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Wang W, Huang J, Hu Y, Feng J, Gao D, Fang W, Xu M, Ma C, Fu Z, Chen Q, Liang X, Lu J. Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:60-73. [PMID: 38147145 DOI: 10.1007/s10126-023-10277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
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Affiliation(s)
- Wenhao Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yan Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianxiang Feng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Dong Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Meng Xu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chunlei Ma
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhenqiang Fu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Qinglong Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xuanguang Liang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China.
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da Fonseca RR, Campos PF, Rey-Iglesia A, Barroso GV, Bergeron LA, Nande M, Tuya F, Abidli S, Pérez M, Riveiro I, Carrera P, Jurado-Ruzafa A, G. Santamaría MT, Faria R, Machado AM, Fonseca MM, Froufe E, C. Castro LF. Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia. Genes (Basel) 2024; 15:170. [PMID: 38397160 PMCID: PMC10888339 DOI: 10.3390/genes15020170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/08/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Paula F. Campos
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark;
| | - Gustavo V. Barroso
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA;
| | - Lucie A. Bergeron
- Section for Ecology and Evolution, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Manuel Nande
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Fernando Tuya
- Grupo en Biodiversidad y Conservación, IU-ECOAQUA, Universidad de Las Palmas de Gran Canaria, 35017 Las Palmas, Spain;
| | - Sami Abidli
- Laboratory of Environment Bio-Monitoring, Faculty of Sciences of Bizerte, University of Carthage, Bizerte 7021, Tunisia;
| | - Montse Pérez
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Isabel Riveiro
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Pablo Carrera
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, IEO-CSIC, 36390 Vigo, Spain; (M.P.); (I.R.); (P.C.)
| | - Alba Jurado-Ruzafa
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - M. Teresa G. Santamaría
- Centro Oceanográfico de Canarias, Instituto Español de Oceanografía, IEO-CSIC, 38180 Santa Cruz de Tenerife, Spain; (A.J.-R.); (M.T.G.S.)
| | - Rui Faria
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - André M. Machado
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Miguel M. Fonseca
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - Elsa Froufe
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
| | - L. Filipe C. Castro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4050-123 Porto, Portugal; (M.N.); (R.F.); (A.M.M.); (M.M.F.); (E.F.)
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
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Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
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Heraghty SD, Jackson JM, Lozier JD. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii. Mol Ecol 2023; 32:5479-5497. [PMID: 37702957 DOI: 10.1111/mec.17125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023]
Abstract
Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.
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Affiliation(s)
- Sam D Heraghty
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jason M Jackson
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, USA
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Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
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Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
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