1
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Zhao H, Guo X, Wang W, Wang Z, Rawson P, Wilbur A, Hare M. Consequences of domestication in eastern oyster: Insights from whole genomic analyses. Evol Appl 2024; 17:e13710. [PMID: 38817396 PMCID: PMC11134191 DOI: 10.1111/eva.13710] [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: 11/10/2023] [Revised: 04/02/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.
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Affiliation(s)
- Honggang Zhao
- Department of Natural Resources & the EnvironmentCornell UniversityIthacaNew YorkUSA
- Present address:
Center for Aquaculture TechnologySan DiegoCaliforniaUSA
| | - Ximing Guo
- Haskin Shellfish Research LaboratoryRutgers UniversityPort NorrisNew JerseyUSA
| | - Wenlu Wang
- Department of Computer SciencesTexas A&M University‐Corpus ChristiCorpus ChristiTexasUSA
| | - Zhenwei Wang
- Haskin Shellfish Research LaboratoryRutgers UniversityPort NorrisNew JerseyUSA
| | - Paul Rawson
- School of Marine SciencesUniversity of MaineOronoMaineUSA
| | - Ami Wilbur
- Shellfish Research Hatchery, Center for Marine ScienceUniversity of North Carolina WilmingtonWilmingtonNorth CarolinaUSA
| | - Matthew Hare
- Department of Natural Resources & the EnvironmentCornell UniversityIthacaNew YorkUSA
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2
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Ropp AJ, Reece KS, Snyder RA, Song J, Biesack EE, McDowell JR. Fine-scale population structure of the northern hard clam ( Mercenaria mercenaria) revealed by genome-wide SNP markers. Evol Appl 2023; 16:1422-1437. [PMID: 37622097 PMCID: PMC10445094 DOI: 10.1111/eva.13577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
Aquaculture is growing rapidly worldwide, and sustainability is dependent on an understanding of current genetic variation and levels of connectivity among populations. Genetic data are essential to mitigate the genetic and ecological impacts of aquaculture on wild populations and guard against unintended human-induced loss of intraspecific diversity in aquacultured lines. Impacts of disregarding genetics can include loss of diversity within and between populations and disruption of local adaptation patterns, which can lead to a decrease in fitness. The northern hard clam, Mercenaria mercenaria (Linnaeus, 1758), is an economically valuable aquaculture species along the North American Atlantic and Gulf coasts. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity among geographic areas is not well understood. To better inform the establishment of site-appropriate aquaculture brood stocks, this study used DArTseq™ genotyping by sequencing to characterize the genetic stock structure of wild clams sampled along the east coast of North America and document genetic diversity within populations. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Stringent data filtering resulted in 4960 single nucleotide polymorphisms from 448 individuals. Five genetic breaks separating six genetically distinct populations were identified: Canada, Maine, Massachusetts, Mid-Atlantic, Chesapeake Bay, and the Carolinas (F ST 0.003-0.046; p < 0.0001). This is the first study to assess population genetic structure of this economically important hard clam along a large portion of its native range with high-resolution genomic markers, enabling identification of previously unrecognized population structure. Results of this study not only broaden insight into the factors shaping the current distribution of M. mercenaria but also reveal the genetic population dynamics of a species with a long pelagic larval dispersal period along the North American Atlantic and Gulf coasts.
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Affiliation(s)
- Ann J. Ropp
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Kimberly S. Reece
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Richard A. Snyder
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jingwei Song
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Ellen E. Biesack
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
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3
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Smith CCR, Tittes S, Ralph PL, Kern AD. Dispersal inference from population genetic variation using a convolutional neural network. Genetics 2023; 224:iyad068. [PMID: 37052957 PMCID: PMC10213498 DOI: 10.1093/genetics/iyad068] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
The geographic nature of biological dispersal shapes patterns of genetic variation over landscapes, making it possible to infer properties of dispersal from genetic variation data. Here, we present an inference tool that uses geographically distributed genotype data in combination with a convolutional neural network to estimate a critical population parameter: the mean per-generation dispersal distance. Using extensive simulation, we show that our deep learning approach is competitive with or outperforms state-of-the-art methods, particularly at small sample sizes. In addition, we evaluate varying nuisance parameters during training-including population density, demographic history, habitat size, and sampling area-and show that this strategy is effective for estimating dispersal distance when other model parameters are unknown. Whereas competing methods depend on information about local population density or accurate inference of identity-by-descent tracts, our method uses only single-nucleotide-polymorphism data and the spatial scale of sampling as input. Strikingly, and unlike other methods, our method does not use the geographic coordinates of the genotyped individuals. These features make our method, which we call "disperseNN," a potentially valuable new tool for estimating dispersal distance in nonmodel systems with whole genome data or reduced representation data. We apply disperseNN to 12 different species with publicly available data, yielding reasonable estimates for most species. Importantly, our method estimated consistently larger dispersal distances than mark-recapture calculations in the same species, which may be due to the limited geographic sampling area covered by some mark-recapture studies. Thus genetic tools like ours complement direct methods for improving our understanding of dispersal.
