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Takenaka M, Yano K, Tojo K. Phylogeography of the true freshwater crab, Geothelphusa dehaani: Detected dual dispersal routes via land and sea. ZOOLOGY 2023; 160:126118. [PMID: 37683516 DOI: 10.1016/j.zool.2023.126118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023]
Abstract
Dispersal is an important factor that determines the potential for colonization to pioneer sites. Although most decapods employ seaward migration for reproduction with a planktonic larval phase, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on true freshwater crabs, Geothelphusa Stimpson, 1858. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans. We collected and genetically analyzed 283 specimens at 138 localities across the Japanese Islands. Phylogenetic analyses were conducted on the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3 regions) and the data set based on the mtDNA COI region. The phylogenetic relationships detected 10 clades that were highly monophyletic. The highlights of this study were the discovery of several cryptic species or undescribed species, and the completely different heterogeneous dual dispersal pathways within a single species; i.e., both land and ocean routes. Although it was concluded that Japanese crabs are basically genetically divided by straits, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"). It was also confirmed that Geothelphusa dehaani (White, 1847) could survive in seawater.
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Affiliation(s)
- Masaki Takenaka
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, Sugadairakogen 1278-294, Ueda 386-2204, Japan
| | - Koki Yano
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Division of Evolutionary Developmental Biology, National Institute for Basic Biology, Nishigonaka 38, Okazaki 444-0867, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.
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2
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Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla. Nat Commun 2022; 13:5861. [PMID: 36195609 PMCID: PMC9532449 DOI: 10.1038/s41467-022-33499-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Gene flow governs the contemporary spatial structure and dynamic of populations as well as their long-term evolution. For species that disperse using atmospheric or oceanic flows, biophysical models allow predicting the migratory component of gene flow, which facilitates the interpretation of broad-scale spatial structure inferred from observed allele frequencies among populations. However, frequent mismatches between dispersal estimates and observed genetic diversity prevent an operational synthesis for eco-evolutionary projections. Here we use an extensive compilation of 58 population genetic studies of 47 phylogenetically divergent marine sedentary species over the Mediterranean basin to assess how genetic differentiation is predicted by Isolation-By-Distance, single-generation dispersal and multi-generation dispersal models. Unlike previous approaches, the latter unveil explicit parents-to-offspring links (filial connectivity) and implicit links among siblings from a common ancestor (coalescent connectivity). We find that almost 70 % of observed variance in genetic differentiation is explained by coalescent connectivity over multiple generations, significantly outperforming other models. Our results offer great promises to untangle the eco-evolutionary forces that shape sedentary population structure and to anticipate climate-driven redistributions, altogether improving spatial conservation planning.
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3
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van Woesik R, Shlesinger T, Grottoli AG, Toonen RJ, Vega Thurber R, Warner ME, Marie Hulver A, Chapron L, McLachlan RH, Albright R, Crandall E, DeCarlo TM, Donovan MK, Eirin‐Lopez J, Harrison HB, Heron SF, Huang D, Humanes A, Krueger T, Madin JS, Manzello D, McManus LC, Matz M, Muller EM, Rodriguez‐Lanetty M, Vega‐Rodriguez M, Voolstra CR, Zaneveld J. Coral-bleaching responses to climate change across biological scales. GLOBAL CHANGE BIOLOGY 2022; 28:4229-4250. [PMID: 35475552 PMCID: PMC9545801 DOI: 10.1111/gcb.16192] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 05/26/2023]
Abstract
The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km2 ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.
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Affiliation(s)
- Robert van Woesik
- Institute for Global EcologyFlorida Institute of TechnologyMelbourneFloridaUSA
| | - Tom Shlesinger
- Institute for Global EcologyFlorida Institute of TechnologyMelbourneFloridaUSA
| | | | - Rob J. Toonen
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | | | - Mark E. Warner
- School of Marine Science and PolicyUniversity of DelawareLewesDelawareUSA
| | - Ann Marie Hulver
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leila Chapron
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Rowan H. McLachlan
- School of Earth SciencesThe Ohio State UniversityColumbusOhioUSA
- Department of MicrobiologyOregon State UniversityCorvallisOregonUSA
| | | | - Eric Crandall
- Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Mary K. Donovan
- Center for Global Discovery and Conservation Science and School of Geographical Sciences and Urban PlanningArizona State UniversityTempeArizonaUSA
| | - Jose Eirin‐Lopez
- Institute of EnvironmentFlorida International UniversityMiamiFloridaUSA
| | - Hugo B. Harrison
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
| | - Scott F. Heron
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
- Physics and Marine Geophysical LaboratoryJames Cook UniversityTownsvilleQueenslandAustralia
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Adriana Humanes
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Thomas Krueger
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Joshua S. Madin
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | - Derek Manzello
- Center for Satellite Applications and ResearchSatellite Oceanography & Climate DivisionNational Oceanic and Atmospheric AdministrationCollege ParkMarylandUSA
| | - Lisa C. McManus
- Hawai'i Institute of Marine Biology, KāneʻoheUniversity of Hawaiʻi at MānoaHonoluluHawaiiUSA
| | - Mikhail Matz
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexasUSA
| | | | | | | | | | - Jesse Zaneveld
- Division of Biological SciencesUniversity of WashingtonBothellWashingtonUSA
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4
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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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5
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Kudla N, McCluskey EM, Lulla V, Grundel R, Moore JA. Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake. Ecol Evol 2021; 11:6276-6288. [PMID: 34141217 PMCID: PMC8207425 DOI: 10.1002/ece3.7480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 02/01/2021] [Indexed: 11/07/2022] Open
Abstract
Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species' range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.
