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Clark RD, Pinsky ML. Global patterns of nuclear and mitochondrial genetic diversity in marine fishes. Ecol Evol 2024; 14:e11365. [PMID: 38711488 PMCID: PMC11070773 DOI: 10.1002/ece3.11365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
Genetic diversity is a fundamental component of biodiversity. Examination of global patterns of genetic diversity can help highlight mechanisms underlying species diversity, though a recurring challenge has been that patterns may vary by molecular marker. Here, we compiled 6862 observations of genetic diversity from 492 species of marine fish and tested among hypotheses for diversity gradients: the founder effect hypothesis, the kinetic energy hypothesis, and the productivity-diversity hypothesis. We fit generalized linear mixed effect models (GLMMs) and explored the extent to which various macroecological drivers (latitude, longitude, temperature (SST), and chlorophyll-a concentration) explained variation in genetic diversity. We found that mitochondrial genetic diversity followed geographic gradients similar to those of species diversity, being highest near the Equator, particularly in the Coral Triangle, while nuclear genetic diversity did not follow clear geographic patterns. Despite these differences, all genetic diversity metrics were correlated with chlorophyll-a concentration, while mitochondrial diversity was also positively associated with SST. Our results provide support for the kinetic energy hypothesis, which predicts that elevated mutation rates at higher temperatures increase mitochondrial but not necessarily nuclear diversity, and the productivity-diversity hypothesis, which posits that resource-rich regions support larger populations with greater genetic diversity. Overall, these findings reveal how environmental variables can influence mutation rates and genetic drift in the ocean, caution against using mitochondrial macrogenetic patterns as proxies for whole-genome diversity, and aid in defining global gradients of genetic diversity.
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Affiliation(s)
- René D. Clark
- Department of BiologyDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Malin L. Pinsky
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
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2
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Genetic Diversity and Connectivity of Ocypode ceratophthalmus in the East and South China Seas and Its Implications for Conservation. BIOLOGY 2023; 12:biology12030437. [PMID: 36979129 PMCID: PMC10044906 DOI: 10.3390/biology12030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
Abstract
The East and South China Seas are rich in marine resources, but they are also under great pressure from climate change and human activities. Maintaining diversity and connectivity between communities is thought to be effective in mitigating these pressures. To assess the diversity and connectivity among the populations of Ocypode ceratophthalmus in the East and South China Seas, 15 populations from or near 15 marine protected areas in the two seas were studied using COI and D-Loop as genetic markers. The results showed that O. ceratophthalmus populations had high diversity, and the results of a hierarchical analysis of molecular variance and fixation index found that there were no significant genetic structures among these populations. High historical gene flow and high migration rates were further observed among populations by Migrate-n. Furthermore, the COI sequences further showed the asymmetric migration rate with a higher migration rate from south to north than from north to south. This information could provide recommendations for the management of marine protected areas in the East and South China Seas.
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3
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Zelada-Mázmela E, Reyes-Flores LE, Sánchez-Velásquez JJ, Ingar C, Santos-Rojas LE. Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses. Ecol Evol 2022; 12:e9276. [PMID: 36177117 PMCID: PMC9463045 DOI: 10.1002/ece3.9276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
The present‐day population structure of a species reflects the combination of oceanographic currents, life‐history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here, we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star‐shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species’ response to future climate change.
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Affiliation(s)
- Eliana Zelada-Mázmela
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences Universidad Nacional del Santa Nuevo Chimbote Peru
| | - Lorenzo E Reyes-Flores
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences Universidad Nacional del Santa Nuevo Chimbote Peru
| | - Julissa J Sánchez-Velásquez
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences Universidad Nacional del Santa Nuevo Chimbote Peru
| | - Claudia Ingar
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences Universidad Nacional del Santa Nuevo Chimbote Peru
| | - Luis E Santos-Rojas
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences Universidad Nacional del Santa Nuevo Chimbote Peru
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Keeley ATH, Fremier AK, Goertler PAL, Huber PR, Sturrock AM, Bashevkin SM, Barbaree BA, Grenier JL, Dilts TE, Gogol-Prokurat M, Colombano DD, Bush EE, Laws A, Gallo JA, Kondolf M, Stahl AT. Governing Ecological Connectivity in Cross-Scale Dependent Systems. Bioscience 2022; 72:372-386. [PMID: 35370478 PMCID: PMC8970826 DOI: 10.1093/biosci/biab140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries.
