1
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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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Tepolt CK, Grosholz ED, de Rivera CE, Ruiz GM. Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity. Mol Ecol 2021; 31:55-69. [PMID: 34431151 DOI: 10.1111/mec.16143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/24/2021] [Accepted: 08/13/2021] [Indexed: 12/30/2022]
Abstract
Adaptation across environmental gradients has been demonstrated in numerous systems with extensive dispersal, despite high gene flow and consequently low genetic structure. The speed and mechanisms by which such adaptation occurs remain poorly resolved, but are critical to understanding species spread and persistence in a changing world. Here, we investigate these mechanisms in the European green crab Carcinus maenas, a globally distributed invader. We focus on a northwestern Pacific population that spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1500 km, we examine genetic structure using 9376 single nucleotide polymorphisms (SNPs). We find high connectivity among five locations, with significant structure between these locations and an enclosed lagoon with limited connectivity to the coast. Among the five highly connected locations, the only structure observed was a cline driven by a handful of SNPs strongly associated with latitude and winter temperature. These SNPs are almost exclusively found in a large cluster of genes in strong linkage disequilibrium that was previously identified as a candidate for cold tolerance adaptation in this species. This region may represent a balanced polymorphism that evolved to promote rapid adaptation in variable environments despite high gene flow, and which now contributes to successful invasion and spread in a novel environment. This research suggests an answer to the paradox of genetically depauperate yet successful invaders: populations may be able to adapt via a few variants of large effect despite low overall diversity.
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Affiliation(s)
- Carolyn K Tepolt
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Edwin D Grosholz
- Department of Environmental Science and Policy, University of California, Davis, California, USA
| | - Catherine E de Rivera
- Department of Environmental Science and Management, Portland State University, Portland, Oregon, USA
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Smithsonian Institution, Edgewater, Maryland, USA
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3
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Blum MJ, Saunders CJ, McLachlan JS, Summers J, Craft C, Herrick JD. A century-long record of plant evolution reconstructed from a coastal marsh seed bank. Evol Lett 2021; 5:422-431. [PMID: 34367666 PMCID: PMC8327947 DOI: 10.1002/evl3.242] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 04/30/2021] [Accepted: 05/20/2021] [Indexed: 11/12/2022] Open
Abstract
Evidence is mounting that climate-driven shifts in environmental conditions can elicit organismal evolution, yet there are sparingly few long-term records that document the tempo and progression of responses, particularly for plants capable of transforming ecosystems. In this study, we "resurrected" cohorts of a foundational coastal marsh sedge (Schoenoplectus americanus) from a time-stratified seed bank to reconstruct a century-long record of heritable variation in response to salinity exposure. Common-garden experiments revealed that S. americanus exhibits heritable variation in phenotypic traits and biomass-based measures of salinity tolerance. We found that responses to salinity exposure differed among the revived cohorts, with plants from the early 20th century exhibiting greater salinity tolerance than those from the mid to late 20th century. Fluctuations in salinity tolerance could reflect stochastic variation but a congruent record of genotypic variation points to the alternative possibility that the loss and gain in functionality are driven by selection, with comparisons to historical rainfall and paleosalinity records suggesting that selective pressures vary according to shifting estuarine conditions. Because salinity tolerance in S. americanus is tightly coupled to primary productivity and other vital ecosystem attributes, these findings indicate that organismal evolution merits further consideration as a factor shaping coastal marsh responses to climate change.
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Affiliation(s)
- Michael J. Blum
- Department of Ecology & Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee37996
| | - Colin J. Saunders
- Southeast Environmental Research CenterFlorida International UniversityMiamiFlorida33199
| | - Jason S. McLachlan
- Department of Biological SciencesUniversity of Notre DameSouth BendIndiana46556
| | - Jennifer Summers
- Department of Ecology & Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee37996
| | - Christopher Craft
- School of Public and Environmental AffairsIndiana UniversityBloomingtonIndiana47405
| | - Jeffrey D. Herrick
- U.S Environmental Protection AgencyOffice of Research and DevelopmentResearch Triangle ParkNorth Carolina27711
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4
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Tepolt CK, Palumbi SR. Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.580701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Widespread species often adapt easily to novel conditions – both those found in new habitats and those generated by climate change. However, rapid adaptation may be hindered in the marine realm, where long-distance dispersal and consequently high gene flow are predicted to limit potential for local adaptation. Here, we use a highly dispersive invasive marine crab to test the nature and speed of adaptation to temperature in the sea. Using single nucleotide polymorphisms (SNPs) generated from cardiac transcriptome sequencing, we characterized six populations of the European green crab (Carcinus maenas) located across parallel thermal gradients in their native and invasive ranges. We compared SNP frequencies with local temperatures and previously generated data on cardiac heat and cold tolerance to identify candidate markers associated with population-level differences in thermal physiology. Of 10,790 SNPs, 104 were identified as frequency outliers, a signal that was strongly driven by association with temperature and/or cold tolerance. Seventy-two of these outlier markers, representing 28 different genes, were in a cluster of SNPs identified as a potential inversion polymorphism using linkage disequilibrium network analysis. This SNP cluster was unique in the data set, which was otherwise characterized by low levels of linkage disequilibrium, and markers in this cluster showed a significant enrichment of coding substitutions relative to the full SNP set. These 72 outlier SNPs appear to be transmitted as a unit, and represent a putative genomic island of divergence which varied in frequency with organismal cold tolerance. This relationship was strikingly similar across both native and invasive populations, all of which showed a very strong correlation with cold tolerance (R2 = 0.96 over all six populations). Notably, three of these populations have diverged recently (<100 years) and show little to no neutral divergence, suggesting that this genomic region may be responding to temperature on a relatively short time scale. This relationship indicates adaptation to temperature based on the action of a putative genomic island of divergence, perhaps partially explaining the extraordinary invasive ability of this species.
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5
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Ivanina AV, Jarrett A, Bell T, Rimkevicius T, Beniash E, Sokolova IM. Effects of seawater salinity and pH on cellular metabolism and enzyme activities in biomineralizing tissues of marine bivalves. Comp Biochem Physiol A Mol Integr Physiol 2020; 248:110748. [PMID: 32590052 DOI: 10.1016/j.cbpa.2020.110748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/31/2023]
Abstract
Molluscan shell formation is a complex energy demanding process sensitive to the shifts in seawater CaCO3 saturation due to changes in salinity and pH. We studied the effects of salinity and pH on energy demand and enzyme activities of biomineralizing cells of the Pacific oyster (Crassostrea gigas) and the hard-shell clam (Mercenaria mercenaria). Adult animals were exposed for 14 days to high (30), intermediate (18), or low (10) salinity at either high (8.0-8.2) or low (7.8) pH. Basal metabolic cost as well as the energy cost of the biomineralization-related cellular processes were determined in isolated mantle edge cells and hemocytes. The total metabolic rates were similar in the hemocytes of the two studied species, but considerably higher in the mantle cells of C. gigas compared with those of M. mercenaria. Cellular respiration was unaffected by salinity in the clams' cells, while in oysters' cells the highest respiration rate was observed at intermediate salinity (18). In both studied species, low pH suppressed cellular respiration. Low pH led to an upregulation of Na+/K+ ATPase activity in biomineralizing cells of oysters and clams. Activities of Ca2+ ATPase and H+ ATPase, as well as the cellular energy costs of Ca2+ and H+ transport in the biomineralizing cells were insensitive to the variation in salinity and pH in the two studied species. Variability in cellular response to low salinity and pH indicates that the disturbance of shell formation under these conditions has different underlying mechanisms in the two studied species.
