
Evan J. Wilson Andrew M. Shedlock |
author_sort |
Evan J. Wilson |
title |
Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
title_short |
Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
title_full |
Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
title_fullStr |
Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
title_full_unstemmed |
Evaluating the Potential Fitness Effects of Chinook Salmon (Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra |
title_sort |
evaluating the potential fitness effects of chinook salmon (oncorhynchus tshawytscha) aquaculture using non-invasive population genomic analyses of mhc nucleotide substitution spectra |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2023 |
url |
https://doi.org/10.3390/ani13040593 |
op_coverage |
agris |
long_lat |
ENVELOPE(-62.167,-62.167,-74.500,-74.500) |
geographic |
Hernandez |
geographic_facet |
Hernandez |
genre |
Ocean acidification Alaska |
genre_facet |
Ocean acidification Alaska |
op_source |
Animals; Volume 13; Issue 4; Pages: 593 |
op_relation |
Animal Genetics and Genomics https://dx.doi.org/10.3390/ani13040593 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/ani13040593 |
container_title |
Animals |
container_volume |
13 |
container_issue |
4 |
container_start_page |
593 |
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1774721687747559424 |