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Hernawan UE, van Dijk K, Kendrick GA, Feng M, Berry O, Kavazos C, McMahon K. Ocean connectivity and habitat characteristics predict population genetic structure of seagrass in an extreme tropical setting. Ecol Evol 2023; 13:e10257. [PMID: 37404702 PMCID: PMC10316484 DOI: 10.1002/ece3.10257] [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: 03/08/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023] Open
Abstract
Understanding patterns of gene flow and processes driving genetic differentiation is important for a broad range of conservation practices. In marine organisms, genetic differentiation among populations is influenced by a range of spatial, oceanographic, and environmental factors that are attributed to the seascape. The relative influences of these factors may vary in different locations and can be measured using seascape genetic approaches. Here, we applied a seascape genetic approach to populations of the seagrass, Thalassia hemprichii, at a fine spatial scale (~80 km) in the Kimberley coast, western Australia, a complex seascape with strong, multidirectional currents greatly influenced by extreme tidal ranges (up to 11 m, the world's largest tropical tides). We incorporated genetic data from a panel of 16 microsatellite markers, overwater distance, oceanographic data derived from predicted passive dispersal on a 2 km-resolution hydrodynamic model, and habitat characteristics from each meadow sampled. We detected significant spatial genetic structure and asymmetric gene flow, in which meadows 12-14 km apart were less connected than ones 30-50 km apart. This pattern was explained by oceanographic connectivity and differences in habitat characteristics, suggesting a combined scenario of dispersal limitation and facilitation by ocean current with local adaptation. Our findings add to the growing evidence for the key role of seascape attributes in driving spatial patterns of gene flow. Despite the potential for long-distance dispersal, there was significant genetic structuring over small spatial scales implicating dispersal and recruitment bottlenecks and highlighting the importance of implementing local-scale conservation and management measures.
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Affiliation(s)
- Udhi E. Hernawan
- School of Science and Centre for Marine Ecosystems ResearchEdith Cowan UniversityJoondalupWestern AustraliaAustralia
- Research Centre for Oceanography (PRO), National Research and Innovation Agency (BRIN)JakartaIndonesia
| | - Kor‐jent van Dijk
- School of Biological SciencesThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Gary A. Kendrick
- School of Biological Sciences and The Ocean InstituteThe University of Western AustraliaCrawleyWestern AustraliaAustralia
- Western Australian Marine Science InstitutionPerthWestern AustraliaAustralia
| | - Ming Feng
- Western Australian Marine Science InstitutionPerthWestern AustraliaAustralia
- CSIRO Environment, Indian Ocean Marine Research CentreCrawleyWestern AustraliaAustralia
| | - Oliver Berry
- Western Australian Marine Science InstitutionPerthWestern AustraliaAustralia
- CSIRO Environment, Indian Ocean Marine Research CentreCrawleyWestern AustraliaAustralia
| | - Christopher Kavazos
- School of Science and Centre for Marine Ecosystems ResearchEdith Cowan UniversityJoondalupWestern AustraliaAustralia
| | - Kathryn McMahon
- School of Science and Centre for Marine Ecosystems ResearchEdith Cowan UniversityJoondalupWestern AustraliaAustralia
- Western Australian Marine Science InstitutionPerthWestern AustraliaAustralia
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The El Niño Southern Oscillation drives multidirectional inter-reef larval connectivity in the Great Barrier Reef. Sci Rep 2022; 12:21290. [PMID: 36494507 PMCID: PMC9734173 DOI: 10.1038/s41598-022-25629-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The El Niño Southern Oscillation (ENSO) is the strongest source of interannual global climate variability, and extreme ENSO events are projected to increase in frequency under climate change. Interannual variability in the Coral Sea circulation has been associated with ENSO, although uncertainty remains regarding ENSO's influence on hydrodynamics and larval dispersal in the adjacent Great Barrier Reef (GBR). We investigated larval connectivity during ENSO events from 2010 to 2017 throughout the GBR, based on biophysical modelling of a widespread predatory reef fish, Lutjanus carponotatus. Our results indicate a well-connected system over the study period with high interannual variability in inter-reef connectivity associated with ENSO. Larval connectivity patterns were highly correlated to variations in the Southern Oscillation Index (SOI). During El Niño conditions and periods of weak SOI, larval dispersal patterns were predominantly poleward in the central and southern regions, reversing to a predominant equatorward flow during very strong SOI and extreme La Niña conditions. These ENSO-linked connectivity patterns were associated with positive connectivity anomalies among reefs. Our findings identify ENSO as an important source of variation in larval dispersal and connectivity patterns in the GBR, which can influence the stability of population dynamics and patterns of biodiversity in the region.