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Affiliation(s)
- Anna V Ivanina
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA; Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Abigail Jarrett
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA; Department of Marine Biology, University of Rostock, Rostock, Germany
| | - Tiffany Bell
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tadas Rimkevicius
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Elia Beniash
- Department of Oral Biology, School of Dental Medicine, University of Pittsburg, Pittsburgh, PA, USA
| | - Inna M Sokolova
- Department of Marine Biology, University of Rostock, Rostock, Germany; Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany.
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6
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Phillips JM, Bricelj VM, Mitch M, Cerrato RM, MacQuarrie S, Connell LB. Biogeography of resistance to paralytic shellfish toxins in softshell clam, Mya arenaria (L.), populations along the Atlantic coast of North America. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2018; 202:196-206. [PMID: 30075308 DOI: 10.1016/j.aquatox.2018.06.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/28/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Blooms of Alexandrium spp., the causative agent of paralytic shellfish poisoning (PSP), recur with varying frequency and intensity on the Northwest Atlantic coast of North America, from New York, USA, to northern Canadian waters. Along this latitudinal range blooms co-occur with abundant, intertidal populations of softshell clams, Mya arenaria. Prior work identified a naturally-occurring genetic mutation in Domain II α-subunit of the clams' voltage-gated sodium channels (NaV), which significantly reduces the binding affinity of the paralytic shellfish toxin, saxitoxin (STX). This mutation provides clams with resistance to the deleterious effects of STX, allowing them to continue feeding during Alexandrium spp. blooms and attain very high tissue toxicities. This study used genetic sequencing of the NaV mutation locus in clams from four coastal regions of the Bay of Fundy-Gulf of Maine and the mid-Atlantic to determine the percentage of clams in each region that possess the resistant NaV mutation. The genotype composition was related to the occurrence and magnitude of PSP outbreaks based on shellfish toxicity, primarily that of mussels, Mytilus edulis, used as a proxy for the prevalence and severity of Alexandrium blooms in each region. As hypothesized, the proportion of clams bearing the resistant mutation generally matched up well with the historical incidence and intensity of Alexandrium spp. blooms. The highest percentage of homozygote resistant clams (RR = 70.0%), and the lowest percentage of sensitive clams (SS = 4.5%) were found in eastern Gulf of Maine populations. Exceptions at a few sites where anomalously high numbers of M. arenaria with the resistant mutation were found despite the absence of blooms, may be attributable to larval gene flow. There was no evidence that Alexandrium blooms occurring in Northport Harbor, Long Island, have resulted in a shift in genotypic composition of the local clam population, presumably due to their low cell toxicity. Seasonal mismatch of highly vulnerable M. arenaria postset with toxic blooms at this latitude may also partly explain this result. This study provides strong supporting evidence that Alexandrium blooms can select for resistance to PSP-toxins in M. arenaria populations and proposes a mechanism for the persistence of the sensitive allele throughout the region. Implications for clam aquaculture (seeding) efforts, as well as for shellfish toxicity monitoring are discussed.
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Affiliation(s)
- Jennifer M Phillips
- School of Marine Sciences and Molecular & Biomedical Sciences, University of Maine, Orono, ME, 04469, USA.
| | - V Monica Bricelj
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, 08901, USA.
| | - Maren Mitch
- School of Marine and Atmospheric Science (SoMAS), Stony Brook University, Stony Brook, NY, 11794, USA
| | - Robert M Cerrato
- School of Marine and Atmospheric Science (SoMAS), Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Scott MacQuarrie
- Aquatic and Crop Resource Development Research Centre, National Research Council, Halifax, NS, B3H 3Z1, Canada.
| | - Laurie B Connell
- School of Marine Sciences and Molecular & Biomedical Sciences, University of Maine, Orono, ME, 04469, USA; Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, 04469, USA.
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7
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Jeffery NW, Stanley RRE, Wringe BF, Guijarro-Sabaniel J, Bourret V, Bernatchez L, Bentzen P, Beiko RG, Gilbey J, Clément M, Bradbury IR. Range-wide parallel climate-associated genomic clines in Atlantic salmon. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171394. [PMID: 29291123 PMCID: PMC5717698 DOI: 10.1098/rsos.171394] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/13/2017] [Indexed: 05/02/2023]
Abstract
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
- Author for correspondence: Nicholas W. Jeffery e-mail:
| | - Ryan R. E. Stanley
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Brendan F. Wringe
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
| | - Javier Guijarro-Sabaniel
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, CanadaB2Y 4A2
| | - Vincent Bourret
- Laboratoire d'expertise biolégale, MFFP, Québec, Québec, CanadaG1P 3W8
| | - Louis Bernatchez
- Department of Biology, Université Laval, Québec, Québec, CanadaG1 V 0A6
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
| | - John Gilbey
- Marine Scotland, Freshwater Fisheries Laboratory, Faskally, Pitlochry PH16 5LB, UK
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St John's, NL, Canada
- Labrador Institute, Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St John's, Newfoundland and Labrador, CanadaA1C 5X1
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4R2
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8
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Pu C, Li H, Zhu A, Chen Y, Zhao Y, Zhan A. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species. PLoS One 2017; 12:e0180728. [PMID: 28704536 PMCID: PMC5507531 DOI: 10.1371/journal.pone.0180728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/20/2017] [Indexed: 11/19/2022] Open
Abstract
One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.
