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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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Popovic I, Bergeron LA, Bozec YM, Waldvogel AM, Howitt SM, Damjanovic K, Patel F, Cabrera MG, Wörheide G, Uthicke S, Riginos C. High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator. PLoS Genet 2024; 20:e1011129. [PMID: 38346089 PMCID: PMC10861045 DOI: 10.1371/journal.pgen.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Lewontin's paradox, the observation that levels of genetic diversity (π) do not scale linearly with census population size (Nc) variation, is an evolutionary conundrum. The most extreme mismatches between π and Nc are found for highly abundant marine invertebrates. Yet, the influences of new mutations on π relative to extrinsic processes such as Nc fluctuations are unknown. Here, we provide the first germline mutation rate (μ) estimate for a marine invertebrate in corallivorous crown-of-thorns sea stars (Acanthaster cf. solaris). We use high-coverage whole-genome sequencing of 14 parent-offspring trios alongside empirical estimates of Nc in Australia's Great Barrier Reef to jointly examine the determinants of π in populations undergoing extreme Nc fluctuations. The A. cf. solaris mean μ was 9.13 x 10-09 mutations per-site per-generation (95% CI: 6.51 x 10-09 to 1.18 x 10-08), exceeding estimates for other invertebrates and showing greater concordance with vertebrate mutation rates. Lower-than-expected Ne (~70,000-180,000) and low Ne/Nc values (0.0047-0.048) indicated weak influences of population outbreaks on long-term π. Our findings are consistent with elevated μ evolving in response to reduced Ne and generation time length, with important implications for explaining high mutational loads and the determinants of genetic diversity in marine invertebrate taxa.
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Affiliation(s)
- Iva Popovic
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | - Lucie A. Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yves-Marie Bozec
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Samantha M. Howitt
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Frances Patel
- Australian Institute of Marine Science, Townsville, Australia
| | | | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | - Sven Uthicke
- Australian Institute of Marine Science, Townsville, Australia
| | - Cynthia Riginos
- School of the Environment, The University of Queensland, St Lucia, Queensland, Australia
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3
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Sutherland BJG, Itoh N, Gilchrist K, Boyle B, Roth M, Green TJ. Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada. G3 (BETHESDA, MD.) 2023; 13:jkad242. [PMID: 37857308 PMCID: PMC10700054 DOI: 10.1093/g3journal/jkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/06/2023] [Accepted: 10/08/2023] [Indexed: 10/21/2023]
Abstract
The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD) sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains, it ranged between 1.35 and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift was observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9 to 26 individuals whereas the wild population was estimated at 25,048-56,291 individuals. Further, a depletion of low-frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.
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Affiliation(s)
- Ben J G Sutherland
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
- Sutherland Bioinformatics, Lantzville, British Columbia V0R 2H0, Canada
| | - Naoki Itoh
- Laboratory of Fish Diseases, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Korrina Gilchrist
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
| | - Brian Boyle
- Plateforme d’Analyses Génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec, Quebec G1V 0A6, Canada
| | - Myron Roth
- BC Ministry of Agriculture and Food, Victoria, British Columbia V8W 9B4, Canada
| | - Timothy J Green
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, British Columbia V9R 5S5, Canada
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4
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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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5
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Bodenstein S, Casas SM, Tiersch TR, Peyre JFL. Energetic budget of diploid and triploid eastern oysters during a summer die-off. FRONTIERS IN MARINE SCIENCE 2023; 10:1194296. [PMID: 38577631 PMCID: PMC10993659 DOI: 10.3389/fmars.2023.1194296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Triploid oysters are widely used in off-bottom aquaculture of eastern oysters, Crassostrea virginica. However, farmers of the Gulf of Mexico (GoM) and Atlantic coast estuaries have observed unresolved, late-spring die-offs of triploid oysters, threatening the sustainability of triploid aquaculture. To investigate this, the physiological processes underlying oyster growth (e.g., feeding, respiration) and mortality of one-year-old diploid and triploid oysters were compared in early summer following an uptick in mortality. It was predicted that higher triploid mortality was the result of energetic imbalances (increased metabolic demands and decreased feeding behavior). Oyster clearance rates, percentage of time valves were open, absorption efficiency, oxygen consumption rates (basal and routine), ammonia excretion rate were measured in the laboratory and scope for growth was calculated. In addition, their condition index, gametogenic stage, Perkinsus marinus infection level, and mortality were measured. Mortality of triploids in the laboratory was greater than for diploids, mirroring mortality observed in a related field study. The physiological parameters measured, however, could not explain triploid mortality. Scope for growth, condition index, and clearance rates of triploids were greater than for diploids, suggesting sufficient energy reserves, while all other measurements where similar between the ploidies. It remains to be determined whether mortality could be caused from disruption of energy homeostasis at the cellular level.
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Affiliation(s)
- Sarah Bodenstein
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Sandra M. Casas
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Terrence R. Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Jerome F. La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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6
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Kuang W, Zinner D, Li Y, Yao X, Roos C, Yu L. Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys ( Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation. Genes (Basel) 2023; 14:genes14050985. [PMID: 37239345 DOI: 10.3390/genes14050985] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/25/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The snub-nosed monkey genus Rhinopithecus (Colobinae) comprises five species (Rhinopithecus roxellana, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus strykeri, and Rhinopithecus avunculus). They are range-restricted species occurring only in small areas in China, Vietnam, and Myanmar. All extant species are listed as endangered or critically endangered by the International Union for Conservation of Nature (IUCN) Red List, all with decreasing populations. With the development of molecular genetics and the improvement and cost reduction in whole-genome sequencing, knowledge about evolutionary processes has improved largely in recent years. Here, we review recent major advances in snub-nosed monkey genetics and genomics and their impact on our understanding of the phylogeny, phylogeography, population genetic structure, landscape genetics, demographic history, and molecular mechanisms of adaptation to folivory and high altitudes in this primate genus. We further discuss future directions in this research field, in particular how genomic information can contribute to the conservation of snub-nosed monkeys.
