Sylvie Oddou-Muratorio | Institut National de la Recherche Agronomique (original) (raw)

Papers by Sylvie Oddou-Muratorio

Molecular Ecology Notes, 2001

This study reports the cloning and characterization of nine microsatellite primer pairs in a scat... more This study reports the cloning and characterization of nine microsatellite primer pairs in a scattered woody species ( Sorbus torminalis ), and shows their potential for further use in 36 species of the Maloideae , a Rosaceae subfamily containing important fruit crop and ornamental species. These primers were designed from a microsatellite library constructed from genomic DNA of S. torminalis and enriched for CA and GA repeats. Genotyping 48 S. torminalis of a natural population with the six best markers yielded a mean of 10.7 alleles per locus, and an expectation of exclusion probability for paternity analysis greater than 0.993.

Ecological Modelling, 2008

Input factor bound Parameter tuning Individual-based spatially explicit model Felling a b s t r a... more Input factor bound Parameter tuning Individual-based spatially explicit model Felling a b s t r a c t A sensitivity analysis on the impact of uncertainty in tree mortality on the predictions of an individual-based spatially explicit forest dynamics model (SELVA) was performed. The model was developed to investigate the impact of felling (logging) on the demography and structure of tree populations in tropical forests (French Guiana). This study addressed questions about (1) the relative impact on model predictions of uncertainty in mortality processes at different stages of tree development; (2) the interactions between the mortality processes and different felling regimes; and (3) the impact of different felling regimes on the demography and structure of tree populations, taking account of answers to and . A global approach of sensitivity analysis based on the decomposition of the output variance was applied. Based on prior knowledge about model uncertainties, mortality processes at the stages germinated seed, standing juvenile, standing adult, and tree-fall were focused as input factors. The input factors were multivariate mortality sub-models involving several parameters with no explicit biological meaning. Thus, an approach based on confidence ellipses of parameter estimates was used to vary input factors homogenously, so that the impact of different input factors on a given model output could be compared. As outputs, the numbers of living, dead and recruited trees, and the tree diameter structure were analysed over 336 years of simulation. An additional local sensitivity analysis provided deeper insights into the relationships between model input and output. The results showed that standing juvenile mortality was the largest source of uncertainty, ahead of standing adult mortality, germinated seed mortality and tree-fall. Moreover, mainly standing juvenile mortality interacted with the felling regime, resulting in changes of the diameter structure of the studied tree population (Dicorynia guianensis Amshoff, Caesalpiniaceae). Felling all trees ≥60 cm diameter of that population every 42 or 84 years was found not sustainable in the long term. But enhancing the description of standing juvenile mortality may alter these predictions. As major conclusions, (i) standing mortality at the juvenile stage should be modelled thoroughly to ensure reliable long-term predictions, and (ii) the interaction of standing juvenile mortality and the felling regime may be an important relationship to be considered in the evaluation of the sustainability of felling regimes.

Forest Ecology and Management, 2010

The comparison between estimates of historical gene flow, using variance in allelic frequencies, ... more The comparison between estimates of historical gene flow, using variance in allelic frequencies, and estimates of contemporary gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at microsatellite loci was used to quantify genetic structure in two wind pollinated, gravity and animaldispersed tree species (Fagus sylvatica L. and Fagus crenata Blum.) and to derive historical estimates of gene flow. The gene dispersal distances estimated assuming effective population density to be 1/4 of the observed density were ∼77 m in European beech and ∼40 m in Japanese beech. Parentage analyses and a neighbourhood model approach were used to estimate contemporary patterns of seed and pollen dispersal. Our results suggest restricted seed dispersal abilities in both European beech (ı s = 10.5 m) and Japanese beech (ı s = 12.4 m), with an exponential shaped seed dispersal kernel. A non-negligible rate of seed immigration (m s = 27%) was detected in European beech sites but not in Japanese beech site. Pollen dispersal within studied sites also appeared limited (ı p = 41.63 m in European beech and ı p = 79.4 m in Japanese beech), despite high rate of pollen immigration (m p = 68% in European beech and m p = 40% m in Japanese beech). Interestingly, contemporary and historical estimates of gene flow were within the same order of magnitude (a few tens of meters).