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Affiliation(s)
- Chuanliang Pu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Haitao Li
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Aijia Zhu
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, Guangdong, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Yan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing, China
- * E-mail:
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9
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Shulman MJ, Bermingham E. EARLY LIFE HISTORIES, OCEAN CURRENTS, AND THE POPULATION GENETICS OF CARIBBEAN REEF FISHES. Evolution 2017; 49:897-910. [DOI: 10.1111/j.1558-5646.1995.tb02325.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/1993] [Accepted: 07/06/1994] [Indexed: 12/01/2022]
Affiliation(s)
- Myra J. Shulman
- Department of Biology University of California Los Angeles California 90024‐1606
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute Apartado 2072 Balboa Republic of Panama
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10
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Stockwell CA, Mulvey M. PHOSPHOGLUCONATE DEHYDROGENASE POLYMORPHISM AND SALINITY IN THE WHITE SANDS PUPFISH. Evolution 2017; 52:1856-1860. [DOI: 10.1111/j.1558-5646.1998.tb02264.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/1998] [Accepted: 06/19/1998] [Indexed: 11/29/2022]
Affiliation(s)
- Craig A. Stockwell
- Department of Zoology, Stevens Hall; North Dakota State University; Fargo North Dakota 58105-5517
| | - Margaret Mulvey
- Savannah River Ecology Laboratory, Drawer E; Aiken South Carolina 29802
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11
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Burton RS. GENETIC EVIDENCE FOR LONG TERM PERSISTENCE OF MARINE INVERTEBRATE POPULATIONS IN AN EPHEMERAL ENVIRONMENT. Evolution 2017; 51:993-998. [PMID: 28568568 DOI: 10.1111/j.1558-5646.1997.tb03681.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/1996] [Accepted: 02/14/1997] [Indexed: 11/28/2022]
Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California, 92093-0202
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12
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McMillan WO, Raff RA, Palumbi SR. POPULATION GENETIC CONSEQUENCES OF DEVELOPMENTAL EVOLUTION IN SEA URCHINS (GENUS HELIOCIDARIS). Evolution 2017; 46:1299-1312. [PMID: 28568989 DOI: 10.1111/j.1558-5646.1992.tb01125.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/1990] [Accepted: 02/06/1992] [Indexed: 11/27/2022]
Abstract
Within the sea urchin genus Heliocidaris, changes in early embryonic and larval development have resulted in dramatic differences in the length of time larvae spend in the plankton before settling. The larvae of one species, H. tuberculata, spend several weeks feeding in the plankton before settling and metamorphosing into juveniles. The other species, H. erythrogramma, has modified this extended planktonic larval stage and develops into a juvenile within 3-4 days after fertilization. We used restriction site polymorphisms in mitochondrial DNA to examine the population genetic consequences of these developmental changes. Ten restriction enzymes were used to assay the mitochondrial genome of 29 individuals from 2 localities for H. tuberculata and 62 individuals from 5 localities for H. erythrogramma. Within H. tuberculata, 11 mitochondrial genotypes were identified. A GST analysis showed high levels of genetic exchange between populations separated by 1,000 kilometers of open ocean. In contrast, in H. erythrogramma, 13 mitochondrial genotypes differing by up to 2.33% were geographically partitioned over spatial scales ranging from 800 to 3,400 kilometers. Between distant localities, there was complete mitochondrial lineage sorting and large sequence divergence between resulting clades. Over much smaller spatial scales (< 1,000 km), genetic differentiation was due to the differential sorting of very similar genotypes. This pattern of mitochondrial variation suggests that these population differences have arisen recently and may reflect the historical interplay between the restricted dispersal capabilities of H. erythrogramma and the climatic and geological changes associated with Pleistocene Ice Ages.
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Affiliation(s)
- W Owen McMillan
- Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI, 96822, USA
| | - Rudolf A Raff
- Institute for Molecular and Cellular Biology and Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Stephen R Palumbi
- Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI, 96822, USA
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13
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Hellberg ME. RELATIONSHIPS BETWEEN INFERRED LEVELS OF GENE FLOW AND GEOGRAPHIC DISTANCE IN A PHILOPATRIC CORAL, BALANOPHYLLIA ELEGANS. Evolution 2017; 48:1829-1854. [DOI: 10.1111/j.1558-5646.1994.tb02218.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/1992] [Accepted: 08/17/1993] [Indexed: 12/01/2022]
Affiliation(s)
- Michael E. Hellberg
- Department of Zoology and Center for Population Biology; University of California; Davis California 95616
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14
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Johnson MS, Black R. PATTERN BENEATH THE CHAOS: THE EFFECT OF RECRUITMENT ON GENETIC PATCHINESS IN AN INTERTIDAL LIMPET. Evolution 2017; 38:1371-1383. [PMID: 28563786 DOI: 10.1111/j.1558-5646.1984.tb05658.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/1983] [Accepted: 05/08/1984] [Indexed: 11/30/2022]
Affiliation(s)
- Michael S. Johnson
- Department of Zoology; University of Western Australia; Nedlands 6009 Western Australia
| | - Robert Black
- Department of Zoology; University of Western Australia; Nedlands 6009 Western Australia
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15
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Vermeij GJ. ENVIRONMENTAL CHANGE AND THE EVOLUTIONARY HISTORY OF THE PERIWINKLE (LITTORINA LITTOREA) IN NORTH AMERICA. Evolution 2017; 36:561-580. [PMID: 28568041 DOI: 10.1111/j.1558-5646.1982.tb05077.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/1981] [Revised: 09/03/1981] [Indexed: 11/29/2022]
Affiliation(s)
- Geerat J Vermeij
- Department of Zoology, University of Maryland, College Park, Maryland, 20742
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16
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Burton RS, Feldman MW. POPULATION GENETICS OF TIGRIOPUS CALIFORNICUS. II. DIFFERENTIATION AMONG NEIGHBORING POPULATIONS. Evolution 2017; 35:1192-1205. [PMID: 28563405 DOI: 10.1111/j.1558-5646.1981.tb04989.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/1980] [Revised: 03/30/1981] [Indexed: 11/27/2022]
Affiliation(s)
- Ronald S Burton
- Department of Biological Sciences, Stanford University, Stanford, California, 94305
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, California, 94305
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17
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Marko PB. HISTORICAL ALLOPATRY AND THE BIOGEOGRAPHY OF SPECIATION IN THE PROSOBRANCH SNAIL GENUS NUCELLA. Evolution 2017; 52:757-774. [PMID: 28565241 DOI: 10.1111/j.1558-5646.1998.tb03700.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/1997] [Accepted: 03/06/1998] [Indexed: 12/01/2022]
Affiliation(s)
- Peter B. Marko
- Section of Evolution and Ecology and Center for Population Biology; University of California; Davis California 95616
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18
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Hilbish TJ, Koehn RK. EXCLUSION OF THE ROLE OF SECONDARY CONTACT IN AN ALLELE FREQUENCY CLINE IN THE MUSSEL MYTILUS EDULIS. Evolution 2017; 39:432-443. [PMID: 28564224 DOI: 10.1111/j.1558-5646.1985.tb05679.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/1984] [Accepted: 09/14/1984] [Indexed: 11/26/2022]
Abstract
We examined the hypothesis that secondary contact generates an allele-frequency cline at the aminopeptidase-I locus (Lap) in the marine mussel, Mytilus edulis. It has been proposed that variation at the Lap locus is neutral and that the cline results from secondary contact between differentiated oceanic and estuarine populations (Levinton, 1980). We tested this hypothesis by comparing the genotypic distributions in samples from the cline to distributions that incorporate mixing effects. We employed a statistical model that determines the degree of contact using a maximum likelihood estimator and then incorporates the mixing estimates into an expected distribution of genotypes. Wahlund effects resulting from possible admixture are thereby incorporated into the expected distribution. Failure of the model to reconcile the observed with the expected distribution of genotypes indicates that the observed population structure does not result from admixture. The null hypothesis of mixing was unable to explain about 33% of the samples. Combined tests demonstrated the general departure from the mixing model to be highly significant. The distribution of heterozygote discrepancies across the cline was inconsistent with the expectations of a mixing model. Therefore we reject explanations for the structure of the Lap cline that involve secondary contact. Selection directed at the Lap locus appears necessary to explain the genotypic structure of clinal populations.