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Affiliation(s)
- Weimin Kuang
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-University of Göttingen, 37077 Göttingen, Germany
- Leibniz-Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Yuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Xueqin Yao
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
| | - Christian Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650500, China
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7
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Bodenstein S, Callam BR, Walton WC, Rikard FS, Tiersch TR, La Peyre JF. Survival and growth of triploid eastern oysters, Crassostrea virginica, produced from wild diploids collected from low-salinity areas. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2023; 564:739032. [PMID: 36778722 PMCID: PMC9910191 DOI: 10.1016/j.aquaculture.2022.739032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Triploid Eastern oysters have been reported to suffer greater mortalities than diploids when exposed to low-salinity (<5) conditions in the U.S. Gulf of Mexico and Atlantic estuaries. As such, the effect of broodstock parentage was investigated on the low-salinity tolerance of triploid progeny produced by mating diploid females (collected from three Louisiana estuaries differing in salinity regimes) with male tetraploids at two hatcheries. Diploid crosses were also produced using the wild broodstocks to verify expected differences in low-salinity tolerance among diploid progeny and between ploidy levels. All progeny were deployed at low and moderate-salinity (averages of 9.3 and 19.4) field sites to monitor monthly growth and mortality. Sex ratio, gametogenic stage, gonad-to-body ratio, condition index, and Perkinsus marinus infection were also measured periodically at both field sites Although high triploid mortality at the low-salinity site prevented complete analysis, results indicated that diploid parentage had little effect on triploid survival at low salinity. Broodstock parentage affected diploid mortality and growth, although results did not match with predictions made based on historical salinity at broodstock collection sites. Ploidy level had the largest effect on triploid survival and growth followed by the hatchery site where the oysters were produced.
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Affiliation(s)
- Sarah Bodenstein
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70820, United States of America
| | - Brian R. Callam
- Louisiana State University and Louisiana Sea Grant Outreach Program, Baton Rouge, LA 70803, United States of America
| | - William C. Walton
- Department of Fisheries Science, Virginia Institute of Marine Science, Gloucester Point, VA 23062, United States of America
| | - F. Scott Rikard
- Auburn University Shellfish Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Dauphin Island, AL 36528, United States of America
| | - Terrence R. Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA 70820, United States of America
| | - Jerome F. La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, United States of America
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Guo X, Puritz JB, Wang Z, Proestou D, Allen S, Small J, Verbyla K, Zhao H, Haggard J, Chriss N, Zeng D, Lundgren K, Allam B, Bushek D, Gomez-Chiarri M, Hare M, Hollenbeck C, La Peyre J, Liu M, Lotterhos KE, Plough L, Rawson P, Rikard S, Saillant E, Varney R, Wikfors G, Wilbur A. Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:174-191. [PMID: 36622459 DOI: 10.1007/s10126-022-10191-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.
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Affiliation(s)
- Ximing Guo
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| | - Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Zhenwei Wang
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Dina Proestou
- USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA
| | - Standish Allen
- Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA
| | - Jessica Small
- Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA
| | | | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Jaime Haggard
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Noah Chriss
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Dan Zeng
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Kathryn Lundgren
- USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA
| | - David Bushek
- Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher Hollenbeck
- Texas A&M University - Corpus Christi, Texas A&M AgriLife Research, 6300 Ocean Drive Unit 5892, Corpus Christi, TX, 78412, USA
| | - Jerome La Peyre
- School of Animal Sciences, Louisiana State University Agricultural Center, 201 Animal and Food Sciences Laboratory Building, Forestry Lane, Baton Rouge, LA, 70803, USA
| | - Ming Liu
- Patuxent Environmental and Aquatic Research Laboratory, Morgan State University, 10545 Mackall Road, Saint Leonard, MD, 20685, USA
| | - Katie E Lotterhos
- Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA
| | - Louis Plough
- Horn Point Lab, University of Maryland, 5745 Lovers Lane, Cambridge, MD, 21613, USA
| | - Paul Rawson
- School of Marine Sciences, University of Maine, 5751 Murray Hall, , Orono, ME, 04469, USA
| | - Scott Rikard
- School of Fisheries Aquaculture and Aquatic Sciences, Auburn University Shellfish Laboratory, Auburn University, 150 Agassiz St., Dauphin Island, AL, 36528, USA
| | - Eric Saillant
- School of Ocean Science and Engineering, The University of Southern Mississippi, 103 McIlwain Drive, Ocean Springs, MS, 39564, USA
| | - Robin Varney
- Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA
| | - Gary Wikfors
- Milford CT Laboratory, NOAA Fisheries, 212 Rogers Avenue, Milford, CT, 06460, USA
| | - Ami Wilbur
- Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA
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9
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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10
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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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11
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Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture. Animal 2022; 16:100642. [PMID: 36183431 PMCID: PMC9553672 DOI: 10.1016/j.animal.2022.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
The extent of application of genetic technologies to aquaculture production varies widely by species and geography. Achieving a more universal application of seed derived from scientifically based breeding programmes is an important goal in order to meet increasing global demands for seafood production. This article reviews the status of genetic technologies across the world’s top 10 highly produced species. Opportunities and barriers to achieving broad-scale uptake of genetic technologies in global aquaculture are discussed. A future outlook for potential disruptive genetic technologies and how they might affect global aquaculture production is given.
Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.
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12
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Bean TP, Tanguy A, Peñaloza C, Gundappa MK, Boutet I, Houston RD, Macqueen DJ, Boudry P. Two parallel chromosome‐level reference genomes to support restoration and aquaculture of European flat oyster
Ostrea edulis. Evol Appl 2022; 15:1709-1712. [PMID: 36426118 PMCID: PMC9679237 DOI: 10.1111/eva.13465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/29/2022] [Accepted: 07/31/2022] [Indexed: 12/15/2022] Open
Abstract
This volume of Evolutionary Applications sees the publication of two genomes for the European native flat oyster Ostrea edulis, a species of significant evolutionary, ecological and commercial value. Each is a highly contiguous chromosome‐level assembly from individuals of different genetic backgrounds, which have been benchmarked against one another. This situation has resulted from the serendipitous discovery that two independent research groups were both deep into the process of building, annotating and investigating separately produced assemblies. Due to constraints with funder requirements and the need to recognize early career researchers for their work, alongside the technical challenge of integrating assemblies from two very different genomes, there was limited capacity to merge the sequences into one publication at the stage of discovery. This issue is likely to become very common over the next few years until the technologies for working with multiple genomes at once, for example, graph genomes, become commonplace in nonmodel species. Consequently, both of our teams have decided to collaborate rather than compete, recognizing the benefit to copublishing two separate genome resources for the research community, each with distinct scientific investigations, and working collaboratively to benchmark the assemblies.
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Affiliation(s)
- Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus Edinburgh UK
| | - Arnaud Tanguy
- CNRS, UMR 7144, Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus Edinburgh UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus Edinburgh UK
| | - Isabelle Boutet
- CNRS, UMR 7144, Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus Edinburgh UK
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Campus Edinburgh UK
| | - Pierre Boudry
- Département Ressources Biologiques et Environnement Ifremer Plouzané France
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13
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Point pattern analysis as a tool for assessing disease spread and population features in remaining sanctuaries of the critically endangered bivalve Pinna nobilis. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Peñaloza C, Barria A, Papadopoulou A, Hooper C, Preston J, Green M, Helmer L, Kean-Hammerson J, Nascimento-Schulze JC, Minardi D, Gundappa MK, Macqueen DJ, Hamilton J, Houston RD, Bean TP. Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis). Front Genet 2022; 13:926638. [PMID: 35983410 PMCID: PMC9380691 DOI: 10.3389/fgene.2022.926638] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 12/11/2022] Open
Abstract
The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.
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Affiliation(s)
- Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Agustin Barria
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Athina Papadopoulou
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, United Kingdom
| | - Chantelle Hooper
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, United Kingdom
| | - Joanne Preston
- Institute of Marine Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Matthew Green
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, United Kingdom
| | - Luke Helmer
- Institute of Marine Sciences, University of Portsmouth, Portsmouth, United Kingdom
- Blue Marine Foundation, London, United Kingdom
- Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | | | - Jennifer C. Nascimento-Schulze
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, United Kingdom
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Diana Minardi
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, United Kingdom
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ross D. Houston
- Benchmark Genetics, Penicuik, United Kingdom
- *Correspondence: Tim P. Bean, ; Ross D. Houston,
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Tim P. Bean, ; Ross D. Houston,
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15
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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16
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Hedgecock D. No evidence for temporally balanced selection on larval Pacific oysters Crassostrea gigas: a comment on Durland et al. (2021). Proc Biol Sci 2022; 289:20212579. [PMID: 35642361 PMCID: PMC9156931 DOI: 10.1098/rspb.2021.2579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
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17
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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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18
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Wang F, Tekle YI. Variation of natural selection in the Amoebozoa reveals heterogeneity across the phylogeny and adaptive evolution in diverse lineages. Front Ecol Evol 2022; 10:851816. [PMID: 36874909 PMCID: PMC9980437 DOI: 10.3389/fevo.2022.851816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial role in understanding the evolution of the supergroup. In this study, we searched for traces of natural selection based on a set of highly conserved protein-coding genes in a phylogenetic framework from a broad sampling of amoebozoans. Using these genes, we estimated substitution rates and inferred patterns of selective pressure in lineages and sites with various models. We also examined the effect of selective pressure on codon usage bias and potential correlations with observed biological traits and habitat. Results showed large heterogeneity of selection across lineages of Amoebozoa, indicating potential species-specific optimization of adaptation to their diverse ecological environment. Overall, lineages in Tubulinea had undergone stronger purifying selection with higher average substitution rates compared to Discosea and Evosea. Evidence of adaptive evolution was observed in some representative lineages and in a gene (Rpl7a) within Evosea, suggesting potential innovation and beneficial mutations in these lineages. Our results revealed that members of the fast-evolving lineages, Entamoeba and Cutosea, all underwent strong purifying selection but had distinct patterns of codon usage bias. For the first time, this study revealed an overall pattern of natural selection across the phylogeny of Amoebozoa and provided significant implications on their distinctive evolutionary processes.
