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Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas / FRANCES RATCLIFFE

Swansea University Author: FRANCES RATCLIFFE

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DOI (Published version): 10.23889/SUthesis.59261

Abstract

The North Celtic and Irish seas are extensively fished and, due to their shallow coastal nature, are particularly vulnerable to climate change stressors. Fish species assemblages in the region are characterised by high levels of diversity and include species of commercial and recreational importance...

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Published: Swansea 2022
Institution: Swansea University
Degree level: Doctoral
Degree name: Ph.D
Supervisor: Consuegra del Olmo, Sonia
URI: https://cronfa.swan.ac.uk/Record/cronfa59261
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first_indexed 2022-01-28T10:28:59Z
last_indexed 2022-01-29T03:42:56Z
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spelling 2022-01-28T10:48:41.8286028 v2 59261 2022-01-28 Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas 705c44c2abe741b81754ba155cf975aa FRANCES RATCLIFFE FRANCES RATCLIFFE true false 2022-01-28 The North Celtic and Irish seas are extensively fished and, due to their shallow coastal nature, are particularly vulnerable to climate change stressors. Fish species assemblages in the region are characterised by high levels of diversity and include species of commercial and recreational importance, however poor larval recruitment and high fishing mortality have led to declines in abundance for some species. Monitoring of larval recruits and heavily exploited fish populations is essential for future sustainable fisheries management in a changing climate. This work aimed to develop and optimize molecular techniques for assessing fish communities in spawning grounds and fine scale population structure using adaptive molecular markers. Firstly, metabarcoding of bulk fish larvae homogenates was optimised by standardizing input material and using conserved priming sites, resulting in quantitative relative abundance estimates. This demonstrated that bulk larvae metabarcoding is a feasible alternative to traditional morphological assessment for assessing community diversity and composition. Secondly, species detections in spawning grounds from water sample and bulk larval sample metabarcoding were compared resulting in a 75% average agreement in detections across sample sites. Thirdly, a class I major histocompatibility complex (MHC) marker was developed and tested to assess sea bass population structure, allelic diversity and positive selection. Private alleles within the Celtic Shelf and Portuguese populations were identified. Finally, signals of positive selection and trans-species functional supertype structure in the MHC class II alpha and beta domains of the clade (series) Eupercaria were compared. Contrary to findings in other vertebrates, both domains exhibited similar levels of selection and should therefore be considered candidate regions for population structure studies in this clade. This thesis demonstrates that the molecular techniques demonstrated supplement, and in some cases improve on, existing monitoring and population assessment techniques and contribute to the sustainable management of fishes in the North Celtic and Irish seas. E-Thesis Swansea Fish larvae, metabarcoding, Dicentrarchus labrax, Major Histocompatibility Complex 28 1 2022 2022-01-28 10.23889/SUthesis.59261 ORCiD identifier: https://orcid.org/0000-0001-5185-9200 COLLEGE NANME COLLEGE CODE Swansea University Consuegra del Olmo, Sonia Doctoral Ph.D Ireland Wales Co-operation Programme 2014 – 2020 (BlueFish project) 2022-01-28T10:48:41.8286028 2022-01-28T10:25:11.5680156 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences FRANCES RATCLIFFE 1 59261__22243__ee1d3babd70d49a7b43b582c4ed6ac87.pdf Ratcliffe_Frances_C_PhD_Thesis_Final_Cronfa.pdf 2022-01-28T10:36:30.7085037 Output 6073951 application/pdf E-Thesis – open access true Copyright: The author, Frances C. Ratcliffe, 2022. true eng
title Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
spellingShingle Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
FRANCES RATCLIFFE
title_short Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
title_full Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
title_fullStr Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
title_full_unstemmed Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
title_sort Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas
author_id_str_mv 705c44c2abe741b81754ba155cf975aa
author_id_fullname_str_mv 705c44c2abe741b81754ba155cf975aa_***_FRANCES RATCLIFFE
author FRANCES RATCLIFFE
author2 FRANCES RATCLIFFE
format E-Thesis
publishDate 2022
institution Swansea University
doi_str_mv 10.23889/SUthesis.59261
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
active_str 0
description The North Celtic and Irish seas are extensively fished and, due to their shallow coastal nature, are particularly vulnerable to climate change stressors. Fish species assemblages in the region are characterised by high levels of diversity and include species of commercial and recreational importance, however poor larval recruitment and high fishing mortality have led to declines in abundance for some species. Monitoring of larval recruits and heavily exploited fish populations is essential for future sustainable fisheries management in a changing climate. This work aimed to develop and optimize molecular techniques for assessing fish communities in spawning grounds and fine scale population structure using adaptive molecular markers. Firstly, metabarcoding of bulk fish larvae homogenates was optimised by standardizing input material and using conserved priming sites, resulting in quantitative relative abundance estimates. This demonstrated that bulk larvae metabarcoding is a feasible alternative to traditional morphological assessment for assessing community diversity and composition. Secondly, species detections in spawning grounds from water sample and bulk larval sample metabarcoding were compared resulting in a 75% average agreement in detections across sample sites. Thirdly, a class I major histocompatibility complex (MHC) marker was developed and tested to assess sea bass population structure, allelic diversity and positive selection. Private alleles within the Celtic Shelf and Portuguese populations were identified. Finally, signals of positive selection and trans-species functional supertype structure in the MHC class II alpha and beta domains of the clade (series) Eupercaria were compared. Contrary to findings in other vertebrates, both domains exhibited similar levels of selection and should therefore be considered candidate regions for population structure studies in this clade. This thesis demonstrates that the molecular techniques demonstrated supplement, and in some cases improve on, existing monitoring and population assessment techniques and contribute to the sustainable management of fishes in the North Celtic and Irish seas.
published_date 2022-01-28T04:16:26Z
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score 11.013148

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