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Bernal-Durán V, Donoso D, Piñones A, Jonsson PR, Benestan L, Landaeta MF, Naretto J, Gerard K, Haye PA, Gonzalez-Wevar C, Poulin E, Segovia NI. Combining population genomics and biophysical modelling to assess connectivity patterns in an Antarctic fish. Mol Ecol 2024; 33:e17360. [PMID: 38656687 DOI: 10.1111/mec.17360] [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: 01/15/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish Harpagifer antarcticus, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modelling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central and (4) the southern area of WAP (Marguerite Bay). These genetic groups exhibited limited gene flow between them, consistent with local oceanographic conditions, which would represent barriers to larval dispersal. The joint effect of geographic distance and larval dispersal by ocean currents had a greater influence on the observed population structure than each variable evaluated separately. The combined effect of geographic distance and a complex oceanographic dynamic would be generating limited levels of population connectivity in the fish H. antarcticus along the WAP. Based on this, population connectivity estimations and priority areas for conservation were discussed, considering the marine protected area proposed for this threatened region of the Southern Ocean.
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Affiliation(s)
- Valentina Bernal-Durán
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile, Santiago, Chile
| | - David Donoso
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
- Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Andrea Piñones
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
- Instituto de Ciencias Marinas y Limnológicas (ICML) y Centro FONDAP IDEAL, Universidad Austral de Chile, Valdivia, Chile
- Centro COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Per R Jonsson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Laura Benestan
- Institut Français de Recherche pour l'Exploitation de la Mer, Centre du Pacifique, Vairao, Tahiti, French Polynesia
| | - Mauricio F Landaeta
- Laboratorio de Ictiología e Interacciones Biofísicas (LABITI), Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Observación Marino para Estudios de Riesgos del Ambiente Costero (COSTA-R), Universidad de Valparaíso, Viña del Mar, Chile
| | | | - Karin Gerard
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
| | - Pilar A Haye
- Instituto Milenio en Socio-ecología Costera (SECOS), Departamento de Biología Marina, Facultadde Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo, Chile
| | - Claudio Gonzalez-Wevar
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
- Instituto de Ciencias Marinas y Limnológicas (ICML) y Centro FONDAP IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Elie Poulin
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y subAntárticos (MIBASE), Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto Milenio de Ecología y Biodiversidad (IEB), Universidad de Chile, Santiago, Chile
| | - Nicolás I Segovia
- Instituto Milenio en Socio-ecología Costera (SECOS), Departamento de Biología Marina, Facultadde Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
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Kemppainen P, Schembri R, Momigliano P. Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data. Mol Biol Evol 2024; 41:msae091. [PMID: 38743590 PMCID: PMC11135943 DOI: 10.1093/molbev/msae091] [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: 12/06/2023] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.
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Affiliation(s)
- Petri Kemppainen
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
| | - Rhiannon Schembri
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Paolo Momigliano
- School of Biological Sciences and Swire Institute of Marine Science, Faculty of Science, The University of Hong Kong, Hong Kong, SAR, People's Republic of China
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Mares-Mayagoitia JA, Lafarga-De la Cruz F, Micheli F, Cruz-Hernández P, de-Anda-Montañez JA, Hyde J, Hernández-Saavedra NY, Mejía-Ruíz P, De Jesús-Bonilla VS, Vargas-Peralta CE, Valenzuela-Quiñonez F. Seascape genomics of the pink abalone (Haliotis corrugata): An insight into a cross-border species in the northeast Pacific coast. J Hered 2024; 115:188-202. [PMID: 38158823 DOI: 10.1093/jhered/esad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024] Open
Abstract
Seascape genomics gives insight into the geographic and environmental factors shaping local adaptations. It improves the understanding of the potential effects of climate change, which is relevant to provide the basis for the international management of fishery resources. The pink abalone (Haliotis corrugata) is distributed from California, United States to Baja California Sur, Mexico, exposed to a latitudinal environmental gradient in the California Current System. Management of the pink abalone contrasts between Mexico and the United States; Mexico has an active fishery organized in four administrative areas, while the United States has kept the fishery in permanent closure since 1996. However, the impact of environmental factors on genetic variation along the species distribution remains unknown, and understanding this relationship is crucial for effective spatial management strategies. This study aims to investigate the neutral and adaptive genomic structure of H. corrugata. A total of 203 samples from 13 locations were processed using ddRADseq, and covering the species' distribution. Overall, 2,231 neutral, nine potentially adaptive and three genomic-environmental association loci were detected. The neutral structure identified two groups: 1) California, United States and 2) Baja California Peninsula, México. In addition, the adaptive structure analysis also detected two groups with genetic divergence observed at Punta Eugenia. Notably, the seawater temperature significantly correlated with the northern group (temperate) and the southern (warmer) group. This study is a valuable foundation for future research and conservation initiatives, emphasizing the importance of considering neutral and adaptive genetic factors when developing management strategies for marine species.
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Affiliation(s)
| | - Fabiola Lafarga-De la Cruz
- Centro de Investigaciones Científicas y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Fiorenza Micheli
- Hopkins Marine Station, Oceans Department, Stanford University, Pacific Grove, CA, United States
| | - Pedro Cruz-Hernández
- Centro de Investigaciones Biológicas del Noroeste S.C., La Paz, Baja California Sur, Mexico
| | | | - John Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, CA, United States
| | | | - Paulina Mejía-Ruíz
- Centro de Investigaciones Científicas y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | | | - Carmen E Vargas-Peralta
- Centro de Investigaciones Científicas y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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4
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Selmoni O, Bay LK, Exposito-Alonso M, Cleves PA. Finding genes and pathways that underlie coral adaptation. Trends Genet 2024; 40:213-227. [PMID: 38320882 DOI: 10.1016/j.tig.2024.01.003] [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: 10/09/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Mass coral bleaching is one of the clearest threats of climate change to the persistence of marine biodiversity. Despite the negative impacts of bleaching on coral health and survival, some corals may be able to rapidly adapt to warming ocean temperatures. Thus, a significant focus in coral research is identifying the genes and pathways underlying coral heat adaptation. Here, we review state-of-the-art methods that may enable the discovery of heat-adaptive loci in corals and identify four main knowledge gaps. To fill these gaps, we describe an experimental approach combining seascape genomics with CRISPR/Cas9 gene editing to discover and validate heat-adaptive loci. Finally, we discuss how information on adaptive genotypes could be used in coral reef conservation and management strategies.
