1
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Da Silva O, Ayata SD, Ser-Giacomi E, Leconte J, Pelletier E, Fauvelot C, Madoui MA, Guidi L, Lombard F, Bittner L. Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea. Environ Microbiol 2022; 24:6086-6099. [PMID: 36053818 PMCID: PMC10087736 DOI: 10.1111/1462-2920.16171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 08/09/2022] [Indexed: 01/12/2023]
Abstract
For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.
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Affiliation(s)
- Ophélie Da Silva
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Sakina-Dorothée Ayata
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France
| | - Enrico Ser-Giacomi
- Sorbonne Université, UMR 7159 CNRS-IRD-MNHN, LOCEAN-IPSL, Paris, France.,Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Cécile Fauvelot
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut de Recherche pour le Développement (IRD), UMR ENTROPIE, Nouméa, New Caledonia
| | - Mohammed-Amin Madoui
- Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France
| | - Lionel Guidi
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Fabien Lombard
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lucie Bittner
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Institut Universitaire de France (IUF), Paris, France
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2
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Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla. Nat Commun 2022; 13:5861. [PMID: 36195609 PMCID: PMC9532449 DOI: 10.1038/s41467-022-33499-z] [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: 09/24/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Gene flow governs the contemporary spatial structure and dynamic of populations as well as their long-term evolution. For species that disperse using atmospheric or oceanic flows, biophysical models allow predicting the migratory component of gene flow, which facilitates the interpretation of broad-scale spatial structure inferred from observed allele frequencies among populations. However, frequent mismatches between dispersal estimates and observed genetic diversity prevent an operational synthesis for eco-evolutionary projections. Here we use an extensive compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by Isolation-By-Distance, single-generation dispersal and multi-generation dispersal models. Unlike previous approaches, the latter unveil explicit parents-to-offspring links (filial connectivity) and implicit links among siblings from a common ancestor (coalescent connectivity). We find that almost 70 % of observed variance in genetic differentiation is explained by coalescent connectivity over multiple generations, significantly outperforming other models. Our results offer great promises to untangle the eco-evolutionary forces that shape sedentary population structure and to anticipate climate-driven redistributions, altogether improving spatial conservation planning.
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3
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Jahnke M, Jonsson PR. Biophysical models of dispersal contribute to seascape genetic analyses. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210024. [PMID: 35067094 PMCID: PMC8784932 DOI: 10.1098/rstb.2021.0024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/23/2021] [Indexed: 12/20/2022] Open
Abstract
Dispersal is generally difficult to directly observe. Instead, dispersal is often inferred from genetic markers and biophysical modelling where a correspondence indicates that dispersal routes and barriers explain a significant part of population genetic differentiation. Biophysical models are used for wind-driven dispersal in terrestrial environments and for propagules drifting with ocean currents in the sea. In the ocean, such seascape genetic or seascape genomic studies provide promising tools in applied sciences, as actions within management and conservation rely on an understanding of population structure, genetic diversity and presence of local adaptations, all dependent on dispersal within the metapopulation. Here, we surveyed 87 studies that combine population genetics and biophysical models of dispersal. Our aim was to understand if biophysical dispersal models can generally explain genetic differentiation. Our analysis shows that genetic differentiation and lack of genetic differentiation can often be explained by dispersal, but the realism of the biophysical model, as well as local geomorphology and species biology also play a role. The review supports the use of a combination of both methods, and we discuss our findings in terms of recommendations for future studies and pinpoint areas where further development is necessary, particularly on how to compare both approaches. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad 45296, Sweden
| | - Per R. Jonsson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad 45296, Sweden
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4
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Atzeni L, Cushman SA, Wang J, Riordan P, Shi K, Bauman D. Evidence of spatial genetic structure in a snow leopard population from Gansu, China. Heredity (Edinb) 2021; 127:522-534. [PMID: 34743188 PMCID: PMC8626472 DOI: 10.1038/s41437-021-00483-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding the spatial structure of genetic diversity provides insights into a populations' genetic status and enables assessment of its capacity to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, a conservation flagship species of Central Asia mountains. Focusing on a snow leopard population in the Qilian mountains of Gansu Province, China, we characterised the spatial genetic patterns by incorporating spatially explicit indices of diversity and multivariate analyses, based on different inertia levels of Principal Component Analysis (PCA). We compared two datasets differing in the number of loci and individuals. We found that genetic patterns were significantly spatially structured and were characterised by a broad geographical division coupled with a fine-scale cline of differentiation. Genetic admixture was detected in two adjoining core areas characterised by higher effective population size and allelic diversity, compared to peripheral localities. The power to detect significant spatial relationships depended primarily on the number of loci, and secondarily on the number of PCA axes. Spatial patterns and indices of diversity highlighted the cryptic structure of snow leopard genetic diversity, likely driven by its ability to disperse over large distances. In combination, the species' low allelic richness and large dispersal ability result in weak genetic differentiation related to major geographical features and isolation by distance. This study illustrates how cryptic genetic patterns can be investigated and analysed at a fine spatial scale, providing insights into the spatially variable isolation effects of both geographic distance and landscape resistance.