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Affiliation(s)
- Chris C R Smith
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Silas Tittes
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Peter L Ralph
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Andrew D Kern
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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4
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Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE. Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges. Ecol Evol 2023; 13:e9945. [PMID: 37066063 PMCID: PMC10099488 DOI: 10.1002/ece3.9945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
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Affiliation(s)
- Diede L. Maas
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity GenomicsSenckenberg Natural History MuseumFrankfurt am MainGermany
- South African National Biodiversity InstituteNational Zoological Gardens of South AfricaPretoriaSouth Africa
| | | | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Computational Genomics Resource Laboratory, California Institute for Quantitative BiosciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Lydia L. Smith
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Ludi P. Aji
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
- Research Centre for Oceanography, Indonesian Institute of SciencesLembaga Ilmu Pengetahuan IndonesiaJakartaIndonesia
| | - Ricardo F. Tapilatu
- Marine Science and Fisheries Departments and Research Center of Pacific Marine ResourcesState University of PapuaManokwariIndonesia
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Leontine E. Becking
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Aquaculture and Fisheries, Naturalis Biodiversity CenterWageningen University & ResearchWageningenThe Netherlands
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5
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Lapègue S, Reisser C, Harrang E, Heurtebise S, Bierne N. Genetic parallelism between European flat oyster populations at the edge of their natural range. Evol Appl 2023; 16:393-407. [PMID: 36793680 PMCID: PMC9923475 DOI: 10.1111/eva.13449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Although all marine ecosystems have experienced global-scale losses, oyster reefs have shown the greatest. Therefore, substantial efforts have been dedicated to restoration of such ecosystems during the last two decades. In Europe, several pilot projects for the restoration of the native European flat oyster, Ostrea edulis, recently begun and recommendations to preserve genetic diversity and to conduct monitoring protocols have been made. In particular, an initial step is to test for genetic differentiation against homogeneity among the oyster populations potentially involved in such programs. Therefore, we conducted a new sampling of wild populations at the European scale and a new genetic analysis with 203 markers to (1) confirm and study in more detail the pattern of genetic differentiation between Atlantic and Mediterranean populations, (2) identify potential translocations that could be due to aquaculture practices and (3) investigate the populations at the fringe of the geographical range, since they seemed related despite their geographic distance. Such information should be useful to enlighten the choice of the animals to be translocated or reproduced in hatcheries for further restocking. After the confirmation of the general geographical pattern of genetic structure and the identification of one potential case of aquaculture transfer at a large scale, we were able to detect genomic islands of differentiation mainly in the form of two groups of linked markers, which could indicate the presence of polymorphic chromosomal rearrangements. Furthermore, we observed a tendency for these two islands and the most differentiated loci to show a parallel pattern of differentiation, grouping the North Sea populations with the Eastern Mediterranean and Black Sea populations, against geography. We discussed the hypothesis that this genetic parallelism could be the sign of a shared evolutionary history of the two groups of populations despite them being at the border of the distribution nowadays.
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Affiliation(s)
- Sylvie Lapègue
- MARBEC, Univ Montpellier, CNRSIfremer, IRDMontpellierFrance
| | - Céline Reisser
- MARBEC, Univ Montpellier, CNRSIfremer, IRDMontpellierFrance
| | | | | | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRDMontpellierFrance
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6
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Seascape genomics of common dolphins (Delphinus delphis) reveals adaptive diversity linked to regional and local oceanography. BMC Ecol Evol 2022; 22:88. [PMID: 35818031 PMCID: PMC9275043 DOI: 10.1186/s12862-022-02038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
High levels of standing genomic variation in wide-ranging marine species may enhance prospects for their long-term persistence. Patterns of connectivity and adaptation in such species are often thought to be influenced by spatial factors, environmental heterogeneity, and oceanographic and geomorphological features. Population-level studies that analytically integrate genome-wide data with environmental information (i.e., seascape genomics) have the potential to inform the spatial distribution of adaptive diversity in wide-ranging marine species, such as many marine mammals. We assessed genotype-environment associations (GEAs) in 214 common dolphins (Delphinus delphis) along > 3000 km of the southern coast of Australia.
