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Silva JC, Soeth M, Hackradt CW, Lima A, Félix-Hackradt FC. Daily age, growth rate, and pelagic larval duration of commercially important snapper species in Abrolhos National Marine Park. JOURNAL OF FISH BIOLOGY 2024; 104:1411-1422. [PMID: 38351593 DOI: 10.1111/jfb.15654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/05/2023] [Accepted: 12/25/2023] [Indexed: 05/22/2024]
Abstract
The age and daily growth of fish are registered through the deposition of increments in their otoliths, which are concretions formed by the precipitation of substances present in the endolymphatic fluid, mainly calcium carbonate (CaCO3). Faced with the need to fill some of the gaps in the knowledge on the occurrence and duration of the initial stages of snapper species' life cycles in the Abrolhos Bank, this study aimed to describe the growth rates, age, and period of pelagic larval duration (PLD) of three snapper species during the larval pre-settlement phase, in the Abrolhos Bank region. The post-larvae were captured using light traps. Otoliths were removed from 117 samples of snapper species; however, only 69 were viable for age estimation, of which 15 were Lutjanus analis, 25 were Lutjanus jocu, and 29 were Lutjanus synagris. Together, the samples presented individuals with total lengths ranging from 16.14 to 24.76 mm and ages from 21 to 39 days. Settlement marks were found for all three species, and the average PLD was ~25 days. The somatic growth of the snapper species was positively correlated with otolith growth. L. jocu presented the greatest daily growth compared to the other species. The three species use the Abrolhos Bank as a larval settlement site, demonstrating plasticity by using different habitats throughout their lives.
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Affiliation(s)
- Jeane Campos Silva
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, Brasil
- Programa de Pós-Graduação em Ciência e Tecnologias Ambientais, Universidade Federal do Sul da Bahia e Instituto Federal de Educação, Ciência e Tecnologia da Bahia, Porto Seguro, Brasil
| | - Marcelo Soeth
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, Brasil
- Programa de Pós-Graduação em Sistemas Costeiros e Oceânicos, Universidade Federal do Paraná, Pontal do Sul, Paraná, Brasil
| | - Carlos Werner Hackradt
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, Brasil
| | - Andre Lima
- Laboratório de Ecologia e Conservação Marinha, Universidade Federal do Sul da Bahia, Porto Seguro, Brasil
- Programa de Pós Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Ilhéus, Brasil
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2
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Peres PA, Mantelatto FL. Demographic changes and life-history strategies predict the genetic diversity in crabs. J Evol Biol 2023; 36:432-443. [PMID: 36537369 DOI: 10.1111/jeb.14138] [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: 06/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.
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Affiliation(s)
- Pedro A Peres
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Fernando L Mantelatto
- Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), Laboratory of Bioecology and Crustacean Systematics (LBSC), Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
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3
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Guo XZ, Wei KJ, Yan RJ, Gardner JPA. Pronounced Mitochondrial DNA Population Genetic Structure in a Brooding Coastal Marine Invertebrate. MALACOLOGIA 2022. [DOI: 10.4002/040.065.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiang-Zhao Guo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Jian Wei
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruo-Jin Yan
- School of Biological Sciences, Victoria University of Wellington, P. O. Box 600, Wellington 6140, New Zealand
| | - Jonathan P. A. Gardner
- School of Biological Sciences, Victoria University of Wellington, P. O. Box 600, Wellington 6140, New Zealand
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4
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Pilger TJ, Gido KB, Propst DL, Whitney JE, Turner TF. Demography predicts genetic effective size in a desert stream fish community. Am Nat 2022; 200:275-291. [DOI: 10.1086/720208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Yamazaki D, Ito S, Miura O, Sasaki T, Chiba S. High-throughput SNPs dataset reveal restricted population connectivity of marine gastropod within the narrow distribution range of peripheral oceanic islands. Sci Rep 2022; 12:2119. [PMID: 35136087 PMCID: PMC8825847 DOI: 10.1038/s41598-022-05026-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022] Open
Abstract
Molecular studies based on the high resolution genetic markers help us to grasp the factor shaping the genetic structure of marine organisms. Ecological factors linking to life history traits have often explained the process of genetic structuring in open and connectable oceanic environments. Besides, population genetic divergence can be affected by fragmented habitat, oceanic current, and past geographical events. In the present study, we demonstrated the genetic differentiation of marine gastropod Monodonta sp. within a narrow range of peripheral oceanic islands, the Ogasawara Islands. Genetic analyses were performed not only with a mitochondrial DNA marker but also with a high-throughput SNPs dataset obtained by ddRAD-seq. The results of the mtDNA analyses did not show genetic divergence among populations, while the SNPs dataset detected population genetic differentiation. Population demographic analyses and gene flow estimation suggested that the genetic structure was formed by sea level fluctuation associated with the past climatic change and regulated by temporal oceanographic conditions. These findings provide important insights into population genetic patterns in open and connectable environments.
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Affiliation(s)
- Daishi Yamazaki
- Center for Northeast Asian Studies, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8576, Japan.
| | - Shun Ito
- Graduate School of Life Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Tetsuro Sasaki
- Institute of Boninology, Chichijima-Aza-Nishimachi, Ogasawara, Tokyo, 100-2101, Japan
| | - Satoshi Chiba
- Center for Northeast Asian Studies, Tohoku University, 41 Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8576, Japan.,Graduate School of Life Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan
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6
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Demmer J, Robins P, Malham S, Lewis M, Owen A, Jones T, Neill S. The role of wind in controlling the connectivity of blue mussels (Mytilus edulis L.) populations. MOVEMENT ECOLOGY 2022; 10:3. [PMID: 35063034 PMCID: PMC8783501 DOI: 10.1186/s40462-022-00301-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/10/2022] [Indexed: 06/10/2023]
Abstract
BACKGROUND Larval connectivity between distinct benthic populations is essential for their persistence. Although connectivity is difficult to measure in situ, it can be predicted via models that simulate biophysical interactions between larval behaviour and ocean currents. The blue mussel (Mytilus Edulis L.) is widespread throughout the northern hemisphere and extensively commercialised worldwide. In the Irish Sea, this industry represents ~ 50% of Welsh shellfisheries, where cultivation is mainly based on wild spat. However, the main sources and amount of spat varied interannually (1100 tonnes harvest in 2014 against zero in 2018). The aim of this study is to characterise the structure and dynamics of the blue mussel metapopulation within the northern part of the Irish Sea. METHODS We develop a Lagrangian particle tracking model, driven by a high-resolution (from 30 to 5000 m) validated unstructured coastal hydrodynamic model of the Irish Sea, to simulate spatial and temporal variability of larval dispersal and connectivity between distinct mussel populations and potential settlement areas. RESULTS Our results showed that: (1) larvae positioned near the surface were strongly influenced by wind-driven currents suggesting that connectivity networks had the potential to span hundreds of kilometres; (2) in contrast, larvae positioned deeper in the water column were driven by tidal currents, producing intricate spatial patterns of connectivity between mussel beds over tens of kilometres that were consistent over time. CONCLUSIONS Dispersal of mussel larvae in the tidally energetic Irish Sea during the April-May spawning season is potentially driven by wind-driven surface currents, as confirmed by fisherman observations of inter-annual variability in wild spat collection. These results have important implications for metapopulation dynamics within the context of climate change and sustainable shellfisheries management (i.e. gain and loss of populations and harvest areas according to wind conditions).
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Affiliation(s)
- Jonathan Demmer
- School of Ocean Sciences, Bangor University, Askew street, Menai Bridge, LL59 5AB UK
| | - Peter Robins
- School of Ocean Sciences, Bangor University, Askew street, Menai Bridge, LL59 5AB UK
| | - Shelagh Malham
- School of Ocean Sciences, Bangor University, Askew street, Menai Bridge, LL59 5AB UK
| | - Matthew Lewis
- School of Ocean Sciences, Bangor University, Askew street, Menai Bridge, LL59 5AB UK
| | - Aaron Owen
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG UK
| | - Trevor Jones
- Extramussel Limited, Refail Llanffinan, Llangefni, Anglesey, LL77 7SN UK
| | - Simon Neill
- School of Ocean Sciences, Bangor University, Askew street, Menai Bridge, LL59 5AB UK
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7
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Liu SYV, Green J, Briggs D, Hastings R, Jondelius Y, Kensinger S, Leever H, Santos S, Throne T, Cheng C, Madduppa H, Toonen RJ, Gaither MR, Crandall ED. Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea. PeerJ 2021; 9:e12063. [PMID: 34540369 PMCID: PMC8415289 DOI: 10.7717/peerj.12063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022] Open
Abstract
Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions This multispecies study provides the most comprehensive examination of the role of Dongsha Atoll in marine connectivity in the South China Sea to date. Combining new and existing population genetic data for nine coral reef species in the region with a graph theoretical analysis, this study provides evidence that Dongsha Atoll is an important hub for sustaining connectivity for the majority of coral-reef species in the region.