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Affiliation(s)
- Fang Wang
- Department of Biology, Spelman College, Atlanta, GA, United States
| | - Yonas I Tekle
- Department of Biology, Spelman College, Atlanta, GA, United States
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19
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Griffiths JS, Johnson KM, Kelly MW. Evolutionary Change in the Eastern Oyster, Crassostrea Virginica, Following Low Salinity Exposure. Integr Comp Biol 2021; 61:1730-1740. [PMID: 34448845 DOI: 10.1093/icb/icab185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The presence of standing genetic variation will play a role in determining a population's capacity to adapt to environmentally relevant stressors. In the Gulf of Mexico, extreme climatic events and anthropogenic changes to local hydrology will expose productive oyster breeding grounds to stressful low salinity conditions. We identified genetic variation for performance under low salinity (due to the combined effects of low salinity and genetic load) using a single-generation selection experiment on larvae from two populations of the eastern oyster, Crassostrea virginica. We used pool-sequencing to test for allele frequency differences at 152 salinity-associated genes for larval families pre- and post-low salinity exposure. Our results have implications for how evolutionary change occurs during early life history stages at environmentally relevant salinities. Consistent with observations of high genetic load observed in oysters, we demonstrate evidence for purging of deleterious alleles at the larval stage in C. virginica. In addition, we observe increases in allele frequencies at multiple loci, suggesting that natural selection for low salinity performance at the larval stage can act as a filter for genotypes found in adult populations.
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Affiliation(s)
- Joanna S Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA
| | - Kevin M Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.,California Sea Grant, University of California San Diego, La Jolla, CA 92093, USA
| | - Morgan W Kelly
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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20
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Yin X, Hedgecock D. Overt and concealed genetic loads revealed by QTL mapping of genotype-dependent viability in the Pacific oyster Crassostrea gigas. Genetics 2021; 219:6382310. [PMID: 34739049 DOI: 10.1093/genetics/iyab165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/19/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F2 oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster's extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance.
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Affiliation(s)
- Xiaoshen Yin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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21
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Vendrami DLJ, Peck LS, Clark MS, Eldon B, Meredith M, Hoffman JI. Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner. SCIENCE ADVANCES 2021; 7:eabj4713. [PMID: 34516767 PMCID: PMC8442859 DOI: 10.1126/sciadv.abj4713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
A long-standing paradox of marine populations is chaotic genetic patchiness (CGP), temporally unstable patterns of genetic differentiation that occur below the geographic scale of effective dispersal. Several mechanisms are hypothesized to explain CGP including natural selection, spatiotemporal fluctuations in larval source populations, self-recruitment, and sweepstake reproduction. Discriminating among them is extremely difficult but is fundamental to understanding how marine organisms reproduce and disperse. Here, we report a notable example of CGP in the Antarctic limpet, an unusually tractable system where multiple confounding explanations can be discounted. Using population genomics, temporally replicated sampling, surface drifters, and forward genetic simulations, we show that CGP likely arises from an extreme sweepstake event together with collective larval dispersal, while selection appears to be unimportant. Our results illustrate the importance of neutral demographic forces in natural populations and have important implications for understanding the recruitment dynamics, population connectivity, local adaptation, and resilience of marine populations.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501 Bielefeld, Germany
| | - Lloyd S. Peck
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Melody S. Clark
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Research, Museum für Naturkunde, 10115 Berlin, Germany
| | - Michael Meredith
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Postfach 100131, 33501 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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22
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Durland E, De Wit P, Langdon C. Temporally balanced selection during development of larval Pacific oysters ( Crassostrea gigas) inherently preserves genetic diversity within offspring. Proc Biol Sci 2021; 288:20203223. [PMID: 34465244 PMCID: PMC8437028 DOI: 10.1098/rspb.2020.3223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favour of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity, while also inherently sheltering genetic load within oyster populations.
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Affiliation(s)
- Evan Durland
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Chris Langdon
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment Station, Hatfield Marine Science Center, Oregon State University, Newport, OR 97365, USA
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23
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Durland E, De Wit P, Meyer E, Langdon C. Larval development in the Pacific oyster and the impacts of ocean acidification: Differential genetic effects in wild and domesticated stocks. Evol Appl 2021; 14:2258-2272. [PMID: 34603497 PMCID: PMC8477599 DOI: 10.1111/eva.13289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The adaptive capacity of marine calcifiers to ocean acidification (OA) is a topic of great interest to evolutionary biologists and ecologists. Previous studies have provided evidence to suggest that larval resilience to high pCO2 seawater for these species is a trait with a genetic basis and variability in natural populations. To date, however, it remains unclear how the selective effects of OA occur within the context of complex genetic interactions underpinning larval development in many of the most vulnerable taxa. Here we evaluated phenotypic and genetic changes during larval development of Pacific oysters (Crassostrea gigas) reared in ambient (~400 µatm) and high (~1600 µatm) pCO2 conditions, both in domesticated and naturalized "wild" oysters from the Pacific Northwest, USA. Using pooled DNA samples, we determined changes in allele frequencies across larval development, from early "D-stage" larvae to metamorphosed juveniles (spat), in both groups and environments. Domesticated larvae had ~26% fewer loci with changing allele frequencies across developmental stages and <50% as many loci affected by acidified culture conditions, compared to larvae from wild broodstock. Functional enrichment analyses of genetic markers with significant changes in allele frequency revealed that the structure and function of cellular membranes were disproportionately affected by high pCO2 conditions in both groups. These results indicate the potential for a rapid adaptive response of oyster populations to OA conditions; however, underlying genetic changes associated with larval development differ between these wild and domesticated oyster stocks and influence their adaptive responses to OA conditions.
