1
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Dong YW. Roles of multi-level temperature-adaptive responses and microhabitat variation in establishing distributions of intertidal species. J Exp Biol 2023; 226:jeb245745. [PMID: 37909420 DOI: 10.1242/jeb.245745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
How intertidal species survive their harsh environment and how best to evaluate and forecast range shifts in species distribution are two important and closely related questions for intertidal ecologists and global change biologists. Adaptive variation in responses of organisms to environmental change across all levels of biological organization - from behavior to molecular systems - is of key importance in setting distribution patterns, yet studies often neglect the interactions of diverse types of biological variation (e.g. differences in thermal optima owing to genetic and acclimation-induced effects) with environmental variation, notably at the scale of microhabitats. Intertidal species have to cope with extreme and frequently changing thermal stress, and have shown high variation in thermal sensitivities and adaptive responses at different levels of biological organization. Here, I review the physiological and biochemical adaptations of intertidal species to environmental temperature on multiple spatial and temporal scales. With fine-scale datasets for the thermal limits of individuals and for environmental temperature variation at the microhabitat scale, we can map the thermal sensitivity for each individual in different microhabitats, and then scale up the thermal sensitivity analysis to the population level and, finally, to the species level by incorporating physiological traits into species distribution models. These more refined mechanistic models that include consideration of physiological variations have higher predictive power than models that neglect these variations, and they will be crucial to answering the questions posed above concerning adaptive mechanisms and the roles they play in governing distribution patterns in a rapidly changing world.
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Affiliation(s)
- Yun-Wei Dong
- Ministry Key Laboratory of Mariculture, Fisheries College, Ocean University of China, Qingdao 266001, China
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2
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Green L, Faust E, Hinchcliffe J, Brijs J, Holmes A, Englund Örn F, Svensson O, Roques JAC, Leder EH, Sandblom E, Kvarnemo C. Invader at the edge - Genomic origins and physiological differences of round gobies across a steep urban salinity gradient. Evol Appl 2023; 16:321-337. [PMID: 36793700 PMCID: PMC9923490 DOI: 10.1111/eva.13437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022] Open
Abstract
Species invasions are a global problem of increasing concern, especially in highly connected aquatic environments. Despite this, salinity conditions can pose physiological barriers to their spread, and understanding them is important for management. In Scandinavia's largest cargo port, the invasive round goby (Neogobius melanostomus) is established across a steep salinity gradient. We used 12,937 SNPs to identify the genetic origin and diversity of three sites along the salinity gradient and round goby from western, central and northern Baltic Sea, as well as north European rivers. Fish from two sites from the extreme ends of the gradient were also acclimated to freshwater and seawater, and tested for respiratory and osmoregulatory physiology. Fish from the high-salinity environment in the outer port showed higher genetic diversity, and closer relatedness to the other regions, compared to fish from lower salinity upstream the river. Fish from the high-salinity site also had higher maximum metabolic rate, fewer blood cells and lower blood Ca2+. Despite these genotypic and phenotypic differences, salinity acclimation affected fish from both sites in the same way: seawater increased the blood osmolality and Na+ levels, and freshwater increased the levels of the stress hormone cortisol. Our results show genotypic and phenotypic differences over short spatial scales across this steep salinity gradient. These patterns of the physiologically robust round goby are likely driven by multiple introductions into the high-salinity site, and a process of sorting, likely based on behaviour or selection, along the gradient. This euryhaline fish risks spreading from this area, and seascape genomics and phenotypic characterization can inform management strategies even within an area as small as a coastal harbour inlet.
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Affiliation(s)
- Leon Green
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden
| | - Ellika Faust
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Gothenburg Global Biodiversity Centre University of Gothenburg Gothenburg Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden
| | - James Hinchcliffe
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Jeroen Brijs
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Institute of Marine Biology University of Hawai'i Kaneohe Hawai'i USA
| | - Andrew Holmes
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
| | - Felix Englund Örn
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
| | - Ola Svensson
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Department of Educational Work University of Borås Borås Sweden
| | - Jonathan A C Roques
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Erica H Leder
- Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden.,Tjärnö Marine Laboratory, Department of Marine Sciences University of Gothenburg Strömstad Sweden.,Natural History Museum University of Oslo Oslo Norway
| | - Erik Sandblom
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden.,Linnaeus Centre for Marine Evolutionary Biology University of Gothenburg Strömstad Sweden
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3
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Martínez M, González-Aravena M, Held C, Abele D. A molecular perspective on the invasibility of the southern ocean benthos: The impact of hypoxia and temperature on gene expression in South American and Antarctic Aequiyoldia bivalves. Front Physiol 2023; 14:1083240. [PMID: 36895632 PMCID: PMC9989211 DOI: 10.3389/fphys.2023.1083240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
When an organism makes a long-distance transition to a new habitat, the associated environmental change is often marked and requires physiological plasticity of larvae, juveniles, or other migrant stages. Exposing shallow-water marine bivalves (Aequiyoldia cf. eightsii) from southern South America (SSA) and the West Antarctic Peninsula (WAP) to changes in temperature and oxygen availability, we investigated changes in gene expression in a simulated colonization experiment of the shores of a new continent after crossing of the Drake Passage, and in a warming scenario in the WAP. Bivalves from SSA were cooled from 7°C (in situ) to 4°C and 2°C (future warmed WAP conditions), WAP bivalves were warmed from 1.5°C (current summer in situ) to 4°C (warmed WAP), gene expression patterns in response to thermal stress by itself and in combination with hypoxia were measured after 10 days. Our results confirm that molecular plasticity may play a vital role for local adaptation. Hypoxia had a greater effect on the transcriptome than temperature alone. The effect was further amplified when hypoxia and temperature acted as combined stressors. The WAP bivalves showed a remarkable ability to cope with short-term exposure to hypoxia by switching to a metabolic rate depression strategy and activating the alternative oxidation pathway, whilst the SSA population showed no comparable response. In SSA, the high prevalence of apoptosis-related differentially expressed genes especially under combined higher temperatures and hypoxia indicated that the SSA Aequiyoldia are operating near their physiological limits already. While the effect of temperature per se may not represent the single most effective barrier to Antarctic colonization by South American bivalves, the current distribution patterns as well as their resilience to future conditions can be better understood by looking at the synergistic effects of temperature in conjunction with short-term exposure to hypoxia.