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Affiliation(s)
- Luciano Atzeni
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Samuel A Cushman
- US Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Jun Wang
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Philip Riordan
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Marwell Wildlife, Winchester, UK
- Department of Biological Sciences, University of Southampton, Southampton, UK
| | - Kun Shi
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
- Eco-Bridge Continental, Beijing, China.
| | - David Bauman
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
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5
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Ledoux J, Ghanem R, Horaud M, López‐Sendino P, Romero‐Soriano V, Antunes A, Bensoussan N, Gómez‐Gras D, Linares C, Machordom A, Ocaña O, Templado J, Leblois R, Ben Souissi J, Garrabou J. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jean‐Baptiste Ledoux
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Institut de Ciències del Mar CSIC Barcelona Spain
| | - Raouia Ghanem
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
| | | | | | | | - Agostinho Antunes
- CIIMAR/CIMAR Centro Interdisciplinar de Investigação Marinha e Ambiental Universidade do Porto Porto Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal
| | | | | | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals Institut de Recerca de la Biodiversitat (IRBIO) Universitat de Barcelona Barcelona Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Oscar Ocaña
- Departamento de Oceanografía Biológica y Biodiversidad Fundación Museo del Mar de Ceuta Ceuta Spain
| | - José Templado
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| | - Raphaêl Leblois
- CBGP INRAE CIRAD IRD Montpellier SupAgro University of Montpellier Montpellier France
- Institut de Biologie Computationnelle University of Montpellier Montpellier France
| | - Jamila Ben Souissi
- Institut National Agronomique de Tunisie Université de Carthage Tunis Tunisie
- Laboratoire de Biodiversité, Biotechnologies et Changements Climatiques (LR11ES09) Université Tunis El Manar Tunis Tunisie
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6
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Boulanger E, Benestan L, Guerin PE, Dalongeville A, Mouillot D, Manel S. Climate differently influences the genomic patterns of two sympatric marine fish species. J Anim Ecol 2021; 91:1180-1195. [PMID: 34716929 DOI: 10.1111/1365-2656.13623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022]
Abstract
Climate influences population genetic variation in marine species. Capturing these impacts remains challenging for marine fishes which disperse over large geographical scales spanning steep environmental gradients. It requires the extensive spatial sampling of individuals or populations, representative of seascape heterogeneity, combined with a set of highly informative molecular markers capable of revealing climatic-associated genetic variations. We explored how space, dispersal and environment shape the genomic patterns of two sympatric fish species in the Mediterranean Sea, which ranks among the oceanic basins most affected by climate change and human pressure. We hypothesized that the population structure and climate-associated genomic signatures of selection would be stronger in the less mobile species, as restricted gene flow tends to facilitate the fixation of locally adapted alleles. To test our hypothesis, we genotyped two species with contrasting dispersal abilities: the white seabream Diplodus sargus and the striped red mullet Mullus surmuletus. We collected 823 individuals and used genotyping by sequencing (GBS) to detect 8,206 single nucleotide polymorphisms (SNPs) for the seabream and 2,794 for the mullet. For each species, we identified highly differentiated genomic regions (i.e. outliers) and disentangled the relative contribution of space, dispersal and environmental variables (climate, marine primary productivity) on the outliers' genetic structure to test the prevalence of gene flow and local adaptation. We observed contrasting patterns of gene flow and adaptive genetic variation between the two species. The seabream showed a distinct Alboran sea population and panmixia across the Mediterranean Sea. The mullet revealed additional differentiation within the Mediterranean Sea that was significantly correlated to summer and winter temperatures, as well as marine primary productivity. Functional annotation of the climate-associated outlier SNPs then identified candidate genes involved in heat tolerance that could be examined to further predict species' responses to climate change. Our results illustrate the key steps of a comparative seascape genomics study aiming to unravel the evolutionary processes at play in marine species, to better anticipate their response to climate change. Defining population adaptation capacities and environmental niches can then serve to incorporate evolutionary processes into species conservation planning.