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Affiliation(s)
- Nathan Kudla
- Biology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | | | - Vijay Lulla
- Department of GeographyIUPUIIndianapolis, INUSA
| | - Ralph Grundel
- Great Lakes Science CenterU.S. Geological SurveyChestertonINUSA
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6
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Benestan L, Fietz K, Loiseau N, Guerin PE, Trofimenko E, Rühs S, Schmidt C, Rath W, Biastoch A, Pérez-Ruzafa A, Baixauli P, Forcada A, Arcas E, Lenfant P, Mallol S, Goñi R, Velez L, Höppner M, Kininmonth S, Mouillot D, Puebla O, Manel S. Restricted dispersal in a sea of gene flow. Proc Biol Sci 2021; 288:20210458. [PMID: 34004134 PMCID: PMC8131118 DOI: 10.1098/rspb.2021.0458] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.
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Affiliation(s)
- L. Benestan
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - K. Fietz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - N. Loiseau
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - P. E. Guerin
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - E. Trofimenko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - S. Rühs
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - C. Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - W. Rath
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - A. Biastoch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - A. Pérez-Ruzafa
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - P. Baixauli
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - A. Forcada
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - E. Arcas
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - P. Lenfant
- Centre de Formation et de Recherche sur les Environnements Méditerranéens, Université Perpignan Via Domitia, CNRS, 66100 Perpignan, France
| | - S. Mallol
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - R. Goñi
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - L. Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - M. Höppner
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - S. Kininmonth
- School of Marine Studies, University of the South Pacific, Fiji
| | - D. Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - O. Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Ecology Department, Leibniz-Centre for Tropical Marine Research, Fahrenheitstraße 6, 28359 Bremen, Germany
| | - S. Manel
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
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7
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Bertola LD, Boehm JT, Putman NF, Xue AT, Robinson JD, Harris S, Baldwin CC, Overcast I, Hickerson MJ. Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity. Proc Biol Sci 2020; 287:20200657. [PMID: 32370669 DOI: 10.1098/rspb.2020.0657] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading to predictions on population-level genetic connectivity and the directionality of effective dispersal. Here, we use genome-wide single nucleotide polymorphism data to investigate whether gene flow directionality in two seahorses (Hippocampus) and three pipefishes (Syngnathus) follows the predominant ocean circulation patterns in the Gulf of Mexico and northwestern Atlantic. In addition, we explore whether gene flow magnitudes are predicted by traits related to active dispersal ability and habitat preference. We inferred demographic histories of these co-distributed syngnathid species, and coalescent model-based estimates indicate that gene flow directionality is in agreement with ocean circulation data that predicts eastward and northward macro-algal transport. However, the magnitude to which ocean currents influence this pattern appears strongly dependent on the species-specific traits related to rafting propensity and habitat preferences. Higher levels of gene flow and stronger directionality are observed in Hippocampus erectus, Syngnathus floridae and Syngnathus louisianae, which closely associated with the pelagic macro-algae Sargassum spp., compared to Hippocampus zosterae and the Syngnathus scovelli/Syngnathus fuscus sister-species pair, which prefer near shore habitats and are weakly associated with pelagic Sargassum. This study highlights how the combination of population genomic inference together with ocean circulation data can help explain patterns of population structure and diversity in marine ecosystems.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Department of Earth and Atmospheric Sciences, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - J T Boehm
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th Street, New York, NY 10024, USA
| | - Nathan F Putman
- LGL Ecological Research Associates, Inc, Bryan, TX 77801, USA.,Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL 33149, USA
| | - Alexander T Xue
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - John D Robinson
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Department of Fisheries and Wildlife, Michigan State University, 480 Wilson Road, East Lansing, MI 48824, USA
| | - Stephen Harris
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th Street and Constitution Avenue NW, Washington, DC 20560, USA
| | - Isaac Overcast
- Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Michael J Hickerson
- Department of Biology, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Subprogram in Ecology, Evolution and Behavior, The Graduate Center of the City University of New York, 365 5th Avenue, New York, NY 10016, USA.,Division of Invertebrate Zoology, American Museum of Natural History, Central Park West and 79th Street, New York, NY 10024, USA
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8
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Species-specific genetic variation in response to deep-sea environmental variation amongst Vulnerable Marine Ecosystem indicator taxa. Sci Rep 2020; 10:2844. [PMID: 32071333 PMCID: PMC7028729 DOI: 10.1038/s41598-020-59210-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/27/2020] [Indexed: 11/15/2022] Open
Abstract
Understanding the ecological processes that shape spatial genetic patterns of population structure is critical for understanding evolutionary dynamics and defining significant evolutionary and management units in the deep sea. Here, the role of environmental factors (topographic, physico-chemical and biological) in shaping the population genetic structure of four deep-sea habitat-forming species (one sponge - Poecillastra laminaris, three corals - Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) was investigated using seascape genetics. Genetic data (nuclear and mitochondrial sequences and microsatellite multilocus genotypes) and environmental variables were employed to build individual-based and population-level models. The results indicated that environmental factors affected genetic variation differently amongst the species, as well as at different geographic scales. For individual-based analyses, different environmental variables explained genetic variation in P. laminaris (dissolved oxygen), G. dumosa (dynamic topography), M. oculata (sea surface temperature and surface water primary productivity), and S. variabilis (tidal current speed). At the population level, factors related to current and food source explained the regional genetic structure in all four species, whilst at the geomorphic features level, factors related to food source and topography were most important. Environmental variation in these parameters may be acting as barriers to gene flow at different scales. This study highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms, and to identify environmental factors that can be used to locate sites for the protection of deep-sea Vulnerable Marine Ecosystems.
