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Arnaud Estoup

Publications and source records attributed to Arnaud Estoup.

17 recordsLinked to original sources
PubMed2006

Microsatellite null alleles and estimation of population differentiation.

Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.

Alleles↗
PubMed2006

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Alleles↗
PubMed2006

Rare sexual reproduction events in the clonal reproduction system of introduced populations of the little fire ant.

A unique reproductive system has previously been described in Wasmannia auropunctata, a widespread invasive ant species, where males are produced clonally, female queens are parthenogens, and female workers are produced sexually. However, these findings were mostly based on samples originating from only a limited part of the native range of the species in South America. We used microsatellite markers to uncover the reproductive modes displayed by a large number of nests collected in various invasive W. auropunctata populations introduced 40 years ago into New Caledonia, where the species now forms a single 450-km-long supercolony. Although the main reproduction system in New Caledonia remained clonality for both male and female reproductives, we found evidence of rare sexual reproduction events that led to the production of both new queen and male clonal lineages. All clonal lineages observed in New Caledonia potentially derived from sexual reproduction, recombination, and mutation events from a single female and a single male genotype. Hence, the male and female gene pools are not strictly separated in New Caledonia and the two sexes do not follow independent evolutionary trajectories. Our results also suggest genetic determination for both parthenogenesis and caste. We discuss the evolutionary implications of the emergence of sex in the clonal reproduction system of introduced populations of W. auropunctata.

Animals↗
PubMed2005

Multiple transatlantic introductions of the western corn rootworm.

The invasion of Europe by the western corn rootworm, North America's most destructive corn pest, is ongoing and represents a serious threat to European agriculture. Because this pest was initially introduced in Central Europe, it was believed that subsequent outbreaks in Western Europe originated from this area. Using model-based Bayesian analyses of the genetic variability of the western corn rootworm, we demonstrate that this belief is false: There have been at least three independent introductions from North America during the past two decades. This result raises questions about changing circumstances that have enabled a sudden burst of transatlantic introductions.

Animals↗
PubMed2005

A general eco-evolutionary framework for understanding bioinvasions.

Studies of bioinvasions have revealed various strategies of invasion, depending on the ecosystem invaded and the alien species concerned. Here, we consider how migration (as a demographic factor), as well as ecological and evolutionary changes, affect invasion success. We propose three main theoretical scenarios that depend on how these factors generate the match between an invader and its new environment. Our framework highlights the features that are common to, or differ among, observed invasion cases, and clarifies some general trends that have been previously highlighted in bioinvasions. We also suggest some new directions of research, such as the assessment of the time sequence of demographic, genetic and environmental changes, using detailed temporal surveys.

Animal Migration↗
PubMed2005

Clonal reproduction by males and females in the little fire ant.

Sexual reproduction can lead to major conflicts between sexes and within genomes. Here we report an extreme case of such conflicts in the little fire ant Wasmannia auropunctata. We found that sterile workers are produced by normal sexual reproduction, whereas daughter queens are invariably clonally produced. Because males usually develop from unfertilized maternal eggs in ants and other haplodiploid species, they normally achieve direct fitness only through diploid female offspring. Hence, although the clonal production of queens increases the queen's relatedness to reproductive daughters, it potentially reduces male reproductive success to zero. In an apparent response to this conflict between sexes, genetic analyses reveal that males reproduce clonally, most likely by eliminating the maternal half of the genome in diploid eggs. As a result, all sons have nuclear genomes identical to those of their father. The obligate clonal production of males and queens from individuals of the same sex effectively results in a complete separation of the male and female gene pools. These findings show that the haplodiploid sex-determination system provides grounds for the evolution of extraordinary genetic systems and new types of sexual conflict.

Alleles↗
PubMed2005

Bayesian analysis of an admixture model with mutations and arbitrarily linked markers.