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Affiliation(s)
- Evan Durland
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment StationHatfield Marine Science CenterOregon State UniversityNewportORUSA
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Pierre De Wit
- Department of Marine SciencesTjärnö Marine LaboratoryUniversity of GothenburgStrömstadSweden
| | - Eli Meyer
- Department of Integrative BiologyOregon State UniversityCorvallisORUSA
| | - Chris Langdon
- Department of Fisheries and Wildlife and Coastal Oregon Marine Experiment StationHatfield Marine Science CenterOregon State UniversityNewportORUSA
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Regan T, Stevens L, Peñaloza C, Houston RD, Robledo D, Bean TP. Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution. Genome Biol Evol 2021; 13:6337976. [PMID: 34343278 PMCID: PMC8382680 DOI: 10.1093/gbe/evab177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bivalve molluscs comprise 20,000 species occupying a wide diversity of marine habitats. As filter feeders and detritivores they act as ecosystem engineers clarifying water, creating reefs, and protecting coastlines. The global decline of natural oyster reefs has led to increased restoration efforts in recent years. Bivalves also play an important role in global food security contributing to >20% of worldwide aquaculture production. Despite this importance, relatively little is known about bivalve evolutionary adaptation strategies. Difficulties previously associated with highly heterozygous and repetitive regions of bivalve genomes have been overcome by long-read sequencing, enabling the generation of accurate bivalve assemblies. With these resources we have analyzed the genomes of 32 species representing each molluscan class, including 15 bivalve species, to identify gene families that have undergone expansion during bivalve evolution. Gene family expansions across bivalve genomes occur at the point of evolutionary pressures. We uncovered two key factors that shape bivalve evolutionary history: expansion of bivalvia into environmental niches with high stress followed by later exposure to specific pathogenic pressures. The conserved expansion of protein recycling gene families we found across bivalvia is mirrored by adaptations to a sedentary lifestyle seen in plants. These results reflect the ability of bivalves to tolerate high levels of environmental stress and constant exposure to pathogens as filter feeders. The increasing availability of accurate genome assemblies will provide greater resolution to these analyses allowing further points of evolutionary pressure to become clear in other understudied taxa and potentially different populations of a single species.
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Affiliation(s)
- Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Lewis Stevens
- Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
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25
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Francisco SM, Castilho R, Lima CS, Almada F, Rodrigues F, Šanda R, Vukić J, Pappalardo AM, Ferrito V, Robalo JI. Genetic hypervariability of a Northeastern Atlantic venomous rockfish. PeerJ 2021; 9:e11730. [PMID: 34306828 PMCID: PMC8280884 DOI: 10.7717/peerj.11730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Understanding the interplay between climate and current and historical factors shaping genetic diversity is pivotal to infer changes in marine species range and communities' composition. A phylogeographical break between the Atlantic and the Mediterranean has been documented for several marine organisms, translating into limited dispersal between the two basins. METHODS In this study, we screened the intraspecific diversity of 150 individuals of the Madeira rockfish (Scorpaena maderensis) across its distributional range (seven sampling locations in the Atlantic and Mediterranean basins) using the mitochondrial control region and the nuclear S7 first intron. RESULTS The present work is the most comprehensive study done for this species, yielding no genetic structure across sampled locations and no detectable Atlantic-Mediterranean break in connectivity. Our results reveal deep and hyper-diverse bush-like genealogies with large numbers of singletons and very few shared haplotypes. The genetic hyper-diversity found for the Madeira rockfish is relatively uncommon in rocky coastal species, whose dispersal capability is limited by local oceanographic patterns. The effect of climate warming on the distribution of the species is discussed.
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Affiliation(s)
- Sara M. Francisco
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Rita Castilho
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Cristina S. Lima
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Frederico Almada
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Francisca Rodrigues
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
| | - Radek Šanda
- Department of Zoology, National Museum, Prague, Czeck Republic
| | - Jasna Vukić
- Faculty of Science, Department of Ecology, Charles University, Prague, Czech Republic
| | - Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Section of Animal Biology Biology ‘‘Marcello La Greca’’, University of Catania, Catania, Italy
| | - Joana I. Robalo
- MARE—Marine and Environmental Sciences Centre, ISPA Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, Lisbon, Portugal
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26
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Alm Rosenblad M, Abramova A, Lind U, Ólason P, Giacomello S, Nystedt B, Blomberg A. Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:402-416. [PMID: 33931810 PMCID: PMC8270832 DOI: 10.1007/s10126-021-10033-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/05/2021] [Indexed: 05/11/2023]
Abstract
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
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Affiliation(s)
- Magnus Alm Rosenblad
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Anna Abramova
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Ulrika Lind
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Páll Ólason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Anders Blomberg
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden.
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27
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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28
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Mortz M, Levivier A, Lartillot N, Dufresne F, Blier PU. Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates. Front Mol Biosci 2021; 8:626042. [PMID: 33791336 PMCID: PMC8005583 DOI: 10.3389/fmolb.2021.626042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023] Open
Abstract
Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.
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Affiliation(s)
- Mathieu Mortz
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Aurore Levivier
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Nicolas Lartillot
- Laboratoire De Biométrie et Biologie Evolutive, UMR CNRS, Université Lyon 1, Villeurbanne, France
| | - France Dufresne
- Laboratoire D'écologie Moléculaire, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada.,Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Pierre U Blier
- Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
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29
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O’Hare JA, Momigliano P, Raftos DA, Stow AJ. Genetic structure and effective population size of Sydney rock oysters in eastern Australia. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01343-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Carducci F, Biscotti MA, Trucchi E, Giuliani ME, Gorbi S, Coluccelli A, Barucca M, Canapa A. Omics approaches for conservation biology research on the bivalve Chamelea gallina. Sci Rep 2020; 10:19177. [PMID: 33154500 PMCID: PMC7645701 DOI: 10.1038/s41598-020-75984-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/30/2020] [Indexed: 12/27/2022] Open
Abstract
The striped venus (Chamelea gallina) is an important economic resource in the Mediterranean Basin; this species has exhibited a strong quantitative decline in the Adriatic Sea. The aim of this work was to provide a comprehensive view of the biological status of C. gallina to elucidate the bioecological characteristics and genetic diversity of wild populations. To the best of our knowledge, this investigation is the first to perform a multidisciplinary study on C. gallina based on two omics approaches integrated with histological, ecotoxicological, and chemical analyses and with the assessment of environmental parameters. The results obtained through RNA sequencing indicated that the striped venus has a notable ability to adapt to different environmental conditions. Moreover, the stock reduction exhibited by this species in the last 2 decades seems not to have negatively affected its genetic diversity. Indeed, the high level of genetic diversity that emerged from our ddRAD dataset analyses is ascribable to the high larval dispersal rate, which might have played a “compensatory role” on local fluctuations, conferring to this species a good adaptive potential to face the environmental perturbations. These findings may facilitate the efforts of conservation biologists to adopt ad hoc management plans for this fishery resource.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Emiliano Trucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Elisa Giuliani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Stefania Gorbi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Coluccelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy.
