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D'Anatro A, Calvelo J, Feijóo M, Giorello FM. Differential expression analyses and detection of SNP loci associated with environmental variables: Are salinity and temperature factors involved in population differentiation and speciation in Odontesthes? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101262. [PMID: 38861850 DOI: 10.1016/j.cbd.2024.101262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/13/2024]
Abstract
Environmental factors play a key role in individual adaptation to different local conditions. Because of this, studies about the physiological and genetic responses of individuals exposed to different natural environments offer clues about mechanisms involved in population differentiation, and as a subsequent result, speciation. Marine environments are especially suited to survey this kind of phenomena because they commonly harbor species adapted to different local conditions along a geographic continuum. Silversides belonging to Odontesthes are commonly distributed in tropical and temperate regions of South America and exhibit noticeable phenotypic plasticity, which allows them to adapt to contrasting environments. In this study, the genetic expression of O. argentinensis sampled along the Uruguayan Atlantic coast and estuarine adjacent areas was investigated. In addition, the correlation between individual genotypes and environmental variables was also analysed in O. argentinensis and O. bonariensis. Results obtained suggest a differential expression pattern of low magnitude among individuals from the different areas sampled and a correlation between several SNP loci and environmental variables. The analyses carried out did not show a clear differentiation among individuals sampled along different salinity regimens, but enriched GOTerms seem to be driven by water oxygen content. On the other hand, a total of 46 SNPs analysed in O. argentinensis and O. bonariensis showed a correlation with salinity and temperature. Although none of the correlated SNPs and corresponding genes from our both analyses were directly associated with hypoxia, genes related to the cardiovascular system and muscle cell differentiation were found. All these genes are interesting candidates for future studies since they are closely related to the differentially expressed genes. Although salinity was also mentioned as an important parameter limiting introgression between O. argentinensis and O. bonariensis, it was found that salinity does not drive differential expression in O. argentinensis, but rather oxygen levels. Moreover, salinity does not directly affect the structure and genetic divergence of the populations, they appear to be structured based on their degree of isolation and geographical distance between them. Further studies, like genome-wide analyses, could help to elucidate additional genes adapted to the different environments in these silverside species.
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Affiliation(s)
- Alejandro D'Anatro
- Laboratorio de Evolución y Sistemática, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Matías Feijóo
- Centro Universitario Regional Este, Sede Treinta y Tres, Universidad de la República, Treinta y Tres, Uruguay
| | - Facundo M Giorello
- Espacio de Biología Vegetal del Noreste, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
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Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [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: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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3
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Atmore LM, Martínez-García L, Makowiecki D, André C, Lõugas L, Barrett JH, Star B. Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics. Proc Natl Acad Sci U S A 2022; 119:e2208703119. [PMID: 36282902 PMCID: PMC9659336 DOI: 10.1073/pnas.2208703119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 10/14/2023] Open
Abstract
The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.
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Affiliation(s)
- Lane M. Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Lourdes Martínez-García
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, 87-100 Toruń, Poland
| | - Carl André
- Department of Marine Sciences–Tjärnö, University of Gothenburg, 452 96 Strömstad, Sweden
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, 10120 Tallinn, Estonia
| | - James H. Barrett
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7012 Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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4
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Xuereb A, Rougemont Q, Dallaire X, Moore J, Normandeau E, Bougas B, Perreault‐Payette A, Koop BF, Withler R, Beacham T, Bernatchez L. Re-evaluating Coho salmon ( Oncorhynchus kisutch) conservation units in Canada using genomic data. Evol Appl 2022; 15:1925-1944. [PMID: 36426130 PMCID: PMC9679250 DOI: 10.1111/eva.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Abstract
Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic data sets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection. We used one of the largest genomic data sets recently published for a nonmodel species, comprising 5662 individual Coho salmon (Oncorhynchus kisutch) from 149 sampling locations and a total of 24,542 high-quality SNPs obtained using genotyping-by-sequencing and mapped to the Coho salmon reference genome to (1) evaluate the current delineation of CUs for Coho in Canada and (2) compare patterns of population structure observed using neutral and outlier loci from genotype-environment association analyses to determine whether separate CUs that capture adaptive diversity are needed. Our results reflected CU boundaries on the whole, with the majority of sampling locations managed in the same CU clustering together within genetic groups. However, additional groups that are not currently represented by CUs were also uncovered. We observed considerable overlap in the genetic clusters identified using neutral or candidate loci, indicating a general congruence in patterns of genetic variation driven by local adaptation and gene flow in this species. Consequently, we suggest that the current CU boundaries for Coho salmon are largely well-suited for meeting the Canadian Wild Salmon Policy's objective of defining biologically distinct groups, but we highlight specific areas where CU boundaries may be refined.
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Affiliation(s)
- Amanda Xuereb
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Quentin Rougemont
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRDUniv Paul Valéry MontpellierMontpellierFrance
| | - Xavier Dallaire
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Jean‐Sébastien Moore
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Eric Normandeau
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Bérénice Bougas
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Alysse Perreault‐Payette
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Ben F. Koop
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Ruth Withler
- Department of Fisheries and OceanPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Terry Beacham
- Department of Fisheries and OceanPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Louis Bernatchez
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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Geburzi JC, Heuer N, Homberger L, Kabus J, Moesges Z, Ovenbeck K, Brandis D, Ewers C. An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea. Ecol Evol 2022; 12:e8868. [PMID: 35600684 PMCID: PMC9121054 DOI: 10.1002/ece3.8868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/14/2022] Open
Abstract
Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.
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Affiliation(s)
- Jonas C. Geburzi
- Mangrove Ecology Leibniz Centre for Tropical Marine Research (ZMT) Bremen Germany
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge Massachusetts USA
- Zoological Museum Kiel University Kiel Germany
| | - Nele Heuer
- Zoological Museum Kiel University Kiel Germany
| | | | - Jana Kabus
- Zoological Museum Kiel University Kiel Germany
- Department Aquatic Ecotoxicology Institute of Ecology Diversity and Evolution Goethe University Frankfurt am Main Frankfurt am Main Germany
| | - Zoe Moesges
- Zoological Museum Kiel University Kiel Germany
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6
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Zhang Z, Li A, She Z, Wang X, Jia Z, Wang W, Zhang G, Li L. Adaptive divergence and underlying mechanisms in response to salinity gradients between two Crassostrea oysters revealed by phenotypic and transcriptomic analyses. Evol Appl 2022; 16:234-249. [PMID: 36793677 PMCID: PMC9923467 DOI: 10.1111/eva.13370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
Comparing the responses of closely related species to environmental changes is an efficient method to explore adaptive divergence, for a better understanding of the adaptive evolution of marine species under rapidly changing climates. Oysters are keystone species thrive in intertidal and estuarine areas where frequent environmental disturbance occurs including fluctuant salinity. The evolutionary divergence of two sister species of sympatric estuarine oysters, Crassostrea hongkongensis and Crassostrea ariakensis, in response to euryhaline habitats on phenotypes and gene expression, and the relative contribution of species effect, environment effect, and their interaction to the divergence were explored. After a 2-month outplanting at high- and low-salinity locations in the same estuary, the high growth rate, percent survival, and high tolerance indicated by physiological parameters suggested that the fitness of C. ariakensis was higher under high-salinity conditions and that of C. hongkongensis was higher under low-salinity conditions. Moreover, a transcriptomic analysis showed the two species exhibited differentiated transcriptional expression in high- and low-salinity habitats, largely caused by the species effect. Several of the important pathways enriched in divergent genes between species were also salinity-responsive pathways. Specifically, the pyruvate and taurine metabolism pathway and several solute carriers may contribute to the hyperosmotic adaptation of C. ariakensis, and some solute carriers may contribute to the hypoosmotic adaptation of C. hongkongensis. Our findings provide insights into the phenotypic and molecular mechanisms underlying salinity adaptation in marine mollusks, which will facilitate the assessment of the adaptive capacity of marine species in the context of climate change and will also provide practical information for marine resource conservation and aquaculture.