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Affiliation(s)
- Emilie Boulanger
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France.,MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Laura Benestan
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Pierre-Edouard Guerin
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | | | - David Mouillot
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Institut Universitaire de France, Paris, France
| | - Stéphanie Manel
- CEFE, University of Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
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7
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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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8
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Dang BT, Truong OT, Tran SQ, Glenner H. Comparative population genetics of swimming crab host ( Portunus pelagicus) and common symbiotic barnacle ( Octolasmis angulata) in Vietnam. PeerJ 2021; 9:e11671. [PMID: 34277149 PMCID: PMC8272463 DOI: 10.7717/peerj.11671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms. Methods Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages. Results Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).
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Affiliation(s)
- Binh Thuy Dang
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Oanh Thi Truong
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Sang Quang Tran
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Khanh Hoa, Vietnam
| | - Henrik Glenner
- Department of Biological Science, University of Bergen, Bergen, Norway
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9
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Reguera-Rouzaud N, Díaz-Viloria N, Pérez-Enríquez R, Espino-Barr E, Rivera-Lucero MI, Munguía-Vega A. Drivers for genetic structure at different geographic scales for Pacific red snapper (Lutjanus peru) and yellow snapper (Lutjanus argentiventris) in the tropical eastern Pacific. JOURNAL OF FISH BIOLOGY 2021; 98:1267-1280. [PMID: 33349917 DOI: 10.1111/jfb.14656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/03/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
The tropical eastern Pacific (TEP) is a highly dynamic region and a model system to study how habitat discontinuities affect the distribution of shorefishes, particularly for species that display ontogenetic habitat shifts, including snappers (Lutjanidae). To evaluate the genetic structure of the Pacific red snapper (Lutjanus peru) and the yellow snapper (Lutjanus argentiventris) throughout their distribution range along the TEP, 13 and 11 microsatellite loci were analysed, respectively. The genetic diversity of L. peru (N = 446) and L. argentiventris (N = 170) was evaluated in 10 and 5 localities, respectively, showing slightly higher but non-significant values in the Gulf of California for both species. The genetic structure analysis identified the presence of significant genetic structure in both species, but the locations of the identified barriers for the gene flow differed between species. The principal driver for the genetic structure at large scales >2500 km was isolation by distance. At smaller scales (<250 km), the habitat discontinuity for juveniles and adults and the environmental differences throughout the distribution range represented potential barriers to gene flow between populations for both species.
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Affiliation(s)
- Nicole Reguera-Rouzaud
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR), La Paz, Mexico
| | - Noé Díaz-Viloria
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional-Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR), La Paz, Mexico
| | - Ricardo Pérez-Enríquez
- Departamento de Acuicultura, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Mexico
| | - Elaine Espino-Barr
- Instituto Nacional de Pesca, CRIP-Manzanillo, Playa Ventana, Colima, Mexico
| | | | - Adrián Munguía-Vega
- Conservation Genetics Laboratory & Desert Laboratory on Tumamoc Hill, University of Arizona, Tucson, Arizona, USA
- @Lab Applied Genomics, La Paz, Mexico
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10
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von Takach B, Ahrens CW, Lindenmayer DB, Banks SC. Scale-dependent signatures of local adaptation in a foundation tree species. Mol Ecol 2021; 30:2248-2261. [PMID: 33740830 DOI: 10.1111/mec.15894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 01/17/2023]
Abstract
Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.