Results
We identified 747 candidate adaptive SNPs out of a filtered panel of 17,327 SNPs, and five putatively locally-adapted populations with high levels of standing genomic variation were disclosed along environmentally heterogeneous coasts. Current velocity, sea surface temperature, salinity, and primary productivity were the key environmental variables associated with genomic variation. These environmental variables are in turn related to three main oceanographic phenomena that are likely affecting the dispersal of common dolphins: (1) regional oceanographic circulation, (2) localised and seasonal upwellings, and (3) seasonal on-shelf circulation in protected coastal habitats. Signals of selection at exonic gene regions suggest that adaptive divergence is related to important metabolic traits.
Conclusion
To the best of our knowledge, this represents the first seascape genomics study for common dolphins (genus Delphinus). Information from the associations between populations and their environment can assist population management in forecasting the adaptive capacity of common dolphins to climate change and other anthropogenic impacts.
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Canales‐Aguirre CB, Larson WA, McKinney GJ, Claure CE, Rocha JD, Ceballos SG, Cádiz MI, Yáñez JM, Gomez‐Uchida D. Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from north Patagonia. Ecol Evol 2022; 12:e9343. [PMID: 36225825 PMCID: PMC9530513 DOI: 10.1002/ece3.9343] [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: 08/19/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor an important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that are currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of E. maclovinus. We used restriction site-associated DNA (RAD) sequencing and outlier tests to obtain neutral and adaptive loci, using FST and GEA approaches. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 (Chepu) to 14,454 (Chaitén) and were influenced more by locality than by salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in E. maclovinus populations. These results suggest a complex interaction between genetic drift, gene flow, and natural selection in this area. Our findings also suggest several evolutionary significant units in this area, and the information should be integrated into the management of this species. We discussed the significance of these results for fishery management and suggest future directions to improve our understanding of how E. maclovinus has adapted to the dynamic waters of Northern Patagonia.
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Affiliation(s)
| | - Wesley A. Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAlaskaUSA
| | | | - C. Eliza Claure
- Centro i~mar, Universidad de Los LagosPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
| | - J. Dellis Rocha
- Centro i~mar, Universidad de Los LagosPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
| | - Santiago G. Ceballos
- Centro Austral de Investigaciones Científicas (CADIC‐CONICET)UshuaiaTierra del FuegoArgentina
- Universidad Nacional de Tierra del Fuego (ICPA‐UNTDF)UshuaiaArgentina
| | - María I. Cádiz
- Núcleo Milenio INVASALConcepciónChile
- Department of BiologyAarhus UniversityAarhus CDenmark
| | - José M. Yáñez
- Núcleo Milenio INVASALConcepciónChile
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileLa PintanaSantiagoChile
| | - Daniel Gomez‐Uchida
- Núcleo Milenio INVASALConcepciónChile
- Genomics in Ecology, Evolution & Conservation Lab (GEECLAB), Departamento de Zoología. Facultad de Ciencias Naturales y OceanográficasUniversidad de ConcepciónConcepciónChile
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Dimond JL, Crim RN, Unsell E, Barry V, Toft JE. Population genomics of the basket cockle Clinocardium nuttallii in the southern Salish Sea: Assessing genetic risks of stock enhancement for a culturally important marine bivalve. Evol Appl 2022; 15:459-470. [PMID: 35386400 PMCID: PMC8965374 DOI: 10.1111/eva.13359] [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: 10/29/2021] [Revised: 01/18/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Coastal Indigenous communities that rely on subsistence harvests are uniquely vulnerable to declines in nearshore species. The basket cockle Clinocardium nuttallii is among the favored foods of Indigenous people along the northwest Pacific coast of North America, yet localized declines in their abundance have led to interest in stock enhancement efforts. We used a population genomics approach to examine potential risks associated with stock enhancement of C. nuttallii in the southern Salish Sea, a large inland estuary that includes Puget Sound. More than 8000 single nucleotide polymorphisms across 349 individuals at 12 locations were assembled de novo using restriction site-associated DNA sequencing. Results indicated that C. nuttallii within the southern Salish Sea were distinct from those along the outer Pacific coast (F ST = 0.021-0.025). Within the southern Salish Sea, C. nuttallii populations appear to be well-connected despite numerous potential impediments to gene flow; Hood Canal, which experiences the lowest flushing rates of all Puget Sound sub-basins, was a minor exception to this strong connectivity. We found evidence of isolation by distance within the southern Salish Sea, but the slope of this relationship was shallow, and F ST values were low (F ST = 0.001-0.004). Meanwhile, outlier analyses did not support the hypothesis that southern Salish Sea sub-populations are locally adapted. Estimates of effective population size had no upper bound, suggesting potentially very high adaptive capacity in C. nuttallii, but also making it difficult to assess potential reductions in effective population size resulting from stock enhancement. We present several strategies to augment cockle populations for subsistence harvest that would limit risk to the genetic diversity of wild cockle populations.