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Affiliation(s)
- Oliver Selmoni
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Line K Bay
- Reef Recovery, Adaptation, and Restoration, Australian Institute of Marine Science; Townsville, QLD 4810, Australia
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Phillip A Cleves
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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5
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Nimbs MJ, Champion C, Lobos SE, Malcolm HA, Miller AD, Seinor K, Smith SD, Knott N, Wheeler D, Coleman MA. Genomic analyses indicate resilience of a commercially and culturally important marine gastropod snail to climate change. PeerJ 2023; 11:e16498. [PMID: 38025735 PMCID: PMC10676721 DOI: 10.7717/peerj.16498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic vulnerability analyses are being increasingly used to assess the adaptability of species to climate change and provide an opportunity for proactive management of harvested marine species in changing oceans. Southeastern Australia is a climate change hotspot where many marine species are shifting poleward. The turban snail, Turbo militaris is a commercially and culturally harvested marine gastropod snail from eastern Australia. The species has exhibited a climate-driven poleward range shift over the last two decades presenting an ongoing challenge for sustainable fisheries management. We investigate the impact of future climate change on T. militaris using genotype-by-sequencing to project patterns of gene flow and local adaptation across its range under climate change scenarios. A single admixed, and potentially panmictic, demographic unit was revealed with no evidence of genetic subdivision across the species range. Significant genotype associations with heterogeneous habitat features were observed, including associations with sea surface temperature, ocean currents, and nutrients, indicating possible adaptive genetic differentiation. These findings suggest that standing genetic variation may be available for selection to counter future environmental change, assisted by widespread gene flow, high fecundity and short generation time in this species. We discuss the findings of this study in the content of future fisheries management and conservation.
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Affiliation(s)
- Matt J. Nimbs
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Curtis Champion
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
| | - Simon E. Lobos
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Hamish A. Malcolm
- NSW Department of Primary Industries, Fisheries Research, Coffs Harbour, NSW, Australia
| | - Adam D. Miller
- Deakin Genomics Centre, Deakin University, Geelong, Vic, Australia
- School of Life and Environmental Sciences, Deakin University, Warrnambool, Vic, Australia
| | - Kate Seinor
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Stephen D.A. Smith
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Aquamarine Australia, Mullaway, NSW, Australia
| | - Nathan Knott
- NSW Department of Primary Industries, Fisheries Research, Huskisson, NSW, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange, NSW, Australia
| | - Melinda A. Coleman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- NSW Department of Primary Industries, Fisheries, National Marine Science Centre, Coffs Harbour, Australia
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6
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Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
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Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
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7
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Guo F, Ye Y, Zhu K, Lin S, Wang Y, Dong Z, Yao R, Li H, Wang W, Liao Z, Guo B, Yan X. Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing. Int J Mol Sci 2023; 24:13641. [PMID: 37686445 PMCID: PMC10488143 DOI: 10.3390/ijms241713641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.
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Affiliation(s)
- Feng Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
| | - Shuangrui Lin
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yuxia Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhenyu Dong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Ronghui Yao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Hongfei Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Weifeng Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
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8
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Laso-Jadart R, O'Malley M, Sykulski AM, Ambroise C, Madoui MA. Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations. BMC Ecol Evol 2023; 23:46. [PMID: 37658324 PMCID: PMC10472650 DOI: 10.1186/s12862-023-02160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method. RESULTS We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors. CONCLUSION Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.
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Affiliation(s)
- Romuald Laso-Jadart
- 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 GO-SEE, 3 rue Michel-Ange, Paris, France
| | - Michael O'Malley
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | - Adam M Sykulski
- STOR-i Centre for Doctoral Training/Department of Mathematics and Statistics, Lancaster University, Lancaster, UK
| | | | - Mohammed-Amin Madoui
- 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 GO-SEE, 3 rue Michel-Ange, Paris, France.
- 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.
- Équipe Écologie Évolutive, UMR CNRS 6282 BioGéoSciences, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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Piertney SB, Wenzel M, Jamieson AJ. Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench. Mol Ecol 2023; 32:2206-2218. [PMID: 36808786 DOI: 10.1111/mec.16887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/20/2023]
Abstract
The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipod Hirondellea gigas in the Mariana Trench at depths of 8126-10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco-evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alan J Jamieson
- Minderoo-UWA Deep-Sea Research Centre, School of Biological Sciences and Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
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10
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De Wit P, Faust E, Green L, Jahnke M, Pereyra RT, Rafajlović M. A decade of progress in marine evolutionary biology. Evol Appl 2023; 16:193-201. [PMID: 36793695 PMCID: PMC9923465 DOI: 10.1111/eva.13523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/11/2022] [Indexed: 12/27/2022] Open
Abstract
This article summarizes the Evolutionary Applications Special Issue, "A decade of progress in Marine Evolutionary Biology." The globally connected ocean, from its pelagic depths to its highly varied coastlines, inspired Charles Darwin to develop the theory of evolution during the voyage of the Beagle. As technology has developed, there has been a dramatic increase in our knowledge about life on our blue planet. This Special Issue, composed of 19 original papers and seven reviews, represents a small contribution to the larger picture of recent research in evolutionary biology, and how such advancements come about through the connection of researchers, their fields, and their knowledge. The first European network for marine evolutionary biology, the Linnaeus Centre for Marine Evolutionary Biology (CeMEB), was developed to study evolutionary processes in the marine environment under global change. Though hosted by the University of Gothenburg in Sweden, the network quickly grew to encompass researchers throughout Europe and beyond. Today, more than a decade after its foundation, CeMEB's focus on the evolutionary consequences of global change is more relevant than ever, and knowledge gained from marine evolution research is urgently needed in management and conservation. This Special Issue, organized and developed through the CeMEB network, contains contributions from all over the world and provides a snapshot of the current state of the field, thus forming an important basis for future research directions.