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Affiliation(s)
- Shang Yin Vanson Liu
- Dongsha Atoll Research Station, College of Marine Sciences, National Sun Yat-sen University, Kaohsiung City, Taiwan.,Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, Taiwan
| | - Jacob Green
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Biological and Environmental Science, University of Rhode Island, Kingston, Rhode Island, United States
| | - Dana Briggs
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Ruth Hastings
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Ylva Jondelius
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Skylar Kensinger
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Hannah Leever
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Sophia Santos
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Trevor Throne
- School of Natural Sciences, California State University, Monterey Bay, California, United States
| | - Chi Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, Taiwan
| | - Hawis Madduppa
- Department of Marine Science and Technology, Institut Pertanian Bogor, Bogor, Indonesia
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, Hawai'i, United States
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Orlando, Florida, United States
| | - Eric D Crandall
- School of Natural Sciences, California State University, Monterey Bay, California, United States.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States
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8
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Assis J, Fragkopoulou E, Serrão EA, Horta E Costa B, Gandra M, Abecasis D. Weak biodiversity connectivity in the European network of no-take marine protected areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145664. [PMID: 33940752 DOI: 10.1016/j.scitotenv.2021.145664] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The need for international cooperation in marine resource management and conservation has been reflected in the increasing number of agreements aiming for effective and well-connected networks of Marine Protected Areas (MPAs). However, the extent to which individual MPAs are connected remains mostly unknown. Here, we use a biophysical model tuned with empirical data on species dispersal ecology to predict connectivity of a vast spectrum of biodiversity in the European network of marine reserves (i.e., no-take MPAs). Our results highlight the correlation between empirical propagule duration data and connectivity potential and show weak network connectivity and strong isolation for major ecological groups, resulting from the lack of direct connectivity corridors between reserves over vast regions. The particularly high isolation predicted for ecosystem structuring species (e.g., corals, sponges, macroalgae and seagrass) might potentially undermine biodiversity conservation efforts if local retention is insufficient and unmanaged populations are at risk. Isolation might also be problematic for populations' persistence in the light of climate change and expected species range shifts. Our findings provide novel insights for management directives, highlighting the location of regions requiring additional marine reserves to function as stepping-stone connectivity corridors.
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Affiliation(s)
- J Assis
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal.
| | - E Fragkopoulou
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - E A Serrão
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - B Horta E Costa
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - M Gandra
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - D Abecasis
- CCMAR - Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
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9
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De Kort H, Prunier JG, Ducatez S, Honnay O, Baguette M, Stevens VM, Blanchet S. Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations. Nat Commun 2021; 12:516. [PMID: 33483517 PMCID: PMC7822833 DOI: 10.1038/s41467-021-20958-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.
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Affiliation(s)
- H De Kort
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium.
| | - J G Prunier
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - S Ducatez
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - O Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
| | - M Baguette
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - V M Stevens
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - S Blanchet
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
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10
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Andrews KR, Copus JM, Wilcox C, Williams AJ, Newman SJ, Wakefield CB, Bowen BW. Range-Wide Population Structure of 3 Deepwater Eteline Snappers Across the Indo-Pacific Basin. J Hered 2020; 111:471-485. [PMID: 32803261 DOI: 10.1093/jhered/esaa029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of 3 tropical deepwater snappers of the genus Etelis that reside at 100-400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for 2 of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these 2 species, as well as a recently exposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow-water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to the management of these valuable food fishes. A total of 1153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first 2 species were analyzed with mtDNA and 9-11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA Ф ST = 0.010 (P = 0.0007), with the isolation of Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA Ф ST = 0.021 (P = 0.0001), with low but significant levels of isolation for Hawai'i, and divergence between Tonga and Fiji. Etelis sp. had mtDNA Ф ST = 0.018 (P = 0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence (similar to near-shore species), and isolation at the fringes of the Indo-Pacific basin in Hawai'i and the western Indian Ocean. While most shallow-water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow-water species. This population structure indicates the capacity for widespread dispersal throughout the Indo-Pacific region.
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Affiliation(s)
- Kimberly R Andrews
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID.,Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Joshua M Copus
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Christie Wilcox
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
| | - Ashley J Williams
- Oceanic Fisheries Programme, The Pacific Community, Noumea, New Caledonia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Marine and Environmental Sciences, James Cook University, Townsville, Queensland, Australia
| | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Corey B Wakefield
- Western Australian Fisheries and Marine Research Laboratories, Department of Primary Industries and Regional Development, Government of Western Australia, North Beach, WA, Australia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, Kaneohe, HI
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11
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Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversity. Sci Rep 2020; 10:12707. [PMID: 32728141 PMCID: PMC7391780 DOI: 10.1038/s41598-020-69374-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The displacement of species from equatorial latitudes to temperate locations following the increase in sea surface temperatures is among the significant reported consequences of climate change. Shifts in the distributional ranges of species result in fish communities tropicalisation, i.e., high latitude colonisations by typically low latitude distribution species. These movements create new interactions between species and new trophic assemblages. The Senegal seabream, Diplodus bellottii, may be used as a model to understand the population genetics of these invasions. In the last decades, this species has undergone an outstanding range expansion from its African area of origin to the Atlantic coast of the Iberian Peninsula, where now occurs abundantly. Mitochondrial and nuclear markers revealed a striking high haplotypic nucleotide and genetic diversity values, along with significant population differentiation throughout the present-day geographical range of the Senegal seabream. These results are not consistent with the central-marginal hypothesis, nor with the expectations of a leptokurtic distribution of individuals, as D. bellottii seems to be able to retain exceptional levels of diversity in marginal and recently colonised areas. We discuss possible causes for hyperdiversity and lack of geographical structure and subsequent implications for fisheries.
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12
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Neves A, Vieira AR, Sequeira V, Paiva RB, Gordo LS, Paulo OS. Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data. Sci Rep 2020; 10:4063. [PMID: 32132605 PMCID: PMC7055218 DOI: 10.1038/s41598-020-61050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/20/2020] [Indexed: 12/24/2022] Open
Abstract
Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.
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Affiliation(s)
- Ana Neves
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Ana Rita Vieira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Vera Sequeira
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Rafaela Barros Paiva
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Leonel Serrano Gordo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Octávio S Paulo
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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13
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Jossart Q, Sands CJ, Sewell MA. Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star. Heredity (Edinb) 2019; 123:622-633. [PMID: 31073238 PMCID: PMC6972741 DOI: 10.1038/s41437-019-0228-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/08/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
Poecilogony, or multiple developmental modes in a single species, is exceedingly rare. Several species described as poecilogenous were later demonstrated to be multiple (cryptic) species with a different developmental mode. The Southern Ocean is known to harbor a high proportion of brooders (Thorson's Rule) but with an increasing number of counter examples over recent years. Here we evaluated poecilogony vs. crypticism in the brittle star Astrotoma agassizii across the Southern Ocean. This species was initially described from South America as a brooder before some pelagic stages were identified in Antarctica. Reproductive and mitochondrial data were combined to unravel geographic and genetic variation of developmental modes. Our results indicate that A. agassizii is composed of seven well-supported and deeply divergent clades (I: Antarctica and South Georgia; II: South Georgia and Sub-Antarctic locations including Kerguelen, Patagonian shelf, and New Zealand; III-VI-VII: Patagonian shelf, IV-V: South Georgia). Two of these clades demonstrated strong size dimorphism when in sympatry and can be linked to differing developmental modes (Clade V: dwarf brooder vs. Clade I: giant broadcaster). Based on their restricted geographic distributions and on previous studies, it is likely that Clades III-VI-VII are brooders. Clade II is composed of different morphological species, A. agassizii and A. drachi, the latter originally used as the outgroup. By integrating morphology, reproductive, and molecular data we conclude that the variation identified in A. agassizii is best described as crypticism rather than poecilogony.