Molecular Ecology, 2008

The comparison between historical estimates of gene flow, using variance in allelic frequencies, ... more The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (Nb = 70 individuals, σe = 417 m) were similar to those inferred from adult genotypes (Nb = 114 individuals, σe = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (σc = 211 m) was ∼twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

Molecular Ecology, 2004

Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed ... more Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in ∼100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.

Molecular Ecology, 2003

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which i... more Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short-term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log-normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis, the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density (d obs /d ep ~13). This value is between the value (~2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value (~30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.

Molecular Ecology, 2008

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which i... more Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short-term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log-normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis, the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density (dobs/dep ~ 13). This value is between the value (~2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value (~30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.

Molecular Ecology, 2005

Knowing the extent of gene movements from parents to offspring is essential to understand the pot... more Knowing the extent of gene movements from parents to offspring is essential to understand the potential of a species to adapt rapidly to a changing environment, and to design appropriate conservation strategies. In this study, we develop a nonlinear statistical model to jointly estimate the pollen dispersal kernel and the heterogeneity in fecundity among phenotypically or environmentally defined groups of males. This model uses genotype data from a sample of fruiting plants, a sample of seeds harvested on each of these plants, and all males within a circumscribed area. We apply this model to a scattered, entomophilous woody species, Sorbus torminalis (L.) Crantz, within a natural population covering more than 470 ha. We estimate a high heterogeneity in male fecundity among ecological groups, both due to phenotype (size of the trees and flowering intensity) and landscape factors (stand density within the neighbourhood). We also show that fat-tailed kernels are the most appropriate to depict the important abilities of long-distance pollen dispersal for this species. Finally, our results reveal that the spatial position of a male with respect to females affects as much its mating success as ecological determinants of male fecundity. Our study thus stresses the interest to account for the dispersal kernel when estimating heterogeneity in male fecundity, and reciprocally.

Molecular Ecology, 2004

Pollen dispersal is a critical process that shapes genetic diversity in natural populations of pl... more Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin-tailed (decreasing faster than exponential), or fat-tailed (decreasing slower than the exponential). In the latter case, rare events of long-distance dispersal will be much more likely. Here we generalize the previously developed TWOGENER method, assuming that the pollen dispersal curve belongs to particular one-or two-parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin-tailed, exponential and fat-tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve -thin-tailed or fat-tailed -and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat-tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of TWOGENER for evaluating the shape of the dispersal curve and the effective density of the population ( d e ).

American Journal of Botany, 2006

Understanding the role of mother plants as pollen recipients in shaping mating patterns is essent... more Understanding the role of mother plants as pollen recipients in shaping mating patterns is essential for understanding the evolution of populations and in particular to predict the consequence of habitat fragmentation. Here, we investigated variation in mating patterns due to maternal phenotypic traits, phenological variance, and landscape features in Sorbus torminalis, a hermaphroditic, insect-pollinated and low-density, European temperate forest tree. The diversity and composition of pollen clouds received by maternal trees in S. torminalis were mainly determined by their conspecific neighborhood: isolated individuals sample more diversity through more even paternal contributions, low relatedness among paternal genes, and high rates of long-distance pollen dispersal within their progenies. Maternal phenotypic traits related to pollinator attractiveness also had an effect, but only when competition was strong: in this case, larger mother trees with more flowers sampled more diversity. The floral architecture of S. torminalis, with multiple-seeded fruit, strongly shaped mating patterns, with higher levels of correlated paternity among seeds belonging to the same fruit (30% full sibs) than among seeds belonging to different fruits (14% full sibs). Finally, flowering phenology affected the distribution of diversity among maternal pollen clouds, but the earliest and latest mother trees did not receive less diversity of pollen than the others.

Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed ... more Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in ∼ ∼ ∼ ∼ 100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.