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Affiliation(s)
- Pierre De Wit
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Marine Sciences, Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Ellika Faust
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Marine Sciences, Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Leon Green
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Marlene Jahnke
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Marine Sciences, Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Ricardo T Pereyra
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Marine Sciences, Tjärnö Marine Laboratory University of Gothenburg Strömstad Sweden
| | - Marina Rafajlović
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Marine Sciences University of Gothenburg Gothenburg Sweden
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11
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Fainburg L, Sabadin D, Díaz de Astarloa JM, Fernández Iriarte P. Population structure of mud flounder Paralichthys orbignyanus from the south-western Atlantic Ocean. JOURNAL OF FISH BIOLOGY 2023; 102:455-464. [PMID: 36427018 DOI: 10.1111/jfb.15271] [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: 12/29/2021] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift.
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Affiliation(s)
- Leandro Fainburg
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - David Sabadin
- Instituto de Investigaciones Marinas y Costeras, Laboratorio Biología de Peces, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Juan Martín Díaz de Astarloa
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Pedro Fernández Iriarte
- Departamento de Biología-Instituto de Investigaciones Marinas y Costeras, Laboratorio de Genética, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
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12
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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13
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Antoniou A, Manousaki T, Ramírez F, Cariani A, Cannas R, Kasapidis P, Magoulas A, Albo-Puigserver M, Lloret-Lloret E, Bellido JM, Pennino MG, Follesa MC, Esteban A, Saraux C, Sbrana M, Spedicato MT, Coll M, Tsigenopoulos CS. Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea. Mol Ecol 2023; 32:1608-1628. [PMID: 36596297 DOI: 10.1111/mec.16840] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/20/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023]
Abstract
By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter includes how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 single nucleotide polymorphisms (SNPs) from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (FST = 0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19°C, a critical threshold for successful sardine spawning, was crucial at all levels of population structuring with implications on the species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium in which population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in a natural system warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key to understanding and predicting future changes and responses of this highly exploited species in the face of climate change.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Francisco Ramírez
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Alessia Cariani
- Dept. Biological, Geological & Environmental Sciences (BiGeA), Alma Mater Studiorum - Università di Bologna, Ravenna, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Rita Cannas
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
| | - Marta Albo-Puigserver
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain.,Centro Oceanográfico de Baleares, Instituto Español de Oceanografía (COB-CNIEO/CSIC), Palma, Spain
| | - Elena Lloret-Lloret
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Jose Maria Bellido
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía, (COMU-CNIEO/CSIC), Murcia, Spain
| | - Maria Grazia Pennino
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (COVI-CNIEO/CSIC), Vigo, Pontevedra, Spain
| | - Maria Cristina Follesa
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Antonio Esteban
- Centro Oceanográfico de Murcia, Instituto Español de Oceanografía, (COMU-CNIEO/CSIC), Murcia, Spain
| | - Claire Saraux
- MARBEC, University of Montpellier, CNRS, IFREMER, IRD, Sète, France
| | - Mario Sbrana
- Consorzio per il Centro Interuniversitario di Biologia Marina ed Ecologia Applicata G, Livorno, Italy
| | | | - Marta Coll
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Costas S Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece
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14
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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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15
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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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16
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Adam AAS, Thomas L, Underwood J, Gilmour J, Richards ZT. Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia. Mol Ecol 2022; 31:3533-3547. [PMID: 35567512 PMCID: PMC9328316 DOI: 10.1111/mec.16498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
Abstract
Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecast future genetic offset in gradient forest and generalised dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming scenario (RCP 2.6), we predicted a general pattern of increasing genetic offset with latitude. Under the extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch between current allele frequencies and those required to cope with local environmental change, compared to populations in the inshore Kimberley region. The study suggests complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.
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Affiliation(s)
- Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia.,Australian Institute of Marine Science, IOMRC, The University of Western Australia, Crawley, Western Australia
| | - Luke Thomas
- Australian Institute of Marine Science, IOMRC, The University of Western Australia, Crawley, Western Australia.,The UWA Oceans Institute, Oceans Graduate School, The University of Western Australia, Crawley, Western Australia
| | - Jim Underwood
- Australian Institute of Marine Science, IOMRC, The University of Western Australia, Crawley, Western Australia
| | - James Gilmour
- Australian Institute of Marine Science, IOMRC, The University of Western Australia, Crawley, Western Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia.,Collections and Research, Western Australian Museum, Welshpool, Western Australia
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17
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Dalongeville A, Nielsen ES, Teske PR, Heyden S. Comparative phylogeography in a marine biodiversity hotspot provides novel insights into evolutionary processes across the Atlantic‐Indian Ocean transition. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Erica S. Nielsen
- Department of Evolution and Ecology University of California, Davis Davis California USA
| | - Peter R. Teske
- Department of Zoology Centre for Ecological Genomics and Wildlife Conservation University of Johannesburg Auckland Park South Africa
| | - Sophie Heyden
- Department of Botany and Zoology Evolutionary Genomics Group Stellenbosch University Stellenbosch South Africa
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18
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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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19
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Knutsen H, Catarino D, Rogers L, Sodeland M, Mattingsdal M, Jahnke M, Hutchings JA, Mellerud I, Espeland SH, Johanneson K, Roth O, Hansen MM, Jentoft S, André C, Jorde PE. Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species. Mol Ecol 2022; 31:2562-2577. [PMID: 35229385 PMCID: PMC9311693 DOI: 10.1111/mec.16415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/11/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double‐digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long‐term (~30‐year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation‐by‐distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps.