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Affiliation(s)
- Ziyan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,University of Chinese Academy of SciencesBeijingChina,Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Ao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Zhicai She
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine SciencesBeibu Gulf UniversityQinzhouChina
| | - Xuegang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Zhen Jia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine SciencesBeibu Gulf UniversityQinzhouChina
| | - Wei Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‐Science, Institute of OceanologyChinese Academy of SciencesQingdaoChina,University of Chinese Academy of SciencesBeijingChina,Laboratory for Marine Fisheries Science and Food Production ProcessesPilot National Laboratory for Marine Science and TechnologyQingdaoChina,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of OceanologyChinese Academy of SciencesQingdaoChina
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7
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Ratcliffe FC, Garcia de Leaniz C, Consuegra S. MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax). Anim Genet 2022; 53:340-351. [PMID: 35274334 PMCID: PMC9314080 DOI: 10.1111/age.13184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/13/2022] [Accepted: 02/20/2022] [Indexed: 01/29/2023]
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 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.
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Affiliation(s)
- Frances C Ratcliffe
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | | | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
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8
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Prentice MB, Bowman J, Murray DL, Khidas K, Wilson PJ. Spatial and environmental influences on selection in a clock gene coding trinucleotide repeat in Canada lynx (Lynx canadensis). Mol Ecol 2020; 29:4637-4652. [PMID: 32989809 DOI: 10.1111/mec.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022]
Abstract
Clock genes exhibit substantial control over gene expression and ultimately life-histories using external cues such as photoperiod, and are thus likely to be critical for adaptation to shifting seasonal conditions and novel environments as species redistribute their ranges under climate change. Coding trinucleotide repeats (cTNRs) are found within several clock genes, and may be interesting targets of selection due to their containment within exonic regions and elevated mutation rates. Here, we conduct inter-specific characterization of the NR1D1 cTNR between Canada lynx and bobcat, and intra-specific spatial and environmental association analyses of neutral microsatellites and our functional cTNR marker, to investigate the role of selection on this locus in Canada lynx. We report signatures of divergent selection between lynx and bobcat, with the potential for hybrid-mediated gene flow in the area of range overlap. We also provide evidence that this locus is under selection across Canada lynx in eastern Canada, with both spatial and environmental variables significantly contributing to the explained variation, after controlling for neutral population structure. These results suggest that cTNRs may play an important role in the generation of functional diversity within some mammal species, and allow for contemporary rates of adaptation in wild populations in response to environmental change. We encourage continued investment into the study of cTNR markers to better understand their broader relevance to the evolution and adaptation of mammals.
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Affiliation(s)
- Melanie B Prentice
- Department of Environmental & Life Sciences, Trent University, Peterborough, ON, Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, ON, Canada
| | - Dennis L Murray
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Kamal Khidas
- Vertebrate Zoology and Beaty Centre for Species Discovery, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Paul J Wilson
- Biology Department, Trent University, Peterborough, ON, Canada
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9
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Seljestad GW, Quintela M, Faust E, Halvorsen KT, Besnier F, Jansson E, Dahle G, Knutsen H, André C, Folkvord A, Glover KA. "A cleaner break": Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse ( Labrus bergylta). Ecol Evol 2020; 10:6120-6135. [PMID: 32607218 PMCID: PMC7319121 DOI: 10.1002/ece3.6404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.
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Affiliation(s)
- Gaute W. Seljestad
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | | - Ellika Faust
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Kim T. Halvorsen
- Institute of Marine ResearchAustevoll Research StationStorebøNorway
| | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchFlødevigenNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Carl André
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Arild Folkvord
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
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10
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Rahman S, Schmidt D, Hughes JM. Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude. PeerJ 2020; 8:e8139. [PMID: 31942250 PMCID: PMC6955102 DOI: 10.7717/peerj.8139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/01/2019] [Indexed: 11/29/2022] Open
Abstract
Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.
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Affiliation(s)
- Sharmeen Rahman
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Daniel Schmidt
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Jane M Hughes
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
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11
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Gkafas GA, Hatziioannou M, Malandrakis EE, Tsigenopoulos CS, Karapanagiotidis IT, Mente E, Vafidis D, Exadactylos A. Heterozygosity fitness correlations and generation interval of the Norway lobster in the Aegean Sea, eastern Mediterranean. ACTA ACUST UNITED AC 2019; 26:14. [PMID: 31728339 PMCID: PMC6842237 DOI: 10.1186/s40709-019-0103-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/18/2019] [Indexed: 11/10/2022]
Abstract
Background Comprehensively detailed information on population dynamics for benthic species is crucial since potential admixture of individuals could shift the genetic subdivision and age structure during a full breeding period. The apparent genetic impact of the potential recruitment strategy of Norway lobster Nephrops norvegicus is still under research. For this reason the present study was focused on genetic variation of the species over a given continuous year period in a semi-enclosed gulf of the Aegean Sea. Results Analyses revealed that the relative smaller size class in females and the apparent faster growth of males may represent a key-role differential strategy for the two sexes, whereas females tend to mature slower. Heterozygosity fitness correlations (HFCs) showed substantially significant associations suggesting that inbreeding depression for females and outbreeding depression for males are the proximate fitness mechanisms, respectively. Conclusions Nephrops norvegicus uniformal genetic composition (background of high gene flow), could be attributed to potential population recolonization, due to a hypothesized passive larval movement from deeper waters, which may suggest that some offspring of local residents and potential male non-breeders from other regions admixture randomly.
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Affiliation(s)
- Georgios A Gkafas
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Marianthi Hatziioannou
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Emmanouil E Malandrakis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Costas S Tsigenopoulos
- 2Institute of Marine Biology and Genetics, Hellenic Centre for Marine Research, Heraklion, Crete Greece
| | - Ioannis T Karapanagiotidis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Elena Mente
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Dimitrios Vafidis
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
| | - Athanasios Exadactylos
- 1Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, Volos, Greece
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12
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Bernard AM, Richards VP, Stanhope MJ, Shivji MS. Transcriptome-Derived Microsatellites Demonstrate Strong Genetic Differentiation in Pacific White Sharks. J Hered 2019; 109:771-779. [PMID: 30204894 DOI: 10.1093/jhered/esy045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/08/2018] [Indexed: 01/25/2023] Open
Abstract
Recent advances in genome-scale sequencing technology have allowed the development of high resolution genetic markers for the study of nonmodel taxa. In particular, transcriptome sequencing has proven to be highly useful in generating genomic markers for use in population genetic studies, allowing for insight into species connectivity, as well as local adaptive processes as many transcriptome-derived markers are found within or associated with functional genes. Herein, we developed a set of 30 microsatellite markers from a heart transcriptome for the white shark (Carcharodon carcharias), a widely distributed and globally vulnerable marine predator. Using these markers as well as 10 published anonymous genomic microsatellite loci, we provide 1) the first nuclear genetic assessment of the cross-Pacific connectivity of white sharks, and 2) a comparison of the levels of inferred differentiation across microsatellite marker sets (i.e., transcriptome vs. anonymous) to assess their respective utility to elucidate the population genetic dynamics of white sharks. Significant (FST = 0.083, P = 0.05; G″ST = 0.200; P = 0.001) genetic differentiation was found between Southwestern Pacific (n = 19) and Northeastern Pacific (n = 20) white sharks, indicating restricted, cross Pacific gene flow in this species. Transcriptome-derived microsatellite marker sets identified much higher (up to 2×) levels of genetic differentiation than anonymous genomic markers, underscoring potential utility of transcriptome markers in identifying subtle population genetic differences within highly vagile, globally distributed marine species.Subject areas: Population structure and phylogeography; Conservation genetics and biodiversity.