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Affiliation(s)
- Thomas J Hilbish
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY, 11794
| | - Richard K Koehn
- Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY, 11794
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Britten HB. META-ANALYSES OF THE ASSOCIATION BETWEEN MULTILOCUS HETEROZYGOSITY AND FITNESS. Evolution 2017; 50:2158-2164. [PMID: 28565689 DOI: 10.1111/j.1558-5646.1996.tb03606.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/1995] [Accepted: 04/30/1996] [Indexed: 11/30/2022]
Abstract
Meta-analyses of published correlation coefficients between multilocus heterozygosity (MLH) and two fitness surrogates, growth rate and fluctuating asymmetry, suggested that the strength of these correlations are generally weak. A variety of plants and animals was included in the meta-analyses. A statistically homogeneous group of MLH-growth rate correlation coefficients that included both plants and animals yielded a common correlation of rz = 0.133. A common correlation of rz = -0.170 was estimated for correlations between MLH and fluctuating asymmetry in three species of salmonid fishes. These results suggest that selection, including overdominance, has at most a weak effect at allozyme loci and cast some doubt on the widely held notion that heterozygosity and individual fitness are strongly correlated.
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Affiliation(s)
- Hugh B Britten
- Biological Resources Research Center, Department of Biology, University of Nevada, Reno, Nevada, 89557
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20
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Hilbish TJ, Koehn RK. THE PHYSIOLOGICAL BASIS OF NATURAL SELECTION AT THE LAP LOCUS. Evolution 2017; 39:1302-1317. [PMID: 28564261 DOI: 10.1111/j.1558-5646.1985.tb05696.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/1985] [Accepted: 07/15/1985] [Indexed: 11/30/2022]
Abstract
An extensive research program was undertaken to evaluate the contribution of genetic variation at the Lap locus to variation in physiological traits under natural conditions. Rates of carbon and nitrogen metabolism were monitored in a population of the mussel Mytilus edulis near the center of the Lap allele frequency cline on the north shore of Long Island. The goal of this research was to establish whether the previously described genotype-dependent differences in physiological phenotype are meaningful in ecologically relevant circumstances. It was predicted from laboratory studies that, in nature, genotype-dependent differences will exist for rates of nitrogen excretion and that other aspects of the animal's physiology, particularly rates of carbon metabolism, will be unaffected by Lap genotype. Rates of amino acid and ammonia excretion were significantly dependent upon Lap genotype; individuals with the Lap94 allele exhibited greater rates of nitrogen loss. These differences among genotypes were most evident in the fall, between September and December. The genotype-dependent component of rates of nitrogen loss were also largest relative to the total rate of excretion during the fall period. As predicted, other aspects of the nitrogen metabolism (acquisition) and rates of carbon metabolism were independent of Lap genotype. There was a striking congruity among a variety of observations that all indicate that phenotypic differences in nitrogen metabolism are the basis of natural selection at the Lap locus in Long Island Sound. Rates of growth were minimal during the fall months (Hilbish, 1985) and mussels are known to lose weight in a genotype-specific manner during this period (Koehn et al., 1980). Rates of elemental gain and loss were summed to produce carbon and nitrogen budgets; these data show the fall to be a period of extended deficit in carbon and nitrogen balance. Genotype-dependent losses of ammonia and amino acids were greatest during the fall months. Finally, selection against the Lap94 allele occurs predominantly in the fall (Hilbish, 1985). The data indicate that the depletion of nitrogen resources provides the basis for selection against Lap94 genotypes during the fall months.
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Affiliation(s)
- Thomas J Hilbish
- Department of Ecology and Evolution, State University of New York, Stony Brook, NY, 11794
| | - Richard K Koehn
- Department of Ecology and Evolution, State University of New York, Stony Brook, NY, 11794
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21
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Haag WR, Garton DW. VARIATION IN GENOTYPE FREQUENCIES DURING THE LIFE HISTORY OF THE BIVALVE,
DREISSENA POLYMORPHA. Evolution 2017; 49:1284-1288. [DOI: 10.1111/j.1558-5646.1995.tb04457.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/1994] [Accepted: 09/06/1994] [Indexed: 12/01/2022]
Affiliation(s)
- Wendell R. Haag
- U.S. Department of Agriculture, Forest Service Forest Hydrology Laboratory P.O. Box 947 Oxford Mississippi 38655
- Department of Zoology Ohio State University Columbus Ohio 43210
| | - David W. Garton
- Department of Biological and Physical Sciences Indiana University 2300 South Washington St. Kokomo Indiana 46904
- Department of Zoology Ohio State University Columbus Ohio 43210
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22
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Similarity of osmoregulatory capacity in coastal and inland alligator gar. Comp Biochem Physiol A Mol Integr Physiol 2017; 209:16-24. [PMID: 28400249 DOI: 10.1016/j.cbpa.2017.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 11/24/2022]
Abstract
The alligator gar Atractosteus spatula is a primitive fish species, occupying a wide range of temperature and salinity habitats. Long-distance movements are limited, leading to genetic differentiation between inland and coastal populations. Unknown is whether physiological capacity differs between geographically separated populations, particularly for traits important to osmoregulation in saline environments. Alligator gar from inland and coastal populations were reared in a similar environment and exposed to temperature (10, 30°C) and salinity (0, 20ppt) extremes to determine whether iono- and osmoregulatory ability differed between populations. There were few differences in osmoregulatory ability between populations, with similar gill, blood and gastrointestinal tract osmoregulatory parameters. Blood plasma osmolality, ion concentrations, intestinal pH and bicarbonate base concentrations, intestinal fluid osmolality, ion concentrations and gill Na+, K+-ATPase (NKA) activity were similar between populations. Notably, gar from both populations did not osmoregulate well at low temperature and high salinity, with elevated plasma osmolality and ion concentrations, low gill NKA, and little evidence of gastrointestinal tract contribution to ionic and base regulation based on a lack of intestinal fluid and low base content. Therefore, the hypothesis that coastal gar would have improved osmotic regulatory ability in saline environments as compared to inland alligator gar was not supported, suggesting physiological capacity may be retained in primitive species possibly due to its importance to their persistence through time.