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Affiliation(s)
- Brenton von Takach
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia.,Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - David B Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
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11
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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12
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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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13
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D'Aloia CC, Andrés JA, Bogdanowicz SM, McCune AR, Harrison RG, Buston PM. Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high-throughput genotyping approaches. Mol Ecol 2020; 29:2189-2203. [PMID: 32147850 DOI: 10.1111/mec.15405] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/05/2020] [Accepted: 03/03/2020] [Indexed: 01/04/2023]
Abstract
Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.
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Affiliation(s)
- Cassidy C D'Aloia
- Department of Biological Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Jose A Andrés
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Peter M Buston
- Department of Biology and Marine Program, Boston University, Boston, MA, USA
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14
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Krueck NC, Treml EA, Innes DJ, Ovenden JR. Ocean currents and the population genetic signature of fish migrations. Ecology 2020; 101:e02967. [PMID: 31925790 DOI: 10.1002/ecy.2967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 10/04/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022]
Abstract
Animal migrations are a fascinating and global phenomenon, yet they are often difficult to study and sometimes poorly understood. Here, we build on classic ecological theory by hypothesizing that some enigmatic spawning migrations across coastal marine habitats can be inferred from the population genetic signature of larval dispersal by ocean currents. We test this assumption by integrating spatially realistic simulations of alternative spawning migration routes, associated patterns of larval dispersal, and associated variation in the population genetic structure of eastern Australian sea mullet (Mugil cephalus). We then use simulation results to assess the implications of alternative spawning destinations for larval replenishment, and we contrast simulated against measured population genetic variation. Both analyses suggest that the spawning migrations of M. cephalus in eastern Australia are likely to be localized (approximately 100 km along the shore), and that spawning is likely to occur in inshore waters. Our conclusions are supported by multiple lines of evidence available through independent studies, but they challenge the more traditional assumption of a single, long-distance migration event with subsequent offshore spawning in the East Australian Current. More generally, our study operationalizes classic theory on the relationship between fish migrations, ocean currents, and reproductive success. However, rather than confirming the traditionally assumed adaptation of migratory behavior to dominant ocean current flow, our findings support the concept of a genetically measurable link between fish migrations and local oceanographic conditions, specifically water temperature and coastal retention of larvae. We believe that future studies using similar approaches for high resolution and spatially realistic ecological-genetic scenario testing can help rapidly advance our understanding of key ecological processes in many other marine species.
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Affiliation(s)
- Nils C Krueck
- School of Biological Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia.,Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Eric A Treml
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, 3216, Australia
| | - David J Innes
- Department of Agriculture and Fisheries, Queensland Government, P.O. Box 6097, Brisbane, Queensland, 4072, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
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15
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Driscoe AL, Nice CC, Busbee RW, Hood GR, Egan SP, Ott JR. Host plant associations and geography interact to shape diversification in a specialist insect herbivore. Mol Ecol 2019; 28:4197-4211. [DOI: 10.1111/mec.15220] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Amanda L. Driscoe
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Robert W. Busbee
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Glen R. Hood
- Department of Biological Sciences Wayne State University Detroit Michigan
| | - Scott P. Egan
- Department of Biosciences Rice University Houston Texas
| | - James R. Ott
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
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16
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Riginos C, Hock K, Matias AM, Mumby PJ, Oppen MJH, Lukoschek V. Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12969] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Cynthia Riginos
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Karlo Hock
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Ambrocio M. Matias
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
- Institute of Biology University of the Philippines Diliman Quezon City Philippines
| | - Peter J. Mumby
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Madeleine J. H. Oppen
- Institute of Biology University of the Philippines Diliman Quezon City Philippines
- School of BioSciences The University of Melbourne Parkville Victoria Australia
- Australian Institute for Marine Sciences Cape Cleveland Queensland Australia
| | - Vimoksalehi Lukoschek
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
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17
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Xuereb A, D’Aloia CC, Daigle RM, Andrello M, Dalongeville A, Manel S, Mouillot D, Guichard F, Côté IM, Curtis JMR, Bernatchez L, Fortin MJ. Marine Conservation and Marine Protected Areas. POPULATION GENOMICS 2019. [DOI: 10.1007/13836_2018_63] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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