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31
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McFarland K, Plough LV, Nguyen M, Hare MP. Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae. PLoS One 2020; 15:e0230222. [PMID: 32603332 PMCID: PMC7326227 DOI: 10.1371/journal.pone.0230222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/03/2020] [Indexed: 11/18/2022] Open
Abstract
Conservation efforts are increasingly being challenged by a rapidly changing environment, and for some aquatic species the use of captive rearing or selective breeding is an attractive option. However, captivity itself can impose unintended artificial selection known as domestication selection (adaptation to culture conditions) and is relatively understudied for most marine species. To test for domestication selection in marine bivalves, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection. Using larvae produced from a wild population of Crassostrea virginica and a selectively bred, disease-resistant line we measured growth and survival during starvation versus standard algal diet conditions. Larvae from both lineages showed a remarkable resilience to food limitation, possibly mediated by an ability to utilize dissolved organic matter for somatic maintenance. Water chemistry analysis showed dissolved organic carbon in filtered tank water to be at concentrations similar to natural river water. We observed that survival in larvae produced from the aquaculture line was significantly lower compared to larvae produced from wild broodstock (8 ± 3% and 21 ± 2%, respectively) near the end of a 10-day period with no food (phytoplankton). All larval cohorts had arrested growth and depressed respiration during the starvation period and took at least two days to recover once food was reintroduced before resuming growth. Respiration rate recovered rapidly and final shell length was similar between the two treatments Phenotypic differences between the wild and aquaculture lines suggest potential differences in the capacity to sustain extended food limitation, but this work requires replication with multiple selection lines and wild populations to make more general inferences about domestication selection. With this contribution we explore the potential for domestication selection in bivalves, discuss the physiological and fitness implications of reduced starvation tolerance, and aim to inspire further research on the topic.
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Affiliation(s)
- Katherine McFarland
- Department of Natural Resources, Cornell University, Ithaca, New York, United States of America
- Center for Environmental Science University of Maryland, Cambridge, Maryland, United States of America
- NOAA Fisheries NEFSC, Milford Laboratory, Milford, CT, United States of America
- * E-mail:
| | - Louis V. Plough
- Center for Environmental Science University of Maryland, Cambridge, Maryland, United States of America
| | - Michelle Nguyen
- Center for Environmental Science University of Maryland, Cambridge, Maryland, United States of America
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Matthew P. Hare
- Department of Natural Resources, Cornell University, Ithaca, New York, United States of America
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32
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Sutherland BJG, Rycroft C, Ferchaud AL, Saunders R, Li L, Liu S, Chan AM, Otto SP, Suttle CA, Miller KM. Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere. Evol Appl 2020; 13:1380-1399. [PMID: 32684965 PMCID: PMC7359842 DOI: 10.1111/eva.12965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 01/09/2023] Open
Abstract
Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here, we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean F ST = 0.0019) and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada F ST = 0.0024; Japan-Canada F ST = 0.0060). Chinese populations were more differentiated (China-Japan F ST = 0.0241). Hatchery-propagated populations had higher interindividual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate were lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting nonlocal origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depend on whether naturalized populations are valued as a locally adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.
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Affiliation(s)
- Ben J G Sutherland
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo BC Canada.,Department of Earth, Ocean and Atmospheric Sciences University of British Columbia Vancouver BC Canada
| | - Claire Rycroft
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo BC Canada.,Department of Earth, Ocean and Atmospheric Sciences University of British Columbia Vancouver BC Canada
| | | | | | - Li Li
- Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Sheng Liu
- Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences University of British Columbia Vancouver BC Canada
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences University of British Columbia Vancouver BC Canada.,Department of Microbiology and Immunology and the Institute for the Oceans and Fisheries University of British Columbia Vancouver BC Canada.,Department of Botany University of British Columbia Vancouver BC Canada
| | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada Nanaimo BC Canada
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33
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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34
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Fishman L, McIntosh M. Standard Deviations: The Biological Bases of Transmission Ratio Distortion. Annu Rev Genet 2019; 53:347-372. [DOI: 10.1146/annurev-genet-112618-043905] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.
