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Calboli FCF, Delahaut V, Deflem I, Hablützel PI, Hellemans B, Kordas A, Raeymaekers JAM, Bervoets L, De Boeck G, Volckaert FAM. Association between Chromosome 4 and mercury accumulation in muscle of the three-spined stickleback ( Gasterosteus aculeatus). Evol Appl 2021; 14:2553-2567. [PMID: 34745343 PMCID: PMC8549617 DOI: 10.1111/eva.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 08/18/2021] [Accepted: 08/29/2021] [Indexed: 11/29/2022] Open
Abstract
Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome-wide association study (GWAS) between 28,450 single nucleotide polymorphisms (SNPs) and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on Chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kb distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback.
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Affiliation(s)
- Federico C. F. Calboli
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
- Present address:
Natural Resources Institute Finland (Luke)HelsinkiFinland
| | - Vyshal Delahaut
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
| | - Io Deflem
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | | | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | - Anna Kordas
- Laboratory of Biodiversity and Evolutionary GenomicsKU LeuvenLeuvenBelgium
| | | | - Lieven Bervoets
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
| | - Gudrun De Boeck
- Department of BiologySystemic Physiological and Ecotoxicological Research (SPHERE)University of AntwerpAntwerpenBelgium
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Schregel J, Kopatz A, Eiken HG, Swenson JE, Hagen SB. Sex-specific genetic analysis indicates low correlation between demographic and genetic connectivity in the Scandinavian brown bear (Ursus arctos). PLoS One 2017; 12:e0180701. [PMID: 28672045 PMCID: PMC5495496 DOI: 10.1371/journal.pone.0180701] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/20/2017] [Indexed: 11/30/2022] Open
Abstract
The degree of gene flow within and among populations, i.e. genetic population connectivity, may closely track demographic population connectivity. Alternatively, the rate of gene flow may change relative to the rate of dispersal. In this study, we explored the relationship between genetic and demographic population connectivity using the Scandinavian brown bear as model species, due to its pronounced male dispersal and female philopatry. Thus, we expected that females would shape genetic structure locally, whereas males would act as genetic mediators among regions. To test this, we used eight validated microsatellite markers on 1531 individuals sampled noninvasively during country-wide genetic population monitoring in Sweden and Norway from 2006 to 2013. First, we determined sex-specific genetic structure and substructure across the study area. Second, we compared genetic differentiation, migration/gene flow patterns, and spatial autocorrelation results between the sexes both within and among genetic clusters and geographic regions. Our results indicated that demographic connectivity was not a reliable indicator of genetic connectivity. Among regions, we found no consistent difference in long-term gene flow and estimated current migration rates between males and females. Within regions/genetic clusters, only females consistently displayed significant positive spatial autocorrelation, indicating male-biased small-scale dispersal. In one cluster, however, males showed a dispersal pattern similar to females. The Scandinavian brown bear population has experienced substantial recovery over the last decades; however, our results did not show any changes in its large-scale population structure compared to previous studies, suggesting that an increase in population size and dispersal of individuals does not necessary lead to increased genetic connectivity. Thus, we conclude that both genetic and demographic connectivity should be estimated, so as not to make false assumptions about the reality of wildlife populations.
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Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
- Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management, Ǻs, Norway
- * E-mail: (JS); (SBH)
| | - Alexander Kopatz
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
| | - Jon E. Swenson
- Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management, Ǻs, Norway
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
- * E-mail: (JS); (SBH)
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Konijnendijk N, Shikano T, Daneels D, Volckaert FAM, Raeymaekers JAM. Signatures of selection in the three-spined stickleback along a small-scale brackish water - freshwater transition zone. Ecol Evol 2015; 5:4174-86. [PMID: 26445666 PMCID: PMC4588664 DOI: 10.1002/ece3.1671] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/13/2015] [Accepted: 07/22/2015] [Indexed: 01/31/2023] Open
Abstract
Local adaptation is often obvious when gene flow is impeded, such as observed at large spatial scales and across strong ecological contrasts. However, it becomes less certain at small scales such as between adjacent populations or across weak ecological contrasts, when gene flow is strong. While studies on genomic adaptation tend to focus on the former, less is known about the genomic targets of natural selection in the latter situation. In this study, we investigate genomic adaptation in populations of the three-spined stickleback Gasterosteus aculeatus L. across a small-scale ecological transition with salinities ranging from brackish to fresh. Adaptation to salinity has been repeatedly demonstrated in this species. A genome scan based on 87 microsatellite markers revealed only few signatures of selection, likely owing to the constraints that homogenizing gene flow puts on adaptive divergence. However, the detected loci appear repeatedly as targets of selection in similar studies of genomic adaptation in the three-spined stickleback. We conclude that the signature of genomic selection in the face of strong gene flow is weak, yet detectable. We argue that the range of studies of genomic divergence should be extended to include more systems characterized by limited geographical and ecological isolation, which is often a realistic setting in nature.
