# Publications

### 2021

• Rescan, M., Grulois, D., Aboud, E. O., de Villemereuil, P., & Chevin, L.. (2021). Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment. PLOS Genetics, 17(6), e1009611. doi:10.1371/journal.pgen.1009611

Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest in population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can be predicted indirectly using simpler measures, which combine environmental time series with population estimates in constant environments. Here we address these questions by using an automated experimental evolution approach. We used a liquid-handling robot to expose over a hundred lines of the micro-alga Dunaliella salina to randomly fluctuating salinity over a continuous range, with controlled mean, variance, and autocorrelation. We then tracked the frequencies of two competing strains through amplicon sequencing of nuclear and choloroplastic barcode sequences. We show that the magnitude of environmental fluctuations (determined by their variance), but also their predictability (determined by their autocorrelation), had large impacts on the average selection coefficient. The variance in frequency change, which quantifies randomness in population genetics, was substantially higher in a fluctuating environment. The reaction norm of selection coefficients against constant salinity yielded accurate predictions for the mean selection coefficient in a fluctuating environment. This selection reaction norm was in turn well predicted by environmental tolerance curves, with population growth rate against salinity. However, both the selection reaction norm and tolerance curves underestimated the variance in selection caused by random environmental fluctuations. Overall, our results provide exceptional insights into the prospects for understanding and predicting genetic evolution in randomly fluctuating environments.

@article{rescan_predicting_2021-perso,
title = {Predicting population genetic change in an autocorrelated random environment: {Insights} from a large automated experiment},
volume = {17},
issn = {1553-7404},
shorttitle = {Predicting population genetic change in an autocorrelated random environment},
url = {http://devillemereuil.legtux.org/publis/Rescan et al. - 2021 - Predicting population genetic change in an autocor.pdf},
doi = {10.1371/journal.pgen.1009611},
abstract = {Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest in population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can be predicted indirectly using simpler measures, which combine environmental time series with population estimates in constant environments. Here we address these questions by using an automated experimental evolution approach. We used a liquid-handling robot to expose over a hundred lines of the micro-alga Dunaliella salina to randomly fluctuating salinity over a continuous range, with controlled mean, variance, and autocorrelation. We then tracked the frequencies of two competing strains through amplicon sequencing of nuclear and choloroplastic barcode sequences. We show that the magnitude of environmental fluctuations (determined by their variance), but also their predictability (determined by their autocorrelation), had large impacts on the average selection coefficient. The variance in frequency change, which quantifies randomness in population genetics, was substantially higher in a fluctuating environment. The reaction norm of selection coefficients against constant salinity yielded accurate predictions for the mean selection coefficient in a fluctuating environment. This selection reaction norm was in turn well predicted by environmental tolerance curves, with population growth rate against salinity. However, both the selection reaction norm and tolerance curves underestimated the variance in selection caused by random environmental fluctuations. Overall, our results provide exceptional insights into the prospects for understanding and predicting genetic evolution in randomly fluctuating environments.},
language = {en},
number = {6},
urldate = {2021-09-27},
journal = {PLOS Genetics},
author = {Rescan, Marie and Grulois, Daphné and Aboud, Enrique Ortega and de Villemereuil, Pierre and Chevin, Luis-Miguel},
month = jun,
year = {2021},
note = {IF: 5.92, Q1},
keywords = {Autocorrelation, Chloroplasts, Evolutionary biology, Genetic loci, Haplotypes, Population genetics, Population growth, Salinity},
pages = {e1009611},
file = {Rescan et al. - 2021 - Predicting population genetic change in an autocor.pdf:/home/pierre/Zotero/storage/SVHNWPPH/Rescan et al. - 2021 - Predicting population genetic change in an autocor.pdf:application/pdf},
}

• Denoyelle, L., de Villemereuil, P., Boyer, F., Khelifi, M., Gaffet, C., Alberto, F., Benjelloun, B., & Pompanon, F.. (2021). Genetic variations and differential DNA methylation to face contrasted climates in small ruminants: an analysis on traditionally-managed sheep and goats. Frontiers in Genetics, 12, 1809. doi:10.3389/fgene.2021.745284

The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (FST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

