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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
Dorant, Yann; Cayuela, Hugo; Wellband, Kyle; Laporte, Martin; Rougemont, Quentin; Mérot, Claire; Normandeau, Éric; Rochette, Rémy; Bernatchez, Louis — 2020-08-19 <p style="text-align: justify;">Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
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Drivers of amphibian population dynamics and asynchrony at local and regional scales
Cayuela, Hugo; Griffiths, Richard A.; Zakaria, Nurul; Arntzen, Jan W.; Priol, Pauline; Léna, Jean-Paul; Besnard, Aurélien; Joly, Pierre — 2020-03-11 <ol> <li style="text-align:justify;">Identifying the drivers of population fluctuations in spatially distinct populations remains a significant challenge for ecologists. Whereas regional climatic factors may generate population synchrony (i.e., the Moran effect), local factors including the level of density-dependence may reduce the level of synchrony. Although divergences in the scaling of population synchrony and spatial environmental variation have been observed, the regulatory factors that underlie such mismatches are poorly understood.</li> <li style="text-align:justify;">Few previous studies have investigated how density-dependent processes and population-specific responses to weather variation influence spatial synchrony at both local and regional scales. We addressed this issue in a pond-breeding amphibian, the great crested newt (<i>Triturus cristatus</i>). We used capture-recapture data collected through long-term surveys in five <i>T. cristatus</i> populations in Western Europe.</li> <li style="text-align:justify;">In all populations – and subpopulations within metapopulations – population size, annual survival and recruitment fluctuated over time. Likewise, there was considerable variation in these demographic rates between populations and within metapopulations. These fluctuations and variations appear to be context-dependent and more related to site-specific characteristics than local or regional climatic drivers. We found a low level of demographic synchrony at both local and regional levels. Weather has weak and spatially variable effects on survival, recruitment and population growth rate. In contrast, density-dependence was a common phenomenon (at least for population growth) in almost all populations and subpopulations.</li> <li style="text-align:justify;">Our findings support the idea that the Moran effect is low in species where the population dynamics more closely depends on local factors (e.g. population density and habitat characteristics) than on large-scale environmental fluctuation (e.g. regional climatic variation). Such responses may have far-reaching consequences for the long-term viability of spatially structured populations and their ability to response to large-scale climatic anomalies.</li> </ol>
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Capture-recapture data with partially known birth date in four populations of yellow-bellied toads
Cayuela, Hugo; Lemaître, Jean-François; Bonnaire, Eric; Pichenot, Julian; Schmidt, Benedikt — 2019-12-19 <p>1.    Patterns of actuarial senescence can be highly variable among species. Previous comparative analyses revealed that both age at the onset of senescence and rates of senescence are linked to species position along the fast-slow life-history continuum. As there are few long-term datasets of wild populations with known-age individuals, intraspecific (i.e. between-population) variation in senescence is understudied and limited to comparisons of wild and captive populations of the same species, mostly birds and mammals. <br> 2.      In this paper, we examined how population position along the fast-slow life history continuum affects intraspecific variation in senescence in an amphibian, Bombina variegata. <br> 3.      We used capture-recapture data collected in four populations with contrasting life history strategies. Senescence trajectories were analyzed using Bayesian capture-recapture models.<br> 4.      We show that in fast populations the onset of actuarial senescence was earlier and individuals aged at a faster rate than individuals in slow populations. <br> 5.      Our study provides one of the few empirical examples of among-population variation in actuarial senescence patterns in the wild and confirms that the fast-slow life history gradient is associated with both macroevolutionary and microevolutionary patterns of actuarial senescence.</p>
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Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations