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Affiliation(s)
- Halvor Knutsen
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Diana Catarino
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Lauren Rogers
- Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Marte Sodeland
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Morten Mattingsdal
- Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Marlene Jahnke
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Jeffrey A Hutchings
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway.,Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Ida Mellerud
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
| | - Sigurd H Espeland
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway.,Centre for Coastal Research, Department of Natural Sciences, University of Agder, 4630, Kristiansand, Norway
| | - Kerstin Johanneson
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Kiel University, Germany
| | - Michael M Hansen
- Department of Biology, Aarhus University, 8000, Aarhus C, Denmark
| | - Sissel Jentoft
- University of Oslo, Department of Biology, 0316, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Per Erik Jorde
- Institute of Marine Research, Nye Flødevigveien 20, 4817, His, Norway
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20
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Pratt EAL, Beheregaray LB, Bilgmann K, Zanardo N, Diaz-Aguirre F, Brauer C, Sandoval-Castillo J, Möller LM. Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity. Mol Ecol 2022; 31:2223-2241. [PMID: 35146819 DOI: 10.1111/mec.16389] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The datasets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8,081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1,000s km) and fine-scales (<100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, 2109, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Department of Environment and Water, Adelaide, 5000, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia.,Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, 5042, South Australia, Australia
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21
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Jahnke M, Moknes P, Le‐Moan A, Martens GA, Jonsson PR. Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab
Carcinus maenas. Mol Ecol 2022; 31:1980-1994. [PMID: 35080070 PMCID: PMC9540756 DOI: 10.1111/mec.16371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/27/2022]
Abstract
Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge for larvae of coastal species is to return to coastal nursery habitats. Shore crab (Carcinus maenas L.) larvae are known to show tidal rhythmicity in vertical migration in tidal areas and circadian rhythmicity in microtidal areas, which seems to increase successful coastal settlement. We studied genome‐wide differentiation based on 24,000 single nucleotide polymorphisms of 12 native populations of shore crab sampled from a large tidal amplitude gradient from macrotidal (~8 m) to microtidal (~0.2 m). Dispersal and recruitment success of larvae was assessed with a Lagrangian biophysical model, which showed a strong effect of larval behaviour on long‐term connectivity, and dispersal barriers that partly coincided with different tidal environments. The genetic population structure showed a subdivision of the samples into three clusters, which represent micro‐, meso‐ and macrotidal areas. The genetic differentiation was mostly driven by 0.5% outlier loci, which showed strong allelic clines located at the limits between the three tidal areas. Demographic modelling suggested that the two genetic barriers have different origins. Differential gene expression of two clock genes (cyc and pdp1) further highlighted phenotypic differences among genetic clusters that are potentially linked to the differences in larval behaviour. Taken together, our seascape genomic study suggests that tidal regime acts as a strong selection force on shore crab population structure, consistent with larval behaviour affecting dispersal and recruitment success.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
| | - Per‐Olav Moknes
- Department of Marine Science University of Gothenburg Gothenburg Sweden
| | - Alan Le‐Moan
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
| | - Gerrit A. Martens
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
- Institute of Zoology University of Hamburg Hamburg Germany
| | - Per R. Jonsson
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
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22
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Delaval A, Frost M, Bendall V, Hetherington SJ, Stirling D, Hoarau G, Jones CS, Noble LR. Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis. Evol Appl 2022; 15:78-94. [PMID: 35126649 PMCID: PMC8792474 DOI: 10.1111/eva.13327] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022] Open
Abstract
The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.
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Affiliation(s)
| | - Michelle Frost
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | - Victoria Bendall
- Centre for EnvironmentFisheries and Aquaculture ScienceLowestoftUK
| | | | | | - Galice Hoarau
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | | | - Leslie R. Noble
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
- School of Biological SciencesUniversity of AberdeenAberdeenUK
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23
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Chen Z, Grossfurthner L, Loxterman JL, Masingale J, Richardson BA, Seaborn T, Smith B, Waits LP, Narum SR. Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies. Evol Appl 2022; 15:3-21. [PMID: 35126645 PMCID: PMC8792483 DOI: 10.1111/eva.13335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research InstituteUniversity of IdahoHagermanIdahoUSA
| | - Lukas Grossfurthner
- Bioinformatics and Computational Biology Graduate ProgramUniversity of IdahoHagermanIdahoUSA
| | - Janet L. Loxterman
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | | | | | - Travis Seaborn
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Brandy Smith
- Department of Biological SciencesIdaho State UniversityPocatelloIdahoUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife ResourcesUniversity of IdahoMoscowIdahoUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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24
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Vera M, Maroso F, Wilmes S, Hermida M, Blanco A, Fernández C, Groves E, Malham SK, Bouza C, Robins PE, Martínez P. Genomic survey of edible cockle (
Cerastoderma edule
) in the Northeast Atlantic: a baseline for sustainable management of its wild resources. Evol Appl 2021; 15:262-285. [PMID: 35233247 PMCID: PMC8867702 DOI: 10.1111/eva.13340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b‐RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (FST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Institute of Aquaculture Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Department of Life Sciences and Biotechnologies University of Ferrara via L. Borsari 46 44124 Ferrara Italy
| | - Sophie‐B. Wilmes
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Institute of Aquaculture Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Institute of Aquaculture Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - Emily Groves
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Shelagh K Malham
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Institute of Aquaculture Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - Peter E. Robins
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology. ACUIGEN group. Faculty of Veterinary Universidade de Santiago de Compostela. Campus of Lugo 27002 Lugo Spain
- Institute of Aquaculture Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
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25
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Soares RX, da Motta-Neto CC, da Costa GWWF, Cioffi MDB, Bertollo LAC, Borges AT, Molina WF. Comparative cytogenetic patterns in Carangidae fishes in association with their distribution range. COMPARATIVE CYTOGENETICS 2021; 15:429-445. [PMID: 34963795 PMCID: PMC8654809 DOI: 10.3897/compcytogen.v15.i4.69638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Carangidae are an important and widespreaded family of pelagic predatory fishes that inhabit reef regions or open ocean areas, some species occupying a vast circumglobal distribution. Cytogenetic comparisons among representatives of its different tribes help to understand the process of karyotype divergence in marine ecosystems due to the variable migratory ability of species. In this sense, conventional cytogenetic investigations (Giemsa staining, Ag-NORs, and C-banding), GC base-specific fluorochrome staining and FISH mapping of ribosomal DNAs were performed. Four species, Elagatisbipinnulata (Quoy et Gaimard, 1825) and Seriolarivoliana (Valenciennes, 1883) (Naucratini), with circumtropical distributions, Gnathanodonspeciosus (Forsskål, 1775) (Carangini), widely distributed in the tropical and subtropical waters of the Indian and Pacific oceans, and Trachinotuscarolinus (Linnaeus, 1766) (Trachinotini), distributed along the western Atlantic Ocean, were analyzed, thus encompassing representatives of three out its four tribes. All species have diploid chromosome number 2n = 48, with karyotypes composed mainly by acrocentric chromosomes (NF = 50-56). The 18S rDNA/Ag-NORs/GC+ and 5S rDNA loci were located on chromosomes likely homeologs. Karyotypes showed a pattern considered basal for the family or with small variations in their structures, apparently due to pericentric inversions. The migratory capacity of large pelagic swimmers, in large distribution areas, likely restricts the fixation of chromosome changes in Carangidae responsible for a low level of karyotype diversification.
