Please note that this Research page has not been updated since 2016 and updating it is still in my to-do-list... For recent updates about my research work checking my publications page would be more accurate for sure :). But the best would always be to contact me if you have any interrogations
Current projects
Making sense of the relationships between Ne, Nb and Nc to define conservation thresholds in Atlantic salmon
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Genotyping of microsatellites across different rivers over 5 consecutive years
Effective population size over a generation (Ne) or over a reproductive cycle (Nb), and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. While Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, Nb represents a metric that may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose an empirical context to Waples et al. (2014), who introduced a correction to bias due to overlapping generations, and propose a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the short-term relationships between Ne, Nb, and Nc in 10 Atlantic salmon populations from Québec, Canada, genotyped at 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a strong positive relationship between Nb and Ne (99%), as well as a positive correlation between Nb and Nc suggesting that, in the case of Atlantic salmon populations, Nb is an indicative parameter for tracking population effective population size and abundance. However, our model allows predicting Nc from Nb values at 31 %, suggesting that a lot of variance in Nb/Nc exist both among populations (37 %) and among years for a same population (19 %). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such approach. Finally, we discuss the importance of these results for the management of wild populations
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Genotyping of microsatellites across different rivers over 5 consecutive years
Effective population size over a generation (Ne) or over a reproductive cycle (Nb), and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. While Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, Nb represents a metric that may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose an empirical context to Waples et al. (2014), who introduced a correction to bias due to overlapping generations, and propose a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the short-term relationships between Ne, Nb, and Nc in 10 Atlantic salmon populations from Québec, Canada, genotyped at 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a strong positive relationship between Nb and Ne (99%), as well as a positive correlation between Nb and Nc suggesting that, in the case of Atlantic salmon populations, Nb is an indicative parameter for tracking population effective population size and abundance. However, our model allows predicting Nc from Nb values at 31 %, suggesting that a lot of variance in Nb/Nc exist both among populations (37 %) and among years for a same population (19 %). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such approach. Finally, we discuss the importance of these results for the management of wild populations
Genotyping by sequencing wild lake trout populations
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Relative importance of drift and selection in shaping the distribution of genetic diversity? Can local adaptation still exist or appear a long time after population foundation? (ddRAD sequencing)
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, by mean of genotyping by sequencing, neutral and adaptive genetic variation in thirty-two lake trout (Salvelinus namaycush) populations from Québec, Canada. Demographic modeling based on 9000 SNPs revealed that half of the populations were likely to have undergone bottlenecks following lake colonization and isolation. Genetic diversity was relatively small and weakly shared among lakes, and mainly influenced by lake size, suggesting a major role for genetic drift. Several outlier loci were found linked to temperature and related to biologically relevant functions notably related to heat-stress immune responses. Outcomes of gene-temperature associations were notably influenced by the inclusion of populations with highest inbreeding coefficients, illustrating challenges in finding gene-environment associations in cases of high genetic drift and weak gene flow, as well as suggesting limitations for adaptations in smaller populations. We discuss the relevance of these findings for the conservation and management of lake trout populations, as other cold-water lake fish populations, notably regarding stocking and genetic rescue.
Population genomics of the brook charr through Quebec province and applications for fisheries
We are currently sequencing 50 natural brook charr populations throughout Quebec province. We aim to (i) assess population structuration in order to check the concordance between current fisheries management and the observed genetic structuration, (ii) assess the level of local adaptation throughout a temperature gradient (from southern to northern Quebec) and (iii) infer the evolutionary history of these population in order to highlight the most likelihood colonization history of this species in Quebec province. We are using a ddRAD approach and currently sequencing 30 individuals for each of the 50 sampled locality.
Past projects
The threespine stickleback, a model to study the response to contemporary evolution inferred by climate change
The threespine stickleback, a model to study the response to contemporary evolution inferred by climate change
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Temporal approach (genetic monitoring): How fast could we observe selection footprints within a population ? study based on morphological patterns and SNP (defined by RAD sequencing)
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Spatial approach (landscape genomics): Detecting footprints of selection along environmental gradient (salinity). Study based on a low density SNP array (defined by RAD sequencing).
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Local adaptation: adaptive divergence approach among heterogeneous habitats (marine populations, large lakes, small ponds). Study based on morphological patterns and SNP (defined by RAD sequencing.
4. Transcriptomic approach: Temperature norm reaction effect from RAD sequencing & qPCR. Assessing different genetic expressions between resident versus anadromous populations experimenting temperature increase
The reptile altitude !
Orsini’s viper (Vipera ursinii), species with large habitat range throughout the Palearctic region: from phylogeny to populations genetics.
1- Genetic structuration of French Orsini’s viper populations and impact of past climatic fluctuations on the observed genetic variation. Study based on mitochondrial sequences and microsatellites defined for the subspecies (Vipera ursinii ursinii). Definition of conservation units based on molecular markers in the scope of a European Life Nature program. Test of Biogeographical scenari using ABC approach highlighted, for the first time in vertebrate species, a refugia situation during inter glacial periods.
2- Landscape genetics for Orsini’s viper French populations. Combination of microsatellites and topographic features to identify barriers to dispersion for a species with low dispersal capabilities.
3- Phylogeography of Vipera ursinii taxonomic complex. Use of mitochondrial markers and molecular datation to precise taxonomy and infer evolutionary history of this complex
The Pyrenean rock lizard (Iberolerta bonnali), a Pyrenean endemic species
1- Evolutionary history of the Pyrenean rock lizard inferrred by mitochondrial sequences
2- Population genetic of the Pyrenean rock lizard. main factors influencing current genetic variation of alpine population. Use of microsatellite markers.