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Affiliation(s)
- Quentin Jossart
- University of Auckland, Auckland, New Zealand.
- British Antarctic Survey, Cambridge, UK.
- Vrije Universiteit Brussel, Brussels, Belgium.
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14
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Otwoma LM, Reuter H. Do differences in mating behaviour lead to differences in connectivity patterns of reef fishes? Insights from two sympatric surgeonfish species in the Indian Ocean. MARINE ENVIRONMENTAL RESEARCH 2019; 151:104760. [PMID: 31358313 DOI: 10.1016/j.marenvres.2019.104760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Disentangling the contribution of biotic and abiotic factors in the structuring of the genetic diversity of reef species is critical to illuminate the diversification of evolutionary lineages in marine environment. Howevr, previous studies have mainly focused on determining the influence of pelagic larval duration on the connectivity and demographic history of reef fishes, whereas few studies have examined the effects of other biotic factors, such as mating behaviour and habitat preference. Here, we use mitochondrial DNA (ATPase 6/8) and ten microsatellite loci to compare the population genetic structure and demographic history of the spawning aggregating Acanthurus triostegus with the monogamous spawning Acanthurus leucosternon. Pairwise comparisons and discriminant analysis of principal components showed that the genetic structuring patterns of the two species are not consistent with the influence of mating behaviour, suggesting the possible role of other biotic and abiotic factors. However, demographic history estimates revealed that these species may have responded differently to sea level fluctuations during the glacial maxima.
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Affiliation(s)
- Levy Michael Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany; Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya.
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany; Faculty Biology and Chemistry, University of Bremen, Germany
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15
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Crandall ED, Toonen RJ, Selkoe KA. A coalescent sampler successfully detects biologically meaningful population structure overlooked by F-statistics. Evol Appl 2019; 12:255-265. [PMID: 30697337 PMCID: PMC6346657 DOI: 10.1111/eva.12712] [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: 05/29/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022] Open
Abstract
Assessing the geographic structure of populations has relied heavily on Sewell Wright's F-statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F-statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model-selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping-stone model. In an example case study, we then re-analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping-stone model (leading to an expected pattern of isolation by distance), but F-statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping-stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to F ST = 0.002), while F-statistics had mixed results. Our re-analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping-stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units.
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Affiliation(s)
- Eric D. Crandall
- School of Natural SciencesCalifornia State University, Monterey BaySeasideCalifornia
- School of Ocean and Earth Science and Technology, Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at ManoaKane‘oheHawaii
| | - Robert J. Toonen
- School of Ocean and Earth Science and Technology, Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at ManoaKane‘oheHawaii
| | - ToBo Laboratory
- School of Ocean and Earth Science and Technology, Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at ManoaKane‘oheHawaii
| | - Kimberly A. Selkoe
- National Center for Ecological Analysis and SynthesisSanta BarbaraCalifornia
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16
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Pfaller JB, Payton AC, Bjorndal KA, Bolten AB, McDaniel SF. Hitchhiking the high seas: Global genomics of rafting crabs. Ecol Evol 2019; 9:957-974. [PMID: 30805133 PMCID: PMC6374717 DOI: 10.1002/ece3.4694] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/04/2022] Open
Abstract
Population differentiation and diversification depend in large part on the ability and propensity of organisms to successfully disperse. However, our understanding of these processes in organisms with high dispersal ability is biased by the limited genetic resolution offered by traditional genotypic markers. Many neustonic animals disperse not only as pelagic larvae, but also as juveniles and adults while drifting or rafting at the surface of the open ocean. In theory, the heightened dispersal ability of these animals should limit opportunities for species diversification and population differentiation. To test these predictions, we used next-generation sequencing of genomewide restriction-site-associated DNA tags (RADseq) and traditional mitochondrial DNA sequencing, to investigate the species-level relationships and global population structure of Planes crabs collected from oceanic flotsam and sea turtles. Our results indicate that species diversity in this clade is low-likely three closely related species-with no evidence of cryptic or undescribed species. Moreover, our results indicate weak population differentiation among widely separated aggregations with genetic indices showing only subtle genetic discontinuities across all oceans of the world (RADseq F ST = 0.08-0.16). The results of this study provide unprecedented resolution of the systematics and global biogeography of this group and contribute valuable information to our understanding of how theoretical dispersal potential relates to actual population differentiation and diversification among marine organisms. Moreover, these results demonstrate the limitations of single gene analyses and the value of genomic-level resolution for estimating contemporary population structure in organisms with large, highly connected populations.
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Affiliation(s)
- Joseph B. Pfaller
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
- Caretta Research ProjectSavannahGeorgia
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida
| | - Karen A. Bjorndal
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
| | - Alan B. Bolten
- Department of Biology, Archie Carr Center for Sea Turtle ResearchUniversity of FloridaGainesvilleFlorida
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17
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Young EF, Tysklind N, Meredith MP, de Bruyn M, Belchier M, Murphy EJ, Carvalho GR. Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations. Evol Appl 2018; 11:978-994. [PMID: 29928304 PMCID: PMC5999207 DOI: 10.1111/eva.12613] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/05/2018] [Indexed: 01/02/2023] Open
Abstract
In the marine environment, understanding the biophysical mechanisms that drive variability in larval dispersal and population connectivity is essential for estimating the potential impacts of climate change on the resilience and genetic structure of populations. Species whose populations are small, isolated and discontinuous in distribution will differ fundamentally in their response and resilience to environmental stress, compared with species that are broadly distributed, abundant and frequently exchange conspecifics. Here, we use an individual-based modelling approach, combined with a population genetics projection model, to consider the impacts of a warming climate on the population connectivity of two contrasting Antarctic fish species, Notothenia rossii and Champsocephalus gunnari. Focussing on the Scotia Sea region, sea surface temperatures are predicted to increase significantly by the end of the 21st century, resulting in reduced planktonic duration and increased egg and larval mortality. With shorter planktonic durations, the results of our study predict reduced dispersal of both species across the Scotia Sea, from Antarctic Peninsula sites to islands in the north and east, and increased dispersal among neighbouring sites, such as around the Antarctic Peninsula. Increased mortality modified the magnitude of population connectivity but had little effect on the overall patterns. Whilst the predicted changes in connectivity had little impact on the projected regional population genetic structure of N. rossii, which remained broadly genetically homogeneous within distances of ~1,500 km, the genetic isolation of C. gunnari populations in the northern Scotia Sea was predicted to increase with rising sea temperatures. Our study highlights the potential for increased isolation of island populations in a warming world, with implications for the resilience of populations and their ability to adapt to ongoing environmental change, a matter of high relevance to fisheries and ecosystem-level management.
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Affiliation(s)
| | - Niklas Tysklind
- School of Biological SciencesBangor UniversityBangorGwyneddUK
- Present address:
INRAUMR8172 EcoFoGAgroParisTechCiradCNRSUniversité des AntillesUniversité de GuyaneKourouFrance
| | | | - Mark de Bruyn
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
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18
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Huang WC, Chang JT, Liao C, Tawa A, Iizuka Y, Liao TY, Shiao JC. Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines. PeerJ 2018; 6:e4741. [PMID: 29761056 PMCID: PMC5949063 DOI: 10.7717/peerj.4741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/19/2018] [Indexed: 11/20/2022] Open
Abstract
The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake moray Uropterygius micropterus and the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochrome b and cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day-1 on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day-1 on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day-1 vs. 1.36 ± 0.16 µm day-1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature.
