MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)

Ratcliffe, Frances; De, Carlos Garcia; del, Sofia Consuegra

doi:10.1111/age.13184

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MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)

Frances Ratcliffe, Carlos Garcia De Leaniz

, Sofia Consuegra del Olmo

Animal Genetics, Volume: 53, Issue: 3, Pages: 340 - 351

Swansea University Authors: Frances Ratcliffe, Carlos Garcia De Leaniz , Sofia Consuegra del Olmo

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DOI (Published version): 10.1111/age.13184

Abstract

Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose st...

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Published in:	Animal Genetics
ISSN:	0268-9146 1365-2052
Published:	Wiley 2022
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URI:	https://cronfa.swan.ac.uk/Record/cronfa59982
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European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite management measures to protect them and identifying their fine population structure is needed for managing their exploitation. As for other marine fishes, neutral genetic markers indicate that eastern Atlantic sea bass form a panmictic population and is currently managed as arbitrarily divided stocks. The genes of the major histocompatibility complex (MHC) are key components of the adaptive immune system and ideal candidates to assess fine structuring arising from local selective pressures. We used Illumina sequencing to characterise allelic composition and signatures of selection at the MHC class I-α region of six D. labrax populations across the Atlantic range. We found high allelic diversity driven by positive selection, corresponding to moderate supertype diversity, with 131 alleles clustering into four to eight supertypes, depending on the Bayesian information criterion threshold applied, and a mean number of 13 alleles per individual. Alleles could not be assigned to particular loci, but private alleles allowed us to detect regional genetic structuring not found previously using neutral markers. Our results suggest that MHC markers can be used to detect cryptic population structuring in marine species where neutral markers fail to identify differentiation. 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spelling	2022-10-10T11:30:34.9133959 v2 59982 2022-05-09 MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax) 613553b7a567deeb0e75d38a2702a5f0 Frances Ratcliffe Frances Ratcliffe true false 1c70acd0fd64edb0856b7cf34393ab02 0000-0003-1650-2729 Carlos Garcia De Leaniz Carlos Garcia De Leaniz true false 241f2810ab8f56be53ca8af23e384c6e 0000-0003-4403-2509 Sofia Consuegra del Olmo Sofia Consuegra del Olmo true false 2022-05-09 SBI Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite management measures to protect them and identifying their fine population structure is needed for managing their exploitation. As for other marine fishes, neutral genetic markers indicate that eastern Atlantic sea bass form a panmictic population and is currently managed as arbitrarily divided stocks. The genes of the major histocompatibility complex (MHC) are key components of the adaptive immune system and ideal candidates to assess fine structuring arising from local selective pressures. We used Illumina sequencing to characterise allelic composition and signatures of selection at the MHC class I-α region of six D. labrax populations across the Atlantic range. We found high allelic diversity driven by positive selection, corresponding to moderate supertype diversity, with 131 alleles clustering into four to eight supertypes, depending on the Bayesian information criterion threshold applied, and a mean number of 13 alleles per individual. Alleles could not be assigned to particular loci, but private alleles allowed us to detect regional genetic structuring not found previously using neutral markers. Our results suggest that MHC markers can be used to detect cryptic population structuring in marine species where neutral markers fail to identify differentiation. This is particularly critical for fisheries management, and of potential use for selective breeding or identifying escapes from sea farms. Journal Article Animal Genetics 53 3 340 351 Wiley 0268-9146 1365-2052 aquaculture; fisheries; non-neutral markers 1 6 2022 2022-06-01 10.1111/age.13184 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University European Regional Development fund. Grant Number: BLUEFISH 2022-10-10T11:30:34.9133959 2022-05-09T09:40:54.7135807 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Frances Ratcliffe 1 Carlos Garcia De Leaniz 0000-0003-1650-2729 2 Sofia Consuegra del Olmo 0000-0003-4403-2509 3 59982__24134__56b72aab9e3e4fe49847a2b39db00228.pdf 59982.pdf 2022-05-20T11:30:31.3802120 Output 4515498 application/pdf Version of Record true © 2022 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License true eng http://creativecommons.org/licenses/by-nc-nd/4.0/
title	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
spellingShingle	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax) Frances Ratcliffe Carlos Garcia De Leaniz Sofia Consuegra del Olmo
title_short	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
title_full	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
title_fullStr	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
title_full_unstemmed	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
title_sort	MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)
author_id_str_mv	613553b7a567deeb0e75d38a2702a5f0 1c70acd0fd64edb0856b7cf34393ab02 241f2810ab8f56be53ca8af23e384c6e
author_id_fullname_str_mv	613553b7a567deeb0e75d38a2702a5f0_*_Frances Ratcliffe 1c70acd0fd64edb0856b7cf34393ab02__Carlos Garcia De Leaniz 241f2810ab8f56be53ca8af23e384c6e_**_Sofia Consuegra del Olmo
author	Frances Ratcliffe Carlos Garcia De Leaniz Sofia Consuegra del Olmo
author2	Frances Ratcliffe Carlos Garcia De Leaniz Sofia Consuegra del Olmo
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container_title	Animal Genetics
container_volume	53
container_issue	3
container_start_page	340
publishDate	2022
institution	Swansea University
issn	0268-9146 1365-2052
doi_str_mv	10.1111/age.13184
publisher	Wiley
college_str	Faculty of Science and Engineering
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description	Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite management measures to protect them and identifying their fine population structure is needed for managing their exploitation. As for other marine fishes, neutral genetic markers indicate that eastern Atlantic sea bass form a panmictic population and is currently managed as arbitrarily divided stocks. The genes of the major histocompatibility complex (MHC) are key components of the adaptive immune system and ideal candidates to assess fine structuring arising from local selective pressures. We used Illumina sequencing to characterise allelic composition and signatures of selection at the MHC class I-α region of six D. labrax populations across the Atlantic range. We found high allelic diversity driven by positive selection, corresponding to moderate supertype diversity, with 131 alleles clustering into four to eight supertypes, depending on the Bayesian information criterion threshold applied, and a mean number of 13 alleles per individual. Alleles could not be assigned to particular loci, but private alleles allowed us to detect regional genetic structuring not found previously using neutral markers. Our results suggest that MHC markers can be used to detect cryptic population structuring in marine species where neutral markers fail to identify differentiation. This is particularly critical for fisheries management, and of potential use for selective breeding or identifying escapes from sea farms.
published_date	2022-06-01T04:17:42Z
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MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax)

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