Charles Perrier | Centre National de la Recherche Scientifique / French National Centre for Scientific Research (original) (raw)

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Research paper thumbnail of Adaptation Genomics in Urban Environments

Urban Evolutionary Biology

The field of urban ecology has provided many fascinating examples of organisms that display novel... more The field of urban ecology has provided many fascinating examples of organisms that display novel biological features in urban environments compared to natural habitats. Quantitative genetics provides a framework that can be used to investigate whether this phenotypic differentiation between urban and natural habitats is adaptive and is the result of heritable changes in response to divergent selection. New generation sequencing tools offer unique opportunities to expand our understanding of the genes and genetic mechanisms implicated in evolution in urban environments. This chapter first reviews quantitative genetics studies investigating the mechanisms of evolution in the city. It then reviews pioneering genomic studies that have shed light on the genes and genetic mechanisms implicated in urban microevolution. The authors discuss how further use of cost-effective high-resolution genomic approaches may improve the comprehension of both genomic and epigenomic mechanisms implicated ...

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Research paper thumbnail of Surface temperatures of non-incubated eggs in great tits (Parus major) are strongly associated with ambient temperature

International Journal of Biometeorology

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Research paper thumbnail of Demographic history and genomics of local adaptation in blue tit populations

Evolutionary Applications

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Research paper thumbnail of Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary p... more Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) admixture with the closely related anadromous L. fluviatilis ecotype having a positive effect on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled in 81 sites upstream and downstream from barriers to migration, in 29 West-European rivers. Linear modelling revealed a strong positive relationship between the distance to the source and genetic diversity, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a mode...

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Research paper thumbnail of Assortative Mating in Animals and Its Role for Speciation

The American Naturalist

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Research paper thumbnail of On the importance of time scales when studying adaptive evolution

Long-term field studies coupled with quantitative genomics offer a powerful means to understand t... more Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effect on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like recombination rate variations. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio-temporal variation in great tit bill length, w...

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Research paper thumbnail of Impact of supplementation on deleterious mutation distribution in an exploited salmonid

Evolutionary Applications

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Research paper thumbnail of Effect of riverscape and exotic introgression on the genetic structure and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a... more How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the introduction of exotic rainbow trout (O. mykiss) for aquaculture. The present study aimed to explore the effect of both genetic introgression from O. mykiss and riverscape variables on the genetic variation of O. chrysogaster. Genotyping-by-sequencing (GBS) was applied to generate 9 767 single nucleotide polymorphisms (SNPs), genotyping 270 O. chrysogaster and aquaculture trout. Population genomics analyses were combined with riverscape genetics approaches. A small degree of admixture was identified between aquaculture and native trout, and significant effects of riverscape variables on genetic diversity were detected, as well as evidence of isolation by riverscape resist...

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Research paper thumbnail of Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Evolutionary Applications

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Research paper thumbnail of Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient

Evolutionary Applications

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Research paper thumbnail of Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Molecular Ecology, 2016

Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among r... more Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.

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Research paper thumbnail of A species-specific microsatellite marker to discriminate European Atlantic salmon, brown trout, and their hybrids

Conservation Genetics Resources, 2011

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Research paper thumbnail of Structure génétique des populations de saumon Atlantique en France

Http Www Theses Fr, 2010

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Research paper thumbnail of Succès reproducteur des saumons ensemencés : Le cas de la rivière Malbaie

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Research paper thumbnail of Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

Understanding genomic signatures of divergent selection underlying long-term adaptation in popula... more Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Qu ebec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene–temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene–environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

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Research paper thumbnail of Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in lake superior

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Research paper thumbnail of Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among r... more Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating paral-lelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.

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Research paper thumbnail of Investigating genomic and phenotypic parallelism between piscivorous and planktivorous Lake Trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses

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Research paper thumbnail of Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

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Research paper thumbnail of Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits

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Research paper thumbnail of Adaptation Genomics in Urban Environments

Urban Evolutionary Biology

The field of urban ecology has provided many fascinating examples of organisms that display novel... more The field of urban ecology has provided many fascinating examples of organisms that display novel biological features in urban environments compared to natural habitats. Quantitative genetics provides a framework that can be used to investigate whether this phenotypic differentiation between urban and natural habitats is adaptive and is the result of heritable changes in response to divergent selection. New generation sequencing tools offer unique opportunities to expand our understanding of the genes and genetic mechanisms implicated in evolution in urban environments. This chapter first reviews quantitative genetics studies investigating the mechanisms of evolution in the city. It then reviews pioneering genomic studies that have shed light on the genes and genetic mechanisms implicated in urban microevolution. The authors discuss how further use of cost-effective high-resolution genomic approaches may improve the comprehension of both genomic and epigenomic mechanisms implicated ...