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Affiliation(s)
- Mariano Martínez
- Funktionelle Ökologie, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | | | - Christoph Held
- Funktionelle Ökologie, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Doris Abele
- Funktionelle Ökologie, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
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4
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Hudson J, Bourne SD, Seebens H, Chapman MA, Rius M. The reconstruction of invasion histories with genomic data in light of differing levels of anthropogenic transport. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210023. [PMID: 35067090 PMCID: PMC8784929 DOI: 10.1098/rstb.2021.0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Unravelling the history of range shifts is key for understanding past, current and future species distributions. Anthropogenic transport of species alters natural dispersal patterns and directly affects population connectivity. Studies have suggested that high levels of anthropogenic transport homogenize patterns of genetic differentiation and blur colonization pathways. However, empirical evidence of these effects remains elusive. We compared two range-shifting species (Microcosmus squamiger and Ciona robusta) to examine how anthropogenic transport affects our ability to reconstruct colonization pathways using genomic data. We first investigated shipping networks from the 18th century onwards, cross-referencing these with regions where the species have records to infer how each species has potentially been affected by different levels of anthropogenic transport. We then genotyped thousands of single-nucleotide polymorphisms from 280 M. squamiger and 190 C. robusta individuals collected across their extensive species' ranges and reconstructed colonization pathways. Differing levels of anthropogenic transport did not preclude the elucidation of population structure, though specific inferences of colonization pathways were difficult to discern in some of the considered scenario sets. We conclude that genomic data in combination with information of underlying introduction drivers provide key insights into the historic spread of range-shifting species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.
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Affiliation(s)
- J Hudson
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - S D Bourne
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK
| | - H Seebens
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt, Germany
| | - M A Chapman
- Department of Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - M Rius
- School of Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton SO14 3ZH, UK.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park 2006, South Africa.,Centre for Advanced Studies of Blanes (CEAB, CSIC), Accés a la Cala Sant Francesc 14, Blanes 17300, Spain
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5
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Jahnke M, Moknes P, Le‐Moan A, Martens GA, Jonsson PR. Seascape genomics identify adaptive barriers correlated to tidal amplitude in the shore crab
Carcinus maenas. Mol Ecol 2022; 31:1980-1994. [PMID: 35080070 PMCID: PMC9540756 DOI: 10.1111/mec.16371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/27/2022]
Abstract
Most marine invertebrates disperse during a planktonic larval stage that may drift for weeks with ocean currents. A challenge for larvae of coastal species is to return to coastal nursery habitats. Shore crab (Carcinus maenas L.) larvae are known to show tidal rhythmicity in vertical migration in tidal areas and circadian rhythmicity in microtidal areas, which seems to increase successful coastal settlement. We studied genome‐wide differentiation based on 24,000 single nucleotide polymorphisms of 12 native populations of shore crab sampled from a large tidal amplitude gradient from macrotidal (~8 m) to microtidal (~0.2 m). Dispersal and recruitment success of larvae was assessed with a Lagrangian biophysical model, which showed a strong effect of larval behaviour on long‐term connectivity, and dispersal barriers that partly coincided with different tidal environments. The genetic population structure showed a subdivision of the samples into three clusters, which represent micro‐, meso‐ and macrotidal areas. The genetic differentiation was mostly driven by 0.5% outlier loci, which showed strong allelic clines located at the limits between the three tidal areas. Demographic modelling suggested that the two genetic barriers have different origins. Differential gene expression of two clock genes (cyc and pdp1) further highlighted phenotypic differences among genetic clusters that are potentially linked to the differences in larval behaviour. Taken together, our seascape genomic study suggests that tidal regime acts as a strong selection force on shore crab population structure, consistent with larval behaviour affecting dispersal and recruitment success.
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Affiliation(s)
- Marlene Jahnke
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
| | - Per‐Olav Moknes
- Department of Marine Science University of Gothenburg Gothenburg Sweden
| | - Alan Le‐Moan
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
| | - Gerrit A. Martens
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
- Institute of Zoology University of Hamburg Hamburg Germany
| | - Per R. Jonsson
- Department of Marine Sciences Tjärnö Marine Laboratory University of Gothenburg SE‐45296 Strömstad Sweden
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6
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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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7
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Prentice MB, Vye SR, Jenkins SR, Shaw PW, Ironside JE. Genetic diversity and relatedness in aquaculture and marina populations of the invasive tunicate Didemnum vexillum in the British Isles. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02615-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractIntroductions of invasive, non-native species in the marine environment are increasing as human activity within coastal areas rises. Genetic datasets are useful tools to identify source populations, track routes of invasions, and illuminate the role of genetic variation in the establishment and subsequent spread of novel introductions. Here, a microsatellite dataset is used to estimate the genetic diversity and population structure of 7 introduced Didemnum vexillum populations in Britain and Ireland, 4 of which are associated with aquaculture and 3 with marinas. Genetic differentiation observed between these populations indicates human-mediated transport as the main mechanism underlying the population structure of D. vexillum in Britain and Ireland. In addition to elucidating patterns of population structure we found that aquaculture sites showed significantly higher genetic diversity (measured as allelic richness) in comparison to the marina sites. We discuss these findings in relation to the history of each invasion, the complex life history of D. vexillum, and available evidence of the relative invasiveness of these populations. Our results show numerous interesting patterns which highlight further research avenues to elucidate the complex factors underlying the global spread of this successful invader.
