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Bernardi G, Azzurro E, Bariche M, Jimenez C, Kalogirou S, Kleitou P. Invasion genomics of lionfish in the Mediterranean Sea. Ecol Evol 2024; 14:e11087. [PMID: 38450316 PMCID: PMC10915480 DOI: 10.1002/ece3.11087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
The rate of biological invasions is steadily increasing, with major ecological and economic impacts accounting for billions of dollars in damage as a result. One spectacular example is the western Atlantic invasion by lionfishes. In the Mediterranean Sea, invasions from the Red Sea via the Suez Canal (termed Lessepsian invasions) comprise more than 100 fish species, including a recent invasion by lionfish. In light of the devastating effects of lionfish in the Caribbean Sea, understanding the dynamics of Mediterranean lionfish invasion is crucial. The Lessepsian lionfish invasion started in 2012, and rapidly spread to the central Mediterranean. Here, we used thousands of RAD seq genomic markers to study the population dynamics of this invasion. While we did not find a reduction in genetic diversity between source (Red Sea) and invasive (Mediterranean) populations (i.e., bottleneck effects), we found evidence of population structure within the invasive range in the Mediterranean Sea. We found that loci that are potentially under selection may play an important role in invasion success (in particular, genes involved in osmoregulation and fin spine sizes). Genomic approaches proved powerful in examining the ecological and evolutionary patterns of successful invaders and may be used as tools to understand and potentially mitigate future invasions.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCaliforniaUSA
| | - Ernesto Azzurro
- CNR‐IRBIM, National Research CouncilInstitute of Biological Resources and Marine BiotechnologiesAnconaItaly
- Zoological Station A. DohrnNaplesItaly
| | - Michel Bariche
- Department of BiologyAmerican University of BeirutBeirutLebanon
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre (ENALIA)NicosiaCyprus
- The Cyprus InstituteEnergy Environment and Water Research CenterNicosiaCyprus
| | - Stefanos Kalogirou
- Hellenic Centre for Marine Research, Institute for Marine Biological Resources and Inland WatersHydrobiological Station of RhodesRhodesGreece
| | - Periklis Kleitou
- Marine & Environmental Research (MER) LabLimassolCyprus
- School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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2
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S Raposo D, A Zufall R, Caruso A, Titelboim D, Abramovich S, Hassenrück C, Kucera M, Morard R. Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction. Sci Rep 2023; 13:12578. [PMID: 37537233 PMCID: PMC10400638 DOI: 10.1038/s41598-023-39652-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Among the most successful Lessepsian invaders is the symbiont-bearing benthic foraminifera Amphistegina lobifera. In its newly conquered habitat, this prolific calcifier and ecosystem engineer is exposed to environmental conditions that exceed the range of its native habitat. To disentangle which processes facilitated the invasion success of A. lobifera into the Mediterranean Sea we analyzed a ~ 1400 bp sequence fragment covering the SSU and ITS gene markers to compare the populations from its native regions and along the invasion gradient. The genetic variability was studied at four levels: intra-genomic, population, regional and geographical. We observed that the invasion is not associated with genetic differentiation, but the invasive populations show a distinct suppression of intra-genomic variability among the multiple copies of the rRNA gene. A reduced genetic diversity compared to the Indopacific is observed already in the Red Sea populations and their high dispersal potential into the Mediterranean appears consistent with a bridgehead effect resulting from the postglacial expansion from the Indian Ocean into the Red Sea. We conclude that the genetic structure of the invasive populations reflects two processes: high dispersal ability of the Red Sea source population pre-adapted to Mediterranean conditions and a likely suppression of sexual reproduction in the invader. This discovery provides a new perspective on the cost of invasion in marine protists: The success of the invasive A. lobifera in the Mediterranean Sea comes at the cost of abandonment of sexual reproduction.