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9
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Sasaki MC, Dam HG. Integrating patterns of thermal tolerance and phenotypic plasticity with population genetics to improve understanding of vulnerability to warming in a widespread copepod. GLOBAL CHANGE BIOLOGY 2019; 25:4147-4164. [PMID: 31449341 DOI: 10.1111/gcb.14811] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Differences in population vulnerability to warming are defined by spatial patterns in thermal adaptation. These patterns may be driven by natural selection over spatial environmental gradients, but can also be shaped by gene flow, especially in marine taxa with high dispersal potential. Understanding and predicting organismal responses to warming requires disentangling the opposing effects of selection and gene flow. We begin by documenting genetic divergence of thermal tolerance and developmental phenotypic plasticity. Ten populations of the widespread copepod Acartia tonsa were collected from sites across a large thermal gradient, ranging from the Florida Keys to Northern New Brunswick, Canada (spanning over 20° latitude). Thermal performance curves (TPCs) from common garden experiments revealed local adaptation at the sampling range extremes, with thermal tolerance increasing at low latitudes and decreasing at high latitudes. The opposite pattern was observed in phenotypic plasticity, which was strongest at high latitudes. No relationship was observed between phenotypic plasticity and environmental variables. Instead, the results are consistent with the hypothesis of a trade-off between thermal tolerance and the strength of phenotypic plasticity. Over a large portion of the sampled range, however, we observed a remarkable lack of differentiation of TPCs. To examine whether this lack of divergence is the result of selection for a generalist performance curve or constraint by gene flow, we analyzed cytochrome oxidase I mtDNA sequences, which revealed four distinct genetic clades, abundant genetic diversity, and widely distributed haplotypes. Strong divergence in thermal performance within genetic clades, however, suggests that the pace of thermal adaptation can be relatively rapid. The combined insight from the laboratory physiological experiments and genetic data indicate that gene flow constrains differentiation of TPCs. This balance between gene flow and selection has implications for patterns of vulnerability to warming. Taking both genetic differentiation and phenotypic plasticity into account, our results suggest that local adaptation does not increase vulnerability to warming, and that low-latitude populations in general may be more vulnerable to predicted temperature change over the next century.
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Affiliation(s)
- Matthew C Sasaki
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Hans G Dam
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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10
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Zbawicka M, Gardner JPA, Wenne R. Cryptic diversity in smooth-shelled mussels on Southern Ocean islands: connectivity, hybridisation and a marine invasion. Front Zool 2019; 16:32. [PMID: 31406494 PMCID: PMC6685288 DOI: 10.1186/s12983-019-0332-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2019] [Indexed: 01/08/2023] Open
Abstract
Background Large numbers of endemic species inhabit subantarctic continental coasts and islands that are characterised by highly variable environmental conditions. Southern hemisphere populations of taxa that are morphologically similar to northern counterparts have traditionally been considered to be extensions of such Northern hemisphere taxa, and may not exhibit differentiation amongst geographically isolated populations in the Southern Ocean. Smooth-shelled blue mussels of the genus Mytilus that exhibit an anti-tropical distribution are a model group to study phylogeography, speciation and hybridisation in the sea, and contribute to the theory and practice of marine biosecurity. Methods We used a single nucleotide polymorphism (SNPs) panel that has the ability to accurately identify reference Northern and Southern hemisphere Mytilus taxa to test for evolutionary differentiation amongst native Southern Ocean island populations. Results Native mussels from the Falkland Islands and the Kerguelen Islands exhibited greatest affinity to native M. platensis d’Orbigny 1846 from the Atlantic coast of South America. The major Southern Ocean current flow from west to east is likely to explain the spreading of M. platensis to remote offshore islands, as adults via the process of rafting or perhaps directly as larvae. SNPs variation revealed that mussels from Tasmania were native and clearly differentiated from all other blue mussel groups in the Southern and Northern hemispheres. The native mussels M. planulatus from Tasmania and from mainland New Zealand (NZ), and tentatively M. aoteanus from the two NZ Southern Ocean offshore island groups (the Auckland Islands and Campbell Island), formed a distinct M. galloprovincialis–like Southern hemisphere group with closest affinity to Northern hemisphere M. galloprovincialis from the Mediterranean Sea. In all cases, the SNPs revealed evidence of hybridisation between two or more distinct taxa. The invasive Northern hemisphere M. galloprovincialis was identified only in Tasmania, amongst native mussels of a distinct Australian M. planulatus lineage. Conclusion Overall, our results reveal that Southern hemisphere island mussels have mixed genome ancestry and are native, not introduced by human activities. The preservation of distinct evolutionary lineages of Southern hemisphere species needs to be an ongoing focus of conservation efforts, given that population sizes on some of the remote offshore oceanic islands will be small and may be more easily adversely affected by invasion and subsequent hybridisation and introgression than larger populations elsewhere. Electronic supplementary material The online version of this article (10.1186/s12983-019-0332-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Małgorzata Zbawicka
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Jonathan P A Gardner
- 2School of Biological Sciences, Victoria University of Wellington, P O Box 600, Wellington, 6140 New Zealand