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23
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Barney BT, Munkholm C, Walt DR, Palumbi SR. Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine. BMC Genomics 2017; 18:271. [PMID: 28359300 PMCID: PMC5374575 DOI: 10.1186/s12864-017-3660-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/25/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Atlantic cod (Gadus morhua), is known to vary genetically across the North Atlantic, Greenland, and Newfoundland. This genetic variation occurs both spatially and temporally through decades of heavy fishing, and is concentrated in three linkage disequilibrium blocks, previously defined by pedigreed linkage mapping analysis. Variation within these genomic regions is correlated with both seawater temperature and behavioral ecotype. The full extent and nature of these linkage groups is important information for interpreting cod genetic structure as a tool for future fisheries management. RESULTS We conducted whole genome sequencing for 31 individual cod from three sub-populations in the Gulf of Maine. Across the genome, we found 3,390,654 intermediate to high frequency Single Nucleotide Polymorphisms (SNPs). We show that pairwise linkage analysis among these SNPs is a powerful tool to detect linkage disequilibrium clusters by recovering the three previously detected linkage groups and identifying the 1031 genes contained therein. Across these genes, we found significant population differentiation among spawning groups in the Gulf of Maine and between Georges Bank and Gulf of Maine. Coordinated divergence among these genes and their differentiation at both short and long spatial scales suggests that they are acting as linked supergenes in local adaptation of cod populations. CONCLUSIONS Differentiation between SNPs in linkage disequilibrium blocks is the major signal of genetic differentiation between all groups tested within the Gulf of Maine. Our data provide a map of genes contained in these blocks, allowing an enhanced search for neutral genetic structure for demographic inference and fisheries modeling. Patterns of selection and the history of populations may be possible to identify in cod using this description of linkage disequilibrium blocks and future data sets to robustly separate neutral and selected genetic markers.
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Affiliation(s)
- Bryan T. Barney
- Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 92950 USA
| | - Christiane Munkholm
- Gloucester Marine Genomics Institute, 55 Blackburn Center, Gloucester, MA 01930 USA
| | - David R. Walt
- Gloucester Marine Genomics Institute, 55 Blackburn Center, Gloucester, MA 01930 USA
| | - Stephen R. Palumbi
- Department of Biology, Hopkins Marine Station, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 92950 USA
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24
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Gharbi A, Farcy E, Van Wormhoudt A, Denis F. Response of the carpet shell clam (Ruditapes decussatus) and the Manila clam (Ruditapes philippinarum) to salinity stress. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Gagnaire PA, Gaggiotti OE. Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Curr Zool 2016; 62:603-616. [PMID: 29491948 PMCID: PMC5804256 DOI: 10.1093/cz/zow088] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/21/2016] [Indexed: 12/27/2022] Open
Abstract
Highly fecund marine species with dispersive life-history stages often display large population sizes and wide geographic distribution ranges. Consequently, they are expected to experience reduced genetic drift, efficient selection fueled by frequent adaptive mutations, and high migration loads. This has important consequences for understanding how local adaptation proceeds in the sea. A key issue in this regard, relates to the genetic architecture underlying fitness traits. Theory predicts that adaptation may involve many genes but with a high variance in effect size. Therefore, the effect of selection on allele frequencies may be substantial for the largest effect size loci, but insignificant for small effect genes. In such a context, the performance of population genomic methods to unravel the genetic basis of adaptation depends on the fraction of adaptive genetic variance explained by the cumulative effect of outlier loci. Here, we address some methodological challenges associated with the detection of local adaptation using molecular approaches. We provide an overview of genome scan methods to detect selection, including those assuming complex demographic models that better describe spatial population structure. We then focus on quantitative genetics approaches that search for genotype-phenotype associations at different genomic scales, including genome-wide methods evaluating the cumulative effect of variants. We argue that the limited power of single locus tests can be alleviated by the use of polygenic scores to estimate the joint contribution of candidate variants to phenotypic variation.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
- ISEM – CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète, 34200, France
| | - Oscar E. Gaggiotti
- Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, KY16 9LB, UK
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26
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Gleason LU, Burton RS. Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis. Mol Ecol 2016; 25:3557-73. [PMID: 27199218 DOI: 10.1111/mec.13703] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 12/19/2022]
Abstract
The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we used double-digest restriction site-associated DNA (ddRAD) sequencing to identify 1861 genomewide, quality-filtered single-nucleotide polymorphism (SNP) loci for C. funebralis collected from three northern and three southern California sites (15 individuals per population). Considering all SNPs, there was no evidence for genetic differentiation among populations or regions (average FST = 0.0042). However, outlier tests revealed 34 loci putatively under divergent selection between northern and southern populations, and structure and SNP tree analyses based on these outliers show clear genetic differentiation between geographic regions. Three of these outliers are known or hypothesized to be involved in stress granule formation, a response to environmental stress such as heat. Combined with previous work that found thermally tolerant southern populations show high baseline expression of stress response genes, these results further suggest that thermal stress is a strong selective pressure across C. funebralis populations. Overall, this study increases our understanding of the factors constraining local adaptation in marine organisms, while suggesting that ecologically driven, strong differentiation can occur at relevant loci in a species with planktonic larvae.
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Affiliation(s)
- Lani U Gleason
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.,Department of Biology, Loyola Marymount University, Los Angeles, CA, 90045, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA
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27
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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29
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Lara M, Binder PM, Figueredo-Fernández MA. Rhythmic natural selection over intertidal and brackish water genotypes: simple formulations for testing hypothesis. Mar Genomics 2014; 14:83-8. [PMID: 24412494 DOI: 10.1016/j.margen.2013.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 12/06/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
Tidal cycles at benthic habitats induce a set of periodic environmental changes in variables like salinity, temperature and sediment water content which are able to stress benthic organisms. Consequently, a natural selection temporally correlated with tides affects the fitness of genotypes (wi) depending on their adaptation degree. Classic population genetics demonstrate that (1) rhythmic wi is more restrictive than equivalent spatial variations to preserve genetic variance, and (2) mean fitness of the population (w¯) does not have to be enhanced by genetic variance (σ(2)w). The present study develops a simple replicator dynamics-based model of continuous selection, where wi of multiple asexual genotypes fluctuates as a sinusoid. The amplitude of w was set as 0.5 (1-wmin), whereas the ratio of tide period to generation time (h) was defined. Overall, the model shows that if h>1, then the success of an advantageous genotype is exposed to randomness, and w¯ may decrease over generations. In contrast, if h<1 the success is deterministic, is limiting co-dominance, and only depends on wmin. The amount of different genotypes buffers the decay of σ(2)w and hence increases cohesiveness. Finally, the reliability of the model is analyzed for a set of target intertidal and brackish water organisms.
