Papers by Pierre Duchesne
Journal of Heredity, 2008
Evolutionary Applications
The intentional introduction of exotic species through classical biological control programs prov... more The intentional introduction of exotic species through classical biological control programs provides unique opportunities to examine the consequences of population movement and ecological processes for the genetic diversity and population structure of introduced species. The weevils Neochetina bruchi and N. eichhorniae (Coleoptera: Curculionidae) have been introduced globally to control the Accepted Article This article is protected by copyright. All rights reserved. invasive floating aquatic weed, Eichhornia crassipes, with variable outcomes. Here, we use the importation history and data from polymorphic microsatellite markers to examine the effects of introduction processes on population genetic diversity and structure. We report the first confirmation of hybridization between these species, which could have important consequences for the biological control program. For both species, there were more rare alleles in weevils from the native range than in weevils from the introduced range. N. eichhorniae also had higher allelic richness in the native range than in the introduced range. Neither the number of individuals initially introduced nor the number of introduction steps appeared to consistently affect genetic diversity. We found evidence of genetic drift, inbreeding and admixture in several populations as well as significant population structure. Analyses estimated two populations and eleven sub-clusters for N. bruchi and four populations and seven sub-clusters for N. eichhorniae, indicating divergence of populations during and after introduction. Genetic differentiation and allocation of introduced populations to source populations generally supported the documented importation history and clarified pathways in cases where multiple introductions occurred. In populations with multiple introductions, genetic admixture may have buffered against the negative effects of serial bottlenecks on genetic diversity. The genetic data combined with the introduction history from this biological control study system provides insight on the accuracy of predicting introduction pathways from genetic data, and the consequences of these pathways for the genetic variation and structure of introduced species.
Behavioral Ecology and Sociobiology
One of the central issues of behavioral ecology focuses on the probability of detecting multiple ... more One of the central issues of behavioral ecology focuses on the probability of detecting multiple paternity in a scenario of polygamy. The main problem for this kind of analysis arises in species with large number of offspring in the same litter and large population sizes in which only a small fraction of progeny and females can be analyzed. Here, we present a method to estimate the statistical power to detect multiple paternity for these species. Since calculations involved handling of very large numbers, Ramanujan's approximation to factorials was used to make them possible in the R software. We exemplified this method using features observed in crabs; (i) females carry thousands or millions of embryos per brood, (ii) typically less than 50% of females show multiple paternity, and (iii) high contribution of a single male (>90%) in a brood. Genetic parental analysis assumes the use of loci
Molecular Ecology Notes, 2005
PASOS is a parental allocation program designed to identify collected parents based on individual... more PASOS is a parental allocation program designed to identify collected parents based on individual multilocus genotypes while detecting missing parents when a proportion of them have not been collected. It makes use of restricted error tolerance in order to distinguish between a partially incorrect genotype from a false parent's genotype. PASOS also introduces the technique of sequence allocation allowing the user to obtain estimates of the proportion of missing parents and of allocation correctness. The PASOS interface is very similar to the one found in PAPA , its closed system counterpart (Duchesne et al. 2002). A help file thoroughly describes all technical terms such as error modelling, parameters and procedures. PASOS can be downloaded free of charge from: http://www.bio.ulaval.ca /louisbernatchez /.
Molecular Ecology Notes, 2002
aflpop is a population allocation and simulator program based on amplified fragment length polymo... more aflpop is a population allocation and simulator program based on amplified fragment length polymorphism markers. The allocation method is an adaptation of Paetkau's method for co-dominant alleles. Besides population allocation of specimens of unknown origin, reallocation of sample genotypes, as well as allocation of artificial (Monte Carlo) specimens, may be run to estimate expected rates of correct allocations. Thanks to its embodied simulator, aflpop can provide information on the rates and types of incorrect allocations and on empirical distributions of likelihood statistics. A filtering procedure within aflpop allows the selection of loci according to user-defined criteria.
Molecular Ecology Notes, 2006
PERM is a permutation program designed to detect statistical connections between grouping structu... more PERM is a permutation program designed to detect statistical connections between grouping structures and grouping factors or correlates. Groups may be of various kinds such as herds, flocks, schools and mating couples provided they make up meaningful social units. Relatedness, population membership and genotypic contents are among several aggregating variables which may be processed. Typically, PERM takes in a collection of grouped data and outputs a P value. The latter is computed on the basis of random membership among groups (H O). All files, including input, output and program, are of Excel type (.xls). PERM can be downloaded free of charge at: www.bio.ulaval.ca/louisbernatchez/downloads.htm.