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Affiliation(s)
- James L. Dimond
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
- Shannon Point Marine CenterWestern Washington UniversityAnacortesWashingtonUSA
| | - Ryan N. Crim
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
| | | | - Viviane Barry
- Fisheries DepartmentSuquamish TribeSuquamishWashingtonUSA
| | - Jodie E. Toft
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
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Vera M, Maroso F, Wilmes SB, Hermida M, Blanco A, Fernández C, Groves E, Malham SK, Bouza C, Robins PE, Martínez P. Genomic survey of edible cockle ( Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources. Evol Appl 2022; 15:262-285. [PMID: 35233247 PMCID: PMC8867702 DOI: 10.1111/eva.13340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Department of Life Sciences and BiotechnologiesUniversity of FerraraFerraraItaly
| | - Sophie B. Wilmes
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Emily Groves
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Shelagh K. Malham
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Peter E. Robins
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
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10
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de Miguel M, Rodríguez-Quilón I, Heuertz M, Hurel A, Grivet D, Jaramillo-Correa JP, Vendramin GG, Plomion C, Majada J, Alía R, Eckert AJ, González-Martínez SC. Polygenic adaptation and negative selection across traits, years and environments in a long-lived plant species (Pinus pinaster Ait., Pinaceae). Mol Ecol 2022; 31:2089-2105. [PMID: 35075727 DOI: 10.1111/mec.16367] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
A decade of genetic association studies in multiple organisms suggests that most complex traits are polygenic, i.e., they have a genetic architecture determined by numerous loci each with small effect-size. Thus, determining the degree of polygenicity and its variation across traits, environments and time is crucial to understand the genetic basis of phenotypic variation. We applied multilocus approaches to estimate the degree of polygenicity of fitness-related traits in a long-lived plant (Pinus pinaster Ait., maritime pine) and to analyze this variation across environments and years. We evaluated five categories of fitness-related traits (survival, height, phenology, functional, and biotic-stress response traits) in a clonal common-garden network, planted in contrasted environments (over 12,500 trees). Most of the analyzed traits showed evidence of local adaptation based on Qst -Fst comparisons. We further observed a remarkably stable degree of polygenicity, averaging 6% (range of 0-27%), across traits, environments and years. We detected evidence of negative selection, which could explain, at least partially, the high degree of polygenicity. Because polygenic adaptation can occur rapidly, our results suggest that current predictions on the capacity of natural forest tree populations to adapt to new environments should be revised, especially in the current context of climate change.
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Affiliation(s)
- Marina de Miguel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France.,EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Isabel Rodríguez-Quilón
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | | | - Agathe Hurel
- INRAE, Univ. Bordeaux, BIOGECO, F-33610, Cestas, France
| | - Delphine Grivet
- Department of Forest Ecology and Genetics, Forest Research Centre, INIA, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Juan-Pablo Jaramillo-Correa
- Department of Evolutionary Ecology, Institute of Ecology, Universidad Nacional Autónoma de México, AP 70-275, México City, CDMX 04510, Mexico
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino (FI), Italy
| | | | - Juan Majada
- Sección Forestal, SERIDA, Finca Experimental ''La Mata'', 33820, Grado, Principado de Asturias, Spain
| | - Ricardo Alía
- EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France
| | - Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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11
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Hornick KM, Plough LV. Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number. Evol Appl 2022; 15:40-59. [PMID: 35126647 PMCID: PMC8792482 DOI: 10.1111/eva.13322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 01/20/2023] Open
Abstract
The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters Crassostrea virginica. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large-scale hatchery-based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long-term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine-scale genetic structure and local adaptation in broadcast-spawning marine species and provide novel information for the management of an important fisheries resource.