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Affiliation(s)
- Wen-Chien Huang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Jui-Tsung Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chun Liao
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Atsushi Tawa
- National Research Institute of Far Seas Fisheries, Japan Fisheries Research and Education Agency, Orido, Shimizu, Shizuoka, Japan
| | | | - Te-Yu Liao
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Jen-Chieh Shiao
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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19
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Costantini F, Ferrario F, Abbiati M. Chasing genetic structure in coralligenous reef invertebrates: patterns, criticalities and conservation issues. Sci Rep 2018; 8:5844. [PMID: 29643422 PMCID: PMC5895814 DOI: 10.1038/s41598-018-24247-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/27/2018] [Indexed: 12/02/2022] Open
Abstract
Conservation of coastal habitats is a global issue, yet biogenic reefs in temperate regions have received very little attention. They have a broad geographic distribution and are a key habitat in marine ecosystems impacted by human activities. In the Mediterranean Sea coralligenous reefs are biodiversity hot spots and are classified as sensitive habitats deserving conservation. Genetic diversity and structure influence demographic, ecological and evolutionary processes in populations and play a crucial role in conservation strategies. Nevertheless, a comprehensive view of population genetic structure of coralligenous species is lacking. Here, we reviewed the literature on the genetic structure of sessile and sedentary invertebrates of the Mediterranean coralligenous reefs. Linear regression models and meta-analytic approaches are used to assess the contributions of genetic markers, phylum, pelagic larval duration (PLD) and geographical distance to the population genetic structure. Our quantitative approach highlight that 1) most species show a significant genetic structure, 2) structuring differs between phyla, and 3) PLD does not appear to be a major driver of the structuring. We discuss the implication of these finding for the management and conservation, suggesting research areas that deserve attention, and providing recommendations for broad assessment and monitoring of genetic diversity in biogenic reefs species.
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Affiliation(s)
- Federica Costantini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, UOS Ravenna, Ravenna, Italy.
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali, Università di Bologna, Via S. Alberto 163, I - 48123, Ravenna, Italy.
- CoNISMa, Piazzale Flaminio 9, 00197, Roma, Italy.
| | | | - Marco Abbiati
- Centro Interdipartimentale di Ricerca per le Scienze Ambientali, Università di Bologna, Via S. Alberto 163, I - 48123, Ravenna, Italy
- CoNISMa, Piazzale Flaminio 9, 00197, Roma, Italy
- Dipartimento di Beni Culturali, Via degli Ariani, 1, 48121, Ravenna, Italy
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine, ISMAR, Via P. Gobetti 101, 40129, Bologna, Italy
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20
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Luttikhuizen PC, van den Heuvel FHM, Rebours C, Witte HJ, van Bleijswijk JDL, Timmermans K. Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp Saccharina latissima (Laminariales, Phaeophyta). Ecol Evol 2018; 8:4265-4277. [PMID: 29721296 PMCID: PMC5916297 DOI: 10.1002/ece3.3968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 01/11/2023] Open
Abstract
Kelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is Saccharina latissima, a northern hemisphere kelp inhabiting temperate to arctic rocky shores. To protect and document its natural genetic variation at the onset of this novel aquaculture, as well as increase knowledge on its taxonomy and phylogeography, we collected new genetic data, both nuclear and mitochondrial, and combined it with previous knowledge to estimate genetic connectivity and infer colonization history. Isolation‐with‐migration coalescent analyses demonstrate that gene flow among the sampled locations is virtually nonexistent. An updated scenario for the origin and colonization history of S. latissima is developed as follows: We propose that the species (or species complex) originated in the northwest Pacific, crossed to the northeast Pacific in the Miocene, and then crossed the Bering Strait after its opening ~5.5 Ma into the Arctic and northeast Atlantic. It subsequently crossed the Atlantic from east to west. During the Pleistocene, it was compressed in the south with evidence for northern refugia in Europe. Postglacial recolonization led to secondary contact in the Canadian Arctic. Saccharina cichorioides is shown to probably belong to the S. latissima species complex and to derive from ancestral populations in the Asian North Pacific. Our novel approach of comparing inferred gene flow based on coalescent analysis versus Wright's island model suggests that equilibrium levels of differentiation have not yet been reached in Europe and, hence, that genetic differentiation is expected to increase further if populations are left undisturbed.
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Affiliation(s)
- Pieternella C Luttikhuizen
- Department of Coastal Systems NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Den Burg The Netherlands
| | | | - Céline Rebours
- Norwegian Institute of Bioeconomy Research (NIBIO) Ås Norway.,Møreforsking Ålesund AS Ålesund Norway
| | - Harry J Witte
- Department of Marine Microbiology NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Den Burg The Netherlands
| | - Judith D L van Bleijswijk
- Hortimare B.V. Heerhugowaard The Netherlands.,Department of Marine Microbiology NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Den Burg The Netherlands
| | - Klaas Timmermans
- Hortimare B.V. Heerhugowaard The Netherlands.,Department of Estuarine and Delta Systems NIOZ Royal Netherlands Institute for Sea Research and Utrecht University Yerseke The Netherlands
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21
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Couvray S, Coupé S. Three-year monitoring of genetic diversity reveals a micro-connectivity pattern and local recruitment in the broadcast marine species Paracentrotus lividus. Heredity (Edinb) 2017; 120:110-124. [PMID: 29180717 DOI: 10.1038/s41437-017-0013-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/14/2017] [Accepted: 09/23/2017] [Indexed: 12/20/2022] Open
Abstract
In conservation and management of marine biological resources, a knowledge of connectivity is necessary to understand how local populations are naturally replenished by the arrival of new recruits from source populations. At small geographical scales, species experiencing moderate to long pelagic larval phases are mostly genetically homogeneous, which hinders inferences about local connectivity. Recent studies demonstrated that assessing genetic relatedness and kinship could provide information about local connectivity in populations with high levels of gene flow. Here, we were interested in deciphering the structure and connectivity of populations of the sea urchin Paracentrotus lividus, by monitoring populations at 11 localities distributed along a 225-km coast-line in the south-eastern French Mediterranean Sea. Using 12 microsatellite loci, we found a weak but significant genetic differentiation and observed a transient genetic differentiation among locations within temporal cohorts, without any correlation with the distance between locations, interpreted as unexplainable chaotic genetic patchiness. Among temporal cohorts, the more related individuals were mainly found within locations and the observed local differentiation (FST) correlated with the proportion of kin within locations, suggesting that larvae dispersed cohesively. Specifically, we could also reveal that populations flanking Cape Sicié were influenced by eastern populations and that local recruitment was a frequent occurrence. Overall, our results contribute to the growing number of studies showing that connectivity can be reliably assessed at a fine spatial scale even in genetically homogenous populations.
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Affiliation(s)
- Sylvain Couvray
- Institut Océanographique Paul Ricard, Ile des Embiez, 83140, Six-Fours-Les-Plages, France
| | - Stéphane Coupé
- Univ Toulon, Aix Marseille Univ, CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France.
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22
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Cahill AE, De Jode A, Dubois S, Bouzaza Z, Aurelle D, Boissin E, Chabrol O, David R, Egea E, Ledoux JB, Mérigot B, Weber AAT, Chenuil A. A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes. Mol Ecol 2017; 26:6563-6577. [PMID: 29087018 DOI: 10.1111/mec.14389] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/18/2017] [Indexed: 12/18/2022]
Abstract
Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
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Affiliation(s)
- Abigail E Cahill
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Biology Department, Albion College, Albion, MI, USA
| | - Aurélien De Jode
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Sophie Dubois
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Zoheir Bouzaza
- Département de Biologie, Faculté des Sciences de la Nature et de la Vie, Université Abdelhamid Ibn Badis, Mostaganem, Algérie
| | - Didier Aurelle
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Olivier Chabrol
- CNRS, Centrale Marseille, I2M, UMR7373, Aix-Marseille Université, Marseille, France
| | - Romain David
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Emilie Egea
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Jean-Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Porto, Portugal.,Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Bastien Mérigot
- UMR MARBEC (CNRS, Ifremer, IRD, UM), Université de Montpellier, Sète, France
| | - Alexandra Anh-Thu Weber
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Anne Chenuil
- Aix Marseille Univ, Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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23
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Zhao L, Yi D, Li C, Sun D, Xu H, Gao T. Phylogeography and population structure of - grypotus (Richardson, 1846) as revealed by mitochondrial control region sequences. Zookeys 2017:143-158. [PMID: 29118616 PMCID: PMC5674069 DOI: 10.3897/zookeys.705.13001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/07/2017] [Indexed: 11/30/2022] Open
Abstract
The 137 individuals of Johniusgrypotus were collected from seven localities from the Bohai Sea to the East China Sea. A 549 base pair (bp) fragment of the hypervariable region of the mtDNA control region was sequenced to examine genetic diversity and population structure. The populations of J.grypotus showed high haplotype diversity (h) with a range from 0.7500 to 0.9740 and low nucleotide diversity (π) with a range from 0.0024 to 0.0067. Low and non-significant genetic differentiation was estimated among populations except for North Yellow Sea population, which has a significant genetic difference with other populations. The demographic history examined by mismatch distribution analyses and Bayesian skyline plot (BSP) analyses revealed that a sudden population expansion occurred almost 20 to 40 thousand years before. Relatively recent population expansion in the last glacial period, large dispersal of eggs or larvae carried by coastal current, and the homogeneity of living environment may have an important influence on the population genetic pattern.