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Affiliation(s)
- Andrea M Bernard
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
| | - Vincent P Richards
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC
| | - Michael J Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center & Guy Harvey Research Institute, Nova Southeastern University, Halmos College of Natural Sciences and Oceanography, North Ocean Drive, Dania Beach, FL
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13
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Macedo D, Caballero I, Mateos M, Leblois R, McCay S, Hurtado LA. Population genetics and historical demographic inferences of the blue crab Callinectes sapidus in the US based on microsatellites. PeerJ 2019; 7:e7780. [PMID: 31632846 PMCID: PMC6796965 DOI: 10.7717/peerj.7780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/28/2019] [Indexed: 01/02/2023] Open
Abstract
The native range of the blue crab Callinectes sapidus spans Nova Scotia to northern Argentina. In the US, it constitutes a keystone species in estuarine habitats of the Atlantic coast and Gulf of Mexico (GOM), serving as both predator and prey to other species, and also has historically represented a multi-billion dollar fishery. Knowledge relevant to effective management and monitoring of this ecologically and economically important species, such as levels of population genetic differentiation and genetic diversity, is necessary. Although several population genetics studies have attempted to address these questions in one or more parts of its distribution, conflicting results and potential problems with the markers used, as well as other issues, have obscured our understanding on them. In this study, we examined large-scale genetic connectivity of the blue crab in the US, using 16 microsatellites, and genotyped individuals from Chesapeake Bay, in the US Atlantic, and from nine localities along the US GOM coast. Consistent with the high long-distance dispersal potential of this species, very low levels of genetic differentiation were detected for the blue crab among the ten US localities examined, suggesting it constitutes a large panmictic population within this region. Estimations of genetic diversity for the blue crab appear to be high in the US, and provide a baseline for monitoring temporal changes in this species. Demographic analyses indicate a recent range expansion of the US population, probably during the Holocene. In addition, capitalizing on published microsatellite data from southern Brazil, our analyses detected high genetic differentiation between localities in the US and Brazil. These results point to the need for examination of genetic diversity and differentiation along the area spanning the US to southern Brazil.
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Affiliation(s)
- Danielle Macedo
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Isabel Caballero
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Raphael Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Shelby McCay
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
| | - Luis A Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, USA
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Prentice MB, Bowman J, Murray DL, Klütsch CFC, Khidas K, Wilson PJ. Evaluating evolutionary history and adaptive differentiation to identify conservation units of Canada lynx (Lynx canadensis). Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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15
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Phair NL, Toonen RJ, Knapp I, von der Heyden S. Shared genomic outliers across two divergent population clusters of a highly threatened seagrass. PeerJ 2019; 7:e6806. [PMID: 31106053 PMCID: PMC6497040 DOI: 10.7717/peerj.6806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.
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Affiliation(s)
- Nikki Leanne Phair
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert John Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Ingrid Knapp
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Sophie von der Heyden
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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Kerr Q, Fuentes‐Pardo AP, Kho J, McDermid JL, Ruzzante DE. Temporal stability and assignment power of adaptively divergent genomic regions between herring ( Clupea harengus) seasonal spawning aggregations. Ecol Evol 2019; 9:500-510. [PMID: 30680131 PMCID: PMC6342187 DOI: 10.1002/ece3.4768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 11/07/2022] Open
Abstract
Atlantic herring (Clupea harengus), a vital ecosystem component and target of the largest Northwest Atlantic pelagic fishery, undergo seasonal spawning migrations that result in elusive sympatric population structure. Herring spawn mostly in fall or spring, and genomic differentiation was recently detected between these groups. Here we used a subset of this differentiation, 66 single nucleotide polymorphisms (SNPs) to analyze the temporal dynamics of this local adaptation and the applicability of SNP subsets in stock assessment. We showed remarkable temporal stability of genomic differentiation corresponding to spawning season, between samples taken a decade apart (2005 N = 90 vs. 2014 N = 71) in the Gulf of St. Lawrence, and new evidence of limited interbreeding between spawning components. We also examined an understudied and overexploited herring population in Bras d'Or lake (N = 97); using highly reduced SNP panels (N SNPs > 6), we verified little-known sympatric spawning populations within this unique inland sea. These results describe consistent local adaptation, arising from asynchronous reproduction in a migratory and dynamic marine species. Our research demonstrates the efficiency and precision of SNP-based assessments of sympatric subpopulations; and indeed, this temporally stable local adaptation underlines the importance of such fine-scale management practices.
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Affiliation(s)
- Quentin Kerr
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | | | - James Kho
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Jenni L. McDermid
- Marine Fish and Mammals Section, Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
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Verrez-Bagnis V, Sotelo CG, Mendes R, Silva H, Kappel K, Schröder U. Methods for Seafood Authenticity Testing in Europe. BIOACTIVE MOLECULES IN FOOD 2019. [DOI: 10.1007/978-3-319-78030-6_69] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Manuzzi A, Zane L, Muñoz-Merida A, Griffiths AM, Veríssimo A. Population genomics and phylogeography of a benthic coastal shark (Scyliorhinus canicula) using 2b-RAD single nucleotide polymorphisms. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly185] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Alice Manuzzi
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej, Silkeborg, Denmark
| | - Lorenzo Zane
- Department of Biology, University of Padova, Padova, Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Roma, Italy
| | - Antonio Muñoz-Merida
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
| | | | - Ana Veríssimo
- CIBIO – U.P. – Research Center for Biodiversity and Genetic Resources, Vairão, Portugal
- Virginia Institute of Marine Science, College of William and Mary, VA, USA
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19
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Jorde PE, Synnes A, Espeland SH, Sodeland M, Knutsen H. Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod. Ecol Evol 2018; 8:12547-12558. [PMID: 30619564 PMCID: PMC6308871 DOI: 10.1002/ece3.4648] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 01/03/2023] Open
Abstract
The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high-graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom-settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high-graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.
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Affiliation(s)
- Per Erik Jorde
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
- Institute of Marine ResearchHisNorway
| | - Ann‐Elin Synnes
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Sigurd Heiberg Espeland
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Marte Sodeland
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
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20
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Lo E, Bonizzoni M, Hemming-Schroeder E, Ford A, Janies DA, James AA, Afrane Y, Etemesi H, Zhou G, Githeko A, Yan G. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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21
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Al-Breiki RD, Kjeldsen SR, Afzal H, Al Hinai MS, Zenger KR, Jerry DR, Al-Abri MA, Delghandi M. Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline. BMC Genomics 2018; 19:690. [PMID: 30231936 PMCID: PMC6146514 DOI: 10.1186/s12864-018-5044-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. RESULTS After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. CONCLUSIONS Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.
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Affiliation(s)
- Rufaida Dhuhai Al-Breiki
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
- College of Agriculture and Marine Sciences, Department of Marine Sciences and Fisheries, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Shannon R. Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Hasifa Afzal
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Manal Saif Al Hinai
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4810 Australia
| | - Mohammed Ali Al-Abri
- College of Agriculture and Marine Sciences, Department of Animal and Veterinary Sciences and Technology, Sultan Qaboos University, P.O. Box 34, Al-Khoud, 123 Muscat, Sultanate of Oman
| | - Madjid Delghandi
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, P.O. Box 50, Al-Khoud, 123 Muscat, Sultanate of Oman
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Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla). Mol Phylogenet Evol 2018; 120:183-195. [DOI: 10.1016/j.ympev.2017.11.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/10/2017] [Accepted: 11/29/2017] [Indexed: 01/23/2023]
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Smith H, Epstein H, Torda G. The molecular basis of differential morphology and bleaching thresholds in two morphs of the coral Pocillopora acuta. Sci Rep 2017; 7:10066. [PMID: 28855618 PMCID: PMC5577224 DOI: 10.1038/s41598-017-10560-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 08/10/2017] [Indexed: 11/24/2022] Open
Abstract
Processes of cnidarian evolution, including hybridization and phenotypic plasticity, have complicated the clear diagnosis of species boundaries within the phylum. Pocillopora acuta, a species of scleractinian coral that was recently split from the widespread Pocillopora damicornis species complex, occurs in at least two distinct morphs on the Great Barrier Reef. Contrasting morphology combined with evidence of differential bleaching thresholds among sympatrically distributed colonies suggest that the taxonomy of this recently described species is not fully resolved and may represent its own species complex. To examine the basis of sympatric differentiation between the two morphs, we combined analyses of micro- and macro-skeletal morphology with genome wide sequencing of the coral host, as well as ITS2 genotyping of the associated Symbiodinium communities. We found consistent differences between morphs on both the macro- and micro-skeletal scale. In addition, we identified 18 candidate functional genes that relate to skeletal formation and morphology that may explain how the two morphs regulate growth to achieve their distinct growth forms. With inconclusive results in endosymbiotic algal community diversity between the two morphs, we propose that colony morphology may be linked to bleaching susceptibility. We conclude that cryptic speciation may be in the early stages within the species P. acuta.