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Affiliation(s)
- Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Mariah McIntosh
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
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35
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Hornick KM, Plough LV. Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs. Heredity (Edinb) 2019; 123:92-105. [PMID: 30833745 PMCID: PMC6781163 DOI: 10.1038/s41437-019-0202-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/18/2019] [Accepted: 02/11/2019] [Indexed: 01/25/2023] Open
Abstract
The release of hatchery-propagated fish and shellfish is occurring on a global scale, but the genetic impacts of these practices are often not fully understood and rarely monitored. Slow recovery of depleted eastern oyster populations in the Chesapeake Bay, USA has prompted a hatchery-based restoration program focused in the Choptank River, Maryland consisting of the mass release of hatchery-produced juveniles from local, wild broodstock. To evaluate potential genetic effects of this program, we (1) examined changes in genetic diversity (allelic richness, heterozygosity) and the effective number of breeders (Nb) over the hatchery production cycle with microsatellite-based parentage of natural, mass- and controlled-spawned cohorts, and (2) compared genetic diversity and effective population size (Ne) of a restored reef to wild source populations. Mass-spawned cohorts showed high variance in reproductive contribution, particularly among males, leading to a 45% average reduction in Nb from spawning adult numbers and higher relatedness-lower magnitude reductions in heterozygosity and significant reductions in allelic richness were also observed. While controlled-spawns (single-male fertilizations of pooled eggs) reduced male variance, overall reproductive variance (Vk) remained high. Finally, oysters sampled from a restored reef displayed comparable Ne, genetic diversity, and relatedness to samples from wild populations, with no significant genetic differentiation among them. Overall, the hatchery-based results and initial field-based population genetic analyses suggest that despite reductions in diversity from parents to offspring owing to high Vk, enhancement with rotated, wild broodstock appears to have maintained genetic diversity in a restored reef population compared to proximal wild populations.
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Affiliation(s)
- Katherine M Hornick
- University of Maryland Center for Environmental Science, Horn Point Laboratory, 2020 Horns Pt. Rd., Cambridge, MD, 21613, USA.
| | - Louis V Plough
- University of Maryland Center for Environmental Science, Horn Point Laboratory, 2020 Horns Pt. Rd., Cambridge, MD, 21613, USA
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36
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Bernatchez S, Xuereb A, Laporte M, Benestan L, Steeves R, Laflamme M, Bernatchez L, Mallet MA. Seascape genomics of eastern oyster ( Crassostrea virginica) along the Atlantic coast of Canada. Evol Appl 2019; 12:587-609. [PMID: 30828376 PMCID: PMC6383708 DOI: 10.1111/eva.12741] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean F ST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype-environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
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Affiliation(s)
- Simon Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
- L’Étang Ruisseau Bar Ltd.ShippaganNew BrunswickCanada
| | - Amanda Xuereb
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Royce Steeves
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Mark Laflamme
- Fisheries and Oceans CanadaMonctonNew BrunswickCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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37
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Godwin JL, Spurgin LG, Michalczyk Ł, Martin OY, Lumley AJ, Chapman T, Gage MJG. Lineages evolved under stronger sexual selection show superior ability to invade conspecific competitor populations. Evol Lett 2018; 2:511-523. [PMID: 30283698 PMCID: PMC6145403 DOI: 10.1002/evl3.80] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022] Open
Abstract
Despite limitations on offspring production, almost all multicellular species use sex to reproduce. Sex gives rise to sexual selection, a widespread force operating through competition and choice within reproduction, however, it remains unclear whether sexual selection is beneficial for total lineage fitness, or if it acts as a constraint. Sexual selection could be a positive force because of selection on improved individual condition and purging of mutation load, summing into lineages with superior fitness. On the other hand, sexual selection could negate potential net fitness through the actions of sexual conflict, or because of tensions between investment in sexually selected and naturally selected traits. Here, we explore these ideas using a multigenerational invasion challenge to measure consequences of sexual selection for the overall net fitness of a lineage. After applying experimental evolution under strong versus weak regimes of sexual selection for 77 generations with the flour beetle Tribolium castaneum, we measured the overall ability of introductions from either regime to invade into conspecific competitor populations across eight generations. Results showed that populations from stronger sexual selection backgrounds had superior net fitness, invading more rapidly and completely than counterparts from weak sexual selection backgrounds. Despite comprising only 10% of each population at the start of the invasion experiment, colonizations from strong sexual selection histories eventually achieved near-total introgression, almost completely eliminating the original competitor genotype. Population genetic simulations using the design and parameters of our experiment indicate that this invasion superiority could be explained if strong sexual selection had improved both juvenile and adult fitness, in both sexes. Using a combination of empirical and modeling approaches, our findings therefore reveal positive and wide-reaching impacts of sexual selection for net population fitness when facing the broad challenge of invading competitor populations across multiple generations.
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Affiliation(s)
- Joanne L. Godwin
- School of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUK
| | - Lewis G. Spurgin
- School of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUK
| | - Łukasz Michalczyk
- Department of EntomologyInstitute of ZoologyJagiellonian University30–387KrakówPoland
| | - Oliver Y. Martin
- ETH ZurichInstitute of Integrative BiologyD‐USYS8092ZürichSwitzerland
| | - Alyson J. Lumley
- School of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUK
| | - Tracey Chapman
- School of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUK
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38
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Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers. PLoS One 2018; 13:e0203866. [PMID: 30208106 PMCID: PMC6135516 DOI: 10.1371/journal.pone.0203866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/29/2018] [Indexed: 11/29/2022] Open
Abstract
The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.
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39
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Gagnaire PA, Lamy JB, Cornette F, Heurtebise S, Dégremont L, Flahauw E, Boudry P, Bierne N, Lapègue S. Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata. Genome Biol Evol 2018; 10:2518-2534. [PMID: 30184067 PMCID: PMC6161763 DOI: 10.1093/gbe/evy194] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2018] [Indexed: 01/01/2023] Open
Abstract
The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and Crassostrea angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and the high degree of morphologic similarity. In particular, whether the presence of ecological and/or intrinsic isolating mechanisms contributes to species divergence is unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation is maintained under new environmental and demographic conditions. We generated a pseudochromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.