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Affiliation(s)
- Linlin Zhao
- The First Institute of Oceanography, SOA, Qingdao, Shandong, 266003, P.R. China
| | - Dan Yi
- The First Institute of Oceanography, SOA, Qingdao, Shandong, 266003, P.R. China
| | - Chunhou Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, P.R. China
| | - Dianrong Sun
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, P.R. China
| | - Hanxiang Xu
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316000, P.R. China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, 316000, P.R. China
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24
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Jossart Q, De Ridder C, Lessios HA, Bauwens M, Motreuil S, Rigaud T, Wattier RA, David B. Highly contrasted population genetic structures in a host-parasite pair in the Caribbean Sea. Ecol Evol 2017; 7:9267-9280. [PMID: 29187967 PMCID: PMC5696394 DOI: 10.1002/ece3.3413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/26/2017] [Accepted: 08/19/2017] [Indexed: 01/05/2023] Open
Abstract
Evolution and population genetic structure of marine species across the Caribbean Sea are shaped by two complex factors: the geological history and the present pattern of marine currents. Characterizing and comparing the genetic structures of codistributed species, such as host-parasite associations, allow discriminating the relative importance of environmental factors and life history traits that influenced gene flow and demographic events. Using microsatellite and Cytochrome Oxidase I markers, we investigated if a host-parasite pair (the heart urchin Meoma ventricosa and its parasitic pea crab Dissodactylus primitivus) exhibits comparable population genetic structures in the Caribbean Sea and how the observed patterns match connectivity regions from predictive models and other taxa. Highly contrasting patterns were found: the host showed genetic homogeneity across the whole studied area, whereas the parasite displayed significant differentiation at regional and local scales. The genetic diversity of the parasitic crabs (both in microsatellites and COI) was distributed in two main groups, Panama-Jamaica-St Croix on the one hand, and the South-Eastern Caribbean on the other. At a smaller geographical scale, Panamanian and Jamaican parasite populations were genetically more similar, while more genetic differentiation was found within the Lesser Antilles. Both species showed a signature of population expansion during the Quaternary. Some results match predictive models or data from previous studies (e.g., the Western-Eastern dichotomy in the parasite) while others do not (e.g., genetic differentiation within the Lesser Antilles). The sharp dissimilarity of genetic structure of these codistributed species outlines the importance of population expansion events and/or contrasted patterns of gene flow. This might be linked to differences in several life history traits such as fecundity (higher for the host), swimming capacity of larval stages (higher for the parasite), and habitat availability (higher for the host).
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Affiliation(s)
- Quentin Jossart
- Département de Biologie des OrganismesLaboratoire de Biologie MarineUniversité Libre de Bruxelles (ULB)BrusselsBelgium
- BiogéosciencesUMR CNRS 6282Université de Bourgogne Franche‐Comté (UBFC)DijonFrance
| | - Chantal De Ridder
- Département de Biologie des OrganismesLaboratoire de Biologie MarineUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | | | - Mathieu Bauwens
- Département de Biologie des OrganismesLaboratoire de Biologie MarineUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Sébastien Motreuil
- BiogéosciencesUMR CNRS 6282Université de Bourgogne Franche‐Comté (UBFC)DijonFrance
| | - Thierry Rigaud
- BiogéosciencesUMR CNRS 6282Université de Bourgogne Franche‐Comté (UBFC)DijonFrance
| | - Rémi A. Wattier
- BiogéosciencesUMR CNRS 6282Université de Bourgogne Franche‐Comté (UBFC)DijonFrance
| | - Bruno David
- BiogéosciencesUMR CNRS 6282Université de Bourgogne Franche‐Comté (UBFC)DijonFrance
- Museum National d'Histoire Naturelle (MNHN)ParisFrance
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25
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Community assembly of coral reef fishes along the Melanesian biodiversity gradient. PLoS One 2017; 12:e0186123. [PMID: 29069096 PMCID: PMC5656311 DOI: 10.1371/journal.pone.0186123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 09/26/2017] [Indexed: 11/19/2022] Open
Abstract
The Indo-Pacific is home to Earth’s most biodiverse coral reefs. Diversity on these reefs decreases from the Coral Triangle east through the islands of Melanesia. Despite this pattern having been identified during the early 20th century, our knowledge about the interaction between pattern and process remains incomplete. To evaluate the structure of coral reef fish communities across Melanesia, we obtained distributional records for 396 reef fish species in five taxa across seven countries. We used hierarchical clustering, nestedness, and multiple linear regression analyses to evaluate the community structure. We also compiled data on life history traits (pelagic larval duration, body size and schooling behavior) to help elucidate the ecological mechanisms behind community structure. Species richness for these taxa along the gradient was significantly related to longitude but not habitat area. Communities are significantly nested, indicating that species-poor communities are largely composed of subsets of the species found on species rich reefs. These trends are robust across taxonomic groups except for the Pomacentridae, which exhibit an anti-nested pattern, perhaps due to a large number of endemic species. Correlations between life history traits and the number of reefs on which species occurred indicate that dispersal and survival ability contribute to determining community structure. We conclude that distance from the Coral Triangle dominates community structure in reef fish; however, conservation of the most species-rich areas will not be sufficient alone to conserve the vivid splendor of this region.
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26
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Baeza JA, Behringer DC. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 2017; 5:e3786. [PMID: 28948100 PMCID: PMC5607919 DOI: 10.7717/peerj.3786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, United States of America.,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
| | - Donald C Behringer
- Program in Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, United States of America.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
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27
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Postaire B, Gélin P, Bruggemann JH, Pratlong M, Magalon H. Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea. Ecol Evol 2017; 7:8170-8186. [PMID: 29075441 PMCID: PMC5648676 DOI: 10.1002/ece3.3236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 01/18/2023] Open
Abstract
Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo‐Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
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Affiliation(s)
- Bautisse Postaire
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France.,IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France
| | - Pauline Gélin
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - J Henrich Bruggemann
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
| | - Marine Pratlong
- IMBE UMR 7263 Aix Marseille Université/CNRS/IRD/Avignon Université Marseille France.,I2M Equipe Evolution Biologique et Modélisation Aix Marseille Université/CNRS/Centrale Marseille Marseille France
| | - Hélène Magalon
- UMR ENTROPIE Université de La Réunion/CNRS/IRD Université de La Réunion Saint Denis France.,Laboratoire d'Excellence CORAIL Perpignan France
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28
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Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
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Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
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29
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Almada F, Francisco SM, Lima CS, FitzGerald R, Mirimin L, Villegas-Ríos D, Saborido-Rey F, Afonso P, Morato T, Bexiga S, Robalo JI. Historical gene flow constraints in a northeastern Atlantic fish: phylogeography of the ballan wrasse Labrus bergylta across its distribution range. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160773. [PMID: 28386433 PMCID: PMC5367310 DOI: 10.1098/rsos.160773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/16/2017] [Indexed: 05/17/2023]
Abstract
The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (Labrus bergylta), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry. The phylogeographic pattern, population structure, potential glacial refugia and recolonization routes for this species were assessed across its full distribution range, using mitochondrial and nuclear markers. The existence of a marked population structure can reflect both recolonization from three distinct glacial refugia and current and past oceanographic circulation patterns. Although isolated in present times, shared haplotypes between continental and Azores populations and historical exchange of migrants in both directions point to a common origin of L. bergylta. This situation is likely to be maintained and/or accentuated by current circulation patterns in the north Atlantic, and may lead to incipient speciation in the already distinct Azorean population. Future monitoring of this species is crucial to evaluate how this species is coping with current environmental changes.