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Affiliation(s)
- Hillary Smith
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia. .,Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia. .,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia. .,AIMS@JCU, James Cook University, Townsville, Queensland 4811, Australia.
| | - Hannah Epstein
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia.,College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia.,AIMS@JCU, James Cook University, Townsville, Queensland 4811, Australia
| | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia.,Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
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Deschepper P, Brys R, Fortuna MA, Jacquemyn H. Analysis of spatial genetic variation reveals genetic divergence among populations of Primula veris associated to contrasting habitats. Sci Rep 2017; 7:8847. [PMID: 28821787 PMCID: PMC5562905 DOI: 10.1038/s41598-017-09154-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/24/2017] [Indexed: 12/01/2022] Open
Abstract
Genetic divergence by environment is a process whereby selection causes the formation of gene flow barriers between populations adapting to contrasting environments and is often considered to be the onset of speciation. Nevertheless, the extent to which genetic differentiation by environment on small spatial scales can be detected by means of neutral markers is still subject to debate. Previous research on the perennial herb Primula veris has shown that plants from grassland and forest habitats showed pronounced differences in phenology and flower morphology, suggesting limited gene flow between habitats. To test this hypothesis, we sampled 33 populations of P. veris consisting of forest and grassland patches and used clustering techniques and network analyses to identify sets of populations that are more connected to each other than to other sets of populations and estimated the timing of divergence. Our results showed that spatial genetic variation had a significantly modular structure and consisted of four well-defined modules that almost perfectly coincided with habitat features. Genetic divergence was estimated to have occurred about 114 generations ago, coinciding with historic major changes in the landscape. Overall, these results illustrate how populations adapting to different environments become structured genetically within landscapes on small spatial scales.
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Affiliation(s)
- Pablo Deschepper
- Division of Plant Ecology and Systematics, Biology Department, University of Leuven, Leuven, Belgium.
| | - Rein Brys
- Research Institute for Forest and Nature, Gaverstraat 4, B-9500, Geraardsbergen, Belgium
| | - Miguel A Fortuna
- Department of Evolutionary Biology and Environmental Studies. University of Zurich, Zurich, Switzerland
| | - Hans Jacquemyn
- Division of Plant Ecology and Systematics, Biology Department, University of Leuven, Leuven, Belgium
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25
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Genetic population structure of Indian oil sardine, Sardinella longiceps assessed using microsatellite markers. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Lin Y, Chen Y, Yi C, Fong JJ, Kim W, Rius M, Zhan A. Genetic signatures of natural selection in a model invasive ascidian. Sci Rep 2017; 7:44080. [PMID: 28266616 PMCID: PMC5339779 DOI: 10.1038/srep44080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 12/26/2022] Open
Abstract
Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta.
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Affiliation(s)
- Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Changho Yi
- Marine Biodiversity Assessment and Management Team, National Marine Biodiversity Institute of Korea, 101-75 Jangsan-ro, Janghang-eup, Seocheon-gun Chungcheongnam-do 33662, Korea
| | - Jonathan J Fong
- Science Unit, Lingnan University, 8 Castle Peak Road, Tuen Mun, New Territories, Hong Kong, China
| | - Won Kim
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Marc Rius
- Ocean and Earth Science, National Oceanography Centre, University of Southampton, European Way, Southampton SO14 3ZH, United Kingdom.,Department of Zoology, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing 100085, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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27
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Gillingham MAF, Béchet A, Courtiol A, Rendón-Martos M, Amat JA, Samraoui B, Onmuş O, Sommer S, Cézilly F. Very high MHC Class IIB diversity without spatial differentiation in the mediterranean population of greater Flamingos. BMC Evol Biol 2017; 17:56. [PMID: 28219340 PMCID: PMC5319168 DOI: 10.1186/s12862-017-0905-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/06/2017] [Indexed: 02/07/2023] Open
Abstract
Background Selective pressure from pathogens is thought to shape the allelic diversity of major histocompatibility complex (MHC) genes in vertebrates. In particular, both local adaptation to pathogens and gene flow are thought to explain a large part of the intraspecific variation observed in MHC allelic diversity. To date, however, evidence that adaptation to locally prevalent pathogens maintains MHC variation is limited to species with limited dispersal and, hence, reduced gene flow. On the one hand high gene flow can disrupt local adaptation in species with high dispersal rates, on the other hand such species are much more likely to experience spatial variation in pathogen pressure, suggesting that there may be intense pathogen mediated selection pressure operating across breeding sites in panmictic species. Such pathogen mediated selection pressure operating across breeding sites should therefore be sufficient to maintain high MHC diversity in high dispersing species in the absence of local adaptation mechanisms. We used the Greater Flamingo, Phoenicopterus roseus, a long-lived colonial bird showing a homogeneous genetic structure of neutral markers at the scale of the Mediterranean region, to test the prediction that higher MHC allelic diversity with no population structure should occur in large panmictic populations of long-distance dispersing birds than in other resident species. Results We assessed the level of allelic diversity at the MHC Class IIB exon 2 from 116 individuals born in four different breeding colonies of Greater Flamingo in the Mediterranean region. We found one of the highest allelic diversity (109 alleles, 2 loci) of any non-passerine avian species investigated so far relative to the number of individuals and loci genotyped. There was no evidence of population structure between the four major Mediterranean breeding colonies. Conclusion Our results suggest that local adaptation at MHC Class IIB in Greater Flamingos is constrained by high gene flow and high MHC diversity appears to be maintained by population wide pathogen-mediated selection rather than local pathogen-mediated selection. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in species with large panmictic populations and high dispersal rates. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0905-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark A F Gillingham
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Albert-Einstein Allee 11, D-89069, Ulm, Germany. .,Université de Bourgogne, Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, 6 bd. Gabriel, 21000, Dijon, France. .,Centre de Recherche de la Tour du Valat, Le Sambuc, 13200, Arles, France. .,Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Alfred-Kowalke-Str. 17, D-10315, Berlin, Germany.
| | - Arnaud Béchet
- Centre de Recherche de la Tour du Valat, Le Sambuc, 13200, Arles, France
| | - Alexandre Courtiol
- Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Alfred-Kowalke-Str. 17, D-10315, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), D-14195, Berlin, Germany
| | - Manuel Rendón-Martos
- R.N. Laguna de Fuente de Piedra, Consejería de Medio Ambiente y Ordenación del Territorio, Junta de Andalucía, Apartado 1, E-29520 Fuente de Piedra, (Málaga), Spain
| | - Juan A Amat
- Department of Wetland Ecology, Estación Biológica de Doñana, (EBD-CSIC), calle Américo Vespucio s/n, E-41092, Sevilla, Spain
| | - Boudjéma Samraoui
- Center of Excellence for Research in Biodiversity, King Saud University, Riyadh, Saudi Arabia.,Laboratoire de recherche et de conservation des zones humides, University of Guelma, Guelma, Algeria
| | - Ortaç Onmuş
- Natural History Museum, Faculty of Sciences, Department of Biology, Ege University, Bornova, İzmir, Turkey
| | - Simone Sommer
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Albert-Einstein Allee 11, D-89069, Ulm, Germany
| | - Frank Cézilly
- Université de Bourgogne, Equipe Ecologie Evolutive, UMR CNRS 6282 Biogéosciences, 6 bd. Gabriel, 21000, Dijon, France.,Institut Universitaire de France, Paris, France
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28
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Semenova AV, Karpov AK, Andreeva AP, Rubtsova GA, Afanas’ev KI. Temporal stability of the population genetic structure of the White Sea herring Сlupea pallasii marisalbi. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795416120127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Lal MM, Southgate PC, Jerry DR, Bosserelle C, Zenger KR. Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. BMC Genomics 2017; 18:66. [PMID: 28073363 PMCID: PMC5225542 DOI: 10.1186/s12864-016-3410-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted. The unique life history characteristics of many marine invertebrates such as high dispersal rates, stochastic survival and variable recruitment are also likely to influence how populations are organised. To examine the microevolutionary forces influencing population structure, connectivity and adaptive variation in a highly-dispersive bivalve, populations of the black-lip pearl oyster Pinctada margaritifera were examined across its ~18,000 km Indo-Pacific distribution. RESULTS Analyses utilising 9,624 genome-wide SNPs and 580 oysters, discovered differing patterns of significant and substantial broad-scale genetic structure between the Indian and Pacific Ocean basins. Indian Ocean populations were markedly divergent (F st = 0.2534-0.4177, p < 0.001), compared to Pacific Ocean oysters, where basin-wide gene flow was much higher (F st = 0.0007-0.1090, p < 0.001). Partitioning of genetic diversity (hierarchical AMOVA) attributed 18.1% of variance between ocean basins, whereas greater proportions were resolved within samples and populations (45.8% and 35.7% respectively). Visualisation of population structure at selectively neutral loci resolved three and five discrete genetic clusters for the Indian and Pacific Oceans respectively. Evaluation of genetic structure at adaptive loci for Pacific populations (89 SNPs under directional selection; F st = 0.1012-0.4371, FDR = 0.05), revealed five clusters identical to those detected at neutral SNPs, suggesting environmental heterogeneity within the Pacific. Patterns of structure and connectivity were supported by Mantel tests of isolation by distance (IBD) and independent hydrodynamic particle dispersal simulations. CONCLUSIONS It is evident that genetic structure and connectivity across the natural range of P. margaritifera is highly complex, and produced by the interaction of ocean currents, IBD and seascape features at a broad scale, together with habitat geomorphology and local adaptation at regional levels. Overall population organisation is far more elaborate than generalised CPH predictions, however valuable insights for regional fishery management, and a greater understanding of range-wide genetic structure in a highly-dispersive marine invertebrate have been gained.