| | - Roman Wenne
- 1Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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11
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Riginos C, Hock K, Matias AM, Mumby PJ, Oppen MJH, Lukoschek V. Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in Great Barrier Reef corals. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12969] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Cynthia Riginos
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Karlo Hock
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Ambrocio M. Matias
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
- Institute of Biology University of the Philippines Diliman Quezon City Philippines
| | - Peter J. Mumby
- School of Biological Sciences The University of Queensland St Lucia Queensland Australia
| | - Madeleine J. H. Oppen
- Institute of Biology University of the Philippines Diliman Quezon City Philippines
- School of BioSciences The University of Melbourne Parkville Victoria Australia
- Australian Institute for Marine Sciences Cape Cleveland Queensland Australia
| | - Vimoksalehi Lukoschek
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville Queensland Australia
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12
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Abdou A, Lord C, Keith P, Galzin R. Phylogéographie de Neritina stumpffi Boettger, 1890 et Neritina canalis Sowerby, 1825 (Gastropoda, Cycloneritida, Neritidae). ZOOSYSTEMA 2019. [DOI: 10.5252/zoosystema2019v41a12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ahmed Abdou
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - Clara Lord
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - Philippe Keith
- Unité Biologie des organismes et écosystèmes aquatiques (BOREA), Muséum national d'Histoire naturelle, Sorbonne Université, Université de Caen Normandie, Université des Antilles, CNRS, IRD, case postale 26, 57 rue Cuvier, F-75231 Paris cedex 05 (Fran
| | - René Galzin
- Laboratoire d'excellence Corail, USR 3278 CNRS-EPHE-UPVD, Centre de Recherches insulaires et Observatoire de l'Environnement (CRIOBE), BP 1013 Papetoai, 98729 Moorea, Polynésie française (France)
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13
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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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14
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Sandoval‐Castillo J, Robinson NA, Hart AM, Strain LWS, Beheregaray LB. Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (
Haliotis laevigata
), along a longitudinal environmental gradient. Mol Ecol 2018; 27:1603-1620. [DOI: 10.1111/mec.14526] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 12/05/2017] [Accepted: 12/15/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
| | - Nick A. Robinson
- Nofima Ås Norway
- Sustainable Aquaculture Laboratory School of BioSciences University of Melbourne Parkville Vic Australia
| | - Anthony M. Hart
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Lachlan W. S. Strain
- Western Australian Fisheries and Marine Research Laboratories Department of Fisheries Western Australia Hillarys WA Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory College of Science and Engineering Flinders University Adelaide SA Australia
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15
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Nolasco R, Gomes I, Peteiro L, Albuquerque R, Luna T, Dubert J, Swearer SE, Queiroga H. Independent estimates of marine population connectivity are more concordant when accounting for uncertainties in larval origins. Sci Rep 2018; 8:2641. [PMID: 29422505 PMCID: PMC5805787 DOI: 10.1038/s41598-018-19833-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 12/21/2017] [Indexed: 11/09/2022] Open
Abstract
Marine larval dispersal is a complex biophysical process that depends on the effects of species biology and oceanography, leading to logistical difficulties in estimating connectivity among populations of marine animals with biphasic life cycles. To address this challenge, the application of multiple methodological approaches has been advocated, in order to increase confidence in estimates of population connectivity. However, studies seldom account for sources of uncertainty associated with each method, which undermines a direct comparative approach. In the present study we explicitly account for the statistical uncertainty in observed connectivity matrices derived from elemental chemistry of larval mussel shells, and compare these to predictions from a biophysical model of dispersal. To do this we manipulate the observed connectivity matrix by applying different confidence levels to the assignment of recruits to source populations, while concurrently modelling the intrinsic misclassification rate of larvae to known sources. We demonstrate that the correlation between the observed and modelled matrices increases as the number of observed recruits classified as unknowns approximates the observed larval misclassification rate. Using this approach, we show that unprecedented levels of concordance in connectivity estimates (r = 0.96) can be achieved, and at spatial scales (20-40 km) that are ecologically relevant.
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Affiliation(s)
- R Nolasco
- Departamento de Física & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal.,Instituto de Investigacións Mariñas (CSIC), Eduardo Cabello 6, 36208, Vigo, Spain
| | - I Gomes
- Departamento de Biologia & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal.,Mar. Biol. Research Group, Ghent University, 9000, Ghent, Belgium
| | - L Peteiro
- Departamento de Biologia & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal.,Coastal Ecology Research Group (EcoCost), Department of Ecology and Animal Biology, University of Vigo, Vigo, Spain
| | - R Albuquerque
- Departamento de Biologia & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - T Luna
- Departamento de Física & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - J Dubert
- Departamento de Física & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - S E Swearer
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - H Queiroga
- Departamento de Física & CESAM - Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, 3810-193, Aveiro, Portugal.