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8
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Stage-specific overcompensation, the hydra effect, and the failure to eradicate an invasive predator. Proc Natl Acad Sci U S A 2021; 118:2003955118. [PMID: 33727416 DOI: 10.1073/pnas.2003955118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As biological invasions continue to increase globally, eradication programs have been undertaken at significant cost, often without consideration of relevant ecological theory. Theoretical fisheries models have shown that harvest can actually increase the equilibrium size of a population, and uncontrolled studies and anecdotal reports have documented population increases in response to invasive species removal (akin to fisheries harvest). Both findings may be driven by high levels of juvenile survival associated with low adult abundance, often referred to as overcompensation. Here we show that in a coastal marine ecosystem, an eradication program resulted in stage-specific overcompensation and a 30-fold, single-year increase in the population of an introduced predator. Data collected concurrently from four adjacent regional bays without eradication efforts showed no similar population increase, indicating a local and not a regional increase. Specifically, the eradication program had inadvertently reduced the control of recruitment by adults via cannibalism, thereby facilitating the population explosion. Mesocosm experiments confirmed that adult cannibalism of recruits was size-dependent and could control recruitment. Genomic data show substantial isolation of this population and implicate internal population dynamics for the increase, rather than recruitment from other locations. More broadly, this controlled experimental demonstration of stage-specific overcompensation in an aquatic system provides an important cautionary message for eradication efforts of species with limited connectivity and similar life histories.
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9
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Resh CA, Galaska MP, Benesh KC, Gardner JPA, Wei KJ, Yan RJ, Mahon AR. Using Genomics to Link Populations of an Invasive Species to Its Potential Sources. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.575599] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The introduction and subsequent range expansion of the Northern snakehead (Channa argus: Channidae, Anabantiformes) is one of a growing number of problematic biological invasions in the United States. This harmful aquatic invasive species is a predatory freshwater fish native to northeastern Asia that, following deliberate introduction, has established itself in multiple water basins in the eastern United States, as well as expanding its range into the Midwest. Previous work assessed the population structure and estimated the long-term effective population sizes of the populations present in the United States, but the source of the initial introduction(s) to the U.S. remains unidentified. Building on earlier work, we used whole genome scans (2b-RAD genomic sequencing) to analyze single nucleotide polymorphisms (SNPs) from C. argus to screen the genomes of these invasive fish from United States waters and from three sites in their native range in China. We recovered 2,822 SNP loci from genomic DNA extracted from 164 fish sampled from the eastern United States and Arkansas (Mississippi River basin), plus 30 fish sampled from three regions of the Yangtze River basin in China (n = 10 individuals per basin). Our results provide evidence supporting the Yangtze River basin in China, specifically the Bohu and/or Liangzi lakes, is a likely source of the C. argus introductions in multiple regions of the U.S., including the Lower Hudson River basin, Upper Hudson River basin and Philadelphia (Lower Delaware River basin). This information, in conjunction with additional sampling from the native range, will help to determine the source(s) of introduction for the other U.S. populations. Additionally, this work will provide valuable information for management to help prevent and manage future introductions into United States waterways, as well as aid in the development of more targeted strategies to regulate established populations and inhibit further spread.
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10
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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11
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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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12
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Segovia NI, González-Wevar CA, Haye PA. Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast. Sci Rep 2020; 10:14098. [PMID: 32839518 PMCID: PMC7445245 DOI: 10.1038/s41598-020-70798-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022] Open
Abstract
The highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29–585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.
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Affiliation(s)
- Nicolás I Segovia
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.,Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile
| | - Claudio A González-Wevar
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Instituto de Ecología Y Biodiversidad IEB, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Marinas Y Limnológicas (ICML), Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,Centro FONDAP de Investigaciones en Dinámica de Ecosistemas de Altas Latitudes (IDEAL), Universidad Austral de Chile, Valdivia, Chile
| | - Pilar A Haye
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile.
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13
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Tepolt CK, Blakeslee AMH, Fowler AE, Darling JA, Torchin ME, Miller AW, Ruiz GM. Strong genetic structure in a widespread estuarine crab: A test of potential versus realized dispersal. JOURNAL OF BIOGEOGRAPHY 2020; 47:2532-2542. [PMID: 38269398 PMCID: PMC10807247 DOI: 10.1111/jbi.13919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 05/03/2020] [Indexed: 01/26/2024]
Abstract
Aim Genetic structure has proven difficult to predict for marine and estuarine species with multi-day pelagic larval durations, since many disperse far less than expected based on passive transport models. In such cases, the gap between potential and realized dispersal may result from larval behaviours that evolved to facilitate retention and settlement in favourable environments. Behaviour is predicted to play a particularly key role in structuring truly estuarine species, which often moderate their behaviour to remain within their natal estuaries. In such systems, this restricted dispersal may lead to high divergence, local adaptation and eventual speciation across their range. Here, we test whether a geographically widespread estuarine crab, known to have behaviour promoting larval retention, exhibits high population structure despite a 2- to 4-week larval duration. Location Atlantic and Gulf Coasts of North America. Taxon White-fingered mud crab, Rhithropanopeus harrisii. Methods Population genomic analyses across nine estuaries from New Hampshire to Louisiana using 12,638 transcriptome-derived SNPs. Results We found highly differentiated genetic signatures among all nine estuaries, separated by 200-5,000 km of coastline. Estimates of gene flow suggest that migration is low and largely symmetrical between sites. We also observed deep phylogenetic divides corresponding to major biogeographical breaks. Main conclusions These results indicate substantial and longstanding constraints to dispersal in the species' native range, likely arising from the emergence of geological and oceanographic barriers and sustained by behaviour that promotes estuarine retention during larval development. This work supports the idea that larval behaviour promoting estuarine retention can be reflected in substantial genetic structure even in species with multi-week pelagic larval durations. Such behaviour-restricted dispersal has implications for predicting adaptation and spread in estuarine species, many of which have been introduced outside their native ranges.