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Affiliation(s)
- Katherine M. Hornick
- University of Maryland Center for Environmental ScienceHorn Point LaboratoryCambridgeMarylandUSA
| | - Louis V. Plough
- University of Maryland Center for Environmental ScienceHorn Point LaboratoryCambridgeMarylandUSA
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12
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O'Leary SJ, Hollenbeck CM, Vega RR, Portnoy DS. Disentangling complex genomic signals to understand population structure of an exploited, estuarine-dependent flatfish. Ecol Evol 2021; 11:13415-13429. [PMID: 34646479 PMCID: PMC8495835 DOI: 10.1002/ece3.8064] [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: 01/16/2021] [Revised: 07/19/2021] [Accepted: 08/09/2021] [Indexed: 11/17/2022] Open
Abstract
Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP-containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf. The distribution of Tajima's D estimated at a genome-wide scale differed significantly from equilibrium in all estuaries, with more negative values occurring in the Gulf. Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. Overall, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection). This leads to conflicting signals in different parts of the genome and creates patterns of divergence that do not correspond to paradigms of strong local directional selection.
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Affiliation(s)
| | - Christopher M. Hollenbeck
- Marine Genomics LaboratoryDepartment of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTexasUSA
| | - Robert R. Vega
- CCA Marine Development CenterTexas Parks and Wildlife DepartmentCorpus ChristiTexasUSA
| | - David S. Portnoy
- Marine Genomics LaboratoryDepartment of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTexasUSA
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13
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Vanhove M, Pina‐Martins F, Coelho AC, Branquinho C, Costa A, Batista D, Príncipe A, Sousa P, Henriques A, Marques I, Belkadi B, Knowles LL, Paulo OS. Using gradient Forest to predict climate response and adaptation in Cork oak. J Evol Biol 2021; 34:910-923. [DOI: 10.1111/jeb.13765] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Affiliation(s)
- Mathieu Vanhove
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Francisco Pina‐Martins
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Ana Cristina Coelho
- Centro de Electrónica, Optoelectronica e Telecomunicações Universidade do Algarve Faro Portugal
| | - Cristina Branquinho
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária Oeiras Portugal
- CENSE ‐ Center for Environmental and Sustainability Research NOVA University of Lisbon Caparica Portugal
| | - Dora Batista
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | - Adriana Príncipe
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Paulo Sousa
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - André Henriques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
| | - Isabel Marques
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
- Forest Research Centre Instituto Superior de Agronomia Universidade de Lisboa Lisboa Portugal
| | | | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Octávio S. Paulo
- Faculdade de Ciências Centre for Ecology, Evolution and Environmental Changes Universidade de Lisboa Lisboa Portugal
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14
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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15
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Marshall DA, Casas SM, Walton WC, Rikard FS, Palmer TA, Breaux N, La Peyre MK, Beseres Pollack J, Kelly M, La Peyre JF. Divergence in salinity tolerance of northern Gulf of Mexico eastern oysters under field and laboratory exposure. CONSERVATION PHYSIOLOGY 2021; 9:coab065. [PMID: 34447578 PMCID: PMC8384081 DOI: 10.1093/conphys/coab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 05/04/2023]
Abstract
The eastern oyster, Crassostrea virginica, is a foundation species within US Gulf of Mexico (GoM) estuaries that has experienced substantial population declines. As changes from management and climate are expected to continue to impact estuarine salinity, understanding how local oyster populations might respond and identifying populations with adaptations to more extreme changes in salinity could inform resource management, including restoration and aquaculture programs. Wild oysters were collected from four estuarine sites from Texas [Packery Channel (PC): 35.5, annual mean salinity, Aransas Bay (AB): 23.0] and Louisiana [Calcasieu Lake (CL): 16.2, Vermilion Bay (VB): 7.4] and spawned. The progeny were compared in field and laboratory studies under different salinity regimes. For the field study, F1 oysters were deployed at low (6.4) and intermediate (16.5) salinity sites in Alabama. Growth and mortality were measured monthly. Condition index and Perkinsus marinus infection intensity were measured quarterly. For the laboratory studies, mortality was recorded in F1 oysters that were exposed to salinities of 2.0, 4.0, 20.0/22.0, 38.0 and 44.0 with and without acclimation. The results of the field study and laboratory study with acclimation indicated that PC oysters are adapted to high-salinity conditions and do not tolerate very low salinities. The AB stock had the highest plasticity as it performed as well as the PC stock at high salinities and as well as Louisiana stocks at the lowest salinity. Louisiana stocks did not perform as well as the Texas stocks at high salinities. Results from the laboratory studies without salinity acclimation showed that all F1 stocks experiencing rapid mortality at low salinities when 3-month oysters collected at a salinity of 24 were used and at both low and high salinities when 7-month oysters collected at a salinity of 14.5 were used.