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Affiliation(s)
- M Lara
- Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, Av. República Saharaui s/n, 11510 Puerto Real, Spain.
| | - P M Binder
- Department of Animal Production, Faculty of Agronomy, University of Buenos Aires, Av. San Martín 4453, C1417DSE Buenos Aires, Argentina
| | - M A Figueredo-Fernández
- Department of Environmental Technologies, Faculty of Marine and Environmental Sciences, University of Cádiz, Av. República Saharaui s/n, 11510 Puerto Real, Spain
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30
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Broquet T, Viard F, Yearsley JM. GENETIC DRIFT AND COLLECTIVE DISPERSAL CAN RESULT IN CHAOTIC GENETIC PATCHINESS. Evolution 2013; 67:1660-75. [DOI: 10.1111/j.1558-5646.2012.01826.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/25/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Broquet
- CNRS, UMR 7144, Team Div & Co; Lab. Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff 29682 Roscoff France
- UPMC Univ Paris 06, UMR 7144 AD2M; Station Biologique de Roscoff 29682 Roscoff France
| | - Frédérique Viard
- CNRS, UMR 7144, Team Div & Co; Lab. Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff 29682 Roscoff France
- UPMC Univ Paris 06, UMR 7144 AD2M; Station Biologique de Roscoff 29682 Roscoff France
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31
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Byrne RJ, Bernardi G, Avise JC. Spatiotemporal Genetic Structure in a Protected Marine Fish, the California Grunion (Leuresthes tenuis), and Relatedness in the Genus Leuresthes. J Hered 2013; 104:521-31. [DOI: 10.1093/jhered/est024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Riquet F, Daguin‐Thiébaut C, Ballenghien M, Bierne N, Viard F. Contrasting patterns of genome‐wide polymorphism in the native and invasive range of the marine molluscCrepidula fornicata. Mol Ecol 2013; 22:1003-18. [PMID: 23286428 DOI: 10.1111/mec.12161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/15/2012] [Accepted: 10/29/2012] [Indexed: 01/03/2023]
Affiliation(s)
- Florentine Riquet
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Claire Daguin‐Thiébaut
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
| | - Marion Ballenghien
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution Laboratory Phylogénie et Evolution moléculaire UMR 5554 Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Nicolas Bierne
- Université Montpellier 2 Place Eugène Bataillon 34095 Montpellier France
- CNRS Institut des Sciences de l'Evolution UMR 5554 Station Méditerranéenne de l'Environnement Littoral, 2 rue des Chantiers 34200 Sète France
| | - Frédérique Viard
- UPMC Univ Paris 06 Team Diversity and Connectivity in Coastal Marine Landscapes UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
- CNRS Laboratory Adaptation and Diversity in the Marine Environment UMR 7144 Station Biologique de Roscoff 29680 Roscoff France
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33
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Sotka EE. Natural selection, larval dispersal, and the geography of phenotype in the sea. Integr Comp Biol 2012; 52:538-45. [PMID: 22634357 DOI: 10.1093/icb/ics084] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Populations evolve generalist, specialist, and plastic strategies in response to environmental heterogeneity. Describing such within-species variation in phenotype and how it arises is central to understanding a variety of ecological and evolutionary topics. The literature on phenotypic differences among populations is highly biased; for every one article published on a marine species, at least 10 articles are published on a terrestrial species and eight focus on terrestrial plants. Here, I outline what we know from the marine literature about geographic variation in phenotype in the sea, with a principal focus on local adaptation. The theory of environmental "grain" predicts that the most likely evolutionary response (e.g., local adaptation, phenotypic plasticity, generalism, and balanced polymorphism) depends on the spatial scale of environmental variation relative to the distance that an organism disperses. Consistent with these predictions, phenotypic plasticity is stronger among invertebrates with geographically broad dispersal versus restricted dispersal (i.e., planktonic-dispersers versus direct-developers). However, contrary to predictions, the relative frequency, and spatial scale of local adaptation is not consistently greater among direct-developers relative to planktonic disperers. This indicates that the likelihood of local adaptation depends on other organismal or environmental traits. Two of the most vexing issues that remain include (1) predicting the extent to which barriers to dispersal are a cause versus consequence of phenotypic differentiation and (2) delineating the relative importance of evolutionary forces that favor or impede local adaptation. Understanding the mechanistic basis of the geography of phenotypic differences, or phenogeography, has gained recent momentum because of a need to predict impacts of global climatic change, anthropogenic disturbances, and dispersal of organisms to non-native habitats.
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Affiliation(s)
- Erik E Sotka
- College of Charleston, Department of Biology, Grice Marine Laboratory, Charleston, SC 29412, USA.
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34
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Fevolden SE, Garner SP. Population genetics ofMytilus edulis(L.) from Oslofjorden, norway, in oil-polluted and non oil-polluted water. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/00364827.1986.10419694] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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35
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Pespeni MH, Garfield DA, Manier MK, Palumbi SR. Genome-wide polymorphisms show unexpected targets of natural selection. Proc Biol Sci 2011; 279:1412-20. [PMID: 21993504 DOI: 10.1098/rspb.2011.1823] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Natural selection can act on all the expressed genes of an individual, leaving signatures of genetic differentiation or diversity at many loci across the genome. New power to assay these genome-wide effects of selection comes from associating multi-locus patterns of polymorphism with gene expression and function. Here, we performed one of the first genome-wide surveys in a marine species, comparing purple sea urchins, Strongylocentrotus purpuratus, from two distant locations along the species' wide latitudinal range. We examined 9112 polymorphic loci from upstream non-coding and coding regions of genes for signatures of selection with respect to gene function and tissue- and ontogenetic gene expression. We found that genetic differentiation (F(ST)) varied significantly across functional gene classes. The strongest enrichment occurred in the upstream regions of E3 ligase genes, enzymes known to regulate protein abundance during development and environmental stress. We found enrichment for high heterozygosity in genes directly involved in immune response, particularly NALP genes, which mediate pro-inflammatory signals during bacterial infection. We also found higher heterozygosity in immune genes in the southern population, where disease incidence and pathogen diversity are greater. Similar to the major histocompatibility complex in mammals, balancing selection may enhance genetic diversity in the innate immune system genes of this invertebrate. Overall, our results show that how genome-wide polymorphism data coupled with growing databases on gene function and expression can combine to detect otherwise hidden signals of selection in natural populations.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, Hopkins Marine Station, Stanford University, Oceanview Boulevard, Pacific Grove, CA 93950, USA.