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Affiliation(s)
- Carolyn K. Tepolt
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Woods Hole Oceanographic Institution, Department of Biology, Woods Hole, MA
| | | | - Amy E. Fowler
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | - John A. Darling
- Center for Environmental Measurement and Modeling, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Mark E. Torchin
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | | | - Gregory M. Ruiz
- Smithsonian Environmental Research Center, Edgewater, MD, USA
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14
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Cornwell BH. Gene flow in the anemone
Anthopleura elegantissima
limits signatures of local adaptation across an extensive geographic range. Mol Ecol 2020; 29:2550-2566. [DOI: 10.1111/mec.15506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/22/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
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15
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Freedman AH, Clamp M, Sackton TB. Error, noise and bias in de novo transcriptome assemblies. Mol Ecol Resour 2020; 21:18-29. [PMID: 32180366 DOI: 10.1111/1755-0998.13156] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/25/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
De novo transcriptome assembly is a powerful tool, and has been widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed transcripts. Using publicly available data for model organisms, we demonstrate that, across assembly algorithms and data sets, these assumptions are consistently violated. Bias exists at the nucleotide level, with genotyping error rates ranging from 30% to 83%. As a result, diversity is underestimated in transcriptome assemblies, with consistent underestimation of heterozygosity in all but the most inbred samples. Even at the gene level, expression estimates show wide deviations from map-to-reference estimates, and positive bias at lower expression levels. Standard filtering of transcriptome assemblies improves the robustness of gene expression estimates but leads to the loss of a meaningful number of protein-coding genes, including many that are highly expressed. We demonstrate a computational method, length-rescaled CPM, to partly alleviate noise and bias in expression estimates. Researchers should consider ways to minimize the impact of bias in transcriptome assemblies.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
| | - Michele Clamp
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
| | - Timothy B Sackton
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, MA, USA
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16
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Popovic I, Matias AMA, Bierne N, Riginos C. Twin introductions by independent invader mussel lineages are both associated with recent admixture with a native congener in Australia. Evol Appl 2020; 13:515-532. [PMID: 32431733 PMCID: PMC7045716 DOI: 10.1111/eva.12857] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 06/27/2019] [Accepted: 07/24/2019] [Indexed: 01/04/2023] Open
Abstract
Introduced species can impose profound impacts on the evolution of receiving communities with which they interact. If native and introduced taxa remain reproductively semi-isolated, human-mediated secondary contact may promote genetic exchange across newly created hybrid zones, potentially impacting native genetic diversity and invasive species spread. Here, we investigate the contributions of recent divergence histories and ongoing (post-introduction) gene flow between the invasive marine mussel, Mytilus galloprovincialis, and a morphologically indistinguishable and taxonomically contentious native Australian taxon, Mytilus planulatus. Using transcriptome-wide markers, we demonstrate that two contemporary M. galloprovincialis introductions into south-eastern Australia originate from genetically divergent lineages from its native range in the Mediterranean Sea and Atlantic Europe, where both introductions have led to repeated instances of admixture between introduced and endemic populations. Through increased genome-wide resolution of species relationships, combined with demographic modelling, we validate that mussels sampled in Tasmania are representative of the endemic Australian taxon (M. planulatus), but share strong genetic affinities to M. galloprovincialis. Demographic inferences indicate late-Pleistocene divergence times and historical gene flow between the Tasmanian endemic lineage and northern M. galloprovincialis, suggesting that native and introduced taxa have experienced a period of historical isolation of at least 100,000 years. Our results demonstrate that many genomic loci and sufficient sampling of closely related lineages in both sympatric (e.g. Australian populations) and allopatric (e.g. northern hemisphere Mytilus taxa) ranges are necessary to accurately (a) interpret patterns of intraspecific differentiation and to (b) distinguish contemporary invasive introgression from signatures left by recent divergence histories in high dispersal marine species. More broadly, our study fills a significant gap in systematic knowledge of native Australian biodiversity and sheds light on the intrinsic challenges for invasive species research when native and introduced species boundaries are not well defined.
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Affiliation(s)
- Iva Popovic
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
| | | | - Nicolas Bierne
- Institut des Sciences de l’EvolutionUMR 5554CNRS‐IRD‐EPHE‐UMUniversité de MontpellierMontpellierFrance
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandSt LuciaQldAustralia
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17
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Verwimp C, Vansteenbrugge L, Derycke S, Kerkhove T, Muylle H, Honnay O, Ruttink T, Roldán‐Ruiz I, Hostens K. Population genomic structure of the gelatinous zooplankton species Mnemiopsis leidyi in its nonindigenous range in the North Sea. Ecol Evol 2020; 10:11-25. [PMID: 31988713 PMCID: PMC6972810 DOI: 10.1002/ece3.5468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 11/07/2022] Open
Abstract
Nonindigenous species pose a major threat for coastal and estuarine ecosystems. Risk management requires genetic information to establish appropriate management units and infer introduction and dispersal routes. We investigated one of the most successful marine invaders, the ctenophore Mnemiopsis leidyi, and used genotyping-by-sequencing (GBS) to explore the spatial population structure in its nonindigenous range in the North Sea. We analyzed 140 specimens collected in different environments, including coastal and estuarine areas, and ports along the coast. Single nucleotide polymorphisms (SNPs) were called in approximately 40 k GBS loci. Population structure based on the neutral SNP panel was significant (F ST .02; p < .01), and a distinct genetic cluster was identified in a port along the Belgian coast (Ostend port; pairwise F ST .02-.04; p < .01). Remarkably, no population structure was detected between geographically distant regions in the North Sea (the Southern part of the North Sea vs. the Kattegat/Skagerrak region), which indicates substantial gene flow at this geographical scale and recent population expansion of nonindigenous M. leidyi. Additionally, seven specimens collected at one location in the indigenous range (Chesapeake Bay, USA) were highly differentiated from the North Sea populations (pairwise F ST .36-.39; p < .01). This study demonstrates the utility of GBS to investigate fine-scale population structure of gelatinous zooplankton species and shows high population connectivity among nonindigenous populations of this recently introduced species in the North Sea. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at: The DNA sequences generated for this study are deposited in the NCBI sequence read archive under SRA accession numbers SRR6950721-SRR6950884, and will be made publically available upon publication of this manuscript.