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Affiliation(s)
- Rodrigo Xavier Soares
- Departament of Cell Biology and Genetics, Biosciences Center, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078970, Brazil
| | - Clóvis Coutinho da Motta-Neto
- Departament of Cell Biology and Genetics, Biosciences Center, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078970, Brazil
| | | | - Marcelo de Bello Cioffi
- Fish Cytogenetics Laboratory, Departament of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, C.P. 676, Brazils
| | - Luiz Antônio Carlos Bertollo
- Fish Cytogenetics Laboratory, Departament of Genetics and Evolution, Universidade Federal de São Carlos, São Carlos, SP, C.P. 676, Brazils
| | - Amanda Torres Borges
- Departament of Cell Biology and Genetics, Biosciences Center, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078970, Brazil
| | - Wagner Franco Molina
- Departament of Cell Biology and Genetics, Biosciences Center, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078970, Brazil
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26
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Paril JF, Balding DJ, Fournier-Level A. Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations. Mol Ecol Resour 2021; 22:137-152. [PMID: 34192415 DOI: 10.1111/1755-0998.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 11/27/2022]
Abstract
Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.
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Affiliation(s)
- Jefferson F Paril
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - David J Balding
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandre Fournier-Level
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia
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27
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Mendiola MJR, Ravago‐Gotanco R. Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Ecol Evol 2021; 11:7951-7969. [PMID: 34188864 PMCID: PMC8216953 DOI: 10.1002/ece3.7625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation ( R adj 2 = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (N e < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea ( R adj 2 = 0.692-0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource.
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Affiliation(s)
| | - Rachel Ravago‐Gotanco
- The Marine Science InstituteUniversity of the Philippines DilimanQuezon CityPhilippines
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28
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Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
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Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
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29
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Benestan L, Fietz K, Loiseau N, Guerin PE, Trofimenko E, Rühs S, Schmidt C, Rath W, Biastoch A, Pérez-Ruzafa A, Baixauli P, Forcada A, Arcas E, Lenfant P, Mallol S, Goñi R, Velez L, Höppner M, Kininmonth S, Mouillot D, Puebla O, Manel S. Restricted dispersal in a sea of gene flow. Proc Biol Sci 2021; 288:20210458. [PMID: 34004134 PMCID: PMC8131118 DOI: 10.1098/rspb.2021.0458] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.
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Affiliation(s)
- L. Benestan
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - K. Fietz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - N. Loiseau
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - P. E. Guerin
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - E. Trofimenko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - S. Rühs
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - C. Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - W. Rath
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - A. Biastoch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - A. Pérez-Ruzafa
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - P. Baixauli
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - A. Forcada
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - E. Arcas
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - P. Lenfant
- Centre de Formation et de Recherche sur les Environnements Méditerranéens, Université Perpignan Via Domitia, CNRS, 66100 Perpignan, France
| | - S. Mallol
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - R. Goñi
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - L. Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - M. Höppner
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - S. Kininmonth
- School of Marine Studies, University of the South Pacific, Fiji
| | - D. Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - O. Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Ecology Department, Leibniz-Centre for Tropical Marine Research, Fahrenheitstraße 6, 28359 Bremen, Germany
| | - S. Manel
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
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30
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Andrews KR, Epstein B, Leslie MS, Fiedler P, Morin PA, Hoelzel AR. Genomic signatures of divergent selection are associated with social behaviour for spinner dolphin ecotypes. Mol Ecol 2021; 30:1993-2008. [PMID: 33645853 DOI: 10.1111/mec.15865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 01/16/2021] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Understanding the genomic basis of adaptation is critical for understanding evolutionary processes and predicting how species will respond to environmental change. Spinner dolphins in the eastern tropical Pacific (ETP) present a unique system for studying adaptation. Within this large geographical region are four spinner dolphin ecotypes with weak neutral genetic divergence and no obvious barriers to gene flow, but strong spatial variation in morphology, behaviour and habitat. These ecotypes have large population sizes, which could reduce the effects of drift and facilitate selection. To identify genomic regions putatively under divergent selective pressures between ecotypes, we used genome scans with 8994 RADseq single nucleotide polymorphisms (SNPs) to identify population differentiation outliers and genotype-environment association outliers. Gene ontology enrichment analyses indicated that outlier SNPs from both types of analyses were associated with multiple genes involved in social behaviour and hippocampus development, including 15 genes associated with the human social disorder autism. Evidence for divergent selection on social behaviour is supported by previous evidence that these spinner dolphin ecotypes differ in mating systems and associated social behaviours. In particular, three of the ETP ecotypes probably have a polygynous mating system characterized by strong premating competition among males, whereas the fourth ecotype probably has a polygynandrous mating system characterized by strong postmating competition such as sperm competition. Our results provide evidence that selection for social behaviour may be an evolutionary force driving diversification of spinner dolphins in the ETP, potentially as a result of divergent sexual selection associated with different mating systems. Future studies should further investigate the potential adaptive role of the candidate genes identified here, and could probably find further signatures of selection using whole genome sequence data.
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Affiliation(s)
- Kimberly R Andrews
- School of Biosciences, Durham University, Durham, UK.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
| | - Brendan Epstein
- Department of Plant & Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | | | - Paul Fiedler
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - A Rus Hoelzel
- School of Biosciences, Durham University, Durham, UK
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31
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Selmoni O, Lecellier G, Magalon H, Vigliola L, Oury N, Benzoni F, Peignon C, Joost S, Berteaux-Lecellier V. Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species. Mol Ecol 2021; 30:1892-1906. [PMID: 33619812 PMCID: PMC8252710 DOI: 10.1111/mec.15857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that have been exposed to recurrent thermal stress over the years and whose corals appear to have been tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover the molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs), frequencies of which were associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress-associated SNPs located in proximity of genes involved in pathways well known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways, and DNA damage-repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underline the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.