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Affiliation(s)
- Monal M. Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
| | - Paul C. Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
- Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558 QLD Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
| | - Cyprien Bosserelle
- Geoscience Division, Secretariat of the Pacific Community, 241 Mead Road, Nabua, Suva Fiji Islands
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, Townsville, QLD 4811 QLD Australia
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30
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Farrell ED, Carlsson JEL, Carlsson J. Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish ( Capros aper). ROYAL SOCIETY OPEN SCIENCE 2016; 3:160651. [PMID: 28083107 PMCID: PMC5210689 DOI: 10.1098/rsos.160651] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Abstract
The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (Capros aper) across the species' range. Microsatellite loci were developed de novo and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies-a crucial element for assessment, sustainable management and conservation of valuable biological resources.
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Affiliation(s)
- Edward D. Farrell
- Area 52 Research Group, School of Biology and Environmental Science/Earth Institute, University College Dublin, Belfield, Dublin 4, Republic of Ireland
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31
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Ofori BY, Beaumont LJ, Stow AJ. Cunningham's skinks show low genetic connectivity and signatures of divergent selection across its distribution. Ecol Evol 2016; 7:48-57. [PMID: 28070274 PMCID: PMC5214970 DOI: 10.1002/ece3.2627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 11/24/2022] Open
Abstract
Establishing corridors of connecting habitat has become a mainstay conservation strategy to maintain gene flow and facilitate climate‐driven range shifts. Yet, little attention has been given to ascertaining the extent to which corridors will benefit philopatric species, which might exhibit localized adaptation. Measures of genetic connectivity and adaptive genetic variation across species’ ranges can help fill this knowledge gap. Here, we characterized the spatial genetic structure of Cunningham's skink (Egernia cunninghami), a philopatric species distributed along Australia's Great Dividing Range, and assessed evidence of localized adaptation. Analysis of 4,274 SNPs from 94 individuals sampled at four localities spanning 500 km and 4° of latitude revealed strong genetic structuring at neutral loci (mean FST ± SD = 0.603 ± 0.237) among the localities. Putatively neutral SNPs and those under divergent selection yielded contrasting spatial patterns, with the latter identifying two genetically distinct clusters. Given low genetic connectivity of the four localities, we suggest that the natural movement rate of this species is insufficient to keep pace with spatial shifts to its climate envelope, irrespective of habitat availability. In addition, our finding of localized adaptation highlights the risk of outbreeding depression should the translocation of individuals be adopted as a conservation management strategy.
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Affiliation(s)
- Benjamin Y Ofori
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia; Department Animal Biology and Conservation Science University of Ghana Legon-Accra Ghana
| | - Linda J Beaumont
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia
| | - Adam J Stow
- Department of Biological Sciences Macquarie University North Ryde Macquarie Park NSW Australia
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32
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Lal MM, Southgate PC, Jerry DR, Bosserelle C, Zenger KR. A Parallel Population Genomic and Hydrodynamic Approach to Fishery Management of Highly-Dispersive Marine Invertebrates: The Case of the Fijian Black-Lip Pearl Oyster Pinctada margaritifera. PLoS One 2016; 11:e0161390. [PMID: 27559735 PMCID: PMC4999145 DOI: 10.1371/journal.pone.0161390] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/04/2016] [Indexed: 11/18/2022] Open
Abstract
Fishery management and conservation of marine species increasingly relies on genetic data to delineate biologically relevant stock boundaries. Unfortunately for high gene flow species which may display low, but statistically significant population structure, there is no clear consensus on the level of differentiation required to resolve distinct stocks. The use of fine-scale neutral and adaptive variation, considered together with environmental data can offer additional insights to this problem. Genome-wide genetic data (4,123 SNPs), together with an independent hydrodynamic particle dispersal model were used to inform farm and fishery management in the Fijian black-lip pearl oyster Pinctada margaritifera, where comprehensive fishery management is lacking, and the sustainability of exploitation uncertain. Weak fine-scale patterns of population structure were detected, indicative of broad-scale panmixia among wild oysters, while a hatchery-sourced farmed population exhibited a higher degree of genetic divergence (Fst = 0.0850-0.102). This hatchery-produced population had also experienced a bottleneck (NeLD = 5.1; 95% C.I. = [5.1-5.3]); compared to infinite NeLD estimates for all wild oysters. Simulation of larval transport pathways confirmed the existence of broad-scale mixture by surface ocean currents, correlating well with fine-scale patterns of population structuring. Fst outlier tests failed to detect large numbers of loci supportive of selection, with 2-5 directional outlier SNPs identified (average Fst = 0.116). The lack of biologically significant population genetic structure, absence of evidence for local adaptation and larval dispersal simulation, all indicate the existence of a single genetic stock of P. margaritifera in the Fiji Islands. This approach using independent genomic and oceanographic tools has allowed fundamental insights into stock structure in this species, with transferability to other highly-dispersive marine taxa for their conservation and management.
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Affiliation(s)
- Monal M. Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Paul C. Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Centre for Pacific Islands Research, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Dean R. Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Cyprien Bosserelle
- Geoscience Division, Secretariat of the Pacific Community, Nabua, Suva, Fiji Islands
| | - Kyall R. Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
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33
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Takeshima H, Iguchi K, Hashiguchi Y, Nishida M. Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis. Mol Ecol 2016; 25:3048-64. [PMID: 27085501 DOI: 10.1111/mec.13650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/21/2016] [Accepted: 04/12/2016] [Indexed: 01/27/2023]
Abstract
In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic variability in, and differentiation between, ayu populations around the Japan-Ryukyu Archipelago were investigated in 4746 individuals collected from 120 localities by genotyping 12 microsatellite markers. These individuals represented the two subspecies of ayu, namely the Ryukyuan subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and landlocked forms of the nominotypical subspecies (P. a. altivelis) along the archipelago. We successfully detected an absence of genetic differentiation within the landlocked form and subtle but significant differentiation and clear geographic patterns of genetic variation among populations of the amphidromous form, which had been considered genetically homogeneous. This suggests that dense locality sampling effectively resolves subtle differences in genetic population structure, reducing stochastic deviation in the detection of genetic differentiation and geographic patterns in local populations of this dispersive species. Resampling analyses based on empirical data sets clearly demonstrate the effectiveness of increasing the number of locality samples for stable and reliable estimations of genetic fixation indices. The genetic population structure observed within the amphidromous form provides useful information for identifying management or conservation units in ayu.