Aquaculture Genome Technologies, 2007
... reviews, our intent here is not to address the suitability of various molecular techniques, n... more ... reviews, our intent here is not to address the suitability of various molecular techniques, nor is it ... The use of diploid codominant markers will be assumed throughout the following discussion. ... nonzero) likelihood, the offspring is not allocated but the output is scored as ambiguous. ...
Proceedings of the Royal Society B: Biological Sciences, 2012
Social structure involving long-term associations with relatives should facilitate the learning o... more Social structure involving long-term associations with relatives should facilitate the learning of complex behaviours such as long-distance migration. In and around Hudson Bay (Canada), three stocks of beluga whales form a panmictic unit, but have different migratory behaviours associated with different summering areas. We analysed genetic variation at 13 microsatellite loci among 1524 belugas, to test hypotheses about social structure in belugas. We found significant proportions of mother–offspring pairs throughout the migratory cycle, but average relatedness extended beyond close kinship only during migration. Average relatedness was significantly above random expectations for pairs caught at the same site but on different days or months of a year, suggesting that belugas maintain associations with a network of relatives during migration. Pairs involving a female (female–female or male–female) were on average more related than pairs of males, and males seemed to disperse from thei...
Proceedings of the Royal Society B: Biological Sciences, 2001
According to the theory of mate choice based on heterozygosity, mates should choose each other in... more According to the theory of mate choice based on heterozygosity, mates should choose each other in order to increase the heterozygosity of their o¡spring. In this study, we tested the`good genes as heterozygosity' hypothesis of mate choice by documenting the mating patterns of wild Atlantic salmon (Salmo salar) using both major histocompatibility complex (MHC) and microsatellite loci. Speci¢cally, we tested the null hypotheses that mate choice in Atlantic salmon is not dependent on the relatedness between potential partners or on the MHC similarity between mates. Three parameters were assessed: (i) the number of shared alleles between partners (x and y) at the MHC (M xy), (ii) the MHC amino-acid genotypic distance between mates' genotypes (AA xy), and (iii) genetic relatedness between mates (r xy). We found that Atlantic salmon choose their mates in order to increase the heterozygosity of their o¡spring at the MHC and, more speci¢cally, at the peptide-binding region, presumably in order to provide them with better defence against parasites and pathogens. This was supported by a signi¢cant di¡erence between the observed and expected AA xy (p 0.0486). Furthermore, mate choice was not a mechanism of overall inbreeding avoidance as genetic relatedness supported a random mating scheme (p 0.445). This study provides the ¢rst evidence that MHC genes in£uence mate choice in ¢sh.
Proceedings of the Royal Society B: Biological Sciences, 2007
Low genetic diversity is predicted to negatively impact species viability and has been a central ... more Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses ( Diomedea exulans and Diomedea amsterdamensis ) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Divergence time of the two species is estimated at 0.84 Myr ago from cytochrome b data. We tested the hypothesis that both albatrosses inherited poor genetic diversity from their common ancestor. Within the wandering albatross, per cent polymorphic loci and expected heterozygosity at amplified fragment length polymorphisms were approximately one-third of the minimal values reported in other vertebrates. Genetic diversity in the Amsterdam albatross, which is recovering from a severe bottleneck, was...
Molecular Ecology Resources, 2009
Identifying and estimating individual and/or population admixture is a very common objective in e... more Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. There are many situations where samples from one or many of the putatively hybridizing entities are not available or easily identified. Here we describe FLOCK, a new method especially designed to provide spatial and/or temporal admixture maps in the absence of one or several source samples. FLOCK is a non-Bayesian method and therefore differs substantially from previous clustering algorithms. Its working principle is repeated re-allocation of all collected specimens (total sample) to the k subsamples, each re-allocation being more effective than the previous one in attracting genetically similar individuals. This snowball effect, more formally referred to as a positive feedback mechanism, makes FLOCK an efficient and quick sorting process. The usage of FLOCK is illustrated with two empirical situations which have been thoroughly analysed previously with other approaches. A number of simulations were run to better assess the power of the FLOCK algorithm. Performance comparisons were made between the FLOCK and Structure algorithms. When non-negligible numbers of pure genotypes were present, the two performed equally well. However, FLOCK proved significantly more powerful in the absence of pure genotypes. Moreover, FLOCK showed more potential for fast processing. Run times were shown to increase linearly with size of total sample and with size of k, the number of reference samples from which admixture mapping is performed.