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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.,UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - Gaël Lecellier
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France.,Université Paris-Saclay, UVSQ, Versailles, France
| | - Hélène Magalon
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, St Denis de la Réunion, France
| | - Laurent Vigliola
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - Nicolas Oury
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, St Denis de la Réunion, France
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christophe Peignon
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - 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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32
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Morin PA, Forester BR, Forney KA, Crossman CA, Hancock-Hanser BL, Robertson KM, Barrett-Lennard LG, Baird RW, Calambokidis J, Gearin P, Hanson MB, Schumacher C, Harkins T, Fontaine MC, Taylor BL, Parsons KM. Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor-quality samples. Mol Ecol 2021; 30:1457-1476. [PMID: 33544423 DOI: 10.1111/mec.15827] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Harbor porpoise in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of single nucleotide polymoirphisms as microhaplotypes (N = 271 samples) in addition to mitochondrial (mtDNA) sequence data (N = 413 samples) to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We confirmed an overall pattern of strong isolation-by-distance, suggesting that individual dispersal is restricted. We also found evidence of regions where genetic differences are larger than expected based on geographical distance alone, implying current or historical barriers to gene flow. In particular, the southernmost population in California is genetically distinct (FST = 0.02 [microhaplotypes]; 0.31 [mtDNA]), with both reduced genetic variability and high frequency of an otherwise rare mtDNA haplotype. At the northern end of our study range, we found significant genetic differentiation of samples from the Strait of Georgia, previously identified as a potential biogeographical boundary or secondary contact zone between harbor porpoise populations. Association of microhaplotypes with remotely sensed environmental variables indicated potential local adaptation, especially at the southern end of the species' range. These results inform conservation and management for this nearshore species, illustrate the value of genomic methods for detecting patterns of genetic structure within a continuously distributed marine species, and highlight the power of microhaplotype genotyping for detecting genetic structure in harbor porpoises despite reliance on poor-quality samples.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Karin A Forney
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Moss Landing, CA, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, USA
| | - Carla A Crossman
- Biology Department, Saint Mary's University, Halifax, NS, Canada.,Cetacean Research Program, Vancouver Aquarium, Vancouver, BC, Canada
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | | | | | | | - Pat Gearin
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | - M Bradley Hanson
- Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
| | | | | | - Michael C Fontaine
- MIVEGEC Research Unit (Université de Montpellier, CNRS, IRD) & Centre for Research on the Ecology and Evolution of Diseases (CREES), Centre IRD de Montpellier, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kim M Parsons
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA.,Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, USA
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33
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Vandamme S, Raeymaekers JAM, Maes GE, Cottenie K, Calboli FCF, Diopere E, Volckaert FAM. Reconciling seascape genetics and fisheries science in three codistributed flatfishes. Evol Appl 2021; 14:536-552. [PMID: 33664793 PMCID: PMC7896710 DOI: 10.1111/eva.13139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/17/2022] Open
Abstract
Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits.
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Affiliation(s)
- Sara Vandamme
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Animal Sciences Unit ‐ Fisheries and Aquatic ProductionFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
- Department of Animal Sciences and Aquatic EcologyGhent UniversityOostendeBelgium
| | - Joost A. M. Raeymaekers
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Gregory E. Maes
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Centre for Sustainable Tropical Fisheries and AquacultureComparative Genomics CentreCollege of Sciences and EngineeringJames Cook UniversityTownsvilleQLDAustralia
- Center for Human GeneticsGenomics CoreKU LeuvenLeuvenBelgium
| | - Karl Cottenie
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | - Eveline Diopere
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | - Filip A. M. Volckaert
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- CeMEBDepartment of Marine SciencesUniversity of GothenburgGothenburgSweden
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34
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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: 11] [Impact Index Per Article: 3.7] [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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35
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Selmoni O, Lecellier G, Vigliola L, Berteaux-Lecellier V, Joost S. Coral cover surveys corroborate predictions on reef adaptive potential to thermal stress. Sci Rep 2020; 10:19680. [PMID: 33184366 PMCID: PMC7661510 DOI: 10.1038/s41598-020-76604-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/21/2020] [Indexed: 11/22/2022] Open
Abstract
As anomalous heat waves are causing the widespread decline of coral reefs worldwide, there is an urgent need to identify coral populations tolerant to thermal stress. Heat stress adaptive potential is the degree of tolerance expected from evolutionary processes and, for a given reef, depends on the arrival of propagules from reefs exposed to recurrent thermal stress. For this reason, assessing spatial patterns of thermal adaptation and reef connectivity is of paramount importance to inform conservation strategies. In this work, we applied a seascape genomics framework to characterize the spatial patterns of thermal adaptation and connectivity for coral reefs of New Caledonia (Southern Pacific). In this approach, remote sensing of seascape conditions was combined with genomic data from three coral species. For every reef of the region, we computed a probability of heat stress adaptation, and two indices forecasting inbound and outbound connectivity. We then compared our indicators to field survey data, and observed that decrease of coral cover after heat stress was lower at reefs predicted with high probability of adaptation and inbound connectivity. Last, we discussed how these indicators can be used to inform local conservation strategies and preserve the adaptive potential of New Caledonian reefs.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
| | - Gaël Lecellier
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
- UVSQ, Université de Paris-Saclay, Versailles, France
| | - Laurent Vigliola
- UMR250/9220 ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, New Caledonia, France
| | | | - Stéphane Joost
- Laboratory of Geographic Information Systems, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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36
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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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37
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Nielsen ES, Henriques R, Beger M, Toonen RJ, von der Heyden S. Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. BMC Evol Biol 2020; 20:121. [PMID: 32938400 PMCID: PMC7493327 DOI: 10.1186/s12862-020-01679-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Technical University of Denmark, National Institute of Aquatic Resources, Section for Marine Living Resources, Velsøvej 39, 8600, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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38
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Alfaya JEF, Tonini MH, Soria G, Penchaszadeh PE, Bigatti G. Nemertean Larval Dispersion Across Biogeographic Provinces of Southwest Atlantic. Zoolog Sci 2020; 37:450-457. [DOI: 10.2108/zs200050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- José E. F. Alfaya