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Affiliation(s)
- Hirohiko Takeshima
- Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Kei'ichiro Iguchi
- Fisheries Research Agency, National Research Institute of Fisheries Science, Komaki 1088, Ueda, Nagano, 386-0031, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Osaka Medical College, Daigaku-machi 2-7, Takatsuki, Osaka, 569-8686, Japan
| | - Mutsumi Nishida
- Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
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34
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Guo B, Li Z, Merilä J. Population genomic evidence for adaptive differentiation in the Baltic Sea herring. Mol Ecol 2016; 25:2833-52. [DOI: 10.1111/mec.13657] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 03/31/2016] [Accepted: 04/14/2016] [Indexed: 01/30/2023]
Affiliation(s)
- Baocheng Guo
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Zitong Li
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
| | - Juha Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; P.O. Box 65 Helsinki FI-00014 Finland
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35
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Liu BJ, Zhang BD, Xue DX, Gao TX, Liu JX. Population Structure and Adaptive Divergence in a High Gene Flow Marine Fish: The Small Yellow Croaker (Larimichthys polyactis). PLoS One 2016; 11:e0154020. [PMID: 27100462 PMCID: PMC4839715 DOI: 10.1371/journal.pone.0154020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/07/2016] [Indexed: 11/18/2022] Open
Abstract
The spatial distribution of genetic diversity has been long considered as a key component of policy development for management and conservation of marine fishes. However, unraveling the population genetic structure of migratory fish species is challenging due to high potential for gene flow. Despite the shallow population differentiation revealed by putatively neutral loci, the higher genetic differentiation with panels of putatively adaptive loci could provide greater resolution for stock identification. Here, patterns of population differentiation of small yellow croaker (Larimichthys polyactis) were investigated by genotyping 15 highly polymorphic microsatellites in 337 individuals of 15 geographic populations collected from both spawning and overwintering grounds. Outlier analyses indicated that the locus Lpol03 might be under directional selection, which showed a strong homology with Grid2 gene encoding the glutamate receptor δ2 protein (GluRδ2). Based on Lpol03, two distinct clusters were identified by both STRUCTURE and PCoA analyses, suggesting that there were two overwintering aggregations of L. polyactis. A novel migration pattern was suggested for L. polyactis, which was inconsistent with results of previous studies based on historical fishing yield statistics. These results provided new perspectives on the population genetic structure and migratory routes of L. polyactis, which could have significant implications for sustainable management and utilization of this important fishery resource.
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Affiliation(s)
- Bing-Jian Liu
- Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bai-Dong Zhang
- Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Xiu Xue
- Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tian-Xiang Gao
- School of Fisheries, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Jin-Xian Liu
- Key Laboratory of Marine Ecology and Environmental Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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36
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Bekkevold D, Gross R, Arula T, Helyar SJ, Ojaveer H. Outlier Loci Detect Intraspecific Biodiversity amongst Spring and Autumn Spawning Herring across Local Scales. PLoS One 2016; 11:e0148499. [PMID: 27050440 PMCID: PMC4822851 DOI: 10.1371/journal.pone.0148499] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities.
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Affiliation(s)
- Dorte Bekkevold
- Technical University of Denmark, National Institute of Aquatic Resources, Charlottenlund, Denmark
- * E-mail:
| | - Riho Gross
- Estonian University of Life Sciences, Institute of Veterinary Medicine and Animal Sciences, Department of Aquaculture, Tartu, Estonia
| | - Timo Arula
- University of Tartu, Estonian Marine Institute, Pärnu, Estonia
| | - Sarah J. Helyar
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Henn Ojaveer
- University of Tartu, Estonian Marine Institute, Pärnu, Estonia
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37
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Faulks LK, Östman Ö. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics. JOURNAL OF FISH BIOLOGY 2016; 88:1564-1583. [PMID: 26940068 DOI: 10.1111/jfb.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended.
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Affiliation(s)
- L K Faulks
- Department of Ecology and Genetics - Animal Ecology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Ö Östman
- Department of Aquatic Resources - Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolvägen 6, 74242, Öregrund, Sweden
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Nikolic N, Duthoy S, Destombes A, Bodin N, West W, Puech A, Bourjea J. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna. PLoS One 2015; 10:e0141830. [PMID: 26544051 PMCID: PMC4636268 DOI: 10.1371/journal.pone.0141830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/13/2015] [Indexed: 11/21/2022] Open
Abstract
Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24–27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species—Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.
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Affiliation(s)
- Natacha Nikolic
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
- * E-mail:
| | | | | | | | - Wendy West
- Department of Agriculture Forestry and Fisheries, Private Bag X2, Roggebaai, 8012, South Africa
| | - Alexis Puech
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
| | - Jérôme Bourjea
- IFREMER, Institut Français de Recherche pour l’Exploitation de la Mer, Délégation de La Réunion, Rue Jean Bertho, BP 60, 97 822 Le Port Cedex, La Réunion, France
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Stronen AV, Jędrzejewska B, Pertoldi C, Demontis D, Randi E, Niedziałkowska M, Borowik T, Sidorovich VE, Kusak J, Kojola I, Karamanlidis AA, Ozolins J, Dumenko V, Czarnomska SD. Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore. Ecol Evol 2015; 5:4410-25. [PMID: 26664688 PMCID: PMC4667828 DOI: 10.1002/ece3.1695] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67‐K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric‐Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome‐wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long‐term separation among population clusters.
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Affiliation(s)
- Astrid Vik Stronen
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Bogumiła Jędrzejewska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Cino Pertoldi
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Aalborg Zoo Mølleparkvej 63 DK-9000 Aalborg Denmark
| | - Ditte Demontis
- Department of Human Genetics University of Aarhus Wilhelm Meyers Allé DK-8000 Aarhus Denmark
| | - Ettore Randi
- Section of Biology and Environmental Science Department of Chemistry and Bioscience Aalborg University Fredrik Bajers Vej 7H DK-9220 Aalborg Øst Denmark ; Laboratorio di Genetica ISPRA via Cà Fornacetta 9 I-40064 Ozzano Emilia (BO) Italy
| | - Magdalena Niedziałkowska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Tomasz Borowik
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
| | - Vadim E Sidorovich
- Institute of Zoology Scientific and Practical Centre for Biological Resources National Academy of Science of Belarus Akademicheskaya Str 27 220072 Minsk Belarus
| | - Josip Kusak
- Department of Biology Faculty of Veterinary Medicine University of Zagreb Zagreb Croatia
| | - Ilpo Kojola
- Natural Resources Institute Finland Box 16 FI-96500 Rovaniemi Finland
| | - Alexandros A Karamanlidis
- ARCTUROS Civil Society for the Protection and Management of Wildlife and the Natural Environment GR-53075 Aetos Greece ; Department of Ecology and Natural Resources Management Norwegian University of Life Sciences NO-1432 Ås Norway
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava" Rīgas 111 LV-2169 Salaspils Latvia
| | - Vitalii Dumenko
- Biosphere Reserve Askania Nova Frunze Str. 13 Askania-Nova Chaplynka District Kherson Region 75230 Ukraine
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences ul. Waszkiewicza 1 PL 17-230 Bialowieza Poland
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Libungan LA, Slotte A, Husebø Å, Godiksen JA, Pálsson S. Latitudinal Gradient in Otolith Shape among Local Populations of Atlantic Herring (Clupea harengus L.) in Norway. PLoS One 2015; 10:e0130847. [PMID: 26101885 PMCID: PMC4478005 DOI: 10.1371/journal.pone.0130847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 11/19/2022] Open
Abstract
Otolith shape analysis of Atlantic herring (Clupea harengus) in Norwegian waters shows significant differentiation among fjords and a latitudinal gradient along the coast where neighbouring populations are more similar to each other than to those sampled at larger distances. The otolith shape was obtained using quantitative shape analysis, the outlines were transformed with Wavelet and analysed with multivariate methods. The observed morphological differences are likely to reflect environmental differences but indicate low dispersal among the local herring populations. Otolith shape variation suggests also limited exchange between the local populations and their oceanic counterparts, which could be due to differences in spawning behaviour. Herring from the most northerly location (69°N) in Balsfjord, which is genetically more similar to Pacific herring (Clupea pallasii), differed in otolith shape from all the other populations. Our results suggest that the semi-enclosed systems, where the local populations live and breed, are efficient barriers for dispersal. Otolith shape can thus serve as a marker to identify the origin of herring along the coast of Norway.