@article{denoyelle_genetic_2021-perso,
title = {Genetic variations and differential {DNA} methylation to face contrasted climates in small ruminants: an analysis on traditionally-managed sheep and goats},
volume = {12},
issn = {1664-8021},
shorttitle = {Genetic variations and differential {DNA} methylation to face contrasted climates in small ruminants},
url = {http://devillemereuil.legtux.org/publis/Denoyelle et al. - 2021 - Genetic variations and differential DNA methylatio.pdf},
doi = {10.3389/fgene.2021.745284},
abstract = {The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (FST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.},
urldate = {2021-10-11},
journal = {Frontiers in Genetics},
author = {Denoyelle, Laure and de Villemereuil, Pierre and Boyer, Frédéric and Khelifi, Meidhi and Gaffet, Clément and Alberto, Florian and Benjelloun, Badr and Pompanon, François},
year = {2021},
pages = {1809},
file = {Denoyelle et al. - 2021 - Genetic variations and differential DNA methylatio.pdf:/home/pierre/Zotero/storage/9NKBAEW9/Denoyelle et al. - 2021 - Genetic variations and differential DNA methylatio.pdf:application/pdf},
}

• Biquet, J., Bonamour, S., de Villemereuil, P., Franceschi, C., & Teplitsky, C.. (2021). Phenotypic plasticity drives phenological changes in a Mediterranean blue tit population. Journal of Evolutionary Biology. doi:10.1111/jeb.13950

Earlier phenology induced by climate change, such as the passerines’ breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds’ laying date has significantly advanced over 40 years, and we here determine whether this response is of plastic or evolutionary origin, by comparing the predictions of the breeder’s and the Robertson-­Price (STS) equations, to the observed genetic changes. We compare the results obtained for two fitness proxies (fledgling and recruitment success), using models accounting for their zero inflation. Because the trait appears heritable and under directional selection, the breeder’s equation predicts that genetic changes could drive a significant part of the phenological change observed. We, however, found that fitness proxies and laying date are not genetically correlated. The STS, therefore, predicts no evolution of the breeding time, predicting correctly the absence of trend in breeding values. Our results also emphasize that when investigating selection on a plastic trait under fluctuating selection, part of the fitness-­trait phenotypic covariance can be due to within individual covariance. In the case of repeated measurements, splitting within and between individual covariance can shift our perspective on the actual intensity of selection over multiple selection episodes, shedding light on the potential for the trait to evolve.

@article{biquet_phenotypic_2021-perso,
title = {Phenotypic plasticity drives phenological changes in a {Mediterranean} blue tit population},
issn = {1010-061X, 1420-9101},
url = {http://devillemereuil.legtux.org/publis/Biquet et al. - 2021 - Phenotypic plasticity drives phenological changes .pdf},
doi = {10.1111/jeb.13950},
abstract = {Earlier phenology induced by climate change, such as the passerines' breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds' laying date has significantly advanced over 40 years, and we here determine whether this response is of plastic or evolutionary origin, by comparing the predictions of the breeder's and the Robertson-­Price (STS) equations, to the observed genetic changes. We compare the results obtained for two fitness proxies (fledgling and recruitment success), using models accounting for their zero inflation. Because the trait appears heritable and under directional selection, the breeder's equation predicts that genetic changes could drive a significant part of the phenological change observed. We, however, found that fitness proxies and laying date are not genetically correlated. The STS, therefore, predicts no evolution of the breeding time, predicting correctly the absence of trend in breeding values. Our results also emphasize that when investigating selection on a plastic trait under fluctuating selection, part of the fitness-­trait phenotypic covariance can be due to within individual covariance. In the case of repeated measurements, splitting within and between individual covariance can shift our perspective on the actual intensity of selection over multiple selection episodes, shedding light on the potential for the trait to evolve.},
language = {en},
urldate = {2021-11-08},
journal = {Journal of Evolutionary Biology},
author = {Biquet, Juliette and Bonamour, Suzanne and de Villemereuil, Pierre and Franceschi, Christophe and Teplitsky, Céline},
month = nov,
year = {2021},
file = {Biquet et al. - 2021 - Phenotypic plasticity drives phenological changes .pdf:/home/pierre/Zotero/storage/C6ZTSGKS/Biquet et al. - 2021 - Phenotypic plasticity drives phenological changes .pdf:application/pdf},
}

### 2020

• de Villemereuil, P., Charmantier, A., Arlt, D., Bize, P., Brekke, P., Brouwer, L., Cockburn, A., Côté, S. D., Dobson, S. F., Evans, S. R., Festa-Bianchet, M., Gamelon, M., Hamel, S., Hegelbach, J., Jerstad, K., Kempenaers, B., Kruuk, L. E. B., Kumpula, J., Kvalnes, T., McAdam, A. G., McFarlane, E. S., Morrissey, M. B., Pärt, T., Pemberton, J. M., Qvarnström, A., Røstad, O., Schroeder, J., Senar, J. C., Sheldon, B. C., van de Pol, M., Visser, M. E., Wheelwright, N. T., Tufto, J., & Chevin, L.. (2020). Fluctuating optimum and temporally variable selection on breeding date in birds and mammals. Proceedings of the National Academy of Sciences, 117(50), 31969–31978. doi:10.1073/pnas.2009003117

Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.