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Affiliation(s)
- Christophe Verwimp
- Animal Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)MelleBelgium
- Department of Biology, Plant Conservation and Population BiologyUniversity of Leuven (KUL)HeverleeBelgium
| | - Lies Vansteenbrugge
- Animal Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
| | - Sofie Derycke
- Animal Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
- Marine Biology Research GroupGhent UniversityGentBelgium
| | - Thomas Kerkhove
- Animal Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
- Marine Biology Research GroupGhent UniversityGentBelgium
| | - Hilde Muylle
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)MelleBelgium
| | - Olivier Honnay
- Department of Biology, Plant Conservation and Population BiologyUniversity of Leuven (KUL)HeverleeBelgium
| | - Tom Ruttink
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)MelleBelgium
| | - Isabel Roldán‐Ruiz
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)MelleBelgium
- Department of Plant Biotechnology and BioinformaticsGhent UniversityZwijnaardeBelgium
| | - Kris Hostens
- Animal Sciences UnitFlanders Research Institute for Agriculture, Fisheries and Food (ILVO)OostendeBelgium
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18
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Abstract
Carcinus maenas (the “shore crab” or “European green crab”) is a very proficient invader (considered to be one of the world’s 100 worst invaders by the IUCN) due to its phenotypic plasticity, wide temperature and salinity tolerance, and an extensive omnivorous diet. Native to Atlantic Europe, it has established two well-studied nonindigenous populations in the northwestern Atlantic and northeastern Pacific and less-studied populations in Australia, Argentina and South Africa. Green crabs are eurythermal and euryhaline as adults, but they are limited to temperate coastlines due to more restrictive temperature requirements for breeding and larval development. They cannot tolerate wave-swept open shores so are found in wave-protected sheltered bays, estuaries and harbors. Carcinus maenas has been the subject of numerous papers, with over 1000 published in the past decade. This review provides an up-to-date account of the current published information on the life history and population dynamics of this very important species, including genetic differentiation, habitat preferences, physical parameter tolerances, reproduction and larval development, sizes of crabs, densities of populations, sex ratios, ecosystem dynamics and ecological impacts in the various established global populations of green crabs.
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19
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Coyle AE, Voss ER, Tepolt CK, Carlon DB. Mitochondrial genotype influences the response to cold stress in the European green crab, Carcinus maenas. J Exp Biol 2019; 222:jeb203521. [PMID: 31285243 DOI: 10.1242/jeb.203521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 12/20/2022]
Abstract
Hybrid zones provide natural experiments in recombination within and between genomes that may have strong effects on organismal fitness. On the East Coast of North America, two distinct lineages of the European green crab (Carcinus maenas) have been introduced in the last two centuries. These two lineages with putatively different adaptive properties have hybridized along the coast of the eastern Gulf of Maine, producing new nuclear and mitochondrial combinations that show clinal variation correlated with water temperature. To test the hypothesis that mitochondrial or nuclear genes have effects on thermal tolerance, we first measured the response to cold stress in crabs collected throughout the hybrid zone, then sequenced the mitochondrial CO1 gene and two nuclear single nucleotide polymorphisms (SNPs) representative of nuclear genetic lineage. Mitochondrial haplotype had a strong association with the ability of crabs to right themselves at 4.5°C that was sex specific: haplotypes originally from northern Europe gave male crabs an advantage while there was no haplotype effect on righting in female crabs. By contrast, the two nuclear SNPs that were significant outliers in a comparison between northern and southern C. maenas populations had no effect on righting response at low temperature. These results add C. maenas to the shortlist of ectotherms in which mitochondrial variation has been shown to affect thermal tolerance, and suggest that natural selection is shaping the structure of the hybrid zone across the Gulf of Maine. Our limited genomic sampling does not eliminate the strong possibility that mito-nuclear co-adaptation may play a role in the differences in thermal phenotypes documented here. Linkage between mitochondrial genotype and thermal tolerance suggests a role for local adaptation in promoting the spread of invasive populations of C. maenas around the world.
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Affiliation(s)
- Aspen E Coyle
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
| | - Erin R Voss
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
| | - Carolyn K Tepolt
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - David B Carlon
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
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20
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Casso M, Turon X, Pascual M. Single zooids, multiple loci: independent colonisations revealed by population genomics of a global invader. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02069-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Silliman K. Population structure, genetic connectivity, and adaptation in the Olympia oyster ( Ostrea lurida) along the west coast of North America. Evol Appl 2019; 12:923-939. [PMID: 31080505 PMCID: PMC6503834 DOI: 10.1111/eva.12766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/28/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023] Open
Abstract
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of O. lurida.