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Affiliation(s)
| | - Jean-Baptiste Lamy
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Florence Cornette
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Serge Heurtebise
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Lionel Dégremont
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Emilie Flahauw
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
| | - Pierre Boudry
- Ifremer, UMR LEMAR, Laboratoire des Sciences de l’Environnement Marin (UBO, CNRS, IRD, Ifremer), Plouzané, France
| | - Nicolas Bierne
- Institut des Sciences de l’Evolution, ISEM-CNRS, UMR5554, Montpellier, France
| | - Sylvie Lapègue
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, La Tremblade, France
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40
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Hollenbeck CM, Johnston IA. Genomic Tools and Selective Breeding in Molluscs. Front Genet 2018; 9:253. [PMID: 30073016 PMCID: PMC6058216 DOI: 10.3389/fgene.2018.00253] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.
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Affiliation(s)
- Christopher M Hollenbeck
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Ian A Johnston
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom.,Xelect Ltd, St Andrews, United Kingdom
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41
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Spatio-temporal patterns of genetic variation in Arbacia lixula, a thermophilous sea urchin in expansion in the Mediterranean. Heredity (Edinb) 2018; 122:244-259. [PMID: 29904170 DOI: 10.1038/s41437-018-0098-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/06/2023] Open
Abstract
The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally. The main break corresponded to the separation of western Atlantic populations from those in eastern Atlantic and the Mediterranean Sea. A less marked, but significant differentiation was also found between Macaronesia (eastern Atlantic) and the Mediterranean. In the latter area, a signal of differentiation between the transitional area (Alboran Sea) and the rest of the Mediterranean was detected. However, no genetic structure is found within the Mediterranean (excluding Alboran) across the Siculo-Tunisian Strait, resulting from either enough gene flow to homogenize distance areas or/and a recent evolutionary history marked by demographic expansion in this basin. Genetic temporal variation at the Alboran Sea is as important as spatial variation, suggesting that temporal changes in hydrological features can affect the genetic composition of the populations. A picture of genetic homogeneity in the Mediterranean emerges, implying that the potential expansion of this keystone species will not be limited by intraspecific genetic features and/or potential impact of postulated barriers to gene flow in the region.
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42
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Riquet F, Comtet T, Broquet T, Viard F. Unexpected collective larval dispersal but little support for sweepstakes reproductive success in the highly dispersive brooding molluscCrepidula fornicata. Mol Ecol 2017; 26:5467-5483. [DOI: 10.1111/mec.14328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/27/2017] [Accepted: 08/07/2017] [Indexed: 01/16/2023]
Affiliation(s)
- Florentine Riquet
- UPMC Univ Paris 06; UMR 7144; Team Diversity and Connectivity in Coastal Marine Landscapes; Station Biologique de Roscoff; Roscoff France
- CNRS; UMR 7144; Lab. Adaptation and Diversity in the Marine Environment; Station Biologique de Roscoff; Roscoff France
| | - Thierry Comtet
- UPMC Univ Paris 06; UMR 7144; Team Diversity and Connectivity in Coastal Marine Landscapes; Station Biologique de Roscoff; Roscoff France
- CNRS; UMR 7144; Lab. Adaptation and Diversity in the Marine Environment; Station Biologique de Roscoff; Roscoff France
| | - Thomas Broquet
- UPMC Univ Paris 06; UMR 7144; Team Diversity and Connectivity in Coastal Marine Landscapes; Station Biologique de Roscoff; Roscoff France
- CNRS; UMR 7144; Lab. Adaptation and Diversity in the Marine Environment; Station Biologique de Roscoff; Roscoff France
| | - Frédérique Viard
- UPMC Univ Paris 06; UMR 7144; Team Diversity and Connectivity in Coastal Marine Landscapes; Station Biologique de Roscoff; Roscoff France
- CNRS; UMR 7144; Lab. Adaptation and Diversity in the Marine Environment; Station Biologique de Roscoff; Roscoff France
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43
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Guinand B, Vandeputte M, Dupont-Nivet M, Vergnet A, Haffray P, Chavanne H, Chatain B. Metapopulation patterns of additive and nonadditive genetic variance in the sea bass ( Dicentrarchus labrax). Ecol Evol 2017; 7:2777-2790. [PMID: 28428868 PMCID: PMC5395432 DOI: 10.1002/ece3.2832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/19/2016] [Accepted: 01/28/2017] [Indexed: 01/30/2023] Open
Abstract
Describing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.
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Affiliation(s)
- Bruno Guinand
- Département Biologie-Ecologie Université de Montpellier Montpellier France.,UMR CNRS IRD EPHE UM Institut des Sciences de l'Evolution de Montpellier Montpellier France
| | - Marc Vandeputte
- INRA UMR 1313 GABI Domaine de Vilvert Jouy-en-Josas France.,Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
| | | | - Alain Vergnet
- Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
| | | | - Hervé Chavanne
- Istituto Sperimentale Lazzaro Spallanzani Rivolta d'Adda Italy
| | - Béatrice Chatain
- Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
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44
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Bierne N, Bonhomme F, Arnaud-Haond S. Dedicated population genomics for the silent world: the specific questions of marine population genetics. Curr Zool 2016; 62:545-550. [PMID: 29491944 PMCID: PMC5804263 DOI: 10.1093/cz/zow107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nicolas Bierne
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - François Bonhomme
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier, Montpellier, France
- Ifremer – MARine Biodiversity, Exploitation and Conservation, UMR 9190 IRD –
IFREMER – UM – CNRS, Sète, France
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