- LARBIM-IBIOMAR, CCT CONICET-CENPAT. Bvd. Brown 2915, U9120ACV Puerto Madryn, Chubut, Argentina
| | | | - Gaspar Soria
- Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (UNPSJB), Bvd. Brown 3100; U9120ACV Puerto Madryn, Chubut, Argentina
| | - Pablo E. Penchaszadeh
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN CONICET), Av. A. Gallardo 470 (C1405DJR), Buenos Aires, Argentina
| | - Gregorio Bigatti
- LARBIM-IBIOMAR, CCT CONICET-CENPAT. Bvd. Brown 2915, U9120ACV Puerto Madryn, Chubut, Argentina
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39
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Selmoni O, Rochat E, Lecellier G, Berteaux‐Lecellier V, Joost S. Seascape genomics as a new tool to empower coral reef conservation strategies: An example on north-western Pacific Acropora digitifera. Evol Appl 2020; 13:1923-1938. [PMID: 32908595 PMCID: PMC7463334 DOI: 10.1111/eva.12944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/10/2020] [Accepted: 02/17/2020] [Indexed: 12/25/2022] Open
Abstract
Coral reefs are suffering a major decline due to the environmental constraints imposed by climate change. Over the last 20 years, three major coral bleaching events occurred in concomitance with anomalous heatwaves, provoking a severe loss of coral cover worldwide. The conservation strategies for preserving reefs, as they are implemented now, cannot cope with global climatic shifts. Consequently, researchers are advocating for preservation networks to be set-up to reinforce coral adaptive potential. However, the main obstacle to this implementation is that studies on coral adaption are usually hard to generalize at the scale of a reef system. Here, we study the relationships between genotype frequencies and environmental characteristics of the sea (seascape genomics), in combination with connectivity analysis, to investigate the adaptive potential of a flagship coral species of the Ryukyu Archipelago (Japan). By associating genotype frequencies with descriptors of historical environmental conditions, we discovered six genomic regions hosting polymorphisms that might promote resistance against heat stress. Remarkably, annotations of genes in these regions were consistent with molecular roles associated with heat responses. Furthermore, we combined information on genetic and spatial distances between reefs to predict connectivity at a regional scale. The combination of these results portrayed the adaptive potential of this population: we were able to identify reefs carrying potential heat stress adapted genotypes and to understand how they disperse to neighbouring reefs. This information was summarized by objective, quantifiable and mappable indices covering the whole region, which can be extremely useful for future prioritization of reefs in conservation planning. This framework is transferable to any coral species on any reef system and therefore represents a valuable tool for empowering preservation efforts dedicated to the protection of coral reefs in warming oceans.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Estelle Rochat
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Gael Lecellier
- UMR250/9220 ENTROPIE IRD‐CNRS‐URLabex CORAILNoumeaNew Caledonia
- UVSQUniversité de Paris‐SaclayVersaillesFrance
| | | | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG)School of Architecture, Civil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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40
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Arnaud-Haond S, Stoeckel S, Bailleul D. New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations. Mol Ecol 2020; 29:3248-3260. [PMID: 32613610 DOI: 10.1111/mec.15532] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/30/2020] [Accepted: 06/11/2020] [Indexed: 01/23/2023]
Abstract
Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowledge of the effect of clonality on the population genetics of natural populations severely limits our understanding of the dynamics and connectivity of meadows. Recent modelling approaches have described the expected distributions of genotypic and genetic descriptors under increasing clonal rates, which may help us better understand and interpret population genetics data obtained for partial asexuals. Here, in the light of these recent theoretical developments, we revisited population genetics data for 165 meadows of four seagrass species. Contrasting shoot lifespan and rhizome turnover led to the prediction that the influence of asexual reproduction would increase along a gradient from Zostera noltii to Zostera marina, Cymodocea nodosa and Posidonia oceanica, with increasing departure from Hardy-Weinberg equilibrium (Fis ), mostly towards heterozygote excess, and decreasing genotypic richness (R). This meta-analysis provides a nested validation of this hypothesis at both the species and meadow scales through a significant relationship between Fis and R within each species. By empirically demonstrating the theoretical expectations derived from recent modelling approaches, this work calls for the use of Hardy-Weinberg equilibrium (Fis ) rather than only the strongly sampling-sensitive R to assess the importance of clonal reproduction (c), at least when the impact of selfing on Fis can be neglected. The results also emphasize the need to revise our appraisal of the extent of clonality and its influence on the dynamics, connectivity and evolutionary trajectory of partial asexuals in general, including in seagrass meadows, to develop the most accurate management strategies.
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Affiliation(s)
| | - Solenn Stoeckel
- IGEPP INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Diane Bailleul
- Université de Montpellier, Ifremer, CNRS, IRD, MARBEC, Sète, France
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41
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Segovia NI, González-Wevar CA, Haye PA. Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast. Sci Rep 2020; 10:14098. [PMID: 32839518 PMCID: PMC7445245 DOI: 10.1038/s41598-020-70798-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022] Open
Abstract
The highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29–585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.
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Affiliation(s)
- Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.,Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile
| | - Claudio A González-Wevar
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Marinas Y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP de Investigaciones en Dinámica de Ecosistemas de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
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Laso‐Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet J, Madoui M. Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecol Evol 2020; 10:8894-8905. [PMID: 32884665 PMCID: PMC7452778 DOI: 10.1002/ece3.6588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Acclimation allowed by variation in gene or allele expression in natural populations is increasingly understood as a decisive mechanism, as much as adaptation, for species evolution. However, for small eukaryotic organisms, as species from zooplankton, classical methods face numerous challenges. Here, we propose the concept of allelic differential expression at the population-scale (psADE) to investigate the variation in allele expression in natural populations. We developed a novel approach to detect psADE based on metagenomic and metatranscriptomic data from environmental samples. This approach was applied on the widespread marine copepod, Oithona similis, by combining samples collected during the Tara Oceans expedition (2009-2013) and de novo transcriptome assemblies. Among a total of 25,768 single nucleotide variants (SNVs) of O. similis, 572 (2.2%) were affected by psADE in at least one population (FDR < 0.05). The distribution of SNVs under psADE in different populations is significantly shaped by population genomic differentiation (Pearson r = 0.87, p = 5.6 × 10-30), supporting a partial genetic control of psADE. Moreover, a significant amount of SNVs (0.6%) were under both selection and psADE (p < .05), supporting the hypothesis that natural selection and psADE tends to impact common loci. Population-scale allelic differential expression offers new insights into the gene regulation control in populations and its link with natural selection.