Molecular Ecology, 2005
Few studies have critically investigated the genetic composition of wild fish schools. Yet, such ... more Few studies have critically investigated the genetic composition of wild fish schools. Yet, such investigations may have profound implications for the understanding of social organization and population differentiation in both fundamental and applied research. Using 20 microsatellite loci, we investigated the composition of 53 schools (total n = 211) of adult and subadult migratory brook charr (Salvelinus fontinalis) sampled from the known feeding areas of two populations inhabiting Mistassini Lake (Québec, Canada). We specifically tested whether (i) school members originated from the same population, (ii) individuals from the same population within schools were kin (half-or full-siblings), and (iii) kin schooling relationships differed between sexes. Randomization tests revealed a tendency for most schools to be population specific, although some schools were population mixtures. Significantly more kin were found within schools than expected at random for both populations (≈ ≈ ≈ ≈ 21-34% of the total number of school members). This result, combined with the observed size range of individuals, indicated that stable associations between kin may occur beyond juvenile stages for up to 4 years. Nevertheless, a high proportion of school members were non-kin (≈ ≈ ≈ ≈ 66-79%). No differences were detected between sexes in the propensity to school with kin. We discuss the hypothesis that the stable kin groups, rather than arising from kin selection, may instead be a by-product of familiarity based on individual selection for the maintenance of local adaptations related to migration (natal and feeding area philopatry). Our results are noteworthy because they suggest that there is some degree of permanence in the composition of wild fish schools. Additionally, they support the hypothesis that schools can be hierarchically structured (from population members down to family groups) and are thus nonrandom genetic entities.
Molecular Ecology, 1999
We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential ... more We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.
Molecular Ecology, 2006
It is generally assumed that larvae of benthic species are thoroughly mixed in the plankton and d... more It is generally assumed that larvae of benthic species are thoroughly mixed in the plankton and distributed randomly at settlement. Yet, it has also been hypothesized that a combination of larval gregarious behaviour coupled with particular oceanographic conditions may prevent larvae from mixing completely, and result in nonrandom spatial distributions following settlement. Using microsatellite markers, the main objective of this study was to investigate the occurrence of statistical connections between relatedness and settlement in the intertidal acorn barnacle from the Gulf of St Lawrence, Canada. A second objective was to test the hypothesis that patches of kin-related individuals came from a common parental site. Our results indicated that a significant number of barnacles within a given sample were more closely related than expected by chance despite the enormous potential for admixture during the planktonic phase. Thus, eight out of 37 samples analysed had relatedness values significantly higher than expected from random settlement. Moreover, analyses of sibship network construction and network complexity tests provided evidence for the occurrence of networks within several samples that were characterized by strong connections among individuals. Thus, nonrandom planktonic dispersal associated with relatively stable oceanic currents, as well as additional ecological factors to be rigorously investigated (e.g. behavioural mechanisms), may be more important in determining patterns of genetic structure in marine benthic invertebrates than generally assumed. Therefore, documenting genetic patterns associated with kin aggregation should be a fruitful and an important avenue for future studies in marine invertebrates.
Molecular Ecology, 2006
We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes ... more We tested the hypothesis that phenotypic parallelism between dwarf and normal whitefish ecotypes (Coregonus clupeaformis, Salmonidae) is accompanied by parallelism in gene transcription. The most striking phenotypic differences between these forms implied energetic metabolism and swimming activity. Therefore, we predicted that genes showing parallel expression should mainly belong to functional groups associated with these phenotypes. Transcriptome profiles were obtained from white muscle by using a 3557 cDNA gene microarray developed for the Atlantic salmon (Salmo salar). A total of 1181 genes expressed in both lake populations hybridized on the array. Significant differential expression between ecotypes was detected for 134 (11.3%) and 195 (16.5%) gene clones in Cliff Lake and Indian Pond, respectively. Fifty-one genes (4.3%) showed parallel differential expression between lakes, among which 35 were expressed in opposite directions. Sixteen genes (1.35%) showed true parallelism of transcription, which mainly belonged to energetic metabolism and regulation of muscle contraction functional groups. Variance in expression was significantly reduced for these genes compared to those not showing directionality in parallelism of expression. Candidate genes associated with parallelism in swimming activity and energetic metabolism based on their level and variance in expression were identified. These results add to the growing evidence that parallel phenotypic evolution also involves parallelism at both the genotypic and regulatory level, which may at least partly be associated with genetic constraints. It also provides further evidence for the determinant role of divergent natural selection in driving phenotypic divergence, and perhaps reproductive isolation, in the adaptive radiation of lake whitefish. This study adds to a nascent field employing microarrays as powerful tools for investigating the evolutionary processes of adaptive divergence among natural populations.