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Affiliation(s)
- Débora S Raposo
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany.
| | - Rebecca A Zufall
- Department of Biology and Biochemistry, University of Houston, Houston, USA
| | - Antonio Caruso
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - Danna Titelboim
- Department of Earth Sciences, University of Oxford, Oxford, UK
| | - Sigal Abramovich
- Department of Earth and Environmental Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Christiane Hassenrück
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock, Warnemünde, Germany
| | - Michal Kucera
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
| | - Raphaël Morard
- Center for Marine Environmental Sciences, MARUM, Universität Bremen, Bremen, Germany
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3
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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] [Grants] [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 SciencesUniversity of GothenburgGothenburgSweden
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
| | - Ellika Faust
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
- Gothenburg Global Biodiversity CentreUniversity of GothenburgGothenburgSweden
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
| | - James Hinchcliffe
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Jeroen Brijs
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Institute of Marine BiologyUniversity of Hawai'iKaneoheHawai'iUSA
| | - Andrew Holmes
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
| | - Felix Englund Örn
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
| | - Ola Svensson
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
- Department of Educational WorkUniversity of BoråsBoråsSweden
| | - Jonathan A. C. Roques
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Erica H. Leder
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
- Tjärnö Marine Laboratory, Department of Marine SciencesUniversity of GothenburgStrömstadSweden
- Natural History MuseumUniversity of OsloOsloNorway
| | - Erik Sandblom
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Charlotta Kvarnemo
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Linnaeus Centre for Marine Evolutionary BiologyUniversity of GothenburgStrömstadSweden
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4
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Konopiński MK, Fijarczyk AM, Biedrzycka A. Complex patterns shape immune genes diversity during invasion of common raccoon in Europe - Selection in action despite genetic drift. Evol Appl 2023; 16:134-151. [PMID: 36699132 PMCID: PMC9850017 DOI: 10.1111/eva.13517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon Procyon lotor invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific single-nucleotide polymorphism markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, that is - less genetically diverse invasive population from the Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.
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Affiliation(s)
| | - Anna M. Fijarczyk
- Laval University Département de BiologieUniversité LavalQuébecQuébecCanada
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Azzurro E, Nourigat M, Cohn F, Ben Souissi J, Bernardi G. Right out of the gate: the genomics of Lessepsian invaders in the vicinity of the Suez Canal. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractMarine organisms that enter the Mediterranean from the Red Sea via the Suez Canal are known as Lessepsian bioinvaders. In general, genetic studies of Lessepsian fishes have shown little structure between Red Sea and Mediterranean populations. Yet notable exceptions suggest the importance of life-history factors that may influence patterns of spatial genetic variation. In this study, by sampling two invasive fishes with different life histories (the rabbitfish Siganus rivulatus and the filefish Stephanolepis diaspros), we looked at evidence of population structure and selection at the boundary between the Red Sea and the Mediterranean (the Suez Canal), using thousands of molecular markers. Results illustrate two divergent patterns of genetic patterns, with little genetic structure in S. rivulatus and strong population structure in S. diaspros, even at such small spatial scale. We discuss differences in ecological characteristics between the two species to account for such differences. In addition, we report that in the face of both high (S. rivulatus) and low (S. diaspros) gene flow, loci under selection were uncovered, and some protein coding genes were identified as being involved with osmoregulation, which seems to be an important feature of individuals crossing the salinity-variable Suez Canal. The presence of genes under selection in populations near the Suez Canal supports the idea that selection may be active and essential for successful invasions right out of the gate.
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Chen Y, Zhao L, Teng H, Shi C, Liu Q, Zhang J, Zhang Y. Population genomics reveal rapid genetic differentiation in a recently invasive population of Rattus norvegicus. Front Zool 2021; 18:6. [PMID: 33499890 PMCID: PMC7836188 DOI: 10.1186/s12983-021-00387-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/17/2021] [Indexed: 12/19/2022] Open
Abstract
Background Invasive species bring a serious effect on local biodiversity, ecosystems, and even human health and safety. Although the genetic signatures of historical range expansions have been explored in an array of species, the genetic consequences of contemporary range expansions have received little attention, especially in mammal species. In this study, we used whole-genome sequencing to explore the rapid genetic change and introduction history of a newly invasive brown rat (Rattus norvegicus) population which invaded Xinjiang Province, China in the late 1970s. Results Bayesian clustering analysis, principal components analysis, and phylogenetic analysis all showed clear genetic differentiation between newly introduced and native rat populations. Reduced genetic diversity and high linkage disequilibrium suggested a severe population bottleneck in this colonization event. Results of TreeMix analyses revealed that the introduced rats were derived from an adjacent population in geographic region (Northwest China). Demographic analysis indicated that a severe bottleneck occurred in XJ population after the split off from the source population, and the divergence of XJ population might have started before the invasion of XJ. Moreover, we detected 42 protein-coding genes with allele frequency shifts throughout the genome for XJ rats and they were mainly associated with lipid metabolism and immunity, which could be seen as a prelude to future selection analyses in the novel environment of XJ. Conclusions This study presents the first genomic evidence on genetic differentiation which developed rapidly, and deepens the understanding of invasion history and evolutionary processes of this newly introduced rat population. This would add to our understanding of how invasive species become established and aid strategies aimed at the management of this notorious pest that have spread around the world with humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-021-00387-z.