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Affiliation(s)
- Romuald Laso‐Jadart
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Kevin Sugier
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
| | - Emmanuelle Petit
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | - Karine Labadie
- CEA, GenoscopeInstitut de Biologie François JacobUniversité Paris‐SaclayEvryFrance
| | | | | | - Patrick Wincker
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
| | - Jean‐Louis Jamet
- Mediterranean Institute of Oceanology (MIO)AMU‐UTLN UM110CNRS UMR7294, IRDUMR235Equipe Ecologie Marine et Biodiversité (EMBIO)Université de ToulonToulon Cedex 9France
| | - Mohammed‐Amin Madoui
- Génomique Métabolique, GenoscopeInstitut François Jacob, CEA, CNRS, Univ EvryUniversité Paris‐SaclayEvryFrance
- Research Federation for the study of Global Ocean Systems Ecology and EvolutionFR2022/Tara Oceans GO‐SEEParisFrance
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43
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Baldwin-Brown JG, Long AD. Genomic Signatures of Local Adaptation in Clam Shrimp (Eulimnadia texana) from Natural Vernal Pools. Genome Biol Evol 2020; 12:1194-1206. [PMID: 32539143 PMCID: PMC7486962 DOI: 10.1093/gbe/evaa120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2020] [Indexed: 12/20/2022] Open
Abstract
Vernal pools are unique in their isolation and the strong selection acting on their resident species. Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, small genomes, and obligate desiccated diapaused eggs. Clam shrimp are also androdioecious (sexes include males and hermaphrodites), and here we use population-scaled recombination rates to support the hypothesis that the heterogametic sex is recombination free in these shrimp. We collected short-read sequence data from pooled samples from different vernal pools to gain insights into local adaptation. We identify genomic regions in which some populations have allele frequencies that differ significantly from the metapopulation. BayPass (Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555-1579.) detected 19 such genomic regions showing an excess of population subdivision. These regions on average are 550 bp in size and had 2.5 genes within 5 kb of them. Genes located near these regions are involved in Malpighian tubule function and osmoregulation, an essential function in vernal pools. It is likely that salinity profiles vary between pools and over time, and variants at these genes are adapted to local salinity conditions.
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Affiliation(s)
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine
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44
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Bertola LD, Boehm JT, Putman NF, Xue AT, Robinson JD, Harris S, Baldwin CC, Overcast I, Hickerson MJ. Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity. Proc Biol Sci 2020; 287:20200657. [PMID: 32370669 DOI: 10.1098/rspb.2020.0657] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading to predictions on population-level genetic connectivity and the directionality of effective dispersal. Here, we use genome-wide single nucleotide polymorphism data to investigate whether gene flow directionality in two seahorses (Hippocampus) and three pipefishes (Syngnathus) follows the predominant ocean circulation patterns in the Gulf of Mexico and northwestern Atlantic. In addition, we explore whether gene flow magnitudes are predicted by traits related to active dispersal ability and habitat preference. We inferred demographic histories of these co-distributed syngnathid species, and coalescent model-based estimates indicate that gene flow directionality is in agreement with ocean circulation data that predicts eastward and northward macro-algal transport. However, the magnitude to which ocean currents influence this pattern appears strongly dependent on the species-specific traits related to rafting propensity and habitat preferences. Higher levels of gene flow and stronger directionality are observed in Hippocampus erectus, Syngnathus floridae and Syngnathus louisianae, which closely associated with the pelagic macro-algae Sargassum spp., compared to Hippocampus zosterae and the Syngnathus scovelli/Syngnathus fuscus sister-species pair, which prefer near shore habitats and are weakly associated with pelagic Sargassum. This study highlights how the combination of population genomic inference together with ocean circulation data can help explain patterns of population structure and diversity in marine ecosystems.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Department of Earth and Atmospheric Sciences, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - J T Boehm
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th Street, New York, NY 10024, USA
| | - Nathan F Putman
- LGL Ecological Research Associates, Inc, Bryan, TX 77801, USA.,Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Alexander T Xue
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John D Robinson
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, MI 48824, USA
| | - Stephen Harris
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street and Constitution Avenue NW, Washington, DC 20560, USA
| | - Isaac Overcast
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Michael J Hickerson
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Division of Invertebrate Zoology, American Museum of Natural History, Central Park West and 79th Street, New York, NY 10024, USA
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45
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Manel S, Guerin PE, Mouillot D, Blanchet S, Velez L, Albouy C, Pellissier L. Global determinants of freshwater and marine fish genetic diversity. Nat Commun 2020; 11:692. [PMID: 32041961 PMCID: PMC7010757 DOI: 10.1038/s41467-020-14409-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 01/06/2020] [Indexed: 01/18/2023] Open
Abstract
Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity. Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.
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Affiliation(s)
- Stéphanie Manel
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Pierre-Edouard Guerin
- CEFE, Univ. Montpellier, CNRS, EPHE-PSL University, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UMR 5321, F-09200, Moulis, France
| | - Laure Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - Camille Albouy
- IFREMER, unité Ecologie et Modèle pour l'Halieutique, Nantes, France
| | - Loïc Pellissier
- Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, Department of Environmental System Science, ETH Zürich, CH-8092, Zürich, Switzerland
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46
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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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Vaux F, Rasmuson LK, Kautzi LA, Rankin PS, Blume MTO, Lawrence KA, Bohn S, O'Malley KG. Sex matters: Otolith shape and genomic variation in deacon rockfish ( Sebastes diaconus). Ecol Evol 2019; 9:13153-13173. [PMID: 31871636 PMCID: PMC6912905 DOI: 10.1002/ece3.5763] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/15/2022] Open
Abstract
Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50-km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.
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Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - Leif K. Rasmuson
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Lisa A. Kautzi
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Polly S. Rankin
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | | | - Kelly A. Lawrence
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
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48
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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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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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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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