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Affiliation(s)
- Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Richard FitzGerald
- Carna Research Station, Ryan Institute, National University of Ireland, Galway, Republic of Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Dublin Road, Galway, Republic of Ireland
| | - David Villegas-Ríos
- Institute of Marine Research (IMR), Flødevigen Marine Research Station, 4817 His, Norway
| | | | - Pedro Afonso
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
- Departamento de Oceanografia e Pescas da Universidade dos Açores, IMAR—Institute of Marine Research, 9901-862 Horta, Portugal
| | - Telmo Morato
- MARE—Marine and Environmental Sciences Centre, Universidade dos Açores, 9901-862 Horta, Portugal
| | - Sérgio Bexiga
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisboa, Portugal
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30
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Postaire B, Magalon H, Bourmaud CAF, Bruggemann JH. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa). Mol Phylogenet Evol 2016; 105:36-49. [DOI: 10.1016/j.ympev.2016.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/16/2016] [Accepted: 08/21/2016] [Indexed: 01/04/2023]
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31
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Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool 2016; 62:581-601. [PMID: 29491947 PMCID: PMC5804261 DOI: 10.1093/cz/zow067] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/25/2016] [Indexed: 11/21/2022] Open
Abstract
Population genomic approaches are making rapid inroads in the study of non-model organisms, including marine taxa. To date, these marine studies have predominantly focused on rudimentary metrics describing the spatial and environmental context of their study region (e.g., geographical distance, average sea surface temperature, average salinity). We contend that a more nuanced and considered approach to quantifying seascape dynamics and patterns can strengthen population genomic investigations and help identify spatial, temporal, and environmental factors associated with differing selective regimes or demographic histories. Nevertheless, approaches for quantifying marine landscapes are complicated. Characteristic features of the marine environment, including pelagic living in flowing water (experienced by most marine taxa at some point in their life cycle), require a well-designed spatial-temporal sampling strategy and analysis. Many genetic summary statistics used to describe populations may be inappropriate for marine species with large population sizes, large species ranges, stochastic recruitment, and asymmetrical gene flow. Finally, statistical approaches for testing associations between seascapes and population genomic patterns are still maturing with no single approach able to capture all relevant considerations. None of these issues are completely unique to marine systems and therefore similar issues and solutions will be shared for many organisms regardless of habitat. Here, we outline goals and spatial approaches for landscape genomics with an emphasis on marine systems and review the growing empirical literature on seascape genomics. We review established tools and approaches and highlight promising new strategies to overcome select issues including a strategy to spatially optimize sampling. Despite the many challenges, we argue that marine systems may be especially well suited for identifying candidate genomic regions under environmentally mediated selection and that seascape genomic approaches are especially useful for identifying robust locus-by-environment associations.
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Affiliation(s)
- Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Eric D. Crandall
- Division of Science and Environmental Policy, California State University, Seaside, CA 93955, USA
| | - Libby Liggins
- Institute of Natural and Mathematical Sciences, Massey University, Auckland 0745, New Zealand
| | - Pim Bongaerts
- Global Change Institute, The University of Queensland, QLD 4072, St Lucia, Australia
| | - Eric A. Treml
- School of BioSciences, The University of Melbourne, VIC, 3010, Australia
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32
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Tay YC, Chng MWP, Sew WWG, Rheindt FE, Tun KPP, Meier R. Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160253. [PMID: 27853600 PMCID: PMC5108950 DOI: 10.1098/rsos.160253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.
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Affiliation(s)
- Y. C. Tay
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
| | - M. W. P. Chng
- Centre for Liveable Cities, Ministry of National Development, The URA Centre, 45 Maxwell Road no. 07-01, Singapore 069118, Republic of Singapore
| | - W. W. G. Sew
- DHI Water and Environment (S) Pte Ltd, 1 Cleantech Loop, Cleantech One, no. 03-05, Singapore 637141, Republic of Singapore
| | - F. E. Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
| | - K. P. P. Tun
- National Parks Board, 1 Cluny Road, Singapore 259569, Republic of Singapore
| | - R. Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore
- Lee Kong Chian Natural History Museum, Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
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33
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Roterman CN, Copley JT, Linse KT, Tyler PA, Rogers AD. Connectivity in the cold: the comparative population genetics of vent-endemic fauna in the Scotia Sea, Southern Ocean. Mol Ecol 2016; 25:1073-88. [PMID: 26919308 DOI: 10.1111/mec.13541] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/18/2023]
Abstract
We report the first comparative population genetics study for vent fauna in the Southern Ocean using cytochrome C oxidase I and microsatellite markers. Three species are examined: the kiwaid squat lobster, Kiwa tyleri, the peltospirid gastropod, Gigantopelta chessoia, and a lepetodrilid limpet, Lepetodrilus sp., collected from vent fields 440 km apart on the East Scotia Ridge (ESR) and from the Kemp Caldera on the South Sandwich Island Arc, ~95 km eastwards. We report no differentiation for all species across the ESR, consistent with panmixia or recent range expansions. A lack of differentiation is notable for Kiwa tyleri, which exhibits extremely abbreviated lecithotrophic larval development, suggestive of a very limited dispersal range. Larval lifespans may, however, be extended by low temperature-induced metabolic rate reduction in the Southern Ocean, muting the impact of dispersal strategy on patterns of population structure. COI diversity patterns suggest all species experienced demographic bottlenecks or selective sweeps in the past million years and possibly at different times. ESR and Kemp limpets are divergent, although with evidence of very recent ESR-Kemp immigration. Their divergence, possibility indicative of incipient speciation, along with the absence of the other two species at Kemp, may be the consequence of differing dispersal capabilities across a ~1000 m depth range and/or different selective regimes between the two areas. Estimates of historic and recent limpet gene flow between the ESR and Kemp are consistent with predominantly easterly currents and potentially therefore, cross-axis currents on the ESR, with biogeographic implications for the region.
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Affiliation(s)
- C N Roterman
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - J T Copley
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - K T Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - P A Tyler
- Ocean and Earth Science, University of Southampton, Waterfront Campus, Southampton, SO14 3ZH, UK
| | - A D Rogers
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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34
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Baco AR, Etter RJ, Ribeiro PA, von der Heyden S, Beerli P, Kinlan BP. A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design. Mol Ecol 2016; 25:3276-98. [PMID: 27146215 DOI: 10.1111/mec.13689] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/12/2016] [Accepted: 05/02/2016] [Indexed: 11/28/2022]
Abstract
With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep-sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep-sea taxa are hypothesized to disperse greater distances than shallow-water taxa, which implies that reserves would need to be larger in size and networks could be more widely spaced; however, this paradigm has not been tested. We compiled population genetic studies of deep-sea fauna and estimated dispersal distances for 51 studies using a method based on isolation-by-distance slopes. Estimates of dispersal distance ranged from 0.24 km to 2028 km with a geometric mean of 33.2 km and differed in relation to taxonomic and life-history factors as well as several study parameters. Dispersal distances were generally greater for fishes than invertebrates with the Mollusca being the least dispersive sampled phylum. Species that are pelagic as adults were more dispersive than those with sessile or sedentary lifestyles. Benthic species from soft-substrate habitats were generally less dispersive than species from hard substrate, demersal or pelagic habitats. As expected, species with pelagic and/or feeding (planktotrophic) larvae were more dispersive than other larval types. Many of these comparisons were confounded by taxonomic or other life-history differences (e.g. fishes being more dispersive than invertebrates) making any simple interpretation difficult. Our results provide the first rough estimate of the range of dispersal distances in the deep sea and allow comparisons to shallow-water assemblages. Overall, dispersal distances were greater for deeper taxa, although the differences were not large (0.3-0.6 orders of magnitude between means), and imbalanced sampling of shallow and deep taxa complicates any simple interpretation. Our analyses suggest the scales of dispersal and connectivity for reserve design in the deep sea might be comparable to or slightly larger than those in shallow water. Deep-sea reserve design will need to consider the enormous variety of taxa, life histories, hydrodynamics, spatial configuration of habitats and patterns of species distributions. The many caveats of our analyses provide a strong impetus for substantial future efforts to assess connectivity of deep-sea species from a variety of habitats, taxonomic groups and depth zones.