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22
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Stepien CA, Snyder MR, Elz AE. Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS One 2019; 14:e0203012. [PMID: 30917127 PMCID: PMC6436794 DOI: 10.1371/journal.pone.0203012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/19/2022] Open
Abstract
In the 1970s, the introduced silver carp Hypophthalmichthys molitrix (which is indigenous to eastern Asia) escaped from southern U.S. aquaculture to spread throughout the Mississippi River basin, and since has steadily moved northward. This large, prolific filter-feeder reduces food availability for other fishes. It now has reached the threshold of the Laurentian Great Lakes, where it likely will significantly impact food chains and fisheries. Our study evaluates population genetic variability and differentiation of the silver carp using 10 nuclear DNA microsatellite loci, and sequences of two mitochondrial genes-cytochrome b and cytochrome c oxidase subunit 1, along with the nuclear ribosomal protein S7 gene intron 1. We analyze population samples from: two primary Great Lakes' invasion fronts (at the Illinois River outside of Chicago, IL in Lake Michigan and in the Wabash River, which leads into the Maumee River and western Lake Erie), the original establishment "core" in the Lower Mississippi River, and expansion areas in the Upper Mississippi and Missouri rivers. We analyze and compare our results with bighead and other invasive carps, and cyprinid relatives. Results reveal that the silver carp invasion possesses moderate levels of genetic diversity, with more mtDNA haplotypes and unique microsatellite alleles in the "core" Lower Mississippi River population, which also diverges the most. The two invasion fronts also significantly genetically differ. About 3% of individuals (including all populations except the Illinois River) contain a unique and very divergent mtDNA haplotype, which likely stems from historic introgression in Asia with female largescale silver carp H. harmandi. The nuclear microsatellites and S7 sequences of the introgressed individuals do not differ from silver carp and are very distant from bighead carp. These sequence variation data are employed to design and evaluate a targeted high-throughput metabarcoding sequence assay that identifies and distinguishes among species of invasive carps (i.e., silver, bighead, grass, black, and common carps, along with goldfish), as well as native cyprinids, using cytochrome b. Our assay further differentiates among selected silver carp haplotypes (including between H. molitrix and H. harmandi), for use in population genetics and future analyses of spread pathways. We test and evaluate this assay on environmental (e)DNA water samples from 48 bait shops in the Great Lakes' region (along the Lake Erie, Lake St. Clair, and Wabash River watersheds), using positive and negative controls and custom bioinformatic processing. Test results discern silver carp eDNA in four of the shops-three in Lake Erie and one in the Wabash River watershed-and bighead carp from one of the same Lake Erie venues, suggesting that retailers (who often source from established southerly populations) comprise another introduction vector. Our overall findings thus provide key population genetic and phylogenetic data for understanding and tracing introductions, vectors, and spread pathways for silver carp, their variants, and their relatives.
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Affiliation(s)
- Carol A. Stepien
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Matthew R. Snyder
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
| | - Anna E. Elz
- NOAA Pacific Marine Environmental Laboratory, Genetics and Genomics Group (G3), Seattle, WA, United States of America
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23
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Bors EK, Herrera S, Morris JA, Shank TM. Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure. Ecol Evol 2019; 9:3306-3320. [PMID: 30962894 PMCID: PMC6434604 DOI: 10.1002/ece3.4952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 01/10/2023] Open
Abstract
Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme-associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an F ST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.
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Affiliation(s)
- Eleanor K. Bors
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
- Marine Mammal Institute, Department of Fisheries and WildlifeOregon State UniversityNewportOregon
| | - Santiago Herrera
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvania
| | - James A. Morris
- National Oceanic and Atmospheric Administration, National Ocean ServiceNational Centers for Coastal Ocean ScienceBeaufortNorth Carolina
| | - Timothy M. Shank
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
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24
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Lehnert SJ, DiBacco C, Jeffery NW, Blakeslee AMH, Isaksson J, Roman J, Wringe BF, Stanley RRE, Matheson K, McKenzie CH, Hamilton LC, Bradbury IR. Temporal dynamics of genetic clines of invasive European green crab ( Carcinus maenas) in eastern North America. Evol Appl 2018; 11:1656-1670. [PMID: 30344634 PMCID: PMC6183463 DOI: 10.1111/eva.12657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We evaluated current clinal structure by quantifying the distribution of lineages and fine-scale hybridization patterns across the eastern North American range (25 locations, ~39 to 49°N) using informative single nucleotide polymorphisms (SNPs; n = 96). In addition, temporal changes in the genetic clines were evaluated using mitochondrial DNA and microsatellite loci (n = 9-11) over a 15-year period (2000-2015). Clinal structure was consistent with prior work demonstrating the existence of both northern and southern lineages with a hybrid zone occurring between southern New Brunswick (NB) and southern NS. Extensive later generation hybrids were detected in this region and in southeastern Newfoundland. Temporal genetic analysis confirmed the southward progression of clines over time; however, the rate of this progression was slower than predicted by forecasting models, and current clines for all marker types deviated significantly from these predictions. Our results suggest that neutral and selective processes contribute to cline dynamics, and ultimately, highlight how selection, hybridization, and dispersal can collectively influence invasion success.