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Affiliation(s)
- Lísa Anne Libungan
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Aril Slotte
- Institute of Marine Research, Bergen, Norway
- Hjort Centre for Marine Ecosystem Dynamics, Bergen, Norway
| | - Åse Husebø
- Institute of Marine Research, Bergen, Norway
| | - Jane A. Godiksen
- Institute of Marine Research, Bergen, Norway
- Hjort Centre for Marine Ecosystem Dynamics, Bergen, Norway
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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Smith BL, Lu CP, García-Cortés B, Viñas J, Yeh SY, Alvarado Bremer JR. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.). PLoS One 2015; 10:e0127979. [PMID: 26057382 PMCID: PMC4461265 DOI: 10.1371/journal.pone.0127979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/21/2015] [Indexed: 12/03/2022] Open
Abstract
Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.
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Affiliation(s)
- Brad L. Smith
- Department of Marine Biology, Texas A&M University at Galveston, OCSB 3029, Galveston, TX 77553, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
- * E-mail:
| | - Ching-Ping Lu
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
| | - Blanca García-Cortés
- Centro Oceanográphico A Coruña, Instituto Español de Oceanografia, Muelle de las Animas s/n P.O. Box 130, 15080 A Coruña, Spain
| | - Jordi Viñas
- Department de Biologia, Universitat de Girona, Campus Montilivi, E-17071 Girona, Spain
| | - Shean-Ya Yeh
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Jaime R. Alvarado Bremer
- Department of Marine Biology, Texas A&M University at Galveston, OCSB 3029, Galveston, TX 77553, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
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Souche EL, Hellemans B, Babbucci M, MacAoidh E, Guinand B, Bargelloni L, Chistiakov DA, Patarnello T, Bonhomme F, Martinsohn JT, Volckaert FAM. Range-wide population structure of European sea bassDicentrarchus labrax. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12572] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Erika L. Souche
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Center of Human Genetics; University of Leuven; O&N I Herestraat 49 - PO Box 602 B-3000 Leuven Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
| | - Massimiliano Babbucci
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Eoin MacAoidh
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Bruno Guinand
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - Dimitry A. Chistiakov
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Medical Nanobiotechnology; Pirogov Russian State Medical University Research Center; Ulitsa Ostrovityanova 1 117997 Moscow Russia
| | - Tomaso Patarnello
- Dipartimento di Biomedicina Comparata e Alimentazione; Università di Padova; I-35124 Padova Italy
| | - François Bonhomme
- Institut des Sciences de l'Evolution de Montpellier; Université de Montpellier; UMR CNRS 5554, Place Eugène Bataillon - cc63 F-34095 Montpellier Cedex 5 France
| | - Jann T. Martinsohn
- Joint Research Centre; Institute for the Protection and Security of the Citizen; European Commission; Maritime Affairs Unit (G.03) - TP051 (Bldg. 51), Via Enrico Fermi nr. 2749 I-21027 Ispra Italy
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics; University of Leuven; Ch. Deberiotstraat 32 - PO Box 2439 B-3000 Leuven Belgium
- Department of Biological and Environmental Sciences; CeMEB; University of Gothenburg; Box 463 SE-405 30 Gothenburg Sweden
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Berg PR, Jentoft S, Star B, Ring KH, Knutsen H, Lien S, Jakobsen KS, André C. Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.). Genome Biol Evol 2015; 7:1644-63. [PMID: 25994933 PMCID: PMC4494048 DOI: 10.1093/gbe/evv093] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
How genomic selection enables species to adapt to divergent environments is a fundamental question in ecology and evolution. We investigated the genomic signatures of local adaptation in Atlantic cod (Gadus morhua L.) along a natural salinity gradient, ranging from 35‰ in the North Sea to 7‰ within the Baltic Sea. By utilizing a 12 K SNPchip, we simultaneously assessed neutral and adaptive genetic divergence across the Atlantic cod genome. Combining outlier analyses with a landscape genomic approach, we identified a set of directionally selected loci that are strongly correlated with habitat differences in salinity, oxygen, and temperature. Our results show that discrete regions within the Atlantic cod genome are subject to directional selection and associated with adaptation to the local environmental conditions in the Baltic- and the North Sea, indicating divergence hitchhiking and the presence of genomic islands of divergence. We report a suite of outlier single nucleotide polymorphisms within or closely located to genes associated with osmoregulation, as well as genes known to play important roles in the hydration and development of oocytes. These genes are likely to have key functions within a general osmoregulatory framework and are important for the survival of eggs and larvae, contributing to the buildup of reproductive isolation between the low-salinity adapted Baltic cod and the adjacent cod populations. Hence, our data suggest that adaptive responses to the environmental conditions in the Baltic Sea may contribute to a strong and effective reproductive barrier, and that Baltic cod can be viewed as an example of ongoing speciation.
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Affiliation(s)
- Paul R Berg
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Kristoffer H Ring
- Centre for Development and the Environment (SUM), University of Oslo, Norway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway Institute of Marine Research (IMR), Flødevigen, His, Norway University of Agder, Kristiansand, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Norway
| | - Carl André
- Department of Biology and Environmental Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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Burridge AK, Goetze E, Raes N, Huisman J, Peijnenburg KTCA. Global biogeography and evolution of Cuvierina pteropods. BMC Evol Biol 2015; 15:39. [PMID: 25880735 PMCID: PMC4443520 DOI: 10.1186/s12862-015-0310-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 02/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world's oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. RESULTS We distinguished six morphotypes based on geometric morphometric analyses of shells from 926 museum and 113 fresh specimens. These morphotypes have distinct geographic distributions across the Atlantic, Pacific and Indian oceans, and belong to three major genetic clades based on COI and 28S DNA sequence data. Using a fossil-calibrated phylogeny, we estimated that these clades separated in the Late Oligocene and Early to Middle Miocene. We found evidence for ecological differentiation among all morphotypes based on ecological niche modelling with sea surface temperature, salinity and phytoplankton biomass as primary determinants. Across all analyses, we found highly congruent patterns of differentiation suggesting species level divergences between morphotypes. However, we also found distinct morphotypes (e.g. in the Atlantic Ocean) that were ecologically, but not genetically differentiated. CONCLUSIONS Given the distinct ecological and phenotypic specializations found among both described and undescribed Cuvierina taxa, they may not respond equally to future ocean changes and may not be equally sensitive to ocean acidification. Our findings support the view that ecological differentiation may be an important driving force in the speciation of zooplankton.
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Affiliation(s)
- Alice K Burridge
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
| | - Erica Goetze
- Department of Oceanography, University of Hawaii at Manoa, 1000 Pope Road, Honolulu, HI, 96822, USA.
| | - Niels Raes
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
| | - Jef Huisman
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
| | - Katja T C A Peijnenburg
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands.
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, Amsterdam, 1090 GE, The Netherlands.