We introduce here a Bayesian analysis of a classical admixture model in which all parameters are simultaneously estimated. Our approach follows the approximate Bayesian computation (ABC) framework, relying on massive simulations and a rejection-regression algorithm. Although computationally intensive, this approach can easily deal with complex mutation models and partially linked loci, and it can be thoroughly validated without much additional computation cost. Compared to a recent maximum-likelihood (ML) method, the ABC approach leads to similarly accurate estimates of admixture proportions in the case of recent admixture events, but it is found superior when the admixture is more ancient. All other parameters of the admixture model such as the divergence time between parental populations, the admixture time, and the population sizes are also well estimated, unlike the ML method. The use of partially linked markers does not introduce any particular bias in the estimation of admixture, but ML confidence intervals are found too narrow if linkage is not specifically accounted for. The application of our method to an artificially admixed domestic bee population from northwest Italy suggests that the admixture occurred in the last 10-40 generations and that the parental Apis mellifera and A. ligustica populations were completely separated since the last glacial maximum.

Animals↗
PubMed2004

A spatial statistical model for landscape genetics.

Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets (e.g., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation (e.g., FST<0.05). The method is then applied to a set of 88 individuals of wolverines (Gulo gulo) sampled in the northwestern United States and genotyped at 10 microsatellites.

Animals↗
PubMed2004

Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power.

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.

Animal Migration↗
PubMed2004

Influence of spatial and temporal heterogeneities on the estimation of demographic parameters in a continuous population using individual microsatellite data.

Drift and migration disequilibrium are very common in animal and plant populations. Yet their impact on methods of estimation of demographic parameters was rarely evaluated especially in complex realistic population models. The effect of such disequilibria on the estimation of demographic parameters depends on the population model, the statistics, and the genetic markers used. Here we considered the estimation of the product Dsigma2 from individual microsatellite data, where D is the density of adults and sigma2 the average squared axial parent-offspring distance in a continuous population evolving under isolation by distance. A coalescence-based simulation algorithm was used to study the effect on Dsigma2 estimation of temporal and spatial fluctuations of demographic parameters. Estimation of present-time Dsigma2 values was found to be robust to temporal changes in dispersal, to density reduction, and to spatial expansions with constant density, even for relatively recent changes (i.e., a few tens of generations ago). By contrast, density increase in the recent past gave Dsigma2 estimations biased largely toward past demographic parameters values. The method was also robust to spatial heterogeneity in density and estimated local demographic parameters when the density is homogenous around the sampling area (e.g., on a surface that equals four times the sampling area). Hence, in the limit of the situations studied in this article, and with the exception of the case of density increase, temporal and spatial fluctuations of demographic parameters appear to have a limited influence on the estimation of local and present-time demographic parameters with the method studied.

Algorithms↗
PubMed2004

Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus.

Inferring the spatial expansion dynamics of invading species from molecular data is notoriously difficult due to the complexity of the processes involved. For these demographic scenarios, genetic data obtained from highly variable markers may be profitably combined with specific sampling schemes and information from other sources using a Bayesian approach. The geographic range of the introduced toad Bufo marinus is still expanding in eastern and northern Australia, in each case from isolates established around 1960. A large amount of demographic and historical information is available on both expansion areas. In each area, samples were collected along a transect representing populations of different ages and genotyped at 10 microsatellite loci. Five demographic models of expansion, differing in the dispersal pattern for migrants and founders and in the number of founders, were considered. Because the demographic history is complex, we used an approximate Bayesian method, based on a rejection-regression algorithm, to formally test the relative likelihoods of the five models of expansion and to infer demographic parameters. A stepwise migration-foundation model with founder events was statistically better supported than other four models in both expansion areas. Posterior distributions supported different dynamics of expansion in the studied areas. Populations in the eastern expansion area have a lower stable effective population size and have been founded by a smaller number of individuals than those in the northern expansion area. Once demographically stabilized, populations exchange a substantial number of effective migrants per generation in both expansion areas, and such exchanges are larger in northern than in eastern Australia. The effective number of migrants appears to be considerably lower than that of founders in both expansion areas. We found our inferences to be relatively robust to various assumptions on marker, demographic, and historical features. The method presented here is the only robust, model-based method available so far, which allows inferring complex population dynamics over a short time scale. It also provides the basis for investigating the interplay between population dynamics, drift, and selection in invasive species.