Evolution, 2001

We examined the spatial distribution of maternally inherited chloroplast DNA markers over the Fre... more We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (G STc ϭ 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen-nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

Evolution, 2001

Abstract.— We examined the spatial distribution of maternally inherited chloroplast DNA markers o... more Abstract.— We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (GSTc= 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen- nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

In plant quantitative genetic studies conducted ex situ, the large number of seeds produced per i... more In plant quantitative genetic studies conducted ex situ, the large number of seeds produced per individual has promoted the use of open-pollinated progeny tests. In subsequent analyses, seeds collected on the same mother-plant are assumed to be half-sibs. The consequences of the departure from half-sib assumption in progeny tests have been investigated since the 1960s using simulation approaches and, more recently, using molecular-based experimental approaches. This review aims to synthesize the results and conclusions of these simulation and empirical studies. We focus on tree species, where controlled crosses are difficult to carry out experimentally and departures from half-sib assumptions occur frequently in natural populations. First, the average level of relatedness expected within maternal progeny for many tree populations is higher than that of half-sibs. This is the consequence of non-random mating resulting from the small number of effective pollen donors per female, unequal male reproductive success and/or selfing. As result, estimates of genetic variance and heritability for quantitative traits may be upward biased. Alternatively, inbreeding depression, dominance effects and the heterogeneity of the male gamete pool among females are often neglected, which may lead to underestimation of the heritability of traits. A correction based on the mean genetic relatedness between offspring and the relatedness between parents is often used to compensate those biases. However, such correction cannot accurately adjust the estimates in situations where variable levels of genetic relatedness among families, dominance effects or inbreeding depression exist within the progeny. An alternative and promising approach is the use of the "animal model" approach, which optimizes the use of molecular data and paternal information to estimate heritability more accurately. This study is part of Julie Gauzere PhD thesis, which aims at understanding the role of adaptation and gene flow in the phenotypic variation of traits related to climate response along an altitudinal gradient of a temperate tree species, Fagus sylvatica. Sylvie Oddou-Muratorio is a population geneticist studying the impact of pollen and seed dispersal and climate-driven selection on adaptive dynamics of forest trees natural populations under climate change. François Lefèvre's research is targeted at the issues of sustainable management of forest genetic resources and adaptation of the forests to climate change. Christian Pichot is a population geneticist and quantitative geneticist studying the role of forest tree genetic resources on population dynamics. Etienne Klein research is targeted on dispersal of plant propagules (pollen and seeds), and their impact on the genetic composition of populations.

Molecular Ecology Notes, 2001

This study reports the cloning and characterization of nine microsatellite primer pairs in a scat... more This study reports the cloning and characterization of nine microsatellite primer pairs in a scattered woody species ( Sorbus torminalis ), and shows their potential for further use in 36 species of the Maloideae , a Rosaceae subfamily containing important fruit crop and ornamental species. These primers were designed from a microsatellite library constructed from genomic DNA of S. torminalis and enriched for CA and GA repeats. Genotyping 48 S. torminalis of a natural population with the six best markers yielded a mean of 10.7 alleles per locus, and an expectation of exclusion probability for paternity analysis greater than 0.993.