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Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography. BMC Ecol Evol 2022; 22:88. [PMID: 35818031 PMCID: PMC9275043 DOI: 10.1186/s12862-022-02038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.
Results
We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.
Conclusion
To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.
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Fairclough DV, Ayvazian SG, Newman SJ. Complementary evidence for small-scale spatial assemblages of the exploited grass emperor (Lethrinus laticaudis) in the Shark Bay World Heritage Area, Western Australia. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105543. [PMID: 34952373 DOI: 10.1016/j.marenvres.2021.105543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Understanding the connectivity of exploited fish populations is critical to their management under both rapid and long-term environmental change. Patterns of connectivity are unknown for most fishes in the Shark Bay World Heritage Area (Western Australia), a large, shallow embayment in the eastern Indian Ocean, vulnerable to marine heatwaves. The composition of oxygen (δ18O) and carbon (δ13C) stable isotopes in whole otoliths of the recreationally-important reef fish Lethrinus laticaudis did not differ between Shark Bay's two large inner gulfs, separated by the Peron Peninsula. However, significant differences were found between pairs of locations with different salinities over a spatial scale of ∼60 km within each gulf. Misclassification of samples was greatest between locations mostly in different gulfs, but with similar salinities (15-41%), and rare between adjacent locations in the same gulf with different salinities (0-5%). This is influenced by the strong correlation (ρ = 0.93) between δ18O in otoliths and the salinity gradient of the two gulfs, and further supported by a lack of correlation in the similarities of isotope compositions and distances between locations (ρ = 0.16). Fish samples from each of the different locations were composed of multiple year-classes, yet the otolith chemistry distinguished them at a minimum distance of 16 km apart, indicating that small-scale connectivity of L. laticaudis is likely during the majority of their life cycle. Physical barriers to movement of post-settlement individuals (land masses, expansive seagrass and sand) between the small, isolated reefs of Shark Bay may reduce large scale connectivity, which instead would occur mostly by egg and larval dispersal. The probable scale of connectivity of post-settlement L. laticaudis indicates that this major recreational fishing target species may be vulnerable to localised over-exploitation and negative environmental effects on population sources and sinks within this shallow embayment. Maintaining sustainable spawning biomass at scales relevant to the extent of connectivity for such a species in a World Heritage Area is an important management consideration.
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Affiliation(s)
- David V Fairclough
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia
| | - Suzanne G Ayvazian
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Atlantic Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI, 02882, USA
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, P.O. Box 20, North Beach, WA, 6920, Australia.
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Donati GFA, Zemp N, Manel S, Poirier M, Claverie T, Ferraton F, Gaboriau T, Govinden R, Hagen O, Ibrahim S, Mouillot D, Leblond J, Julius P, Velez L, Zareer I, Ziyad A, Leprieur F, Albouy C, Pellissier L. Species ecology explains the spatial components of genetic diversity in tropical reef fishes. Proc Biol Sci 2021; 288:20211574. [PMID: 34583586 PMCID: PMC8479362 DOI: 10.1098/rspb.2021.1574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/03/2021] [Indexed: 11/12/2022] Open
Abstract
Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α, β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.