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Affiliation(s)
- Nellie Konijnendijk
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Takahito Shikano
- Ecological Genetics Research Unit Department of Biosciences University of Helsinki P.O. Box 65 FI-000 14 Helsinki Finland
| | - Dorien Daneels
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
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Engler JO, Balkenhol N, Filz KJ, Habel JC, Rödder D. Comparative landscape genetics of three closely related sympatric Hesperid butterflies with diverging ecological traits. PLoS One 2014; 9:e106526. [PMID: 25184414 PMCID: PMC4153614 DOI: 10.1371/journal.pone.0106526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 08/07/2014] [Indexed: 12/02/2022] Open
Abstract
To understand how landscape characteristics affect gene flow in species with diverging ecological traits, it is important to analyze taxonomically related sympatric species in the same landscape using identical methods. Here, we present such a comparative landscape genetic study involving three closely related Hesperid butterflies of the genus Thymelicus that represent a gradient of diverging ecological traits. We analyzed landscape effects on their gene flow by deriving inter-population connectivity estimates based on different species distribution models (SDMs), which were calculated from multiple landscape parameters. We then used SDM output maps to calculate circuit-theoretic connectivity estimates and statistically compared these estimates to actual genetic differentiation in each species. We based our inferences on two different analytical methods and two metrics of genetic differentiation. Results indicate that land use patterns influence population connectivity in the least mobile specialist T. acteon. In contrast, populations of the highly mobile generalist T. lineola were panmictic, lacking any landscape related effect on genetic differentiation. In the species with ecological traits in between those of the congeners, T. sylvestris, climate has a strong impact on inter-population connectivity. However, the relative importance of different landscape factors for connectivity varies when using different metrics of genetic differentiation in this species. Our results show that closely related species representing a gradient of ecological traits also show genetic structures and landscape genetic relationships that gradually change from a geographical macro- to micro-scale. Thus, the type and magnitude of landscape effects on gene flow can differ strongly even among closely related species inhabiting the same landscape, and depend on their relative degree of specialization. In addition, the use of different genetic differentiation metrics makes it possible to detect recent changes in the relative importance of landscape factors affecting gene flow, which likely change as a result of contemporary habitat alterations.
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Affiliation(s)
- Jan O. Engler
- Zoological Research Museum Alexander Koenig, Bonn, Germany
- Department of Wildlife Sciences, University of Göttingen, Göttingen, Germany
- * E-mail:
| | - Niko Balkenhol
- Department of Wildlife Sciences, University of Göttingen, Göttingen, Germany
| | - Katharina J. Filz
- Department of Biogeography, Trier University, Trier, Germany
- Museum of Natural History Dortmund, Dortmund, Germany
| | - Jan C. Habel
- Department of Ecology and Ecosystemmanagement, Technical University Munich, Freising-Weihenstephan, Germany
| | - Dennis Rödder
- Zoological Research Museum Alexander Koenig, Bonn, Germany
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Lega M, Fior S, Li M, Leonardi S, Varotto C. Genetic Drift Linked to Heterogeneous Landscape and Ecological Specialization Drives Diversification in the Alpine Endemic Columbine Aquilegia thalictrifolia. J Hered 2014; 105:542-554. [PMID: 24864044 DOI: 10.1093/jhered/esu028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 02/10/2014] [Indexed: 11/13/2022] Open
Abstract
The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this work, we used 9 microsatellite loci to study the genetic structure and diversity of 11 populations of Aquilegia thalictrifolia Schott & Kotschy, an alpine taxon characterized by a marked ecological specificity. We found that, despite the endemic and fragmented distribution, A. thalictrifolia has overall high levels of heterozygosity, which is consistent to the substantial inbreeding depression that characterizes the genus. Strong spatial genetic structuring of populations suggests a historical prevalence of genetic drift over gene flow, with natural barriers and ecological niche hindering migration. An analytical comparison of fixation and population differentiation indexes allowed us to infer hypotheses of the postglacial history and more recent demographic events that have influenced the genetics of the species. Overall, our results indicate allopatry as a major force of differentiation in the European scenario, likely to underlie the development of taxonomic boundaries in a broader geographic context. This adds to previous notions on the primary evolutionary forces shaping the Aquilegia radiation in Europe.