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16
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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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17
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Van Wynsberge S, Andréfouët S, Gaertner-Mazouni N, Tiavouane J, Grulois D, Lefèvre J, Pinsky ML, Fauvelot C. Considering reefscape configuration and composition in biophysical models advance seascape genetics. PLoS One 2017; 12:e0178239. [PMID: 28542261 PMCID: PMC5444781 DOI: 10.1371/journal.pone.0178239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 05/10/2017] [Indexed: 01/10/2023] Open
Abstract
Previous seascape genetics studies have emphasized the role of ocean currents and geographic distances to explain the genetic structure of marine species, but the role of benthic habitat has been more rarely considered. Here, we compared the population genetic structure observed in West Pacific giant clam populations against model simulations that accounted habitat composition and configuration, geographical distance, and oceanic currents. Dispersal determined by geographical distance provided a modelled genetic structure in better agreement with the observations than dispersal by oceanic currents, possibly due to insufficient spatial resolution of available oceanographic and coastal circulation models. Considering both habitat composition and configuration significantly improved the match between simulated and observed genetic structures. This study emphasizes the importance of a reefscape genetics approach to population ecology, evolution and conservation in the sea.
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Affiliation(s)
- Simon Van Wynsberge
- UMR-241 EIO, Université de la Polynésie Française, Laboratoire d’Excellence CORAIL, Faa’a, Tahiti, French Polynesia
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
- * E-mail:
| | - Serge Andréfouët
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Nabila Gaertner-Mazouni
- UMR-241 EIO, Université de la Polynésie Française, Laboratoire d’Excellence CORAIL, Faa’a, Tahiti, French Polynesia
| | - Josina Tiavouane
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Daphné Grulois
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
| | - Jérôme Lefèvre
- UMR-065 LEGOS and UMR-235 MIO, Centre IRD de Nouméa, Nouméa, New Caledonia
| | - Malin L. Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
- Institute of Earth, Ocean, and Atmospheric Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Cécile Fauvelot
- UMR-9220 ENTROPIE (Institut de Recherche pour le Développement, Université de La Réunion, CNRS), Laboratoire d’excellence-CORAIL, centre IRD de Nouméa, Nouméa, New Caledonia
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18
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Puritz JB, Keever CC, Addison JA, Barbosa SS, Byrne M, Hart MW, Grosberg RK, Toonen RJ. Life-history predicts past and present population connectivity in two sympatric sea stars. Ecol Evol 2017; 7:3916-3930. [PMID: 28616188 PMCID: PMC5468144 DOI: 10.1002/ece3.2938] [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: 11/15/2016] [Revised: 02/24/2017] [Accepted: 03/03/2017] [Indexed: 12/31/2022] Open
Abstract
Life‐history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic‐developing sea star, Parvulastra exigua, has lower levels of within‐ and among‐population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima (LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic‐developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic‐developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post‐Pleistocene introgression.
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Affiliation(s)
- Jonathan B Puritz
- Marine Science Center Northeastern University Nahant MA USA.,Hawai'i Institute of Marine Biology School of Ocean and Earth Science and Technology University of Hawai'i at Mānoa Kāne'ohe HI USA
| | - Carson C Keever
- Department of Biology Kwantlen Polytechnic University Surrey BC Canada.,Department of Biological Sciences Simon Fraser University Burnaby BC Canada
| | - Jason A Addison
- Department of Biology University of New Brunswick Fredericton NB Canada
| | - Sergio S Barbosa
- Schools of Medical and Biological Sciences University of Sydney Sydney NSW Australia
| | - Maria Byrne
- Schools of Medical and Biological Sciences University of Sydney Sydney NSW Australia
| | - Michael W Hart
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada.,Crawford LabCentre for Evolutionary Studies Simon Fraser University Burnaby BC Canada
| | - Richard K Grosberg
- Department of Evolution and Ecology College of Biological Sciences University of California Davis Davis CA USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology School of Ocean and Earth Science and Technology University of Hawai'i at Mānoa Kāne'ohe HI USA
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19
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Krueck NC, Ahmadia GN, Green A, Jones GP, Possingham HP, Riginos C, Treml EA, Mumby PJ. Incorporating larval dispersal into MPA design for both conservation and fisheries. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:925-941. [PMID: 28039952 DOI: 10.1002/eap.1495] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 12/04/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
Larval dispersal by ocean currents is a critical component of systematic marine protected area (MPA) design. However, there is a lack of quantitative methods to incorporate larval dispersal in support of increasingly diverse management objectives, including local population persistence under multiple types of threats (primarily focused on larval retention within and dispersal between protected locations) and benefits to unprotected populations and fisheries (primarily focused on larval export from protected locations to fishing grounds). Here, we present a flexible MPA design approach that can reconcile multiple such potentially conflicting management objectives by balancing various associated treatments of larval dispersal information. We demonstrate our approach based on alternative dispersal patterns, combinations of threats to populations, management objectives, and two different optimization strategies (site vs. network-based). Our outcomes highlight a consistently high effectiveness in selecting priority locations that are self-replenishing, inter-connected, and/or important larval sources. We find that the opportunity to balance these three dispersal attributes flexibly can help not only to prevent meta-population collapse, but also to ensure effective fisheries recovery, with average increases in the number of recruits at fishing grounds at least two times higher than achieved by standard habitat-based or ad-hoc MPA designs. Future applications of our MPA design approach should therefore be encouraged, specifically where management tools other than MPAs are not feasible.