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Affiliation(s)
- Giulia Francesca Azzurra Donati
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zürich, CH8092 Zürich, Switzerland
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
| | - Maude Poirier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Thomas Claverie
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Centre Universitaire de formation et de recherche de Mayotte, Dembeni 97660, France
| | - Franck Ferraton
- Centre National de la Recherche Scientifique (CNRS), UMR 248 MARBEC, Montpellier, France
| | - Théo Gaboriau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | | | - Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
| | - Shameel Ibrahim
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - David Mouillot
- CEFE, Univ Montpellier, CNRS EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Julien Leblond
- Wildlife Conservation Society, Madagascar Program, Antananarivo, Madagascar
| | | | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
| | - Irthisham Zareer
- Maldives Whale Shark Research Programme, Popeshead Court Offices, Peter Lane, York, Yorkshire Y01 8SU, UK
| | - Adam Ziyad
- Ministry of Fisheries and Agriculture, Malé, Republic of Maldives
| | - Fabien Leprieur
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier 34095, France
- Institut Universitaire de France, Paris, France
| | - Camille Albouy
- IFREMER, Unité Écologie et Modèles pour l'Halieutique, rue de l'Ile d'Yeu, BP21105, 44311 Nantes cedex 3, France
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, CH8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH8903 Birmensdorf, Switzerland
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Cortez T, Amaral RV, Sobral-Souza T, Andrade SCS. Genome-wide assessment elucidates connectivity and the evolutionary history of the highly dispersive marine invertebrate Littoraria flava (Littorinidae: Gastropoda). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
An important goal of marine population genetics is to understand how spatial connectivity patterns are influenced by historical and evolutionary factors. In this study, we evaluate the demographic history and population structure of Littoraria flava, a highly dispersive marine gastropod in the Brazilian intertidal zone. To test the hypotheses that the species has (1) historically high levels of gene flow on a macrogeographical spatial scale and (2) a distribution in rocky shores that consists of subpopulations, we collected specimens along the Brazilian coastline and combined different sets of genetic markers (mitochondrial DNA, ITS-2 and single nucleotide polymorphisms) with niche-based modelling to predict its palaeodistribution. Low genetic structure was observed, as well as high gene flow over long distances. The demographic analyses suggest that L. flava has had periods of population bottlenecks followed by expansion. According to both palaeodistribution and coalescent simulations, these expansion events occurred during the Pleistocene interglacial cycles (21 kya) and the associated climatic changes were the probable drivers of the distribution of the species. This is the first phylogeographical study of a marine gastropod on the South American coast based on genomic markers associated with niche modelling.
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Affiliation(s)
- Thainá Cortez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Rafael V Amaral
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
| | - Thadeu Sobral-Souza
- Departamento de Botânica e Ecologia, Universidade Federal do Mato Grosso, Cuiabá, MTBrazil
| | - Sónia C S Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, SPBrazil
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Evans RD, McMahon KM, van Dijk KJ, Dawkins K, Nilsson Jacobi M, Vikrant A. Identification of dispersal barriers for a colonising seagrass using seascape genetic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:143052. [PMID: 33189383 DOI: 10.1016/j.scitotenv.2020.143052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Seagrasses are important habitats providing many ecological services. Most species have broad distributions with maximum dispersal distances of 100's of kms, however there is limited understanding of dispersal distances of colonising species like Halodule uninervis. It commonly grows in disturbed environments and could disperse to other meadows via clonal fragments. Effective conservation management requires greater understanding of genetic structure, dispersal barriers, and connectivity timescales to predict recovery following disturbance. Despite fragment viability of up to 28 days in a congenera, this theory remains untested in situ. Using 80 neutral single nucleotide polymorphisms, we investigated genetic diversity, gene flow patterns and structure among 15 populations of H. uninervis along 2000 km of Western Australian coastline. These data were combined with a multi-generational oceanographic dispersal model and a barrier dispersal analysis to identify dispersal barriers and determine which fragment dispersal duration (FDD) and timescale over which stepping-stone connectivity occurred, best matched the observed genetic structure. The 2-7 day FDD best matched the genetic structure with 4-12 clusters, with barriers to dispersal that persisted for up to 100 years. Modelling suggested greater fragmentation of metapopulations towards the southern edge of the species distribution, but genetic diversity did not decline. Several long-term boundaries were identified even with fragment viability of up to 28 days. This suggests H. uninervis dispersal is spatially limited by factors like oceanographic features and habitat continuity which may limit dispersal of this species. This study reiterates that potential dispersal does not equal realised dispersal, and management scales of 10's of kilometers are required to maintain existing meadows. Recruitment from distances further than this scale are unlikely to aid recovery after extreme disturbance events, particularly towards the range edge of H. uninervis distribution.