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Affiliation(s)
- Danielle A Marshall
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sandra M Casas
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - William C Walton
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - F Scott Rikard
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, USA
| | - Terence A Palmer
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Natasha Breaux
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Megan K La Peyre
- US Geological Survey, Louisiana Fish and Wildlife Cooperative Research Unit, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Jennifer Beseres Pollack
- Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi, TX, 78412, USA
| | - Morgan Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jerome F La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Corresponding author: School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA. Tel: (225) 578-5419.
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16
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Elizabeth Alter S, Tariq L, Creed JK, Megafu E. Evolutionary responses of marine organisms to urbanized seascapes. Evol Appl 2021; 14:210-232. [PMID: 33519966 PMCID: PMC7819572 DOI: 10.1111/eva.13048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022] Open
Abstract
Many of the world's major cities are located in coastal zones, resulting in urban and industrial impacts on adjacent marine ecosystems. These pressures, which include pollutants, sewage, runoff and debris, temperature increases, hardened shorelines/structures, and light and acoustic pollution, have resulted in new evolutionary landscapes for coastal marine organisms. Marine environmental changes influenced by urbanization may create new selective regimes or may influence neutral evolution via impacts on gene flow or partitioning of genetic diversity across seascapes. While some urban selective pressures, such as hardened surfaces, are similar to those experienced by terrestrial species, others, such as oxidative stress, are specific to aquatic environments. Moreover, spatial and temporal scales of evolutionary responses may differ in the ocean due to the spatial extent of selective pressures and greater capacity for dispersal/gene flow. Here, we present a conceptual framework and synthesis of current research on evolutionary responses of marine organisms to urban pressures. We review urban impacts on genetic diversity and gene flow and examine evidence that marine species are adapting, or are predicted to adapt, to urbanization over rapid evolutionary time frames. Our findings indicate that in the majority of studies, urban stressors are correlated with reduced genetic diversity. Genetic structure is often increased in urbanized settings, but artificial structures can also act as stepping stones for some hard-surface specialists, promoting range expansion. Most evidence for rapid adaptation to urban stressors comes from studies of heritable tolerance to pollutants in a relatively small number of species; however, the majority of marine ecotoxicology studies do not test directly for heritability. Finally, we highlight current gaps in our understanding of evolutionary processes in marine urban environments and present a framework for future research to address these gaps.
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Affiliation(s)
- S. Elizabeth Alter
- Department of Biology & ChemistryCalifornia State University, Monterey BayChapman Academic Science CenterSeasideCAUSA
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Laraib Tariq
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
| | - James Keanu Creed
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Emmanuel Megafu
- Department of BiologyYork CollegeCity University of New YorkJamaicaNYUSA
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17
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Vu NTT, Zenger KR, Guppy JL, Sellars MJ, Silva CNS, Kjeldsen SR, Jerry DR. Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis. BMC Genomics 2020; 21:669. [PMID: 32993495 PMCID: PMC7526253 DOI: 10.1186/s12864-020-07084-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 09/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management. RESULTS Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001-0.107; p < 0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations. CONCLUSION This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.
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Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia. .,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Melony J Sellars
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,CSIRO Agriculture & Food, Integrated Sustainable Aquaculture Production Program, Queensland Bioscience Precinct, St Lucia, 4067, Australia.,Present address: Genics Pty Ltd, Level 5, Gehrmann Building. 60 Research Road, St Lucia, QLD, 4067, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
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18
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Nielsen ES, Henriques R, Beger M, Toonen RJ, von der Heyden S. Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species. BMC Evol Biol 2020; 20:121. [PMID: 32938400 PMCID: PMC7493327 DOI: 10.1186/s12862-020-01679-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species' potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). RESULTS Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. CONCLUSION The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change.
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Affiliation(s)
- Erica S Nielsen
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Technical University of Denmark, National Institute of Aquatic Resources, Section for Marine Living Resources, Velsøvej 39, 8600, Silkeborg, Denmark
| | - Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
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19
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Coscia I, Wilmes SB, Ironside JE, Goward-Brown A, O'Dea E, Malham SK, McDevitt AD, Robins PE. Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach. Evol Appl 2020; 13:1854-1867. [PMID: 32908590 PMCID: PMC7463313 DOI: 10.1111/eva.12932] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/21/2020] [Indexed: 12/11/2022] Open
Abstract
Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine-scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April-September), factoring in larval duration and interannual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean F ST = 0.021) within a relatively fine spatial scale in the north-west Atlantic. Environmental association analysis indicates that oceanographic currents and geographic proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperature extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographic scale.