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Affiliation(s)
- Nils C Krueck
- Marine Spatial Ecology Lab and Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
| | - Gabby N Ahmadia
- Oceans Conservation, World Wildlife Fund (WWF), Washington, D.C., 20037, USA
| | - Alison Green
- The Nature Conservancy, 245 Riverside Drive, West End, Queensland, 4101, Australia
| | - Geoffrey P Jones
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia
| | - Hugh P Possingham
- School of Biological Sciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
- Australian Research Council Centre of Excellence for Environmental Decisions, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
| | - Eric A Treml
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Peter J Mumby
- Marine Spatial Ecology Lab and Australian Research Council Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia Campus, Brisbane, Queensland, 4072, Australia
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20
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Antoniou A, Kasapidis P, Kotoulas G, Mylonas CC, Magoulas A. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. ACTA ACUST UNITED AC 2017; 24:3. [PMID: 28239596 PMCID: PMC5314471 DOI: 10.1186/s40709-017-0062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/28/2017] [Indexed: 11/25/2022]
Abstract
Background Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species’ reproduction. Results Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study’s sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
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Buonomo R, Assis J, Fernandes F, Engelen AH, Airoldi L, Serrão EA. Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea. Mol Ecol 2017; 26:766-780. [PMID: 27997043 DOI: 10.1111/mec.13960] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/29/2022]
Abstract
Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping-stone oceanographic transport and habitat continuity, using as model an ecosystem-structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping-stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life-history traits. Our results highlight the importance of spatially explicit modelling of stepping-stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications.
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Affiliation(s)
- Roberto Buonomo
- CCMAR-CIMAR Laboratorio Associado, F.C.T.- Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, UO Conisma, University of Bologna, Via S. Alberto 163, 48123, Ravenna, Italy
| | - Jorge Assis
- CCMAR-CIMAR Laboratorio Associado, F.C.T.- Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Francisco Fernandes
- CCMAR-CIMAR Laboratorio Associado, F.C.T.- Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Aschwin H Engelen
- CCMAR-CIMAR Laboratorio Associado, F.C.T.- Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Laura Airoldi
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, UO Conisma, University of Bologna, Via S. Alberto 163, 48123, Ravenna, Italy
| | - Ester A Serrão
- CCMAR-CIMAR Laboratorio Associado, F.C.T.- Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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Wren JLK, Kobayashi DR, Jia Y, Toonen RJ. Modeled Population Connectivity across the Hawaiian Archipelago. PLoS One 2016; 11:e0167626. [PMID: 27930680 PMCID: PMC5145177 DOI: 10.1371/journal.pone.0167626] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/17/2016] [Indexed: 11/18/2022] Open
Abstract
We present the first comprehensive estimate of connectivity of passive pelagic particles released from coral reef habitat throughout the Hawaiian Archipelago. Potential connectivity is calculated using a Lagrangian particle transport model coupled offline with currents generated by an oceanographic circulation model, MITgcm. The connectivity matrices show a surprising degree of self-recruitment and directional dispersal towards the northwest, from the Main Hawaiian Islands (MHI) to the northwestern Hawaiian Islands (NWHI). We identify three predicted connectivity breaks in the archipelago, that is, areas in the mid and northern part of the archipelago that have limited connections with surrounding islands and reefs. Predicted regions of limited connectivity generally match observed patterns of genetic structure reported for coral reef species in the uninhabited NWHI, but multiple genetic breaks observed in the inhabited MHI are not explained by passive dispersal. The better congruence in our modeling results based on physical transport of passive particles in the low-lying atolls of the uninhabited NWHI, but not in the anthropogenically impacted high islands of the MHI begs the question: what ultimately controls connectivity in this system?
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Affiliation(s)
- Johanna L. K. Wren
- Joint Institute for Marine and Atmospheric Research, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, United States of America
- Hawaiʻi Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaiʻi at Mānoa, Kāne‘ohe, Hawaiʻi, United States of America
- * E-mail:
| | - Donald R. Kobayashi
- Ecosystems and Oceanography Program, Pacific Islands Fisheries Science Center, National Oceanographic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Yanli Jia
- International Pacific Research Center, University of Hawaiʻi at Mānoa, Honolulu, Hawai‘i, United States of America
| | - Robert J. Toonen
- Hawaiʻi Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaiʻi at Mānoa, Kāne‘ohe, Hawaiʻi, United States of America
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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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24
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Eizaguirre C. Evolution: Ocean Models Reveal Life in Deep Seas. Curr Biol 2016; 26:R853-R855. [PMID: 27676306 DOI: 10.1016/j.cub.2016.07.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Even though the deep sea represents the largest area in the world, evolution of species from those environments remains largely unstudied. A series of recent papers indicate that combining molecular tools with biophysical models can help us resolve some of these deep mysteries.
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Affiliation(s)
- Christophe Eizaguirre
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, E14NS, London, UK.