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36
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Clarke LM, Munch SB, Thorrold SR, Conover DO. High connectivity among locally adapted populations of a marine fish (Menidia menidia). Ecology 2011; 91:3526-37. [PMID: 21302825 DOI: 10.1890/09-0548.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Patterns of connectivity are important in understanding the geographic scale of local adaptation in marine populations. While natural selection can lead to local adaptation, high connectivity can diminish the potential for such adaptation to occur. Connectivity, defined as the exchange of individuals among subpopulations, is presumed to be significant in most marine species due to life histories that include widely dispersive stages. However, evidence of local adaptation in marine species, such the Atlantic silverside, Menidia menidia, raises questions concerning the degree of connectivity. We examined geochemical signatures in the otoliths, or ear bones, of adult Atlantic silversides collected in 11 locations along the northeastern coast of the United States from New Jersey to Maine in 2004 and eight locations in 2005 using laser ablation inductively coupled plasma mass spectrometry (ICP-MS) and isotope ratio monitoring mass spectrometry (irm-MS). These signatures were then compared to baseline signatures of juvenile fish of known origin to determine natal origin of these adult fish. We then estimated migration distances and the degree of mixing from these data. In both years, fish generally had the highest probability of originating from the same location in which they were captured (0.01-0.80), but evidence of mixing throughout the sample area was present. Furthermore, adult M. menidia exhibit highly dispersive behavior with some fish migrating over 700 km. The probability of adult fish returning to natal areas differed between years, with the probability being, on average, 0.2 higher in the second year. These findings demonstrate that marine species with largely open populations are capable of local adaptation despite apparently high gene flow.
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Affiliation(s)
- Lora M Clarke
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794-5000, USA.
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37
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Bierne N. The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population. Evolution 2011; 64:3254-72. [PMID: 20550573 DOI: 10.1111/j.1558-5646.2010.01050.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Loci with higher levels of population differentiation than the neutral expectation are traditionally interpreted as evidence of ongoing selection that varies in space. This article emphasizes an alternative explanation that has been largely overlooked to date: in species subdivided into large subpopulations, enhanced differentiation can also be the signature left by the fixation of an unconditionally favorable mutation on its chromosomal neighborhood. This is because the hitchhiking effect is expected to diminish as the favorable mutation spreads from the deme in which it originated to other demes. To discriminate among the two alternative scenarios one needs to investigate how genetic structure varies along the chromosomal region of the locus. Local hitchhiking is shown to generate a single sharp peak of differentiation centered on the adaptive polymorphism and the standard signature of a selective sweep only in those subpopulations in which the allele is favored. Global hitchhiking produces two domes of differentiation on either side of the fixed advantageous mutation and signatures of a selective sweep in every subpopulation, albeit of different magnitude. Investigating population differentiation around a locus that strongly differentiates two otherwise genetically similar populations of the marine mussel Mytilus edulis, plausible evidence for the global hitchhiking hypothesis has been obtained. Global hitchhiking is a neglected phenomenon that might prove to be important in species with large population sizes such as many marine invertebrates.
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Affiliation(s)
- Nicolas Bierne
- Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France.
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38
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39
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Armbruster GFJ. Selection and habitat-specific allozyme variation in the self-fertilizing land snailCochlicopa lubrica(O. F. Müller). J NAT HIST 2010. [DOI: 10.1080/00222930150215323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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40
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Genetic variation and population structure of the carpet shell clam Ruditapes decussatus along the Tunisian coast inferred from mtDNA and ITS1 sequence analysis. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0069-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Hart MW, Marko PB. It's about time: divergence, demography, and the evolution of developmental modes in marine invertebrates. Integr Comp Biol 2010; 50:643-61. [PMID: 21558230 DOI: 10.1093/icb/icq068] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Differences in larval developmental mode are predicted to affect ecological and evolutionary processes ranging from gene flow and population bottlenecks to rates of population recovery from anthropogenic disturbance and capacity for local adaptation. The most powerful tests of these predictions use comparisons among species to ask how phylogeographic patterns are correlated with the evolution and loss of prolonged planktonic larval development. An important and largely untested assumption of these studies is that interspecific differences in population genetic structure are mainly caused by differences in dispersal and gene flow (rather than by differences in divergence times among populations or changes in effective population sizes), and that species with similar patterns of spatial genetic variation have similar underlying temporal demographic histories. Teasing apart these temporal and spatial patterns is important for understanding the causes and consequences of evolutionary changes in larval developmental mode. New analytical methods that use the coalescent history of allelic diversity can reveal these temporal patterns, test the strength of traditional population-genetic explanations for variation in spatial structure based on differences in dispersal, and identify strongly supported alternative explanations for spatial structure based on demographic history rather than on gene flow alone. We briefly review some of these recent analytical developments, and show their potential for refining ideas about the correspondence between the evolution of larval developmental mode, population demographic history, and spatial genetic variation.
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Affiliation(s)
- Michael W Hart
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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42
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Pespeni MH, Oliver TA, Manier MK, Palumbi SR. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays. Genome Biol 2010; 11:R44. [PMID: 20403197 PMCID: PMC2884547 DOI: 10.1186/gb-2010-11-4-r44] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 04/07/2010] [Accepted: 04/19/2010] [Indexed: 12/28/2022] Open
Abstract
A method for the simultaneous identification of polymorphic loci and the quantitative genotyping of thousands of loci in individuals is presented. High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, Stanford University, Hopkins Marine Station, Oceanview Blvd Pacific Grove, CA 93950, USA.
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43
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Kelly RP, Palumbi SR. Genetic structure among 50 species of the northeastern Pacific rocky intertidal community. PLoS One 2010; 5:e8594. [PMID: 20062807 PMCID: PMC2799524 DOI: 10.1371/journal.pone.0008594] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/07/2009] [Indexed: 11/18/2022] Open
Abstract
Comparing many species' population genetic patterns across the same seascape can identify species with different levels of structure, and suggest hypotheses about the processes that cause such variation for species in the same ecosystem. This comparative approach helps focus on geographic barriers and selective or demographic processes that define genetic connectivity on an ecosystem scale, the understanding of which is particularly important for large-scale management efforts. Moreover, a multispecies dataset has great statistical advantages over single-species studies, lending explanatory power in an effort to uncover the mechanisms driving population structure. Here, we analyze a 50-species dataset of Pacific nearshore invertebrates with the aim of discovering the most influential structuring factors along the Pacific coast of North America. We collected cytochrome c oxidase I (COI) mtDNA data from populations of 34 species of marine invertebrates sampled coarsely at four coastal locations in California, Oregon, and Alaska, and added published data from 16 additional species. All nine species with non-pelagic development have strong genetic structure. For the 41 species with pelagic development, 13 show significant genetic differentiation, nine of which show striking FST levels of 0.1-0.6. Finer scale geographic investigations show unexpected regional patterns of genetic change near Cape Mendocino in northern California for five of the six species tested. The region between Oregon and Alaska is a second focus of intraspecific genetic change, showing differentiation in half the species tested. Across regions, strong genetic subdivision occurs more often than expected in mid-to-high intertidal species, a result that may reflect reduced gene flow due to natural selection along coastal environmental gradients. Finally, the results highlight the importance of making primary research accessible to policymakers, as unexpected barriers to marine dispersal break the coast into separate demographic zones that may require their own management plans.
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Affiliation(s)
- Ryan P Kelly
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California, United States of America.