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Affiliation(s)
- Amy R Baco
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, 117 N. Woodward Ave, Tallahassee, FL, 32306, USA
| | - Ron J Etter
- Biology Department, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA, 02125, USA
| | - Pedro A Ribeiro
- Department of Oceanography and Fisheries, MARE- Marine and Environmental Sciences Centre & IMAR- Institute of Marine Research, University of the Azores, 9901-862, Horta, Portugal.,Okeanos- R&D Center, University of the Azores, 9901-862, Horta, Portugal
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, 150-T Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Brian P Kinlan
- NOAA National Ocean Service, National Centers for Coastal Ocean Science, Center for Coastal Monitoring and Assessment, Biogeography Branch, 1305 East-West Hwy, N/SCI-1, Silver Spring, MD, 20910-3281, USA.,CSS-Dynamac Inc., 10301 Democracy Lane, Suite 300, Fairfax, VA, 22030, USA
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35
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Ellingson RA, Krug PJ. Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod. Evolution 2015; 70:18-37. [PMID: 26635309 DOI: 10.1111/evo.12830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/17/2015] [Indexed: 01/01/2023]
Abstract
Population-level consequences of dispersal ability remain poorly understood, especially for marine animals in which dispersal is typically considered a species-level trait governed by oceanographic transport of microscopic larvae. Transitions from dispersive (planktotrophic) to nondispersive, aplanktonic larvae are predicted to reduce connectivity, genetic diversity within populations, and the spatial scale at which reproductive isolation evolves. However, larval dimorphism within a species is rare, precluding population-level tests. We show the sea slug Costasiella ocellifera expresses both larval morphs in Florida and the Caribbean, regions with divergent mitochondrial lineages. Planktotrophy predominated at 11 sites, 10 of which formed a highly connected and genetically diverse Caribbean metapopulation. Four populations expressed mainly aplanktonic development and had markedly reduced connectivity, and lower genetic diversity at one mitochondrial and six nuclear loci. Aplanktonic dams showed partial postzygotic isolation in most interpopulation crosses, regardless of genetic or geographic distance to the sire's source, suggesting that outbreeding depression affects fragmented populations. Dams from genetically isolated and neighboring populations also exhibited premating isolation, consistent with reinforcement contingent on historical interaction. By increasing self-recruitment and genetic drift, the loss of dispersal may thus initiate a feedback loop resulting in the evolution of reproductive isolation over small spatial scales in the sea.
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Affiliation(s)
- Ryan A Ellingson
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, California, 90032-8201
| | - Patrick J Krug
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, California, 90032-8201.
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36
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Young EF, Belchier M, Hauser L, Horsburgh GJ, Meredith MP, Murphy EJ, Pascoal S, Rock J, Tysklind N, Carvalho GR. Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species. Evol Appl 2015; 8:486-509. [PMID: 26029262 PMCID: PMC4430772 DOI: 10.1111/eva.12259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/27/2015] [Indexed: 01/27/2023] Open
Abstract
Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.
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Affiliation(s)
| | | | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Gavin J Horsburgh
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK
| | | | | | - Sonia Pascoal
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
| | - Jennifer Rock
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, UK ; School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Department of Zoology, University of Otago Dunedin, 9054, New Zealand
| | - Niklas Tysklind
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK ; Present address: Campus Agronomique BP 709-97387, Kourou Cedex, France
| | - Gary R Carvalho
- School of Biological Sciences, Bangor University Bangor, Gwynedd, UK
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37
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Treml EA, Roberts J, Halpin PN, Possingham HP, Riginos C. The emergent geography of biophysical dispersal barriers across the Indo-West Pacific. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12307] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Eric A. Treml
- School of BioSciences; University of Melbourne; Melbourne Vic. 3010 Australia
| | - Jason Roberts
- Marine Geospatial Ecology Laboratory; A324 LSRC Building; Nicholas School of the Environment; Duke University; Durham NC USA
| | - Patrick N. Halpin
- Marine Geospatial Ecology Laboratory; A324 LSRC Building; Nicholas School of the Environment; Duke University; Durham NC USA
| | - Hugh P. Possingham
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
| | - Cynthia Riginos
- School of Biological Sciences; The University of Queensland; St. Lucia Qld 4072 Australia
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38
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Pusack TJ, Christie MR, Johnson DW, Stallings CD, Hixon MA. Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success. Mol Ecol 2014; 23:3396-408. [DOI: 10.1111/mec.12824] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 05/09/2014] [Accepted: 05/21/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Timothy J. Pusack
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331-2914 USA
- College of Marine Science; University of South Florida; St. Petersburg FL 33701-5016 USA
| | - Mark R. Christie
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331-2914 USA
- Department of Biological Sciences and Department of Forestry and Natural Resources; Purdue University; West Lafayette IN 47907 USA
| | - Darren W. Johnson
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331-2914 USA
- Department of Biological Sciences; California State University Long Beach; 1250 Bellflower Blvd Long Beach CA 90840 USA
| | - Christopher D. Stallings
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331-2914 USA
- College of Marine Science; University of South Florida; St. Petersburg FL 33701-5016 USA
| | - Mark A. Hixon
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331-2914 USA
- Department of Biology; University of Hawai'i at Manoa; Honolulu HI 96822-2216 USA
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39
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Selkoe KA, Gaggiotti OE, Bowen BW, Toonen RJ. Emergent patterns of population genetic structure for a coral reef community. Mol Ecol 2014; 23:3064-79. [DOI: 10.1111/mec.12804] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Kimberly A. Selkoe
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
- National Center for Ecological Analysis and Synthesis; 735 State St. Santa Barbara CA 93101 USA
| | - Oscar E. Gaggiotti
- Scottish Oceans Institute; School of Biology; University of St Andrews; St Andrews Fife KY16 8LB UK
| | - Brian W. Bowen
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
| | - Robert J. Toonen
- Hawai ̀i Institute of Marine Biology; University of Hawai ̀i; Kāne ̀ohe HI 97644 USA
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40
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Poortvliet M, Longo GC, Selkoe K, Barber PH, White C, Caselle JE, Perez-Matus A, Gaines SD, Bernardi G. Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality. Ecol Evol 2013; 3:4558-71. [PMID: 24340195 PMCID: PMC3856754 DOI: 10.1002/ece3.840] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 11/06/2022] Open
Abstract
In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation.
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Affiliation(s)
- Marloes Poortvliet
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
- Department of Marine Benthic Ecology and Evolution, Centre for Ecological and Evolutionary Studies, University of GroningenNijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Gary C Longo
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
| | - Kimberly Selkoe
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
- Hawai'i Institute of Marine Biology, University of Hawai'iKane'ohe, Hawaii, 96744
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology and the Institute of the Environment and Sustainability, University of California Los Angeles621 Charles E. Young Dr. South, Los Angeles, California, 90095
| | - Crow White
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
- Biological Sciences Department, California Polytechnic State UniversitySan Luis Obispo, California, 93407
| | - Jennifer E Caselle
- Marine Science Institute, University of California Santa BarbaraSanta Barbara, California, 93106
| | - Alejandro Perez-Matus
- Subtidal Ecology Laboratory & Center for Marine Conservation, Pontificia Universidad Católica de Chile, Estación Costera de Investigaciones MarinasCasilla 114-D, Santiago, Las Cruces, Chile
| | - Steven D Gaines
- Bren School of Environmental Science and Management, University of CaliforniaSanta Barbara, California, 93106
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa CruzSanta Cruz, California, 95076
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41
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Bernardi G. Speciation in fishes. Mol Ecol 2013; 22:5487-502. [PMID: 24118417 DOI: 10.1111/mec.12494] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/08/2013] [Accepted: 08/14/2013] [Indexed: 12/27/2022]
Abstract
The field of speciation has seen much renewed interest in the past few years, with theoretical and empirical advances that have moved it from a descriptive field to a predictive and testable one. The goal of this review is to provide a general background on research on speciation as it pertains to fishes. Three major components to the question are first discussed: the spatial, ecological and sexual factors that influence speciation mechanisms. We then move to the latest developments in the field of speciation genomics. Affordable and rapidly available, massively parallel sequencing data allow speciation studies to converge into a single comprehensive line of investigation, where the focus has shifted to the search for speciation genes and genomic islands of speciation. We argue that fish present a very diverse array of scenarios, making them an ideal model to study speciation processes.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 100 Shaffer Road, Santa Cruz, CA, 95076, USA
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42
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Anadón JD, del Mar Mancha-Cisneros M, Best BD, Gerber LR. Habitat-specific larval dispersal and marine connectivity: implications for spatial conservation planning. Ecosphere 2013. [DOI: 10.1890/es13-00119.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Iacchei M, Ben-Horin T, Selkoe KA, Bird CE, García-Rodríguez FJ, Toonen RJ. Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene-flow populations. Mol Ecol 2013; 22:3476-94. [PMID: 23802550 PMCID: PMC3749441 DOI: 10.1111/mec.12341] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 03/10/2013] [Accepted: 03/12/2013] [Indexed: 11/28/2022]
Abstract
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; D(est_Chao) = 0.025) and seven nuclear microsatellites (F(ST) = 0.004, P < 0.001; D(est_Chao) = 0.03), despite the species' 240- to 330-day pelagic larval duration. Significant population structure does not correlate with distance between sampling locations, and pairwise FST between adjacent sites often exceeds that among geographically distant locations. This result would typically be interpreted as unexplainable, chaotic genetic patchiness. However, kinship levels differ significantly among sites (pseudo-F(16,988) = 1.39, P = 0.001), and ten of 17 sample sites have significantly greater numbers of kin than expected by chance (P < 0.05). Moreover, a higher proportion of kin within sites strongly correlates with greater genetic differentiation among sites (D(est_Chao), R(2) = 0.66, P < 0.005). Sites with elevated mean kinship were geographically proximate to regions of high upwelling intensity (R(2) = 0.41, P = 0.0009). These results indicate that P. interruptus does not maintain a single homogenous population, despite extreme dispersal potential. Instead, these lobsters appear to either have substantial localized recruitment or maintain planktonic larval cohesiveness whereby siblings more likely settle together than disperse across sites. More broadly, our results contribute to a growing number of studies showing that low F(ST) and high family structure across populations can coexist, illuminating the foundations of cryptic genetic patterns and the nature of marine dispersal.