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25
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Lasker HR, Porto-Hannes I. Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas. PeerJ 2015; 3:e1019. [PMID: 26157606 PMCID: PMC4493681 DOI: 10.7717/peerj.1019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/24/2015] [Indexed: 11/20/2022] Open
Abstract
Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal.
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Affiliation(s)
- Howard R Lasker
- Department of Geology, University at Buffalo , Buffalo, NY , USA ; Graduate Program in Evolution, Ecology and Behavior, University at Buffalo , Buffalo, NY , USA
| | - Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo , Buffalo, NY , USA
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26
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Treml EA, Ford JR, Black KP, Swearer SE. Identifying the key biophysical drivers, connectivity outcomes, and metapopulation consequences of larval dispersal in the sea. MOVEMENT ECOLOGY 2015; 3:17. [PMID: 26180636 PMCID: PMC4502943 DOI: 10.1186/s40462-015-0045-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/19/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Population connectivity, which is essential for the persistence of benthic marine metapopulations, depends on how life history traits and the environment interact to influence larval production, dispersal and survival. Although we have made significant advances in our understanding of the spatial and temporal dynamics of these individual processes, developing an approach that integrates the entire population connectivity process from reproduction, through dispersal, and to the recruitment of individuals has been difficult. We present a population connectivity modelling framework and diagnostic approach for quantifying the impact of i) life histories, ii) demographics, iii) larval dispersal, and iv) the physical seascape, on the structure of connectivity and metapopulation dynamics. We illustrate this approach using the subtidal rocky reef ecosystem of Port Phillip Bay, were we provide a broadly-applicable framework of population connectivity and quantitative methodology for evaluating the relative importance of individual factors in determining local and system outcomes. RESULTS The spatial characteristics of marine population connectivity are primarily influenced by larval mortality, the duration of the pelagic larval stage, and the settlement competency characteristics, with significant variability imposed by the geographic setting and the timing of larval release. The relative influence and the direction and strength of the main effects were strongly consistent among 10 connectivity-based metrics. CONCLUSIONS These important intrinsic factors (mortality, length of the pelagic larval stage, and the extent of the precompetency window) and the spatial and temporal variability represent key research priorities for advancing our understanding of the connectivity process and metapopulation outcomes.
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Affiliation(s)
- Eric A. Treml
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010 Australia
| | - John R. Ford
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010 Australia
| | - Kerry P. Black
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010 Australia
| | - Stephen E. Swearer
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010 Australia
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27
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Dutton PH, Jensen MP, Frey A, LaCasella E, Balazs GH, Zárate P, Chassin-Noria O, Sarti-Martinez AL, Velez E. Population structure and phylogeography reveal pathways of colonization by a migratory marine reptile (Chelonia mydas) in the central and eastern Pacific. Ecol Evol 2014; 4:4317-31. [PMID: 25540693 PMCID: PMC4267870 DOI: 10.1002/ece3.1269] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/22/2014] [Accepted: 09/03/2014] [Indexed: 11/07/2022] Open
Abstract
Climate, behavior, ecology, and oceanography shape patterns of biodiversity in marine faunas in the absence of obvious geographic barriers. Marine turtles are an example of highly migratory creatures with deep evolutionary lineages and complex life histories that span both terrestrial and marine environments. Previous studies have focused on the deep isolation of evolutionary lineages (>3 mya) through vicariance; however, little attention has been given to the pathways of colonization of the eastern Pacific and the processes that have shaped diversity within the most recent evolutionary time. We sequenced 770 bp of the mtDNA control region to examine the stock structure and phylogeography of 545 green turtles from eight different rookeries in the central and eastern Pacific. We found significant differentiation between the geographically separated nesting populations and identified five distinct stocks (FST = 0.08–0.44, P < 0.005). Central and eastern Pacific Chelonia mydas form a monophyletic group containing 3 subclades, with Hawaii more closely related to the eastern Pacific than western Pacific populations. The split between sampled central/eastern and western Pacific haplotypes was estimated at around 0.34 mya, suggesting that the Pacific region west of Hawaii has been a more formidable barrier to gene flow in C. mydas than the East Pacific Barrier. Our results suggest that the eastern Pacific was colonized from the western Pacific via the Central North Pacific and that the Revillagigedos Islands provided a stepping-stone for radiation of green turtles from the Hawaiian Archipelago to the eastern Pacific. Our results fit with a broader paradigm that has been described for marine biodiversity, where oceanic islands, such as Hawaii and Revillagigedo, rather than being peripheral evolutionary “graveyards”, serve as sources and recipients of diversity and provide a mechanism for further radiation.