@article{devillemereuil_fluctuating_2020-perso,
title = {Fluctuating optimum and temporally variable selection on breeding date in birds and mammals},
volume = {117},
issn = {0027-8424, 1091-6490},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2020 - Fluctuating optimum and temporally variable select.pdf},
doi = {10.1073/pnas.2009003117},
abstract = {Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.},
language = {en},
number = {50},
journal = {Proceedings of the National Academy of Sciences},
author = {de Villemereuil, Pierre and Charmantier, Anne and Arlt, Debora and Bize, Pierre and Brekke, Patricia and Brouwer, Lyanne and Cockburn, A. and Côté, Steve D. and Dobson, F. Stephen and Evans, Simon R. and Festa-Bianchet, Marco and Gamelon, Marlène and Hamel, Sandra and Hegelbach, Johann and Jerstad, Kurt and Kempenaers, Bart and Kruuk, Loeske E. B. and Kumpula, Jouko and Kvalnes, Thomas and McAdam, Andrew G. and McFarlane, S. Eryn and Morrissey, Michael B. and Pärt, Tomas and Pemberton, Josephine M. and Qvarnström, Anna and Røstad, Ole-Wiggo and Schroeder, Julia and Senar, Juan Carlos and Sheldon, Ben C and van de Pol, Martijn and Visser, Marcel E. and Wheelwright, Nathaniel T. and Tufto, Jarle and Chevin, Luis-Miguel},
year = {2020},
note = {IF: 9.58, Q1},
keywords = {phenotypic plasticity, adaptation, meta-analysis, fluctuating environment, fitness landscape},
pages = {31969--31978},
file = {de Villemereuil et al. - 2020 - Fluctuating optimum and temporally variable select.pdf:/home/pierre/Zotero/storage/UEMFA4KX/de Villemereuil et al. - 2020 - Fluctuating optimum and temporally variable select.pdf:application/pdf},
}

• Andrello, M., de Villemereuil, P., Carboni, M., Busson, D., Fortin, M., Gaggiotti, O. E., & Till‐Bottraud, I.. (2020). Accounting for stochasticity in demographic compensation along the elevational range of an alpine plant. Ecology Letters, 23(5), 870–880. doi:10.1111/ele.13488

Demographic compensation arises when vital rates change in opposite directions across populations, buffering the variation in population growth rates, and is a mechanism often invoked to explain the stability of species geographic ranges. However, studies on demographic compensation have disregarded the effects of temporal variation in vital rates and their temporal correlations, despite theoretical evidence that stochastic dynamics can affect population persistence in temporally varying environments. We carried out a seven-year-long demographic study on the perennial plant Arabis alpina (L.) across six populations encompassing most of its elevational range. We discovered demographic compensation in the form of negative correlations between the means of plant vital rates, but also between their temporal coefﬁcients of variation, correlations and elasticities. Even if their contribution to demographic compensation was small, this highlights a previously overlooked, but potentially important, role of stochastic processes in stabilising population dynamics at range margins.

@article{andrello_2020_accounting-perso,
title = {Accounting for stochasticity in demographic compensation along the elevational range of an alpine plant},
volume = {23},
issn = {1461-023X, 1461-0248},
url = {http://devillemereuil.legtux.org/publis/Andrello et al. - 2020 - Accounting for stochasticity in demographic compen.pdf},
doi = {10.1111/ele.13488},
abstract = {Demographic compensation arises when vital rates change in opposite directions across populations, buffering the variation in population growth rates, and is a mechanism often invoked to explain the stability of species geographic ranges. However, studies on demographic compensation have disregarded the effects of temporal variation in vital rates and their temporal correlations, despite theoretical evidence that stochastic dynamics can affect population persistence in temporally varying environments. We carried out a seven-year-long demographic study on the perennial plant Arabis alpina (L.) across six populations encompassing most of its elevational range. We discovered demographic compensation in the form of negative correlations between the means of plant vital rates, but also between their temporal coefﬁcients of variation, correlations and elasticities. Even if their contribution to demographic compensation was small, this highlights a previously overlooked, but potentially important, role of stochastic processes in stabilising population dynamics at range margins.},
number = {5},
urldate = {2020-04-22},
journal = {Ecology Letters},
author = {Andrello, Marco and de Villemereuil, Pierre and Carboni, Marta and Busson, Delphine and Fortin, Marie‐Josée and Gaggiotti, Oscar E. and Till‐Bottraud, Irène},
month = may,
year = {2020},
note = {IF: 8.70, Q1},
keywords = {ephe},
pages = {870--880},
file = {Andrello et al. - 2020 - Accounting for stochasticity in demographic compen.pdf:/home/pierre/Zotero/storage/NZL8ENHR/Andrello et al. - 2020 - Accounting for stochasticity in demographic compen.pdf:application/pdf},
}