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Research paper thumbnail of Surface temperatures of non-incubated eggs in great tits (Parus major) are strongly associated with ambient temperature

International Journal of Biometeorology

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Demographic history and genomics of local adaptation in blue tit populations

Evolutionary Applications

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Riverscape genetics in brook lamprey: genetic diversity is less influenced by river fragmentation than by gene flow with the anadromous ecotype

Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary p... more Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident brook lamprey (Lampetra planeri) that has a low ability to pass obstacles to migration. We also tested the hypotheses of i) asymmetric gene flow following water current and ii) admixture with the closely related anadromous L. fluviatilis ecotype having a positive effect on L. planeri genetic diversity. We genotyped 2472 individuals, including 225 L. fluviatilis, sampled in 81 sites upstream and downstream from barriers to migration, in 29 West-European rivers. Linear modelling revealed a strong positive relationship between the distance to the source and genetic diversity, consistent with expected patterns of decreased gene flow into upstream populations. However, the presence of anthropogenic barriers had a mode...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Assortative Mating in Animals and Its Role for Speciation

The American Naturalist

Bookmarks Related papers MentionsView impact

Research paper thumbnail of On the importance of time scales when studying adaptive evolution

Long-term field studies coupled with quantitative genomics offer a powerful means to understand t... more Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with strikingly rapid phenotypic changes in data series, it remains unpredictable in the long term. Second, while the temporal dynamics of some loci with large effect on phenotypic variation and fitness have been characterized, this task can be complicated in cases of highly polygenic trait architecture implicating numerous small effect size loci, or when statistical tests are sensitive to the heterogeneity of some key characteristics of the genome, like recombination rate variations. After introducing these aforementioned challenges, we discuss a recent investigation of the genomic architecture and spatio-temporal variation in great tit bill length, w...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Impact of supplementation on deleterious mutation distribution in an exploited salmonid

Evolutionary Applications

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Effect of riverscape and exotic introgression on the genetic structure and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)

How environmental and anthropogenic factors influence genetic variation and local adaptation is a... more How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the introduction of exotic rainbow trout (O. mykiss) for aquaculture. The present study aimed to explore the effect of both genetic introgression from O. mykiss and riverscape variables on the genetic variation of O. chrysogaster. Genotyping-by-sequencing (GBS) was applied to generate 9 767 single nucleotide polymorphisms (SNPs), genotyping 270 O. chrysogaster and aquaculture trout. Population genomics analyses were combined with riverscape genetics approaches. A small degree of admixture was identified between aquaculture and native trout, and significant effects of riverscape variables on genetic diversity were detected, as well as evidence of isolation by riverscape resist...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Evolutionary Applications

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Research paper thumbnail of Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient

Evolutionary Applications

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Research paper thumbnail of Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Molecular Ecology, 2016

Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among r... more Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating parallelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A species-specific microsatellite marker to discriminate European Atlantic salmon, brown trout, and their hybrids

Conservation Genetics Resources, 2011

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Structure génétique des populations de saumon Atlantique en France

Http Www Theses Fr, 2010

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Succès reproducteur des saumons ensemencés : Le cas de la rivière Malbaie

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

Understanding genomic signatures of divergent selection underlying long-term adaptation in popula... more Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Qu ebec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene–temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene–environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in lake superior

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Inferring the demographic history underlying parallel genomic divergence among pairs of parasitic and nonparasitic lamprey ecotypes

Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among r... more Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident nonparasitic brook lamprey (Lampetra planeri) in nine population pairs displaying variable levels of geographic connectivity. We genotyped 338 individuals with RAD sequencing and inferred the demographic divergence history of each population pair using a diffusion approximation method. Divergence patterns in geographically connected population pairs were better explained by introgression after secondary contact, whereas disconnected population pairs have retained a signal of ancient migration. In all ecotype pairs, models accounting for differential introgression among loci outperformed homogeneous migration models. Generating neutral predictions from the inferred divergence scenarios to detect highly differentiated markers identified greater proportions of outliers in disconnected population pairs than in connected pairs. However, increased similarity in the most divergent genomic regions was found among connected ecotype pairs, indicating that gene flow was instrumental in generating paral-lelism at the molecular level. These results suggest that heterogeneous genomic differentiation and parallelism among replicate ecotype pairs have partly emerged through restricted introgression in genomic islands.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Investigating genomic and phenotypic parallelism between piscivorous and planktivorous Lake Trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Low but contrasting neutral genetic differentiation shaped by winter temperature in European great tits

Bookmarks Related papers MentionsView impact