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Affiliation(s)
- Peter H Dutton
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration 8901 La Jolla Shores Drive, La Jolla, California, 92037
| | - Michael P Jensen
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration 8901 La Jolla Shores Drive, La Jolla, California, 92037
| | - Amy Frey
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration 8901 La Jolla Shores Drive, La Jolla, California, 92037
| | - Erin LaCasella
- Marine Mammal & Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration 8901 La Jolla Shores Drive, La Jolla, California, 92037
| | - George H Balazs
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration 1845 Wasp Blvd., Honolulu, Hawaii, 96818
| | - Patricia Zárate
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida PO Box 118525, Gainesville, Florida, 32611
| | - Omar Chassin-Noria
- Facultad de Biología, Centro Multidisciplinario de Estudios en Biotecnología- UMSNH Morelia, Michoacán, 58030, México
| | - Adriana Laura Sarti-Martinez
- Dirección de Especies Prioritarias para la Conservación, CONANP Camino al Ajusco 200, 2° piso Ala Sur, Col. Jardines en la Montaña, México, DF, 14210, México
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Munguia-Vega A, Jackson A, Marinone SG, Erisman B, Moreno-Baez M, Girón-Nava A, Pfister T, Aburto-Oropeza O, Torre J. Asymmetric connectivity of spawning aggregations of a commercially important marine fish using a multidisciplinary approach. PeerJ 2014; 2:e511. [PMID: 25165626 PMCID: PMC4137664 DOI: 10.7717/peerj.511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 07/22/2014] [Indexed: 12/02/2022] Open
Abstract
Understanding patterns of larval dispersal is key in determining whether no-take marine reserves are self-sustaining, what will be protected inside reserves and where the benefits of reserves will be observed. We followed a multidisciplinary approach that merged detailed descriptions of fishing zones and spawning time at 17 sites distributed in the Midriff Island region of the Gulf of California with a biophysical oceanographic model that simulated larval transport at Pelagic Larval Duration (PLD) 14, 21 and 28 days for the most common and targeted predatory reef fish, (leopard grouper Mycteroperca rosacea). We tested the hypothesis that source–sink larval metapopulation dynamics describing the direction and frequency of larval dispersal according to an oceanographic model can help to explain empirical genetic data. We described modeled metapopulation dynamics using graph theory and employed empirical sequence data from a subset of 11 sites at two mitochondrial genes to verify the model predictions based on patterns of genetic diversity within sites and genetic structure between sites. We employed a population graph describing a network of genetic relationships among sites and contrasted it against modeled networks. While our results failed to explain genetic diversity within sites, they confirmed that ocean models summarized via graph and adjacency distances over modeled networks can explain seemingly chaotic patterns of genetic structure between sites. Empirical and modeled networks showed significant similarities in the clustering coefficients of each site and adjacency matrices between sites. Most of the connectivity patterns observed towards downstream sites (Sonora coast) were strictly asymmetric, while those between upstream sites (Baja and the Midriffs) were symmetric. The best-supported gene flow model and analyses of modularity of the modeled networks confirmed a pulse of larvae from the Baja Peninsula, across the Midriff Island region and towards the Sonoran coastline that acts like a larval sink, in agreement with the cyclonic gyre (anti-clockwise) present at the peak of spawning (May–June). Our approach provided a mechanistic explanation of the location of fishing zones: most of the largest areas where fishing takes place seem to be sustained simultaneously by high levels of local retention, contribution of larvae from upstream sites and oceanographic patterns that concentrate larval density from all over the region. The general asymmetry in marine connectivity observed highlights that benefits from reserves are biased towards particular directions, that no-take areas need to be located upstream of targeted fishing zones, and that some fishing localities might not directly benefit from avoiding fishing within reserves located adjacent to their communities. We discuss the implications of marine connectivity for the current network of marine protected areas and no-take zones, and identify ways of improving it.
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Affiliation(s)
- Adrian Munguia-Vega
- PANGAS Science Coordination, Comunidad y Biodiversidad A.C. , Guaymas, Sonora , México ; Conservation Genetics Laboratory, School of Natural Resources and the Environment, The University of Arizona , Tucson, AZ , USA
| | - Alexis Jackson
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz , Santa Cruz, CA , USA
| | - Silvio Guido Marinone
- Departamento de Oceanografía Física, Centro de Investigación Científica y de Educación Superior de Ensenada , Ensenada, Baja California , México
| | - Brad Erisman
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California , San Diego, La Jolla, CA , USA
| | - Marcia Moreno-Baez
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California , San Diego, La Jolla, CA , USA
| | - Alfredo Girón-Nava
- Universidad Autónoma de Baja California , Ensenada, Baja California , México
| | - Tad Pfister
- School of Natural Resources and the Environment, Center for Latin American Studies, The University of Arizona , Tucson, AZ , USA
| | - Octavio Aburto-Oropeza
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California , San Diego, La Jolla, CA , USA
| | - Jorge Torre
- PANGAS Science Coordination, Comunidad y Biodiversidad A.C. , Guaymas, Sonora , México
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Reynolds TV, Matthee CA, von der Heyden S. The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia). PLoS One 2014; 9:e102115. [PMID: 25054971 PMCID: PMC4108325 DOI: 10.1371/journal.pone.0102115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/15/2014] [Indexed: 11/19/2022] Open
Abstract
The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041-0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.
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Affiliation(s)
- Terry V. Reynolds
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Conrad A. Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- * E-mail:
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30
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Thinking outside the barrier: neutral and adaptive divergence in Indo-Pacific coral reef faunas. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9724-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Taillebois L, Castelin M, Lord C, Chabarria R, Dettaï A, Keith P. New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: Insights on systematics and ancestral areas. Mol Phylogenet Evol 2014; 70:260-71. [DOI: 10.1016/j.ympev.2013.09.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 09/20/2013] [Accepted: 09/27/2013] [Indexed: 10/26/2022]
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Alvarado-Serrano DF, Knowles LL. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 2013; 14:233-48. [DOI: 10.1111/1755-0998.12184] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Diego F. Alvarado-Serrano
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
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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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