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Affiliation(s)
- R D Evans
- Department of Biodiversity, Conservation and Attractions, 17 Dick Perry Ave, Kensington 6151, Australia; Oceans Institute, the University of Western Australia, Perth, WA 6009, Australia.
| | - K M McMahon
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Australia; Centre for Marine Ecosystems Research, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Australia
| | - K-J van Dijk
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - K Dawkins
- School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Australia; Centre for Ecosystem Management, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Australia
| | - M Nilsson Jacobi
- Department of Space, Earth and Environment, Chalmers University of Technology, Maskingränd 2, 412 58 Gothenburg, Sweden
| | - A Vikrant
- Department of Space, Earth and Environment, Chalmers University of Technology, Maskingränd 2, 412 58 Gothenburg, Sweden
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Short- and long-term effects of copper on anammox under gradually increased copper concentrations. Biodegradation 2021; 32:273-286. [PMID: 33745118 DOI: 10.1007/s10532-021-09934-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
This study aims to determine both short- and long-term response of enriched anammox culture to Cu. Assessment of short-term inhibition is based both on total applied Cu concentration and potential bioavailable fractions like intracellular, surface-bound, soluble and free Cu ion. The half maximal inhibitory concentration (IC50) values for total applied, soluble, intracellular and cell-associated concentrations were determined as 4.57 mg/L, 1.97 mg/L, 0.71 mg/L, 1.11 mg/L, respectively. Correlation between the surface-bound fraction of Cu and inhibition response was weak, suggesting that Cu sorbed to biomass was not directly responsible for the effects on anammox activity. There was a disparity between the results of short- and long-term experiments in terms of inhibition threshold concentration (i.e. short-term IC50 = 4.57 mg/L vs long-term IC50 = 6.74 mg/L). Candidatus Kuenenia (59.8%) and Candidatus Brocadia (40.2%) were the two main anammox genera within the initial biomass sample. One of the most interesting finding of the study is the demonstration that a complete wash-out of C. Brocadia genus at an applied Cu concentration of 6.5 mg/L. This strongly indicates that C. Brocadia were not able to tolerate high copper concentrations and all nitrogen conversion was carried out by C. Kuenenia during the Cu exposure period.
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Thia JA, McGuigan K, Liggins L, Figueira WF, Bird CE, Mather A, Evans JL, Riginos C. Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation. Mol Ecol 2021; 30:4392-4414. [PMID: 33544414 DOI: 10.1111/mec.15829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/12/2021] [Accepted: 01/28/2021] [Indexed: 11/28/2022]
Abstract
Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.
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Affiliation(s)
- Joshua A Thia
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia.,School of BioSciences, The University of Melbourne, Melbourne, VIC., Australia
| | - Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Libby Liggins
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Will F Figueira
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Christopher E Bird
- Department of Life Sciences, Texas A&M University Corpus Christi, Corpus Christi, TX, USA
| | - Andrew Mather
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Jennifer L Evans
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Saint Lucia, QLD, Australia
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West K, Travers MJ, Stat M, Harvey ES, Richards ZT, DiBattista JD, Newman SJ, Harry A, Skepper CL, Heydenrych M, Bunce M. Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13228] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Katrina West
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael J. Travers
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Michael Stat
- School of Environmental and Life Sciences The University of Newcastle Callaghan NSW Australia
| | - Euan S. Harvey
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Australian Museum Australian Museum Research Institute Sydney NSW Australia
| | - Stephen J. Newman
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Alastair Harry
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Craig L. Skepper
- Western Australian Fisheries and Marine Research Laboratories Department of Primary Industries and Regional Development Government of Western AustraliaNorth Beach WA Australia
| | - Matthew Heydenrych
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Environmental Protection Authority Wellington New Zealand
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Underwood JN, Richards Z, Berry O, Oades D, Howard A, Gilmour JP. Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north-west Australia. Evol Appl 2020; 13:2404-2421. [PMID: 33005230 PMCID: PMC7513722 DOI: 10.1111/eva.13033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022] Open
Abstract
Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter- and intra-specific genetic diversity. We characterized patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef-building corals to explore the eco-evolutionary processes that sustain populations in north-west Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter-archipelago (tens to hundreds of kilometres), inter-reef (kilometres to tens of kilometres) and within-reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co-occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp-c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales <35 kilometres. Further, we observed four discrete clusters and a semi-permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity.