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Affiliation(s)
- Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI 96744, USA.
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44
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Hoffman JI, Clarke A, Clark MS, Peck LS. Hierarchical population genetic structure in a direct developing antarctic marine invertebrate. PLoS One 2013; 8:e63954. [PMID: 23691125 PMCID: PMC3653801 DOI: 10.1371/journal.pone.0063954] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/10/2013] [Indexed: 12/02/2022] Open
Abstract
Understanding the relationship between life-history variation and population structure in marine invertebrates is not straightforward. This is particularly true of polar species due to the difficulty of obtaining samples and a paucity of genomic resources from which to develop nuclear genetic markers. Such knowledge, however, is essential for understanding how different taxa may respond to climate change in the most rapidly warming regions of the planet. We therefore used over two hundred polymorphic Amplified Fragment Length Polymorphisms (AFLPs) to explore population connectivity at three hierachical spatial scales in the direct developing Antarctic topshell Margarella antarctica. To previously published data from five populations spanning a 1500 km transect along the length of the Western Antarctic Peninsula, we added new AFLP data for four populations separated by up to 6 km within Ryder Bay, Adelaide Island. Overall, we found a nonlinear isolation-by-distance pattern, suggestive of weaker population structure within Ryder Bay than is present over larger spatial scales. Nevertheless, significantly positive Fst values were obtained in all but two of ten pairwise population comparisons within the bay following Bonferroni correction for multiple tests. This is in contrast to a previous study of the broadcast spawner Nacella concinna that found no significant genetic differences among several of the same sites. By implication, the topshell's direct-developing lifestyle may constrain its ability to disperse even over relatively small geographic scales.
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Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- * E-mail:
| | - Andrew Clarke
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Melody S. Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Lloyd S. Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
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45
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Gaither MR, Bowen BW, Toonen RJ. Population structure in the native range predicts the spread of introduced marine species. Proc Biol Sci 2013; 280:20130409. [PMID: 23595272 PMCID: PMC3652461 DOI: 10.1098/rspb.2013.0409] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Forecasting invasion success remains a fundamental challenge in invasion biology. The effort to identify universal characteristics that predict which species become invasive has faltered in part because of the diversity of taxa and systems considered. Here, we use an alternative approach focused on the spread stage of invasions. FST, a measure of alternative fixation of alleles, is a common proxy for realized dispersal among natural populations, summarizing the combined influences of life history, behaviour, habitat requirements, population size, history and ecology. We test the hypothesis that population structure in the native range (FST) is negatively correlated with the geographical extent of spread of marine species in an introduced range. An analysis of the available data (29 species, nine phyla) revealed a significant negative correlation (R(2) = 0.245-0.464) between FST and the extent of spread of non-native species. Mode FST among pairwise comparisons between populations in the native range demonstrated the highest predictive power (R(2) = 0.464, p < 0.001). There was significant improvement when marker type was considered, with mtDNA datasets providing the strongest relationship (n = 21, R(2) = 0.333-0.516). This study shows that FST can be used to make qualitative predictions concerning the geographical extent to which a non-native marine species will spread once established in a new area.
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Affiliation(s)
- Michelle R Gaither
- Section of Ichthyology, California Academy of Sciences, , 55 Music Concourse Drive, San Francisco, CA 94118, USA.
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46
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Reitzel AM, Herrera S, Layden MJ, Martindale MQ, Shank TM. Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics. Mol Ecol 2013; 22:2953-70. [PMID: 23473066 DOI: 10.1111/mec.12228] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 12/11/2012] [Indexed: 12/20/2022]
Abstract
Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.
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Affiliation(s)
- A M Reitzel
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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47
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Zakas C, Wares JP. Consequences of a poecilogonous life history for genetic structure in coastal populations of the polychaete Streblospio benedicti. Mol Ecol 2012; 21:5447-60. [PMID: 23057973 PMCID: PMC4643657 DOI: 10.1111/mec.12040] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 08/06/2012] [Accepted: 08/15/2012] [Indexed: 11/29/2022]
Abstract
In many species, alternative developmental pathways lead to the production of two distinct phenotypes, promoting the evolution of morphological novelty and diversification. Offspring type in marine invertebrates influences transport time by ocean currents, which dictate dispersal potential and gene flow, and thus has sweeping evolutionary effects on the potential for local adaptation and on rates of speciation, extinction and molecular evolution. Here, we use the polychaete Streblospio benedicti to investigate the effects of dimorphic offspring type on gene flow and genetic structure in coastal populations. We use 84 single nucleotide polymorphism (SNP) markers for this species to assay populations on the East and West Coasts of the United States. Using these markers, we found that in their native East Coast distribution, populations of S. benedicti have high-population genetic structure, but this structure is associated primarily with geographic separation rather than developmental differences. Interestingly, very little genetic differentiation is recovered between individuals of different development types when they occur in the same or nearby populations, further supporting that this is a true case of poecilogony. In addition, we were able to demonstrate that the recently introduced (~100 ya) West Coast populations probably originated from a lecithotrophic population near Delaware.
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Affiliation(s)
- Christina Zakas
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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48
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Crandall ED, Treml EA, Barber PH. Coalescent and biophysical models of stepping-stone gene flow in neritid snails. Mol Ecol 2012; 21:5579-98. [PMID: 23050562 DOI: 10.1111/mec.12031] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 08/02/2012] [Accepted: 08/10/2012] [Indexed: 11/28/2022]
Abstract
Marine species in the Indo-Pacific have ranges that can span thousands of kilometres, yet studies increasingly suggest that mean larval dispersal distances are less than historically assumed. Gene flow across these ranges must therefore rely to some extent on larval dispersal among intermediate 'stepping-stone' populations in combination with long-distance dispersal far beyond the mean of the dispersal kernel. We evaluate the strength of stepping-stone dynamics by employing a spatially explicit biophysical model of larval dispersal in the tropical Pacific to construct hypotheses for dispersal pathways. We evaluate these hypotheses with coalescent models of gene flow among high-island archipelagos in four neritid gastropod species. Two of the species live in the marine intertidal, while the other two are amphidromous, living in fresh water but retaining pelagic dispersal. Dispersal pathways predicted by the biophysical model were strongly favoured in 16 of 18 tests against alternate hypotheses. In regions where connectivity among high-island archipelagos was predicted as direct, there was no difference in gene flow between marine and amphidromous species. In regions where connectivity was predicted through stepping-stone atolls only accessible to marine species, gene flow estimates between high-island archipelagos were significantly higher in marine species. Moreover, one of the marine species showed a significant pattern of isolation by distance consistent with stepping-stone dynamics. While our results support stepping-stone dynamics in Indo-Pacific species, we also see evidence for nonequilibrium processes such as range expansions or rare long-distance dispersal events. This study couples population genetic and biophysical models to help to shed light on larval dispersal pathways.
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