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Affiliation(s)
- Ilaria Coscia
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Sophie B Wilmes
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Joseph E Ironside
- Institute of Biological, Environmental and Rural Sciences Aberystwyth University, Penglais Aberystwyth UK
| | - Alice Goward-Brown
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | | | - Shelagh K Malham
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
| | - Allan D McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford UK
| | - Peter E Robins
- School of Ocean Sciences Marine Centre Wales Bangor University Menai Bridge UK
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20
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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21
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Muir AP, Dubois SF, Ross RE, Firth LB, Knights AM, Lima FP, Seabra R, Corre E, Le Corguillé G, Nunes FLD. Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.). BMC Evol Biol 2020; 20:100. [PMID: 32778052 PMCID: PMC7418442 DOI: 10.1186/s12862-020-01658-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/17/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment association tests were used to attempt to identify loci under selection in relation to local temperature data. RESULTS We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as a distinct population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal. CONCLUSIONS As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.
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Affiliation(s)
- Anna P Muir
- Conservation Biology Research Group, Department of Biological Sciences, University of Chester, Parkgate Road, Chester, CH1 4BJ, UK.
- Laboratoire des Sciences de l'Environnement Marin, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, Université de Brest (UBO), Université Européenne de Bretagne (UEB), Institut Universitaire Européen de la Mer (IUEM), 29280, Plouzané, France.
| | - Stanislas F Dubois
- Ifremer, DYNECO, Laboratory of Coastal Benthic Ecology, F-29280, Plouzané, France
| | - Rebecca E Ross
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
- Institute of Marine Research, 1870 Nordnes, 5817, Bergen, Norway
| | - Louise B Firth
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Antony M Knights
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL4 8AA, UK
| | - Fernando P Lima
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Rui Seabra
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique de Roscoff, 29680, Roscoff, France
| | - Flavia L D Nunes
- Laboratoire des Sciences de l'Environnement Marin, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, Université de Brest (UBO), Université Européenne de Bretagne (UEB), Institut Universitaire Européen de la Mer (IUEM), 29280, Plouzané, France
- Ifremer, DYNECO, Laboratory of Coastal Benthic Ecology, F-29280, Plouzané, France
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22
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Clark MS, Peck LS, Arivalagan J, Backeljau T, Berland S, Cardoso JCR, Caurcel C, Chapelle G, De Noia M, Dupont S, Gharbi K, Hoffman JI, Last KS, Marie A, Melzner F, Michalek K, Morris J, Power DM, Ramesh K, Sanders T, Sillanpää K, Sleight VA, Stewart-Sinclair PJ, Sundell K, Telesca L, Vendrami DLJ, Ventura A, Wilding TA, Yarra T, Harper EM. Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics. Biol Rev Camb Philos Soc 2020; 95:1812-1837. [PMID: 32737956 DOI: 10.1111/brv.12640] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/17/2020] [Accepted: 07/17/2020] [Indexed: 12/20/2022]
Abstract
Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO3 crystals form complex biocomposites with proteins, which although typically less than 5% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO3 precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.
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Affiliation(s)
- Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Lloyd S Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K
| | - Jaison Arivalagan
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France.,Proteomics Center of Excellence, Northwestern University, 710 N Fairbanks Ct, Chicago, IL, U.S.A
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium.,Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, Antwerp, B-2610, Belgium
| | - Sophie Berland
- UMR 7208 CNRS/MNHN/UPMC/IRD Biologie des Organismes Aquatiques et Ecosystèmes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Joao C R Cardoso
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Carlos Caurcel
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Gauthier Chapelle
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Michele De Noia
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany.,Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, U.K
| | - Sam Dupont
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Karim Gharbi
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Kim S Last
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Arul Marie
- UMR 7245 CNRS/MNHN Molécules de Communications et Adaptations des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kati Michalek
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - James Morris
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, Brussels, B-1000, Belgium
| | - Deborah M Power
- Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Kirti Ramesh
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Trystan Sanders
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
| | - Kirsikka Sillanpää
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Victoria A Sleight
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, U.K
| | | | - Kristina Sundell
- Swemarc, Department of Biological and Environmental Science, University of Gothenburg, Box 463, Gothenburg, SE405 30, Sweden
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
| | - David L J Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, Bielefeld, 33615, Germany
| | - Alexander Ventura
- Department of Biological and Environmental Sciences, University of Göteburg, Box 463, Göteburg, SE405 30, Sweden
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, U.K
| | - Tejaswi Yarra
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, U.K.,Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, U.K
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, U.K
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23
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González‐Serna MJ, Cordero PJ, Ortego J. Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust ( Dociostaurus maroccanus). Ecol Evol 2020; 10:3991-4008. [PMID: 32489626 PMCID: PMC7244894 DOI: 10.1002/ece3.6165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.