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Affiliation(s)
- Yi Chen
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Chengmin Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Quansheng Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jianxu Zhang
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
| | - Yaohua Zhang
- The State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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7
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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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Wegner KM, Lokmer A, John U. Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.567049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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9
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Charbonnel N, Galan M, Tatard C, Loiseau A, Diagne C, Dalecky A, Parrinello H, Rialle S, Severac D, Brouat C. Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal. Sci Rep 2020; 10:18257. [PMID: 33106535 PMCID: PMC7589499 DOI: 10.1038/s41598-020-75060-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/28/2020] [Indexed: 01/09/2023] Open
Abstract
Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.
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Affiliation(s)
- Nathalie Charbonnel
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Caroline Tatard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Christophe Diagne
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- Départment de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Fann, Dakar, Senegal
| | | | - Hugues Parrinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Stephanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Carine Brouat
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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Wesselmann M, Anton A, Duarte CM, Hendriks IE, Agustí S, Savva I, Apostolaki ET, Marbà N. Tropical seagrass Halophila stipulacea shifts thermal tolerance during Mediterranean invasion. Proc Biol Sci 2020; 287:20193001. [PMID: 32156215 PMCID: PMC7126082 DOI: 10.1098/rspb.2019.3001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
Exotic species often face new environmental conditions that are different from those that they are adapted to. The tropical seagrass Halophila stipulacea is a Lessepsian migrant that colonized the Mediterranean Sea around 100 years ago, where at present the minimum seawater temperature is cooler than in its native range in the Red Sea. Here, we tested if the temperature range in which H. stipulacea can exist is conserved within the species or if the exotic populations have shifted their thermal breadth and optimum due to the cooler conditions in the Mediterranean. We did so by comparing the thermal niche (e.g. optimal temperatures, and upper and lower thermal limits) of native (Saudi Arabia in the Red Sea) and exotic (Greece and Cyprus in the Mediterranean Sea) populations of H. stipulacea. We exposed plants to 12 temperature treatments ranging from 8 to 40°C for 7 days. At the end of the incubation period, we measured survival, rhizome elongation, shoot recruitment, net population growth and metabolic rates. Upper and lower lethal thermal thresholds (indicated by 50% plant mortality) were conserved across populations, but minimum and optimal temperatures for growth and oxygen production were lower for Mediterranean populations than for the Red Sea one. The displacement of the thermal niche of exotic populations towards the colder Mediterranean Sea regime could have occurred within 175 clonal generations.
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Affiliation(s)
- Marlene Wesselmann
- Global Change Research Group, IMEDEA (CSIC-UIB), Institut Mediterrani d'Estudis Avançats, Miquel Marquès 21, 07190, Esporles, Illes Balears, Spain
| | - Andrea Anton
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M. Duarte
- Red Sea Research Centre (RSRC) and Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Iris E. Hendriks
- Global Change Research Group, IMEDEA (CSIC-UIB), Institut Mediterrani d'Estudis Avançats, Miquel Marquès 21, 07190, Esporles, Illes Balears, Spain
| | - Susana Agustí
- Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ioannis Savva
- Marine and Environmental Research (MER) Lab, Limassol 4533, Cyprus
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, PO Box 2214, 71003 Heraklion, Crete, Greece
| | - Núria Marbà
- Global Change Research Group, IMEDEA (CSIC-UIB), Institut Mediterrani d'Estudis Avançats, Miquel Marquès 21, 07190, Esporles, Illes Balears, Spain
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11
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Garcia E, Simison WB, Bernardi G. Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis). J Hered 2020; 111:57-69. [DOI: 10.1093/jhered/esz071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractStudying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.