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Affiliation(s)
| | | | - Pascale A L Goertler
- Delta Stewardship Council, Delta Science Program, Sacramento, California, United States
| | - Patrick R Huber
- University of California, Davis, Davis, California, United States
| | | | | | - Blake A Barbaree
- Point Blue Conservation Science, based Petaluma, California, United States
| | - J Letitia Grenier
- San Francisco Estuary Institute, Richmond, California, United States
| | | | - Melanie Gogol-Prokurat
- California Department of Fish and Wildlife's Biogeographic Data Branch in Sacramento, California, United States
| | | | - Eva E Bush
- Delta Stewardship Council Delta Science Program, Sacramento, California, United States
| | - Angela Laws
- The Xerces Society, Portland, Oregon, United States
| | - John A Gallo
- Conservation Biology Institute, Corvallis, Oregon, United States
| | - Mathias Kondolf
- University of California, Berkeley, Berkeley, California, United States
| | - Amanda T Stahl
- Washington State University, Pullman, Washington, United States
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5
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Tang Q, Shingate P, Wardiatno Y, John A, Tay BH, Tay YC, Yap L, Lim J, Tong HY, Tun K, Venkatesh B, Rheindt FE. The different fates of two Asian horseshoe crab species with different dispersal abilities. Evol Appl 2021; 14:2124-2133. [PMID: 34429753 PMCID: PMC8372080 DOI: 10.1111/eva.13271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022] Open
Abstract
Impending anthropogenic climate change will severely impact coastal organisms at unprecedented speed. Knowledge on organisms' evolutionary responses to past sea-level fluctuations and estimation of their evolutionary potential is therefore indispensable in efforts to mitigate the effects of future climate change. We sampled tens of thousands of genomic markers of ~300 individuals in two of the four extant horseshoe crab species across the complex archipelagic Singapore Straits. Carcinoscorpius rotundicauda Latreille, a less mobile mangrove species, has finer population structure and lower genetic diversity compared with the dispersive deep-sea Tachypleus gigas Müller. Even though the source populations of both species during the last glacial maximum exhibited comparable effective population sizes, the less dispersive C. rotundicauda seems to lose genetic diversity much more quickly because of population fragmentation. Contra previous studies' results, we predict that the more commonly sighted C. rotundicauda faces a more uncertain conservation plight, with a continuing loss in evolutionary potential and higher vulnerability to future climate change. Our study provides important genomic baseline data for the redirection of conservation measures in the face of climate change and can be used as a blueprint for assessment and mitigation of the adverse effects of impending sea-level rise in other systems.
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Affiliation(s)
- Qian Tang
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Prashant Shingate
- Institute of Molecular and Cell BiologyA*STARBiopolisSingapore CitySingapore
| | | | - Akbar John
- Institute of Oceanography and Maritime Studies (INOCEM)Kulliyyah of ScienceInternational Islamic University Malaysia (IIUM)KuantanPahangMalaysia
| | - Boon Hui Tay
- Institute of Molecular and Cell BiologyA*STARBiopolisSingapore CitySingapore
| | | | - Laura‐Marie Yap
- School of Applied SciencesRepublic PolytechnicSingapore CitySingapore
| | - Jasmin Lim
- School of Applied SciencesRepublic PolytechnicSingapore CitySingapore
| | | | | | - Byrappa Venkatesh
- Institute of Molecular and Cell BiologyA*STARBiopolisSingapore CitySingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
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Francisco SM, Castilho R, Lima CS, Almada F, Rodrigues F, Šanda R, Vukić J, Pappalardo AM, Ferrito V, Robalo JI. Genetic hypervariability of a Northeastern Atlantic venomous rockfish. PeerJ 2021; 9:e11730. [PMID: 34306828 PMCID: PMC8280884 DOI: 10.7717/peerj.11730] [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: 01/15/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. METHODS In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. RESULTS The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.
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Affiliation(s)
- Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Francisca Rodrigues
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Radek Šanda
- Department of Zoology, National Museum, Prague, Czeck Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University, Prague, Czech Republic
| | - Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
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7
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Robalo JI, Farias I, Francisco SM, Avellaneda K, Castilho R, Figueiredo I. Genetic population structure of the Blackspot seabream ( Pagellus bogaraveo): contribution of mtDNA control region to fisheries management. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:115-119. [PMID: 33576693 DOI: 10.1080/24701394.2021.1882445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Marine fisheries management models have traditionally considered biological parameters and geopolitical boundaries. The result is the existence of fisheries management units that do not match genetic populations. However, this panorama is changing with the contribution of genetic and genomic data. Pagellus bogaraveo is a commercially important sparid in the northeast Atlantic, with three stock components being considered by ICES: the Celtic Sea and Bay of Biscay, Atlantic Iberian waters and the Azores. The northern stock collapsed (1975-1985) and is essential to characterize the genetic makeup of the species, particularly in the Iberian Peninsula, where it is managed as a single stock. The mitochondrial control region was used to screen the intraspecific diversity and population structure of individuals from six locations across the species range. The genetic diversity found is similar among sites, and there is differentiation between the Azores and the remaining locations.
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Affiliation(s)
- Joana I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Inês Farias
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
| | - Sara M Francisco
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Karen Avellaneda
- MARE - Marine and Environmental Sciences Centre, ISPA Instituto Universitário, Lisboa, Portugal
| | - Rita Castilho
- University of the Algarve, Faro, Portugal.,Faculty of Science and Technology, Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - Ivone Figueiredo
- Portuguese Institute for Sea and Atmosphere (IPMA), Algés, Portugal
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