Animals↗
PubMed2003

Influence of mutational and sampling factors on the estimation of demographic parameters in a "continuous" population under isolation by distance.

In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the average squared parent-offspring distance. We evaluated the influence on this method of both mutation rate and mutation model, with a particular reference to microsatellite markers, as well as that of the spatial scale of sampling. Moreover, we developed and tested a nonparametric bootstrap procedure allowing the construction of confidence intervals for the estimation of Dsigma2. These two objectives prompted us to develop a computer simulation algorithm based on the coalescent theory giving individual genotypes for a continuous population under isolation by distance. Our results show that the characteristics of mutational processes at microsatellite loci, namely the allele size homoplasy generated by stepwise mutations, constraints on allele size, and change of slippage rate with repeat number, have little influence on the estimation of Dsigma2. In contrast, a high genetic diversity (approximately 0.7-0.8), as is commonly observed for microsatellite markers, substantially increases the precision of the estimation. However, very high levels of genetic diversity (>0.85) were found to bias the estimation. We also show that statistics taking into account allele size differences give unreliable estimations (i.e., high variance of Dsigma2 estimation) even under a strict stepwise mutation model. Finally, although we show that this method is reasonably robust with respect to the sampling scale, sampling individuals at a local geographical scale gives more precise estimations of Dsigma2.

Animals↗
PubMed2002

Genetic consequences of sequential founder events by an island-colonizing bird.

The importance of founder events in promoting evolutionary changes on islands has been a subject of long-running controversy. Resolution of this debate has been hindered by a lack of empirical evidence from naturally founded island populations. Here we undertake a genetic analysis of a series of historically documented, natural colonization events by the silvereye species-complex (Zosterops lateralis), a group used to illustrate the process of island colonization in the original founder effect model. Our results indicate that single founder events do not affect levels of heterozygosity or allelic diversity, nor do they result in immediate genetic differentiation between populations. Instead, four to five successive founder events are required before indices of diversity and divergence approach that seen in evolutionarily old forms. A Bayesian analysis based on computer simulation allows inferences to be made on the number of effective founders and indicates that founder effects are weak because island populations are established from relatively large flocks. Indeed, statistical support for a founder event model was not significantly higher than for a gradual-drift model for all recently colonized islands. Taken together, these results suggest that single colonization events in this species complex are rarely accompanied by severe founder effects, and multiple founder events and/or long-term genetic drift have been of greater consequence for neutral genetic diversity.

Animals↗
PubMed2002

Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish.

We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences, comparative mapping, and population genetic studies.

Animals↗
PubMed2002

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis.

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

Biological Evolution↗
PubMed2002

Microevolution in island forms: the roles of drift and directional selection in morphological divergence of a passerine bird.

Theory predicts that in small isolated populations random genetic drift can lead to phenotypic divergence; however this prediction has rarely been tested quantitatively in natural populations. Here we utilize natural repeated island colonization events by members of the avian species complex, Zosterops lateralis, to assess whether or not genetic drift alone is an adequate explanation for the observed patterns of microevolutionary divergence in morphology. Morphological and molecular genetic characteristics of island and mainland populations are compared to test three predictions of drift theory: (1) that the pattern of morphological change is idiosyncratic to each island; (2) that there is concordance between morphological and neutral genetic shifts across island populations; and (3) for populations whose time of colonization is known, that the rate of morphological change is sufficiently slow to be accounted for solely by genetic drift. Our results are not consistent with these predictions. First, the direction of size shifts was consistently towards larger size, suggesting the action of a nonrandom process. Second, patterns of morphological divergence among recently colonized populations showed little concordance with divergence in neutral genetic characters. Third, rate tests of morphological change showed that effective population sizes were not small enough for random processes alone to account for the magnitude of microevolutionary change. Altogether, these three lines of evidence suggest that drift alone is not an adequate explanation of morphological differentiation in recently colonized island Zosterops and therefore we suggest that the observed microevolutionary changes are largely a result of directional natural selection.

Animals↗