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44
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Geller JB, Darling JA, Carlton JT. Genetic perspectives on marine biological invasions. ANNUAL REVIEW OF MARINE SCIENCE 2010; 2:367-93. [PMID: 21141669 DOI: 10.1146/annurev.marine.010908.163745] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The extent to which the geographic distributions of marine organisms have been reshaped by human activities remains underappreciated, and so does, consequently, the impact of invasive species on marine ecosystems. The application of molecular genetic data in fields such as population genetics, phylogeography, and evolutionary biology have improved our ability to make inferences regarding invasion histories. Genetic methods have helped to resolve longstanding questions regarding the cryptogenic status of marine species, facilitated recognition of cryptic marine biodiversity, and provided means to determine the sources of introduced marine populations and to begin to recover the patterns of anthropogenic reshuffling of the ocean's biota. These approaches stand to aid materially in the development of effective management strategies and sustainable science-based policies. Continued advancements in the statistical analysis of genetic data promise to overcome some existing limitations of current approaches. Still other limitations will be best addressed by concerted collaborative and multidisciplinary efforts that recognize the important synergy between understanding the extent of biological invasions and coming to a more complete picture of both modern-day and historical marine biogeography.
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Affiliation(s)
- Jonathan B Geller
- Moss Landing Marine Laboratories, Moss Landing, California 95039, USA.
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45
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Renwrantz L, Lam A. Soluble and surface-bound aminopeptidase in eosinophilic blood cells from Mytilus edulis. J Invertebr Pathol 2010; 103:68-70. [DOI: 10.1016/j.jip.2009.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 10/01/2009] [Accepted: 10/06/2009] [Indexed: 11/25/2022]
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46
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Marshall DJ, Monro K, Bode M, Keough MJ, Swearer S. Phenotype-environment mismatches reduce connectivity in the sea. Ecol Lett 2009; 13:128-40. [PMID: 19968695 DOI: 10.1111/j.1461-0248.2009.01408.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The connectivity of marine populations is often surprisingly lower than predicted by the dispersal capabilities of propagules alone. Estimates of connectivity, moreover, do not always scale with distance and are sometimes counterintuitive. Population connectivity requires more than just the simple exchange of settlers among populations: it also requires the successful establishment and reproduction of exogenous colonizers. Marine organisms often disperse over large spatial scales, encountering very different environments and suffering extremely high levels of post-colonization mortality. Given the growing evidence that such selection pressures often vary over spatial scales that are much smaller than those of dispersal, we argue that selection will bias survival against exogenous colonizers. We call this selection against exogenous colonizers a phenotype-environment mismatch and argue that phenotype-environment mismatches represent an important barrier to connectivity in the sea. Crucially, these mismatches may operate independently of distance and thereby have the potential to explain the counterintuitive patterns of connectivity often seen in marine environments. We discuss how such mismatches might alter our understanding and management of marine populations.
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Affiliation(s)
- D J Marshall
- School of Biological Sciences, The University of Queensland, Queensland, 4072 Qld, Australia.
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47
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Addison JA, Ort BS, Mesa KA, Pogson GH. Range-wide genetic homogeneity in the California sea mussel (Mytilus californianus): a comparison of allozymes, nuclear DNA markers, and mitochondrial DNA sequences. Mol Ecol 2009; 17:4222-32. [PMID: 19378402 DOI: 10.1111/j.1365-294x.2008.03905.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We tested for genetic differentiation among six populations of California sea mussels (Mytilus californianus) sampled across 4000 km of its geographical range by comparing patterns of variation at four independent types of genetic markers: allozymes, single-copy nuclear DNA markers, and DNA sequences from the male and female mitochondrial genomes. Despite our extensive sampling and genotyping efforts, we detected no significant differences among localities and no signal of isolation by distance suggesting that M. californianus is genetically homogeneous throughout its range. This concordance differs from similar studies on other mytilids, especially in the role of postsettlement selection generating differences between exposed coastal and estuarine habitats. To assess if this homogeneity was due to M. californianus not inhabiting estuarine environments, we reviewed studies comparing allozymes with other classes of nuclear DNA markers. Although both types of markers gave broadly consistent results, there was a bias favouring studies in which allozymes were more divergent than DNA markers (nine to three) and a disproportionate number of these cases involved marine taxa (seven). Furthermore, allozymes were significantly more heterogeneous than DNA markers in three of the four studies that sampled coastal and estuarine habitats. We conclude that the genetic uniformity exhibited by M. californianus may result from a combination of extensive gene flow and the lack of exposure to strong selective gradients across its range.
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Affiliation(s)
- Jason A Addison
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.
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48
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Post-settlement viability in the American oyster (Crassostrea virginica): an overdominant phenotype. Genet Res (Camb) 2009. [DOI: 10.1017/s0016672300021327] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
SUMMARYThe degree of heterozygosity as determined by electrophoretic analysis of three or four polymorphic loci correlates positively with survival in age groups of the American oyster (Crassostrea virginica) collected as spat from two different natural populations. The phenomenon is shown to operate in ages from 2 weeks (post-settlement) to 3 years and appears to be general in populations of marine molluscs. The most likely explanation for this result is that heterozygosity improves survival through its effect on growth (heterozygotes grow faster). The effects of individual loci on viability are independent of each other. A direct involvement of the enzyme polymorphisms is the most probable genetic interpretation of the data, but associative overdominance cannot be excluded.
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49
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Hutchinson WF. The dangers of ignoring stock complexity in fishery management: the case of the North Sea cod. Biol Lett 2009; 4:693-5. [PMID: 18782730 DOI: 10.1098/rsbl.2008.0443] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The plight of the marine fisheries is attracting increasing attention as unsustainably high exploitation levels, exacerbated by more extreme climatic conditions, are driving stocks to the point of collapse. The North Atlantic cod (Gadus morhua), a species which until recently formed a major component of the demersal fisheries, has undergone significant declines across its range. The North Sea stock is typical of many, with a spawning stock biomass that has remained below the safe biological limit since 2000 and recruitment levels near the lowest on record. Cod within the North Sea are currently managed as a single stock, and yet mounting empirical evidence supports the existence of a metapopulation of regionally variable, genetically distinct, sub-stocks. Applying the same management strategies to multiple stocks that differ in their resilience to exploitation inevitably results in the overfishing and likely collapse of the weaker components. Indeed, recent studies have identified two North Sea spawning stocks that have undergone disproportionally large collapses with very substantial reductions in egg production. Similarly affected cod stocks in the northwest Atlantic have shown little evidence of recovery, despite fishery closures. The possible implications of ignoring sub-structuring within management units for biocomplexity, local adaptation and ecosystem stability are considered.
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50
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Schmidt PS, Serrão EA, Pearson GA, Riginos C, Rawson PD, Hilbish TJ, Brawley SH, Trussell GC, Carrington E, Wethey DS, Grahame JW, Bonhomme F, Rand DM. Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci. Ecology 2009; 89:S91-107. [PMID: 19097487 DOI: 10.1890/07-1162.1] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.
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Affiliation(s)
- Paul S Schmidt
- Department of Biology, 433 South University Avenue, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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