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Affiliation(s)
- Jim N Underwood
- Australian Institute of Marine Science Indian Oceans Marine Research Centre, Crawley Perth WA Australia
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
| | - Zoe Richards
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Welshpool WA Australia
| | - Oliver Berry
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
- CSIRO Oceans and Atmosphere Indian Oceans Marine Research Centre, Crawley Perth WA Australia
| | - Daniel Oades
- Bardi Jawi Rangers Kimberley Land Council Broome WA Australia
| | - Azton Howard
- Bardi Jawi Rangers Kimberley Land Council Broome WA Australia
| | - James P Gilmour
- Australian Institute of Marine Science Indian Oceans Marine Research Centre, Crawley Perth WA Australia
- Western Australian Marine Science Institution Indian Ocean Marine Research Centre Crawley WA Australia
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12
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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13
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Fietz K, Trofimenko E, Guerin PE, Arnal V, Torres-Oliva M, Lobréaux S, Pérez-Ruzafa A, Manel S, Puebla O. New genomic resources for three exploited Mediterranean fishes. Genomics 2020; 112:4297-4303. [PMID: 32629099 DOI: 10.1016/j.ygeno.2020.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 10/23/2022]
Abstract
Extensive fishing has led to fish stock declines throughout the last decades. While clear stock identification is required for designing management schemes, stock delineation is problematic due to generally low levels of genetic structure in marine species. The development of genomic resources can help to solve this issue. Here, we present the first mitochondrial and nuclear draft genome assemblies of three economically important Mediterranean fishes, the white seabream, the striped red mullet, and the comber. The assemblies are between 613 and 785 Mbp long and contain between 27,222 and 32,375 predicted genes. They were used as references to map Restriction-site Associated DNA markers, which were developed with a single-digest approach. This approach provided between 15,710 and 21,101 Single Nucleotide Polymorphism markers per species. These genomic resources will allow uncovering subtle genetic structure, identifying stocks, assigning catches to populations and assessing connectivity. Furthermore, the annotated genomes will help to characterize adaptive divergence.
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Affiliation(s)
- Katharina Fietz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Elena Trofimenko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Pierre-Edouard Guerin
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Véronique Arnal
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Montserrat Torres-Oliva
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stéphane Lobréaux
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble-Alpes, Grenoble, France
| | - Angel Pérez-Ruzafa
- Departmento de Ecología e Hidrología, Facultad de Biología, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Oscar Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany; Leibniz Centre for Tropical Marine Research, Fahrenheitstrasse 6, 28359 Bremen, Germany
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14
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DiBattista JD, Saenz‐Agudelo P, Piatek MJ, Cagua EF, Bowen BW, Choat JH, Rocha LA, Gaither MR, Hobbs JA, Sinclair‐Taylor TH, McIlwain JH, Priest MA, Braun CD, Hussey NE, Kessel ST, Berumen ML. Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula. Ecol Evol 2020; 10:4314-4330. [PMID: 32489599 PMCID: PMC7246217 DOI: 10.1002/ece3.6199] [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: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.