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Affiliation(s)
- Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Claudio DiBacco
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Nicholas W. Jeffery
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | | | - Jonatan Isaksson
- Gund Institute for EnvironmentUniversity of VermontBurlingtonVermont
| | - Joe Roman
- Gund Institute for EnvironmentUniversity of VermontBurlingtonVermont
| | - Brendan F. Wringe
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | - Kyle Matheson
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Cynthia H. McKenzie
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
| | - Lorraine C. Hamilton
- Aquatic Biotechnology LaboratoryBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundlandCanada
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25
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Jeffery NW, Bradbury IR, Stanley RRE, Wringe BF, Van Wyngaarden M, Lowen JB, McKenzie CH, Matheson K, Sargent PS, DiBacco C. Genomewide evidence of environmentally mediated secondary contact of European green crab ( Carcinus maenas) lineages in eastern North America. Evol Appl 2018; 11:869-882. [PMID: 29928296 PMCID: PMC5999199 DOI: 10.1111/eva.12601] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
Genetic-environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation by distance. Here, we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of the invasive European green crab (Carcinus maenas) in eastern North America. Green crab populations in eastern North America are associated with two independent invasions, previously shown to consist of distinct northern and southern ecotypes, with a contact zone in southern Nova Scotia, Canada. Using a RAD-seq panel of 9,137 genomewide SNPs, we detected 41 SNPs (0.49%) whose allele frequencies were highly correlated with environmental data. A principal components analysis of 25 environmental variables differentiated populations into northern, southern, and admixed sites in concordance with the observed genomic spatial structure. Furthermore, a spatial principal components analysis conducted on genomic and geographic data revealed a high degree of global structure (p < .0001) partitioning a northern and southern ecotype. Redundancy and partial redundancy analyses revealed that among the environmental variables tested, winter sea surface temperature had the strongest association with spatial structuring, suggesting that it is an important factor defining range and expansion limits of each ecotype. Understanding environmental thresholds associated with intraspecific diversity will facilitate the ability to manage current and predict future distributions of this aquatic invasive species.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Faculty of Computer ScienceDalhousie UniversityHalifaxNSCanada
- Department of Ocean SciencesMemorial University of NewfoundlandSt. John’sNLCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Brendan F. Wringe
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | | | - J. Ben Lowen
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
| | - Cynthia H. McKenzie
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Kyle Matheson
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Philip S. Sargent
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Claudio DiBacco
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNSCanada
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26
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Bourne SD, Hudson J, Holman LE, Rius M. Marine Invasion Genomics: Revealing Ecological and Evolutionary Consequences of Biological Invasions. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/13836_2018_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Wellband KW, Pettitt-Wade H, Fisk AT, Heath DD. Standing genetic diversity and selection at functional gene loci are associated with differential invasion success in two non-native fish species. Mol Ecol 2018; 27:1572-1585. [PMID: 29573310 DOI: 10.1111/mec.14557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 02/25/2018] [Accepted: 03/07/2018] [Indexed: 12/30/2022]
Abstract
Invasive species are expected to experience a unique combination of high genetic drift due to demographic factors while also experiencing strong selective pressures. The paradigm that reduced genetic diversity should limit the evolutionary potential of invasive species, and thus, their potential for range expansion has received little empirical support, possibly due to the choice of genetic markers. Our goal was to test for effects of genetic drift and selection at functional genetic markers as they relate to the invasion success of two paired invasive goby species, one widespread (successful) and one with limited range expansion (less successful). We genotyped fish using two marker types: single nucleotide polymorphisms (SNPs) in known-function, protein-coding genes and microsatellites to contrast the effects of neutral genetic processes. We identified reduced allelic variation in the invaded range for the less successful tubenose goby. SNPs putatively under selection were responsible for the observed differences in population structure between marker types for round goby (successful) but not tubenose goby (less successful). A higher proportion of functional loci experienced divergent selection for round goby, suggesting increased evolutionary potential in invaded ranges may be associated with round goby's greater invasion success. Genes involved in thermal tolerance were divergent for round goby populations but not tubenose goby, consistent with the hypothesis that invasion success for fish in temperate regions is influenced by capacity for thermal tolerance. Our results highlight the need to incorporate functional genetic markers in studies to better assess evolutionary potential for the improved conservation and management of species.
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Affiliation(s)
- Kyle W Wellband
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Harri Pettitt-Wade
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Aaron T Fisk
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada.,Department of Biological Sciences, University of Windsor, Windsor, ON, Canada
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28
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Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms. Sci Rep 2018; 8:5062. [PMID: 29567984 PMCID: PMC5864727 DOI: 10.1038/s41598-018-23339-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 03/07/2018] [Indexed: 12/01/2022] Open
Abstract
Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish’s long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (FSTp-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.
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29
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Herrmann M, Ravindran SP, Schwenk K, Cordellier M. Population transcriptomics in Daphnia
: The role of thermal selection. Mol Ecol 2017; 27:387-402. [DOI: 10.1111/mec.14450] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 10/22/2017] [Accepted: 11/02/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Maike Herrmann
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
| | | | - Klaus Schwenk
- Institute for Environmental Sciences; University Koblenz-Landau; Landau in der Pfalz Germany
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30
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Dexter E, Bollens SM, Cordell J, Soh HY, Rollwagen-Bollens G, Pfeifer SP, Goudet J, Vuilleumier S. A genetic reconstruction of the invasion of the calanoid copepod Pseudodiaptomus inopinus across the North American Pacific Coast. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1649-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Benestan L, Moore JS, Sutherland BJG, Le Luyer J, Maaroufi H, Rougeux C, Normandeau E, Rycroft N, Atema J, Harris LN, Tallman RF, Greenwood SJ, Clark FK, Bernatchez L. Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems. Mol Ecol 2017; 26:6767-6783. [DOI: 10.1111/mec.14217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/23/2017] [Accepted: 03/29/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Laura Benestan
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jean-Sébastien Moore
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Ben J. G. Sutherland
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Jérémy Le Luyer
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Halim Maaroufi
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Clément Rougeux
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Eric Normandeau
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | | | - Jelle Atema
- Department of Biology; Boston University; Boston MA USA
| | - Les N. Harris
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Ross F. Tallman
- Fisheries and Oceans Canada; Freshwater Institute; Winnipeg MB Canada
| | - Spencer J. Greenwood
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Fraser K. Clark
- Department of Biomedical Sciences & AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown PE Canada
| | - Louis Bernatchez
- Département de Biologie; Université Laval; Québec QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
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32
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Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic. Heredity (Edinb) 2017; 119:154-165. [PMID: 28422135 DOI: 10.1038/hdy.2017.22] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/20/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022] Open
Abstract
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site-associated DNA sequencing (RAD-seq), microsatellite loci and cytochrome c oxidase subunit I mitochondrial DNA (mtDNA) sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2) and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.
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33
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Mao X, Tsagkogeorga G, Bailey SE, Rossiter SJ. Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xiuguang Mao
- Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Sebastian E. Bailey
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Stephen J. Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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34
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Jeffery NW, DiBacco C, Van Wyngaarden M, Hamilton LC, Stanley RRE, Bernier R, FitzGerald J, Matheson K, McKenzie CH, Nadukkalam Ravindran P, Beiko R, Bradbury IR. RAD sequencing reveals genomewide divergence between independent invasions of the European green crab ( Carcinus maenas) in the Northwest Atlantic. Ecol Evol 2017; 7:2513-2524. [PMID: 28428843 PMCID: PMC5395438 DOI: 10.1002/ece3.2872] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/08/2017] [Accepted: 02/10/2017] [Indexed: 01/10/2023] Open
Abstract
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction‐site‐associated DNA sequencing‐derived SNPs to explore fine‐scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.
