Population structure of the critically endangered Brazilian guitarfish Pseudobatos horkelii (Rhinobatidae) revealed by double‐digest restriction site‐associated DNA sequencing

Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most threatened groups of vertebrates, with about one‐third of the species subject to some degree of threat. This is the case for Pseudobatos horkelii,...

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Veröffentlicht in:	Aquatic conservation Jg. 34; H. 1
Hauptverfasser:	Torres, Yan, Rotundo, Matheus Marcos, Vianna, Marcelo, Charvet, Patricia, Faria, Vicente Vieira, Oliveira, Claudio, Foresti, Fausto, Cruz, Vanessa Paes
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	Oxford Wiley Subscription Services, Inc 01.01.2024
Schlagworte:	Brazil Clusters coasts Conservation Deoxyribonucleic acid DNA DNA sequences DNA sequencing elasmobranchs Endangered & extinct species Endangered species freshwater Gene flow Genetic diversity Genetic structure Genetic variation genetics genomic Habitat fragmentation Heterozygosity Marine fishes Nucleotides Ocean circulation Overfishing Polymorphism Population genetics Population structure Population studies Populations Pseudobatos horkelii Rare species Rhinobatidae Single-nucleotide polymorphism SNPs Species diversity threatened species Upwelling Vertebrates Wildlife conservation Brazil Rio de Janeiro Brazil
ISSN:	1052-7613, 1099-0755
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Abstract	Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most threatened groups of vertebrates, with about one‐third of the species subject to some degree of threat. This is the case for Pseudobatos horkelii, the Brazilian guitarfish, which has suffered severe population reductions (>80%) in recent decades, mainly through coastal overfishing. Understanding the genetic diversity of this species is paramount to applying adequate management and conservation strategies. In this context, the present study evaluated the genetic diversity of P. horkelii, employing single‐nucleotide polymorphism (SNP) nuclear markers obtained by double‐digest restriction site‐associated DNA sequencing (ddRADseq). Samples collected in three areas along the Brazilian Coast (Rio de Janeiro, São Paulo, and Rio Grande do Sul) provided an average of 1,565,339 reads and 2,846 SNPs. The results indicate the presence of at least two genetically distinct populations along the Brazilian Coast, with molecular diversity differences noted among clusters. The heterozygosity excess observed in all populations is likely the result of a bottleneck, probably resulting from overfishing and habitat fragmentation. Moreover, the upwelling phenomenon in Cabo Frio, in the state of Rio de Janeiro, may have a significant influence over the observed genetic structure. The gene flow between the clusters was estimated and was noted as asymmetric between the populations studied. The observed patterns may be the result of the combination of biological characteristics and overfishing pressure in the past decades. The evidence of structured populations presenting genetic diversity differences provides insightful information for the development of stock management and conservation strategies for the Brazilian guitarfish.
AbstractList	Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most threatened groups of vertebrates, with about one‐third of the species subject to some degree of threat. This is the case for Pseudobatos horkelii, the Brazilian guitarfish, which has suffered severe population reductions (>80%) in recent decades, mainly through coastal overfishing. Understanding the genetic diversity of this species is paramount to applying adequate management and conservation strategies.In this context, the present study evaluated the genetic diversity of P. horkelii, employing single‐nucleotide polymorphism (SNP) nuclear markers obtained by double‐digest restriction site‐associated DNA sequencing (ddRADseq). Samples collected in three areas along the Brazilian Coast (Rio de Janeiro, São Paulo, and Rio Grande do Sul) provided an average of 1,565,339 reads and 2,846 SNPs.The results indicate the presence of at least two genetically distinct populations along the Brazilian Coast, with molecular diversity differences noted among clusters. The heterozygosity excess observed in all populations is likely the result of a bottleneck, probably resulting from overfishing and habitat fragmentation. Moreover, the upwelling phenomenon in Cabo Frio, in the state of Rio de Janeiro, may have a significant influence over the observed genetic structure.The gene flow between the clusters was estimated and was noted as asymmetric between the populations studied. The observed patterns may be the result of the combination of biological characteristics and overfishing pressure in the past decades. The evidence of structured populations presenting genetic diversity differences provides insightful information for the development of stock management and conservation strategies for the Brazilian guitarfish. Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most threatened groups of vertebrates, with about one‐third of the species subject to some degree of threat. This is the case for Pseudobatos horkelii , the Brazilian guitarfish, which has suffered severe population reductions (>80%) in recent decades, mainly through coastal overfishing. Understanding the genetic diversity of this species is paramount to applying adequate management and conservation strategies. In this context, the present study evaluated the genetic diversity of P. horkelii , employing single‐nucleotide polymorphism (SNP) nuclear markers obtained by double‐digest restriction site‐associated DNA sequencing (ddRADseq). Samples collected in three areas along the Brazilian Coast (Rio de Janeiro, São Paulo, and Rio Grande do Sul) provided an average of 1,565,339 reads and 2,846 SNPs. The results indicate the presence of at least two genetically distinct populations along the Brazilian Coast, with molecular diversity differences noted among clusters. The heterozygosity excess observed in all populations is likely the result of a bottleneck, probably resulting from overfishing and habitat fragmentation. Moreover, the upwelling phenomenon in Cabo Frio, in the state of Rio de Janeiro, may have a significant influence over the observed genetic structure. The gene flow between the clusters was estimated and was noted as asymmetric between the populations studied. The observed patterns may be the result of the combination of biological characteristics and overfishing pressure in the past decades. The evidence of structured populations presenting genetic diversity differences provides insightful information for the development of stock management and conservation strategies for the Brazilian guitarfish. Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most threatened groups of vertebrates, with about one‐third of the species subject to some degree of threat. This is the case for Pseudobatos horkelii, the Brazilian guitarfish, which has suffered severe population reductions (>80%) in recent decades, mainly through coastal overfishing. Understanding the genetic diversity of this species is paramount to applying adequate management and conservation strategies. In this context, the present study evaluated the genetic diversity of P. horkelii, employing single‐nucleotide polymorphism (SNP) nuclear markers obtained by double‐digest restriction site‐associated DNA sequencing (ddRADseq). Samples collected in three areas along the Brazilian Coast (Rio de Janeiro, São Paulo, and Rio Grande do Sul) provided an average of 1,565,339 reads and 2,846 SNPs. The results indicate the presence of at least two genetically distinct populations along the Brazilian Coast, with molecular diversity differences noted among clusters. The heterozygosity excess observed in all populations is likely the result of a bottleneck, probably resulting from overfishing and habitat fragmentation. Moreover, the upwelling phenomenon in Cabo Frio, in the state of Rio de Janeiro, may have a significant influence over the observed genetic structure. The gene flow between the clusters was estimated and was noted as asymmetric between the populations studied. The observed patterns may be the result of the combination of biological characteristics and overfishing pressure in the past decades. The evidence of structured populations presenting genetic diversity differences provides insightful information for the development of stock management and conservation strategies for the Brazilian guitarfish.
Author	Faria, Vicente Vieira Oliveira, Claudio Vianna, Marcelo Charvet, Patricia Torres, Yan Cruz, Vanessa Paes Rotundo, Matheus Marcos Foresti, Fausto
Author_xml	– sequence: 1 givenname: Yan orcidid: 0000-0001-5520-4092 surname: Torres fullname: Torres, Yan email: yanttp@gmail.com organization: Universidade Federal do Ceará – sequence: 2 givenname: Matheus Marcos surname: Rotundo fullname: Rotundo, Matheus Marcos organization: Universidade Santa Cecília, UNISANTA – sequence: 3 givenname: Marcelo surname: Vianna fullname: Vianna, Marcelo organization: IMAM – AquaRio, Rio de Janeiro Aquarium Research Center – sequence: 4 givenname: Patricia surname: Charvet fullname: Charvet, Patricia organization: Universidade Federal do Ceará – sequence: 5 givenname: Vicente Vieira surname: Faria fullname: Faria, Vicente Vieira organization: Universidade Federal do Ceará – sequence: 6 givenname: Claudio surname: Oliveira fullname: Oliveira, Claudio organization: Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP) – sequence: 7 givenname: Fausto surname: Foresti fullname: Foresti, Fausto organization: Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP) – sequence: 8 givenname: Vanessa Paes surname: Cruz fullname: Cruz, Vanessa Paes organization: Instituto de Biociências de Botucatu, Universidade Estadual Paulista (UNESP)
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Notes	Funding information This study was supported by a grant from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grant no. 426365/2018‐6) to VPC and a doctoral scholarship from the Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico (FUNCAP) to YT. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
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Snippet	Molecular analysis is a powerful tool for assessing and developing conservation strategies for endangered species. Elasmobranchs comprise one of the most...
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SubjectTerms	Brazil Clusters coasts Conservation Deoxyribonucleic acid DNA DNA sequences DNA sequencing elasmobranchs Endangered & extinct species Endangered species freshwater Gene flow Genetic diversity Genetic structure Genetic variation genetics genomic Habitat fragmentation Heterozygosity Marine fishes Nucleotides Ocean circulation Overfishing Polymorphism Population genetics Population structure Population studies Populations Pseudobatos horkelii Rare species Rhinobatidae Single-nucleotide polymorphism SNPs Species diversity threatened species Upwelling Vertebrates Wildlife conservation
Title	Population structure of the critically endangered Brazilian guitarfish Pseudobatos horkelii (Rhinobatidae) revealed by double‐digest restriction site‐associated DNA sequencing
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