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Affiliation(s)
- María José González‐Serna
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
- Departamento de Ciencia y Tecnología Agroforestal y GenéticaEscuela Técnica Superior de Ingenieros Agrónomos (ETSIA)Universidad de Castilla‐La Mancha (UCLM)Ciudad RealSpain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana – EBD – (CSIC)SevilleSpain
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24
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Johnson KM, Kelly MW. Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico. Evol Appl 2020; 13:945-959. [PMID: 32431745 PMCID: PMC7232765 DOI: 10.1111/eva.12912] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/23/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of F ST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low F ST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in F ST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean F ST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.
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Affiliation(s)
- Kevin M. Johnson
- Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
| | - Morgan W. Kelly
- Department of Biological SciencesLouisiana State UniversityBaton RougeLAUSA
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25
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Takeuchi T, Masaoka T, Aoki H, Koyanagi R, Fujie M, Satoh N. Divergent northern and southern populations and demographic history of the pearl oyster in the western Pacific revealed with genomic SNPs. Evol Appl 2020; 13:837-853. [PMID: 32211071 PMCID: PMC7086055 DOI: 10.1111/eva.12905] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022] Open
Abstract
In the open ocean without terrain boundaries, marine invertebrates with pelagic larvae can migrate long distances using ocean currents, suggesting reduced genetic diversification. Contrary to this assumption, however, genetic differentiation is often observed in marine invertebrates. In the present study, we sought to explain how population structure is established in the western Pacific Ocean, where the strong Kuroshio Current maintains high levels of gene flow from south to north, presumably promoting genetic homogeneity. We determined the population structure of the pearl oyster, Pinctada fucata, in the Indo-Pacific Ocean using genome-wide genotyping data from multiple sampling localities. Cluster analysis showed that the western Pacific population is distinct from that of the Indian Ocean, and that it is divided into northern (Japanese mainland) and southern (Nansei Islands, China, and Cambodia) populations. Genetic differentiation of P. fucata can be explained by geographic barriers in the Indian Ocean and a local lagoon, and by environmental gradients of sea surface temperature (SST) and oxygen concentration in the western Pacific. A genome scan showed evidence of adaptive evolution in genomic loci, possibly associated with changes in environmental factors, including SST and oxygen concentration. Furthermore, Bayesian simulation demonstrated that the past population expansion and division are congruent with ocean warming after the last glacial period. It is highly likely that the environmental gradient forms a genetic barrier that diversifies P. fucata populations in the western Pacific. This hypothesis helps to explain genetic differentiation and possible speciation of marine invertebrates.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Tetsuji Masaoka
- Aquaculture Technology DivisionNational Research Institute of Aquaculture, Fisheries Research and Education AgencyTamaki‐choJapan
| | - Hideo Aoki
- Mie Prefecture Fisheries Research InstituteShimaJapan
| | - Ryo Koyanagi
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Manabu Fujie
- DNA Sequencing SectionOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
| | - Noriyuki Satoh
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaJapan
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26
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Schwaner C, Barbosa M, Connors P, Park TJ, de Silva D, Griffith A, Gobler CJ, Pales Espinosa E, Allam B. Experimental acidification increases susceptibility of Mercenaria mercenaria to infection by Vibrio species. MARINE ENVIRONMENTAL RESEARCH 2020; 154:104872. [PMID: 32056698 DOI: 10.1016/j.marenvres.2019.104872] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
Ocean acidification alters seawater carbonate chemistry, which can have detrimental impacts for calcifying organisms such as bivalves. This study investigated the physiological cost of resilience to acidification in Mercenaria mercenaria, with a focus on overall immune performance following exposure to Vibrio spp. Larval and juvenile clams reared in seawater with high pCO2 (~1200 ppm) displayed an enhanced susceptibility to bacterial pathogens. Higher susceptibility to infection in clams grown under acidified conditions was derived from a lower immunity to infection more so than an increase in growth of bacteria under high pCO2. A reciprocal transplant of juvenile clams demonstrated the highest mortality amongst animals transplanted from low pCO2/high pH to high pCO2/low pH conditions and then exposed to bacterial pathogens. Collectively, these results suggest that increased pCO2 will result in immunocompromised larvae and juveniles, which could have complex and pernicious effects on hard clam populations.
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Affiliation(s)
- Caroline Schwaner
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
| | - Michelle Barbosa
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
| | - Peter Connors
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
| | - Tae-Jin Park
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
| | - Darren de Silva
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, 11968, USA.
| | - Andrew Griffith
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, 11968, USA.
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, 11968, USA.
| | | | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11790, USA.
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