Molecular Ecology, 2003
Individual-based population assignment tests have thus far mainly relied on the use of microsatel... more Individual-based population assignment tests have thus far mainly relied on the use of microsatellite loci. However, the logistic difficulty of screening large numbers of loci required to reach sufficient statistical power hampers the usefulness of microsatellites in situations of weak population structuring. Amplified fragment length polymorphisms (AFLP) represents an alternative for overcoming this logistical issue as the technique allows the user to characterize a much larger number of loci with a comparable analytical effort. In this study, an assignment test based on maximum likelihood for dominant markers was used to investigate the potential usefulness of AFLP for population assignment. We also compared assignment success achieved with AFLP with that obtained using microsatellites in a case study of low population differentiation involving whitefish (Coregonus clupeaformis) sympatric ecotypes. The analytical investigation showed that the minimum number of AFLP loci required to reach an assignment success of 95% stood within values that are easily achievable in many situations. This also showed how assignment success varied according to the number of AFLP loci used, their absolute frequency and their frequency differential and sampling errors, as well as the number of putative source populations. The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring.
Journal of Heredity, 2012
Identifying groups of individuals forming coherent genetic clusters is relevant to many fields of... more Identifying groups of individuals forming coherent genetic clusters is relevant to many fields of biology. This paper addresses the K-partition problem: given a collection of genotypes, partition those genotypes into K groups, each group being a sample of the K source populations that are represented in the collection of genotypes. This problem involves allocating genotypes to genetic groups while building those groups at the same time without the use of any other a priori information. FLOCK is a non-Markov chain Monte Carlo (MCMC) algorithm that uses an iterative method to partition a collection of genotypes into k groups. Rules to estimate K are formulated and their validity firmly established by running simulations under several migration rates, migration regimes, number of loci, and values of K. FLOCK tended to build clusters largely consistent with the source samples. The performance of FLOCK was also compared with that of STRUCTURE and BAPS. FLOCK provided more accurate allocations to clusters and more reliable estimates of K; it also ran much faster than STRUCTURE. FLOCK is based on an entirely novel approach and provides a true alternative to the existing, MCMC based, algorithms. FLOCK v.
Journal of Evolutionary Biology, 2006
Conservation Genetics, 2008
Reintroduction programs aim at reinstalling a self-sustained population into the wild via a perio... more Reintroduction programs aim at reinstalling a self-sustained population into the wild via a period of supplementation with captive-bred individuals. This procedure can rapidly generate inbreeding among offspring because of the mating scheme and this inbreeding might be further enhanced by the reintroduction scenario. First, we used simulations to assess the consequences of breeding designs on mean inbreeding index F among offspring when the genetic diversity of breeders, the number and sex ratios of breeders, and the proportion of successful crosses vary. A high number of breeders, a balanced sex ratio, a high proportion of effective crosses and a genetically diverse source population generally contribute to lower F values. However, moderately high (‡20) numbers of breeders combined with all but the most biased sex ratios produced mean F values near minimal values. The variability in F was negligible in all parameter combinations except for a very small number of breeders (5) and very biased sex ratios (£ 1M : 19F). We also simulated the long-term inbreeding dynamics in the introduced population under various demographic scenarios. Our main finding was that the annual number of introduced offspring is a decisive factor in establishing long-term F values in the supplemented population. Low supplementation levels (10 2) quickly generated an almost completely inbred population whereas high levels (‡ 10 4) produced stable F values close to that of the introduced offspring. Simulations were run based on the life history and specific demographics of the bloater (Coregonus hoyi), whose reintroduction in Lake Ontario is being considered.
Conservation Genetics, 2012
Migratory connectivity between areas frequented by wide-ranging animals provides crucial informat... more Migratory connectivity between areas frequented by wide-ranging animals provides crucial information for conservation and management. In and around Hudson Bay (Canada), three stocks of beluga whales (Delphinapterus leucas) are associated with distinct summering areas. We analyzed genetic variation at mtDNA and 13 microsatellite loci among individuals (N [ 1400) harvested by 23 Inuit communities to identify mating units and assess temporal and spatial differences in the way stocks use common migratory pathways. Strong structure at mtDNA and a lack of convincing evidence for nuclear genetic differentiation indicate that both males and females adopt distinct migratory routes towards summering grounds while probably interbreeding on wintering grounds. Spatiotemporal variation in stock composition indicates that subsistence hunting targets all three stocks. While representing ca. 5% of belugas in Hudson Bay, the endangered Eastern Hudson Bay stock accounts for 17% of the overall subsistence harvest by Inuit communities of northern Nunavik (Quebec), and ca. 30% of the spring harvest along northeastern Hudson Bay. Despite interbreeding, cultural conservatism of maternally transmitted migration routes seems to prevent the re-establishment of stocks in previously frequented estuaries. This phenomenon supports the current use of demographic population models based on stock composition for developing behavior-based management strategies. Keywords Beluga Á Hudson Bay Á Migratory connectivity Á mtDNA Á Microsatellites Á Mixed stock analysis Electronic supplementary material The online version of this article (
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Papers by Pierre Duchesne