Ecological Modelling, 2008

Input factor bound Parameter tuning Individual-based spatially explicit model Felling a b s t r a... more Input factor bound Parameter tuning Individual-based spatially explicit model Felling a b s t r a c t A sensitivity analysis on the impact of uncertainty in tree mortality on the predictions of an individual-based spatially explicit forest dynamics model (SELVA) was performed. The model was developed to investigate the impact of felling (logging) on the demography and structure of tree populations in tropical forests (French Guiana). This study addressed questions about (1) the relative impact on model predictions of uncertainty in mortality processes at different stages of tree development; (2) the interactions between the mortality processes and different felling regimes; and (3) the impact of different felling regimes on the demography and structure of tree populations, taking account of answers to and . A global approach of sensitivity analysis based on the decomposition of the output variance was applied. Based on prior knowledge about model uncertainties, mortality processes at the stages germinated seed, standing juvenile, standing adult, and tree-fall were focused as input factors. The input factors were multivariate mortality sub-models involving several parameters with no explicit biological meaning. Thus, an approach based on confidence ellipses of parameter estimates was used to vary input factors homogenously, so that the impact of different input factors on a given model output could be compared. As outputs, the numbers of living, dead and recruited trees, and the tree diameter structure were analysed over 336 years of simulation. An additional local sensitivity analysis provided deeper insights into the relationships between model input and output. The results showed that standing juvenile mortality was the largest source of uncertainty, ahead of standing adult mortality, germinated seed mortality and tree-fall. Moreover, mainly standing juvenile mortality interacted with the felling regime, resulting in changes of the diameter structure of the studied tree population (Dicorynia guianensis Amshoff, Caesalpiniaceae). Felling all trees ≥60 cm diameter of that population every 42 or 84 years was found not sustainable in the long term. But enhancing the description of standing juvenile mortality may alter these predictions. As major conclusions, (i) standing mortality at the juvenile stage should be modelled thoroughly to ensure reliable long-term predictions, and (ii) the interaction of standing juvenile mortality and the felling regime may be an important relationship to be considered in the evaluation of the sustainability of felling regimes.

Forest Ecology and Management, 2010

The comparison between estimates of historical gene flow, using variance in allelic frequencies, ... more The comparison between estimates of historical gene flow, using variance in allelic frequencies, and estimates of contemporary gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at microsatellite loci was used to quantify genetic structure in two wind pollinated, gravity and animaldispersed tree species (Fagus sylvatica L. and Fagus crenata Blum.) and to derive historical estimates of gene flow. The gene dispersal distances estimated assuming effective population density to be 1/4 of the observed density were ∼77 m in European beech and ∼40 m in Japanese beech. Parentage analyses and a neighbourhood model approach were used to estimate contemporary patterns of seed and pollen dispersal. Our results suggest restricted seed dispersal abilities in both European beech (ı s = 10.5 m) and Japanese beech (ı s = 12.4 m), with an exponential shaped seed dispersal kernel. A non-negligible rate of seed immigration (m s = 27%) was detected in European beech sites but not in Japanese beech site. Pollen dispersal within studied sites also appeared limited (ı p = 41.63 m in European beech and ı p = 79.4 m in Japanese beech), despite high rate of pollen immigration (m p = 68% in European beech and m p = 40% m in Japanese beech). Interestingly, contemporary and historical estimates of gene flow were within the same order of magnitude (a few tens of meters).

Molecular Ecology, 2008

The comparison between historical estimates of gene flow, using variance in allelic frequencies, ... more The comparison between historical estimates of gene flow, using variance in allelic frequencies, and contemporary estimates of gene flow, using parentage assignment, is expected to provide insights into ecological and evolutionary processes at work within and among populations. Genetic variation at six microsatellite loci was used to quantify genetic structure in the insect-pollinated, animal-dispersed, low-density tree Sorbus torminalis L. Crantz, and to derive historical estimates of gene flow. The neighbourhood size and root-mean-squared dispersal distance inferred from seedling genotypes (Nb = 70 individuals, σe = 417 m) were similar to those inferred from adult genotypes (Nb = 114 individuals, σe = 472 m). We also used parentage analyses and a neighbourhood model approach after an evaluation of the statistical properties of this method on simulated data. From our data, we estimated even contributions of seed- and pollen-mediated dispersal to the genetic composition of established seedlings, with both fat-tailed pollen and seed dispersal kernels, and slightly higher mean distance of pollen dispersal (248 m) as compared to seed dispersal (135 m). The resulting contemporary estimate of gene dispersal distance (σc = 211 m) was ∼twofold smaller than the historical estimates. Besides different assumptions and statistical nuances of both approaches, this discrepancy is likely to reflect a recent restriction in the scale of gene flow which requires manager's attention in a context of increasing forest fragmentation.

Molecular Ecology, 2004

Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed ... more Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in ∼100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.

Molecular Ecology, 2003

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which i... more Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short-term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log-normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis, the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density (d obs /d ep ~13). This value is between the value (~2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value (~30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.