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Moore JS, Bourret V, Dionne M, Bradbury I, O'Reilly P, Kent M, Chaput G, Bernatchez L. Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol 2014; 23:5680-97. [DOI: 10.1111/mec.12972] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
- Direction de la Protection de la Faune; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Mélanie Dionne
- Direction de la Faune Aquatique; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Ian Bradbury
- Science Branch; Fisheries and Oceans Canada; 80 East White Road St. John's Newfoundland A1C 5X1 Canada
| | - Patrick O'Reilly
- Science Branch; Fisheries and Oceans Canada; Bedford Institute of Oceanography; 1 Challenger Drive Dartmouth Nova Scotia B2Y 4A2 Canada
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE); Department of Animal and Aquacultural Sciences (IHA); Norwegian University of Life Sciences; PO Box 5003 1432 Aas Norway
| | - Gérald Chaput
- Fisheries and Oceans Canada; PO Box 5030 Moncton New Brunswick E1C 9B6 Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
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Eggers F, Slotte A, Libungan LA, Johannessen A, Kvamme C, Moland E, Olsen EM, Nash RDM. Seasonal dynamics of Atlantic herring (Clupea harengus L.) populations spawning in the vicinity of marginal habitats. PLoS One 2014; 9:e111985. [PMID: 25372461 PMCID: PMC4221434 DOI: 10.1371/journal.pone.0111985] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 10/10/2014] [Indexed: 11/18/2022] Open
Abstract
Gillnet sampling and analyses of otolith shape, vertebral count and growth indicated the presence of three putative Atlantic herring (Clupea harengus L.) populations mixing together over the spawning season February–June inside and outside an inland brackish water lake (Landvikvannet) in southern Norway. Peak spawning of oceanic Norwegian spring spawners and coastal Skagerrak spring spawners occurred in March–April with small proportions of spawners entering the lake. In comparison, spawning of Landvik herring peaked in May–June with high proportions found inside the lake, which could be explained by local adaptations to the environmental conditions and seasonal changes of this marginal habitat. The 1.85 km2 lake was characterized by oxygen depletion occurring between 2.5 and 5 m depth between March and June. This was followed by changes in salinity from 1–7‰ in the 0–1 m surface layer to levels of 20–25‰ deeper than 10 m. In comparison, outside the 3 km long narrow channel connecting the lake with the neighboring fjord, no anoxic conditions were found. Here salinity in the surface layer increased over the season from 10 to 25‰, whereas deeper than 5 m it was stable at around 35‰. Temperature at 0–5 m depth increased significantly over the season in both habitats, from 7 to 14°C outside and 5 to 17°C inside the lake. Despite differences in peak spawning and utilization of the lake habitat between the three putative populations, there was an apparent temporal and spatial overlap in spawning stages suggesting potential interbreeding in accordance with the metapopulation concept.
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Affiliation(s)
- Florian Eggers
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
| | - Aril Slotte
- Institute of Marine Research, Bergen, Norway
| | - Lísa Anne Libungan
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | - Even Moland
- Institute of Marine Research, Flødevigen, Norway
| | - Esben M. Olsen
- Institute of Marine Research, Flødevigen, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Natural Sciences, Faculty of Science and Engineering, University of Agder, Kristiansand, Norway
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Population genetic structure of chub mackerel Scomber japonicus in the Northwestern Pacific inferred from microsatellite analysis. Mol Biol Rep 2014; 42:373-82. [PMID: 25366174 DOI: 10.1007/s11033-014-3777-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 09/22/2014] [Indexed: 10/24/2022]
Abstract
Marine pelagic fishes are usually characterized by subtle but complex patterns of genetic differentiation, which are influenced by both historical process and contemporary gene flow. Genetic population differentiation of chub mackerel, Scomber japonicus, was examined across most of its range in the Northwestern Pacific by screening variation of eight microsatellite loci. Our genetic analysis detected a weak but significant genetic structure of chub mackerel, which was characterized by areas of gene flow and isolation by distance. Consistent with previous estimates of stock structure, we found genetic discontinuity between Japan and China samples. Local-scale pattern of genetic differentiation was observed between samples from the Bohai Sea and North Yellow Sea and those from the East China Sea, which we ascribed to differences in spawning time and migratory behavior. Furthermore, the observed homogeneity among collections of chub mackerel from the East and South China Seas could be the result of an interaction between biological characteristics and marine currents. The present study underlies the importance of understanding the biological significance of genetic differentiation to establish management strategies for exploited fish populations.
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48
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Drift rather than selection dominates MHC class II allelic diversity patterns at the biogeographical range scale in natterjack toads Bufo calamita. PLoS One 2014; 9:e100176. [PMID: 24937211 PMCID: PMC4061088 DOI: 10.1371/journal.pone.0100176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 05/23/2014] [Indexed: 12/31/2022] Open
Abstract
Study of major histocompatibility complex (MHC) loci has gained great popularity in recent years, partly due to their function in protecting vertebrates from infections. This is of particular interest in amphibians on account of major threats many species face from emergent diseases such as chytridiomycosis. In this study we compare levels of diversity in an expressed MHC class II locus with neutral genetic diversity at microsatellite loci in natterjack toad (Bufo (Epidalea) calamita) populations across the whole of the species' biogeographical range. Variation at both classes of loci was high in the glacial refugium areas (REF) and much lower in postglacial expansion areas (PGE), especially in range edge populations. Although there was clear evidence that the MHC locus was influenced by positive selection in the past, congruence with the neutral markers suggested that historical demographic events were the main force shaping MHC variation in the PGE area. Both neutral and adaptive genetic variation declined with distance from glacial refugia. Nevertheless, there were also some indications from differential isolation by distance and allele abundance patterns that weak effects of selection have been superimposed on the main drift effect in the PGE zone.
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Stronen AV, Navid EL, Quinn MS, Paquet PC, Bryan HM, Darimont CT. Population genetic structure of gray wolves (Canis lupus) in a marine archipelago suggests island-mainland differentiation consistent with dietary niche. BMC Ecol 2014; 14:11. [PMID: 24915756 PMCID: PMC4050401 DOI: 10.1186/1472-6785-14-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/15/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Emerging evidence suggests that ecological heterogeneity across space can influence the genetic structure of populations, including that of long-distance dispersers such as large carnivores. On the central coast of British Columbia, Canada, wolf (Canis lupus L., 1758) dietary niche and parasite prevalence data indicate strong ecological divergence between marine-oriented wolves inhabiting islands and individuals on the coastal mainland that interact primarily with terrestrial prey. Local holders of traditional ecological knowledge, who distinguish between mainland and island wolf forms, also informed our hypothesis that genetic differentiation might occur between wolves from these adjacent environments. RESULTS We used microsatellite genetic markers to examine data obtained from wolf faecal samples. Our results from 116 individuals suggest the presence of a genetic cline between mainland and island wolves. This pattern occurs despite field observations that individuals easily traverse the 30 km wide study area and swim up to 13 km among landmasses in the region. CONCLUSIONS Natal habitat-biased dispersal (i.e., the preference for dispersal into familiar ecological environments) might contribute to genetic differentiation. Accordingly, this working hypothesis presents an exciting avenue for future research where marine resources or other components of ecological heterogeneity are present.
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Affiliation(s)
- Astrid V Stronen
- Mammal Research Institute, Polish Academy of Sciences, ul. Waszkiewicza 1, Białowieża 17-230, Poland
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 57, Aalborg 9000, Denmark
| | - Erin L Navid
- Faculty of Environmental Design, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N 1 N4, Canada
| | - Michael S Quinn
- Institute for Environmental Sustainability, Mount Royal University, 4825 Mount Royal Gate SW, Calgary, Alberta T3E 6 K6, Canada
| | - Paul C Paquet
- Department of Geography, University of Victoria, PO Box 3060 STN CSC, Victoria, British Columbia V8W 3R4, Canada
- Raincoast Conservation Foundation, PO Box 86 Denny Island, British Columbia V0T 1B0, Canada
| | - Heather M Bryan
- Department of Geography, University of Victoria, PO Box 3060 STN CSC, Victoria, British Columbia V8W 3R4, Canada
- Raincoast Conservation Foundation, PO Box 86 Denny Island, British Columbia V0T 1B0, Canada
- Hakai Beach Institute, Box 309, Heriot Bay, British Columbia V0P 1H0, Canada
| | - Christopher T Darimont
- Department of Geography, University of Victoria, PO Box 3060 STN CSC, Victoria, British Columbia V8W 3R4, Canada
- Raincoast Conservation Foundation, PO Box 86 Denny Island, British Columbia V0T 1B0, Canada
- Hakai Beach Institute, Box 309, Heriot Bay, British Columbia V0P 1H0, Canada
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50
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Olsen MT, Pampoulie C, Daníelsdóttir AK, Lidh E, Bérubé M, Víkingsson GA, Palsbøll PJ. Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences. Ecol Evol 2014; 4:1787-803. [PMID: 24963377 PMCID: PMC4063476 DOI: 10.1002/ece3.1046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 11/07/2022] Open
Abstract
The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.
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Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | | | | | - Emmelie Lidh
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | - Martine Bérubé
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
| | | | - Per J Palsbøll
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
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