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Affiliation(s)
- Nicholas W Jeffery
- Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's NL Canada
| | - Claudio DiBacco
- Bedford Institute of Oceanography Fisheries and Oceans Canada Dartmouth NS Canada
| | - Mallory Van Wyngaarden
- Ocean Sciences Center and Biology Department Memorial University of Newfoundland St John's NL Canada
| | - Lorraine C Hamilton
- Aquatic Biotechnology Laboratory Bedford Institute of Oceanography Dartmouth Nova Scotia Canada
| | - Ryan R E Stanley
- Bedford Institute of Oceanography Fisheries and Oceans Canada Dartmouth NS Canada
| | - Renée Bernier
- Gulf Fisheries Centre Fisheries and Oceans Canada Moncton New Brunswick Canada
| | - Jennifer FitzGerald
- Bedford Institute of Oceanography Fisheries and Oceans Canada Dartmouth NS Canada
| | - K Matheson
- Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's NL Canada
| | - C H McKenzie
- Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's NL Canada
| | | | - Robert Beiko
- Faculty of Computer Science Dalhousie University Halifax Nova Scotia Canada
| | - Ian R Bradbury
- Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada St. John's NL Canada
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35
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Snyder MR, Stepien CA. Genetic patterns across an invasion's history: a test of change versus stasis for the Eurasian round goby in North America. Mol Ecol 2017; 26:1075-1090. [PMID: 28029720 DOI: 10.1111/mec.13997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 01/11/2023]
Abstract
Biological invasions comprise accidental evolutionary experiments, whose genetic compositions underlie relative success, spread and persistence in new habitats. However, little is known about whether, or how, their population genetic patterns change temporally and/or spatially across the invasion's history. Theory predicts that most would undergo founder effect, exhibit low genetic divergence across the new range and gain variation over time via new arriving propagules. To test these predictions, we analyse population genetic diversity and divergence patterns of the Eurasian round goby Neogobius melanostomus across the two decades of its North American invasion in the Laurentian Great Lakes, comparing results from 13 nuclear DNA microsatellite loci and mitochondrial DNA cytochrome b sequences. We test whether 'genetic stasis', 'genetic replacement' and/or 'genetic supplement' scenarios have occurred at the invasion's core and expansion sites, in comparison with its primary native source population in the Dnieper River, Black Sea. Results reveal pronounced genetic divergence across the exotic range, with population areas remaining genetically distinct and statistically consistent across two decades, supporting 'genetic stasis' and 'founder takes most'. The original genotypes continue to predominate, whose high population growth likely outpaced the relative success of later arrivals. The original invasion core has stayed the most similar to the native source. Secondary expansion sites indicate slight allelic composition convergence towards the core population over time, attributable to some early 'genetic supplementation'. The geographic and temporal coverage of this investigation offers a rare opportunity to discern population dynamics over time and space in context of invasion genetic theory vs. reality.
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Affiliation(s)
- Matthew R Snyder
- Great Lakes Genetics/Genomics Laboratory, The Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH, 43606, USA.,NOAA Pacific Marine Environmental Laboratory, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
| | - Carol A Stepien
- Great Lakes Genetics/Genomics Laboratory, The Lake Erie Center and Department of Environmental Sciences, The University of Toledo, Toledo, OH, 43606, USA.,NOAA Pacific Marine Environmental Laboratory, 7600 Sand Point Way NE, Seattle, WA, 98115, USA
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36
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Viard F, David P, Darling JA. Marine invasions enter the genomic era: three lessons from the past, and the way forward. Curr Zool 2016; 62:629-642. [PMID: 29491950 PMCID: PMC5804250 DOI: 10.1093/cz/zow053] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/15/2016] [Indexed: 01/22/2023] Open
Abstract
The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, non-indigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments.
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Affiliation(s)
- Frédérique Viard
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Lab. Adaptation Et Diversité En Milieu Marin, Team Div&Co, Station Biologique De Roscoff, Roscoff 29682, France
| | - Patrice David
- CEFE UMR 5175, CNRS-Université De Montpellier-UM III-EPHE, 1919 Route De Mende, Montpellier Cedex 34293, France
| | - John A. Darling
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
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37
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Benestan L, Quinn BK, Maaroufi H, Laporte M, Clark FK, Greenwood SJ, Rochette R, Bernatchez L. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Mol Ecol 2016; 25:5073-5092. [DOI: 10.1111/mec.13811] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Laura Benestan
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Brady K. Quinn
- Department of Biological Sciences; University of New Brunswick; P.O. Box 5050 Saint John NB Canada E2L 4L5
| | - Halim Maaroufi
- Institut de Biologie Integrative et des Systemes (IBIS); Pavillon Charles-Eugène Marchand; 1030, Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Martin Laporte
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Fraser K. Clark
- Department of Biomedical Sciences; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
- AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
| | - Spencer J. Greenwood
- Department of Biomedical Sciences; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
- AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
| | - Rémy Rochette
- Department of Biological Sciences; University of New Brunswick; P.O. Box 5050 Saint John NB Canada E2L 4L5
| | - Louis Bernatchez
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
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38
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Humble E, Thorne MAS, Forcada J, Hoffman JI. Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success. BMC Res Notes 2016; 9:418. [PMID: 27562535 PMCID: PMC5000416 DOI: 10.1186/s13104-016-2209-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/06/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. RESULTS Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. CONCLUSIONS Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms.
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Affiliation(s)
- Emily Humble
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany. .,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK.
| | - Michael A S Thorne
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501, Bielefeld, Germany
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39
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DeBiasse MB, Kelly MW. Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1. J Hered 2015; 107:71-81. [DOI: 10.1093/jhered/esv073] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 08/06/2015] [Indexed: 01/02/2023] Open
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