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Affiliation(s)
- Margherita Lega
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Simone Fior
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Mingai Li
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Stefano Leonardi
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi)
| | - Claudio Varotto
- From the Department of Biodiversity and Molecular Ecology, Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy (Lega, Fior, Li, and Varotto); the Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland (Fior), and the Dipartimento di Bioscienze, Università di Parma, Parma, Italy (Leonardi).
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Raeymaekers JAM, Konijnendijk N, Larmuseau MHD, Hellemans B, De Meester L, Volckaert FAM. A gene with major phenotypic effects as a target for selection vs. homogenizing gene flow. Mol Ecol 2013; 23:162-81. [PMID: 24192132 DOI: 10.1111/mec.12582] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/20/2013] [Accepted: 10/28/2013] [Indexed: 01/28/2023]
Abstract
Genes with major phenotypic effects facilitate quantifying the contribution of genetic vs. plastic effects to adaptive divergence. A classical example is Ectodysplasin (Eda), the major gene controlling lateral plate phenotype in three-spined stickleback. Completely plated marine stickleback populations evolved repeatedly towards low-plated freshwater populations, representing a prime example of parallel evolution by natural selection. However, many populations remain polymorphic for lateral plate number. Possible explanations for this polymorphism include relaxation of selection, disruptive selection or a balance between divergent selection and gene flow. We investigated 15 polymorphic stickleback populations from brackish and freshwater habitats in coastal North-western Europe. At each site, we tracked changes in allele frequency at the Eda gene between subadults in fall, adults in spring and juveniles in summer. Eda genotypes were also compared for body size and reproductive investment. We observed a fitness advantage for the Eda allele for the low morph in freshwater and for the allele for the complete morph in brackish water. Despite these results, the differentiation at the Eda gene was poorly correlated with habitat characteristics. Neutral population structure was the best predictor of spatial variation in lateral plate number, suggestive of a substantial effect of gene flow. A meta-analysis revealed that the signature of selection at Eda was weak compared to similar studies in stickleback. We conclude that a balance between divergent selection and gene flow can maintain stickleback populations polymorphic for lateral plate number and that ecologically relevant genes may not always contribute much to local adaptation, even when targeted by selection.
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Affiliation(s)
- Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Ch. Deberiotstraat 32, Leuven, B-3000, Belgium; Zoological Institute, University of Basel, Vesalgasse 1, Basel, CH-4051, Switzerland
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Swaegers J, Mergeay J, Therry L, Larmuseau MHD, Bonte D, Stoks R. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly. Heredity (Edinb) 2013; 111:422-9. [PMID: 23820582 DOI: 10.1038/hdy.2013.64] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 04/03/2013] [Accepted: 05/15/2013] [Indexed: 01/14/2023] Open
Abstract
Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations.
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Affiliation(s)
- J Swaegers
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, Leuven, Belgium
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Harniman R, Merritt TJS, Chapman LJ, Lesbarrères D, Martinez ML. Population differentiation of the African cyprinid Barbus neumayeri across dissolved oxygen regimes. Ecol Evol 2013; 3:1495-506. [PMID: 23789062 PMCID: PMC3686186 DOI: 10.1002/ece3.561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 11/10/2022] Open
Abstract
Population level response to hypoxia has become an issue of global significance because of increased frequency and intensity of hypoxic events worldwide, and the potential for global warming to exacerbate hypoxic stress. In this study, we sequenced two nuclear intronic regions and a single mitochondrial region across seven populations of the African cyprinid, Barbus neumayeri from two river drainages in Uganda: the Rwembaita Swamp-Njuguta River System and the Dura River. We then examined two indices of population structure, G ST and Jost's D, to detect links between oxygen availability and genetic variation and to determine if population genetic structure was associated with (i) dissolved oxygen regime (hypoxia or normoxia), (ii) geographical distance, or (iii) a combination of dissolved oxygen regime and geographical distance. Our results indicate that over a large scale (between drainages), geographical distance significantly affects the genetic structure of populations. However, within a single drainage, dissolved oxygen regime plays a key role in determining the genetic structure of populations. Within the Rwembaita-Njuguta system, gene flow was high between locations of similar oxygen regimes, but low between areas characterized by divergent oxygen regimes. Interestingly, G ST analyses appear to yield less realistic measures of population structure than Jost's D, suggesting that caution must be taken when interpreting and comparing the results from different studies. These results support the idea that aquatic dissolved oxygen can act as a selective force limiting gene flow among populations of aquatic species and therefore should be considered when implementing conservation plans and assessing environmental impact of human activities.
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Affiliation(s)
- Robert Harniman
- Department of Biology, Laurentian University 935 Ramsey Lake Road, Sudbury, Ontario, P3E 2C6, Canada
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