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Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Pablo Saenz‐Agudelo
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Marek J. Piatek
- Computational Bioscience Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Edgar Fernando Cagua
- Centre for Integrative EcologySchool of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - John Howard Choat
- School of Marine and Tropical BiologyJames Cook UniversityTownsvilleQldAustralia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Michelle R. Gaither
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Genomics and Bioinformatics ClusterDepartment of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Tane H. Sinclair‐Taylor
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | | | - Mark A. Priest
- Marine Spatial Ecology LabSchool of Biological Sciences and ARC Centre of Excellence for Coral Reef StudiesUniversity of QueenslandSt. LuciaQldAustralia
| | - Camrin D. Braun
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Steven T. Kessel
- Daniel P. Haerther Center for Conservation and ResearchJohn G. Shedd AquariumChicagoILUSA
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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15
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Selmoni O, Vajana E, Guillaume A, Rochat E, Joost S. Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach. Mol Ecol Resour 2019; 20:154-169. [PMID: 31550072 PMCID: PMC6972490 DOI: 10.1111/1755-0998.13095] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/05/2019] [Accepted: 09/18/2019] [Indexed: 02/06/2023]
Abstract
An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographical representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites (20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Annie Guillaume
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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16
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Otwoma LM, Reuter H. Do differences in mating behaviour lead to differences in connectivity patterns of reef fishes? Insights from two sympatric surgeonfish species in the Indian Ocean. MARINE ENVIRONMENTAL RESEARCH 2019; 151:104760. [PMID: 31358313 DOI: 10.1016/j.marenvres.2019.104760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Disentangling the contribution of biotic and abiotic factors in the structuring of the genetic diversity of reef species is critical to illuminate the diversification of evolutionary lineages in marine environment. Howevr, previous studies have mainly focused on determining the influence of pelagic larval duration on the connectivity and demographic history of reef fishes, whereas few studies have examined the effects of other biotic factors, such as mating behaviour and habitat preference. Here, we use mitochondrial DNA (ATPase 6/8) and ten microsatellite loci to compare the population genetic structure and demographic history of the spawning aggregating Acanthurus triostegus with the monogamous spawning Acanthurus leucosternon. Pairwise comparisons and discriminant analysis of principal components showed that the genetic structuring patterns of the two species are not consistent with the influence of mating behaviour, suggesting the possible role of other biotic and abiotic factors. However, demographic history estimates revealed that these species may have responded differently to sea level fluctuations during the glacial maxima.
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Affiliation(s)
- Levy Michael Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany; Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya.
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany
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17
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Hosoya S, Hirase S, Kikuchi K, Nanjo K, Nakamura Y, Kohno H, Sano M. Random PCR-based genotyping by sequencing technology GRAS-Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes. Mol Ecol Resour 2019; 19:1153-1163. [PMID: 31009151 DOI: 10.1111/1755-0998.13025] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/06/2019] [Accepted: 04/15/2019] [Indexed: 01/15/2023]
Abstract
While various technologies for high-throughput genotyping have been developed for ecological studies, simple methods tolerant to low-quality DNA samples are still limited. In this study, we tested the availability of a random PCR-based genotyping-by-sequencing technology, genotyping by random amplicon sequencing, direct (GRAS-Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000-9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next-generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation-by-distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS-Di for fine-grained genetic analysis using field samples, including mangrove fishes.
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Affiliation(s)
- Sho Hosoya
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, Hamamatsu, Japan
| | - Kusuto Nanjo
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Japan
| | - Yohei Nakamura
- Department of Agriculture, Graduate School of Integrated Arts and Sciences, Kochi University, Nankoku, Japan
| | - Hiroyoshi Kohno
- Okinawa Regional Research Center, Tokai University, Taketomi, Japan
| | - Mitsuhiko Sano
- Department of Ecosystem Studies, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
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18
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Bernatchez S, Xuereb A, Laporte M, Benestan L, Steeves R, Laflamme M, Bernatchez L, Mallet MA. Seascape genomics of eastern oyster ( Crassostrea virginica) along the Atlantic coast of Canada. Evol Appl 2019; 12:587-609. [PMID: 30828376 PMCID: PMC6383708 DOI: 10.1111/eva.12741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean F ST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype-environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
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Affiliation(s)
- Simon Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
- L’Étang Ruisseau Bar Ltd.ShippaganNew BrunswickCanada
| | - Amanda Xuereb
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Royce Steeves
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Mark Laflamme
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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19
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Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
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Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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20
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Green ME, D’Anastasi BR, Hobbs JPA, Feldheim K, McAuley R, Peverell S, Stapley J, Johnson G, Appleyard SA, White WT, Simpfendorfer CA, van Herwerden L. Mixed-marker approach suggests maternal philopatry and sex-biased behaviours of narrow sawfish Anoxypristis cuspidata. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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