Cayuela, Hugo — 2020-01-13 <p>There is growing evidence that anthropogenic landscapes can strongly influence the evolution of dispersal, particularly through fragmentation, and may drive organisms into an evolutionary trap by suppressing dispersal. However, the influence on dispersal evolution of anthropogenic variation in habitat patch turnover has so far been largely overlooked. In this study, we examined how human-driven variation in patch persistence affects dispersal rates and distances, determines dispersal-related phenotypic specialization, and drives neutral genetic structure in spatially structured populations. We addressed this issue in an amphibian, Bombina variegata, using an integrative approach combining capture-recapture modeling, demographic simulation, common garden experiments, and population genetics. B. variegata reproduces in small ponds that occur either in habitat patches that are persistent (i.e. several decades or more), located in riverine environments with negligible human activity, or in patches that are highly temporary (i.e. a few years), created by logging operations in intensively harvested woodland. Our capture-recapture models revealed that natal and breeding dispersal rates and distances were drastically higher in spatially structured populations (SSPs) in logging environments than in riverine SSPs. Population simulations additionally showed that dispersal costs and benefits drive the fate of logging SSPs, which cannot persist without dispersal. The common garden experiments revealed that toadlets reared in laboratory conditions have morphological and behavioral specialization that depends on their habitat of origin. Toadlets from logging SSPs were found to have higher boldness and exploration propensity than those from riverine SSPs, indicating transgenerationally transmitted dispersal syndromes. We also found contrasting patterns of neutral genetic diversity and gene flow in riverine and logging SSPs, with genetic diversity and effective population size considerably higher in logging than in riverine SSPs. In parallel, intra-patch inbreeding and relatedness levels were lower in logging SSPs. Controlling for the effect of genetic drift and landscape connectivity, gene flow was found to be higher in logging than in riverine SSPs. Taken together, these results indicate that anthropogenic variation in habitat patch turnover may have an effect at least as important as landscape fragmentation on dispersal evolution and the long-term viability and genetic structure of wild populations.</p>
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Data from: Shared ancestral polymorphism and chromosomal rearrangements as potential drivers of local adaptation in a marine fish
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Cayuela, Hugo; Rougemont, Quentin; Bernatchez, Louis — 2020-06-16 <p>Gene flow has tremendous importance on local adaptation, by influencing the fate of <i>de novo</i> mutations, maintaining standing genetic variation, and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of evolutionary mechanisms impending or favoring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (<i>Mallotus villosus</i>). We first assembled a 490 Mbp draft genome of <i>M. villosus</i> to map our RAD sequence reads. Then, we used a large dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they likely diverged from 3.8 to 1.8 MyA and experienced secondary contacts. Within each lineage, our analyses provided evidence for large <i>N</i><sub><i>e</i></sub> and high gene flow among spawning sites. Within the NWA lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that, both shared polymorphism among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.</p>
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Copy Number variants in Mallotus villosus
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Cayuela, Hugo; Bernatchez, Louis — 2021-01-18 <p>Taking advantage of recent developments allowing CNV analysis from RAD-seq data (<a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15565?_sg%5B0%5D=-uwA9TZisRRXnspI5ElYUaPv2ChLuHLDZPIJZABoML2rc-geS2mVnZVIt2u4FAB6_SPD-DeRxtzyN3RjHivkmfmvEg.JqPMUYewJwfNoZvoALtl54UTEL4BWYI0NA87y3HrK16wm8cRVOG0c0owiV4QoaSysHfAZCLPkLmn-UaqCdolJQ">10.1111/mec.15565</a>), we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (<i>Mallotus villosus</i>). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. Raw sequencing data for GBS libraries have been published in a previous study (Cayuela et al. 2020,  <a class="nova-e-link nova-e-link--color-inherit nova-e-link--theme-decorated" href="https://www.researchgate.net/deref/http%3A%2F%2Fdx.doi.org%2F10.1111%2Fmec.15499?_sg%5B0%5D=OGdqMkvPArx5ICrgLrdT_ifFufXzoOZp0J7gLQEctL4EWpJv-h9FK8yFaom_h68N368lpxVYXRREN9BRpAi7lH0n8A.ylPnOWuObAEr1NJn9bzfYxNNAAwvYDvN0jDBR05xnfdW8Azf-PmnI7jDZFhecO1Kt1aTdFuxG0Yr3ff2e10XCg">10.1111/mec.15499</a>) and are available under accession no. PRJNA631144. Here, we provide the files of normalized read depth for the 6620 putative CNVs and environmental data used in our CNV analyses.</p>

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(auteur : Cayuela, Hugo)

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