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Affiliation(s)
- Eric Garcia
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
- Department of Biological Sciences, Old Dominion University, Norfolk, VA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - Giacomo Bernardi
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
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12
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Vaux F, Rasmuson LK, Kautzi LA, Rankin PS, Blume MTO, Lawrence KA, Bohn S, O'Malley KG. Sex matters: Otolith shape and genomic variation in deacon rockfish ( Sebastes diaconus). Ecol Evol 2019; 9:13153-13173. [PMID: 31871636 PMCID: PMC6912905 DOI: 10.1002/ece3.5763] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/15/2022] Open
Abstract
Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50-km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.
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Affiliation(s)
- Felix Vaux
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - Leif K. Rasmuson
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Lisa A. Kautzi
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Polly S. Rankin
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | | | - Kelly A. Lawrence
- Marine Resources ProgramOregon Department of Fish and WildlifeNewportORUSA
| | - Sandra Bohn
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
| | - Kathleen G. O'Malley
- State Fisheries Genomics LabCoastal Oregon Marine Experiment StationDepartment of Fisheries and WildlifeHatfield Marine Science CenterOregon State UniversityNewportORUSA
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13
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The genomics of invasion: characterization of red lionfish (Pterois volitans) populations from the native and introduced ranges. Biol Invasions 2019. [DOI: 10.1007/s10530-019-01992-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Berumen ML, Roberts MB, Sinclair-Taylor TH, DiBattista JD, Saenz-Agudelo P, Isari S, He S, Khalil MT, Hardenstine RS, Tietbohl MD, Priest MA, Kattan A, Coker DJ. Fishes and Connectivity of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Chen Y, Shenkar N, Ni P, Lin Y, Li S, Zhan A. Rapid microevolution during recent range expansion to harsh environments. BMC Evol Biol 2018; 18:187. [PMID: 30526493 PMCID: PMC6286502 DOI: 10.1186/s12862-018-1311-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/27/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Adaptive evolution is one of the crucial mechanisms for organisms to survive and thrive in new environments. Recent studies suggest that adaptive evolution could rapidly occur in species to respond to novel environments or environmental challenges during range expansion. However, for environmental adaptation, many studies successfully detected phenotypic features associated with local environments, but did not provide ample genetic evidence on microevolutionary dynamics. It is therefore crucial to thoroughly investigate the genetic basis of rapid microevolution in response to environmental changes, in particular on what genes and associated variation are responsible for environmental challenges. Here, we genotyped genome-wide gene-associated microsatellites to detect genetic signatures of rapid microevolution of a marine tunicate invader, Ciona robusta, during recent range expansion to the harsh environment in the Red Sea. RESULTS The Red Sea population was significantly differentiated from the other global populations. The genome-wide scan, as well as multiple analytical methods, successfully identified a set of adaptive genes. Interestingly, the allele frequency largely varied at several adaptive loci in the Red Sea population, and we found significant correlations between allele frequency and local environmental factors at these adaptive loci. Furthermore, a set of genes were annotated to get involved in local temperature and salinity adaptation, and the identified adaptive genes may largely contribute to the invasion success to harsh environments. CONCLUSIONS All the evidence obtained in this study clearly showed that environment-driven selection had left detectable signatures in the genome of Ciona robusta within a few generations. Such a rapid microevolutionary process is largely responsible for the harsh environmental adaptation and therefore contributes to invasion success in different aquatic ecosystems with largely varied environmental factors.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, 6997801, Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel-Aviv, Israel
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yaping Lin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China.
- University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing, 100049, China.
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16
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Bernardi G, Nelson P, Paddack M, Rulmal J, Crane N. Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes. Ecol Evol 2018; 8:8676-8685. [PMID: 30271536 PMCID: PMC6157655 DOI: 10.1002/ece3.4417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/15/2022] Open
Abstract
The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.