Molecular Ecology, 2008

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which i... more Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short-term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log-normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis, the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density (dobs/dep ~ 13). This value is between the value (~2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value (~30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.

Molecular Ecology, 2005

Knowing the extent of gene movements from parents to offspring is essential to understand the pot... more Knowing the extent of gene movements from parents to offspring is essential to understand the potential of a species to adapt rapidly to a changing environment, and to design appropriate conservation strategies. In this study, we develop a nonlinear statistical model to jointly estimate the pollen dispersal kernel and the heterogeneity in fecundity among phenotypically or environmentally defined groups of males. This model uses genotype data from a sample of fruiting plants, a sample of seeds harvested on each of these plants, and all males within a circumscribed area. We apply this model to a scattered, entomophilous woody species, Sorbus torminalis (L.) Crantz, within a natural population covering more than 470 ha. We estimate a high heterogeneity in male fecundity among ecological groups, both due to phenotype (size of the trees and flowering intensity) and landscape factors (stand density within the neighbourhood). We also show that fat-tailed kernels are the most appropriate to depict the important abilities of long-distance pollen dispersal for this species. Finally, our results reveal that the spatial position of a male with respect to females affects as much its mating success as ecological determinants of male fecundity. Our study thus stresses the interest to account for the dispersal kernel when estimating heterogeneity in male fecundity, and reciprocally.

Molecular Ecology, 2004

Pollen dispersal is a critical process that shapes genetic diversity in natural populations of pl... more Pollen dispersal is a critical process that shapes genetic diversity in natural populations of plants. Estimating the pollen dispersal curve can provide insight into the evolutionary dynamics of populations and is essential background for making predictions about changes induced by perturbations. Specifically, we would like to know whether the dispersal curve is exponential, thin-tailed (decreasing faster than exponential), or fat-tailed (decreasing slower than the exponential). In the latter case, rare events of long-distance dispersal will be much more likely. Here we generalize the previously developed TWOGENER method, assuming that the pollen dispersal curve belongs to particular one-or two-parameter families of dispersal curves and estimating simultaneously the parameters of the dispersal curve and the effective density of reproducing individuals in the population. We tested this method on simulated data, using an exponential power distribution, under thin-tailed, exponential and fat-tailed conditions. We find that even if our estimates show some bias and large mean squared error (MSE), we are able to estimate correctly the general trend of the curve -thin-tailed or fat-tailed -and the effective density. Moreover, the mean distance of dispersal can be correctly estimated with low bias and MSE, even if another family of dispersal curve is used for the estimation. Finally, we consider three case studies based on forest tree species. We find that dispersal is fat-tailed in all cases, and that the effective density estimated by our model is below the measured density in two of the cases. This latter result may reflect the difficulty of estimating two parameters, or it may be a biological consequence of variance in reproductive success of males in the population. Both the simulated and empirical findings demonstrate the strong potential of TWOGENER for evaluating the shape of the dispersal curve and the effective density of the population ( d e ).

American Journal of Botany, 2006

Understanding the role of mother plants as pollen recipients in shaping mating patterns is essent... more Understanding the role of mother plants as pollen recipients in shaping mating patterns is essential for understanding the evolution of populations and in particular to predict the consequence of habitat fragmentation. Here, we investigated variation in mating patterns due to maternal phenotypic traits, phenological variance, and landscape features in Sorbus torminalis, a hermaphroditic, insect-pollinated and low-density, European temperate forest tree. The diversity and composition of pollen clouds received by maternal trees in S. torminalis were mainly determined by their conspecific neighborhood: isolated individuals sample more diversity through more even paternal contributions, low relatedness among paternal genes, and high rates of long-distance pollen dispersal within their progenies. Maternal phenotypic traits related to pollinator attractiveness also had an effect, but only when competition was strong: in this case, larger mother trees with more flowers sampled more diversity. The floral architecture of S. torminalis, with multiple-seeded fruit, strongly shaped mating patterns, with higher levels of correlated paternity among seeds belonging to the same fruit (30% full sibs) than among seeds belonging to different fruits (14% full sibs). Finally, flowering phenology affected the distribution of diversity among maternal pollen clouds, but the earliest and latest mother trees did not receive less diversity of pollen than the others.

Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed ... more Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in ∼ ∼ ∼ ∼ 100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.

Evolution, 2001

We examined the spatial distribution of maternally inherited chloroplast DNA markers over the Fre... more We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (G STc ϭ 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen-nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

Evolution, 2001

Abstract.— We examined the spatial distribution of maternally inherited chloroplast DNA markers o... more Abstract.— We examined the spatial distribution of maternally inherited chloroplast DNA markers over the French part of the range of Sorbus torminalis, a scattered temperate forest tree native to most of Europe. The survey by restriction analysis of polymerase-chain-reaction amplified fragments for 880 individuals distributed among 55 populations allowed the detection of 25 haplotypes. The coefficient of differentiation among populations computed on the basis of haplotype frequency (GSTc= 0.34) was one of the lowest found in forest trees so far, and the mean within-population diversity was relatively high, indicating multiple-mother foundation events. A significant but slight geographical pattern was observed, up to distances of about 100 km. This pattern of differentiation was compared to the genetic structure of the same populations revealed by biparentally inherited markers (isoenzymes), and a new method to quantify the relative importance of seed and pollen dispersal was derived, based on isolation-by-distance models. Neither pollen- nor seed-mediated gene flow was predominant in S. torminalis, a finding that differs from those for the majority of tree species studied so far. This result was most likely due to an extinction-recolonization dynamics based on efficient seed dispersal strategies. The joint screening of 31 individuals of the related Sorbus aria and of 163 hybrid individuals shows that hybridization occurs predominantly in one direction and is rarely followed by cytoplasmic introgression. As a consequence, interspecific gene flow should not significantly affect the diversity dynamics within S. torminalis.

In plant quantitative genetic studies conducted ex situ, the large number of seeds produced per i... more In plant quantitative genetic studies conducted ex situ, the large number of seeds produced per individual has promoted the use of open-pollinated progeny tests. In subsequent analyses, seeds collected on the same mother-plant are assumed to be half-sibs. The consequences of the departure from half-sib assumption in progeny tests have been investigated since the 1960s using simulation approaches and, more recently, using molecular-based experimental approaches. This review aims to synthesize the results and conclusions of these simulation and empirical studies. We focus on tree species, where controlled crosses are difficult to carry out experimentally and departures from half-sib assumptions occur frequently in natural populations. First, the average level of relatedness expected within maternal progeny for many tree populations is higher than that of half-sibs. This is the consequence of non-random mating resulting from the small number of effective pollen donors per female, unequal male reproductive success and/or selfing. As result, estimates of genetic variance and heritability for quantitative traits may be upward biased. Alternatively, inbreeding depression, dominance effects and the heterogeneity of the male gamete pool among females are often neglected, which may lead to underestimation of the heritability of traits. A correction based on the mean genetic relatedness between offspring and the relatedness between parents is often used to compensate those biases. However, such correction cannot accurately adjust the estimates in situations where variable levels of genetic relatedness among families, dominance effects or inbreeding depression exist within the progeny. An alternative and promising approach is the use of the "animal model" approach, which optimizes the use of molecular data and paternal information to estimate heritability more accurately. This study is part of Julie Gauzere PhD thesis, which aims at understanding the role of adaptation and gene flow in the phenotypic variation of traits related to climate response along an altitudinal gradient of a temperate tree species, Fagus sylvatica. Sylvie Oddou-Muratorio is a population geneticist studying the impact of pollen and seed dispersal and climate-driven selection on adaptive dynamics of forest trees natural populations under climate change. François Lefèvre's research is targeted at the issues of sustainable management of forest genetic resources and adaptation of the forests to climate change. Christian Pichot is a population geneticist and quantitative geneticist studying the role of forest tree genetic resources on population dynamics. Etienne Klein research is targeted on dispersal of plant propagules (pollen and seeds), and their impact on the genetic composition of populations.