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Affiliation(s)
- Giacomo Bernardi
- Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | | | | | - John Rulmal
- Ulithi Falalop Community Action ProgramYapFederated States of Micronesia
| | - Nicole Crane
- Department of BiologyCabrillo CollegeAptosCalifornia
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17
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Stern N, Jimenez C, Huseyinoglu MF, Andreou V, Hadjioannou L, Petrou A, Öztürk B, Golani D, Rothman SBS. Constructing the genetic population demography of the invasive lionfish Pterois miles in the Levant Basin, Eastern Mediterranean. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:249-255. [DOI: 10.1080/24701394.2018.1482284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Nir Stern
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Carlos Jimenez
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | | | - Vasilis Andreou
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | | | - Antonis Petrou
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | - Bayram Öztürk
- Faculty of Fisheries, İstanbul University, İstanbul, Turkey
| | - Daniel Golani
- Department of Ecology, Evolution and Behavior and the National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shevy B. S. Rothman
- School of Zoology, The George S. Wise Faculty of Life Sciences and the Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
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18
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Successful worldwide invasion of the veined rapa whelk, Rapana venosa, despite a dramatic genetic bottleneck. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1774-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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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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20
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Leydet KP, Grupstra CGB, Coma R, Ribes M, Hellberg ME. Host-targeted RAD-Seq reveals genetic changes in the coralOculina patagonicaassociated with range expansion along the Spanish Mediterranean coast. Mol Ecol 2018; 27:2529-2543. [DOI: 10.1111/mec.14702] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Karine Posbic Leydet
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
| | - Carsten G. B. Grupstra
- Institute for Biodiversity and Ecosystem Dynamics; University of Amsterdam; Amsterdam The Netherlands
- Institut de Ciències del mar; Barcelona Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes; Blanes Girona Spain
| | - Marta Ribes
- Institut de Ciències del mar; Barcelona Spain
| | - Michael E. Hellberg
- Department of Biological Sciences; Louisiana State University; Baton Rouge Louisiana
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21
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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22
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Wang YZ, Li BY, Hoffmann AA, Cao LJ, Gong YJ, Song W, Zhu JY, Wei SJ. Patterns of genetic variation among geographic and host-plant associated populations of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae). BMC Evol Biol 2017; 17:265. [PMID: 29262770 PMCID: PMC5738824 DOI: 10.1186/s12862-017-1116-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/14/2017] [Indexed: 11/29/2022] Open
Abstract
Background Populations of herbivorous insects may become genetically differentiated because of local adaptation to different hosts and climates as well as historical processes, and further genetic divergence may occur following the development of reproductive isolation among populations. Here we investigate the population genetic structure of the orchard pest peach fruit moth (PFM) Carposina sasakii (Lepidoptera: Carposinidae) in China, which shows distinct biological differences when characterized from different host plants. Genetic diversity and genetic structure were assessed among populations from seven plant hosts and nine regions using 19 microsatellite loci and a mitochondrial sequence. Results Strong genetic differentiation was found among geographical populations representing distinct geographical regions, but not in host-associated populations collected from the same area. Mantel tests based on microsatellite loci indicated an association between genetic differentiation and geographical distance, and to a lesser extent environmental differentiation. Approximate Bayesian Computation analyses supported the scenario that PFM likely originated from a southern area and dispersed northwards before the last glacial maximum during the Quaternary. Conclusions Our analyses suggested a strong impact of geographical barriers and historical events rather than host plants on the genetic structure of the PFM; however, uncharacterized environmental factors and host plants may also play a role. Studies on adaptive shifts in this moth should take into account geographical and historical factors. Electronic supplementary material The online version of this article (10.1186/s12862-017-1116-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- You-Zhu Wang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Bing-Yan Li
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China.,Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Ary Anthony Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Li-Jun Cao
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Ya-Jun Gong
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Wei Song
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, 650224, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguanghuayuan Middle Road, Haidian District, Beijing, 100097, China.
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23
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Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering. Sci Rep 2017; 7:17598. [PMID: 29242627 PMCID: PMC5730610 DOI: 10.1038/s41598-017-16810-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/15/2017] [Indexed: 12/17/2022] Open
Abstract
The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher FST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.
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24
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Huang X, Li S, Ni P, Gao Y, Jiang B, Zhou Z, Zhan A. Rapid response to changing environments during biological invasions: DNA methylation perspectives. Mol Ecol 2017; 26:6621-6633. [PMID: 29057612 DOI: 10.1111/mec.14382] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 10/01/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Abstract
Dissecting complex interactions between species and their environments has long been a research hot spot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well-explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly molecular mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environmental adaptation. Here, we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole-genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1 hr of high-temperature exposure or after 3 hr of low-salinity challenge. In addition, we detected time-dependent hemimethylation changes and increased intragroup epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hr) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole-genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation.
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Affiliation(s)
- Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bei Jiang
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Research Institute, Dalian, Liaoning, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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25
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Azzurro E, Maynou F, Belmaker J, Golani D, Crooks JA. Lag times in Lessepsian fish invasion. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1184-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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