• Rutschmann, A., Rozen-Rechels, D., Dupoué, A., Blaimont, P., de Villemereuil, P., Miles, D., Richard, M., & Clobert, J.. (2020). Climate dependent heating efficiency in the common lizard. Ecology and Evolution, 10(15), 8007–8017. doi:10.1002/ece3.6241

Regulation of body temperature is crucial for optimizing physiological performance in ectotherms but imposes constraints in time and energy. Time and energy spent thermoregulating can be reduced through behavioral (e.g., basking adjustments) or biophysical (e.g., heating rate physiology) means. In a heterogeneous environment, we expect thermoregulation costs to vary according to local, climatic conditions and therefore to drive the evolution of both behavioral and biophysical thermoregulation. To date, there are limited data showing that thermal physiological adjustments have a direct relationship to climatic conditions. In this study, we explored the effect of environmental conditions on heating rates in the common lizard (Zootoca vivipara). We sampled lizards from 10 populations in the Massif Central Mountain range of France and measured whether differences in heating rates of individuals correlated with phenotypic traits (i.e., body condition and dorsal darkness) or abiotic factors (temperature and rainfall). Our results show that heat gain is faster for lizards with a higher body condition, but also for individuals from habitats with higher amount of precipitation. Altogether, they demonstrate that environmentally induced constraints can shape biophysical aspects of thermoregulation.

@article{rutschmann_climate_2020-perso,
title = {Climate dependent heating efficiency in the common lizard},
volume = {10},
issn = {2045-7758},
url = {http://devillemereuil.legtux.org/publis/Rutschmann et al. - 2020 - Climate dependent heating efficiency in the common.pdf},
doi = {10.1002/ece3.6241},
abstract = {Regulation of body temperature is crucial for optimizing physiological performance in ectotherms but imposes constraints in time and energy. Time and energy spent thermoregulating can be reduced through behavioral (e.g., basking adjustments) or biophysical (e.g., heating rate physiology) means. In a heterogeneous environment, we expect thermoregulation costs to vary according to local, climatic conditions and therefore to drive the evolution of both behavioral and biophysical thermoregulation. To date, there are limited data showing that thermal physiological adjustments have a direct relationship to climatic conditions. In this study, we explored the effect of environmental conditions on heating rates in the common lizard (Zootoca vivipara). We sampled lizards from 10 populations in the Massif Central Mountain range of France and measured whether differences in heating rates of individuals correlated with phenotypic traits (i.e., body condition and dorsal darkness) or abiotic factors (temperature and rainfall). Our results show that heat gain is faster for lizards with a higher body condition, but also for individuals from habitats with higher amount of precipitation. Altogether, they demonstrate that environmentally induced constraints can shape biophysical aspects of thermoregulation.},
language = {en},
number = {15},
journal = {Ecology and Evolution},
author = {Rutschmann, Alexis and Rozen-Rechels, David and Dupoué, Andreaz and Blaimont, Pauline and de Villemereuil, Pierre and Miles, Donald and Richard, Murielle and Clobert, Jean},
year = {2020},
note = {IF: 2.40, Q1},
keywords = {ephe, ectotherms, heating efficiency, heating rate, thermoregulation behavior, time budget},
pages = {8007--8017},
file = {Rutschmann et al. - 2020 - Climate dependent heating efficiency in the common.pdf:/home/pierre/Zotero/storage/9GXV5G9Q/Rutschmann et al. - 2020 - Climate dependent heating efficiency in the common.pdf:application/pdf},
}

• Salloum, P., de Villemereuil, P., Santure, A. W., Waters, J. M., & Lavery, S. D.. (2020). Hitchhiking consequences for genetic and morphological patterns: the influence of kelp rafting on a brooding chiton. Biological Journal of the Linnean Society, 130(4), 756–770. doi:10.1093/biolinnean/blaa073

Abstract. Onithochiton neglectus is a morphologically variable, brooding chiton inhabiting coastal reefs throughout New Zealand and its Sub-Antarctic Islands.

@article{salloum_hitchhiking_2020-perso,
title = {Hitchhiking consequences for genetic and morphological patterns: the influence of kelp rafting on a brooding chiton},
volume = {130},
issn = {0024-4066},
shorttitle = {Hitchhiking consequences for genetic and morphological patterns},
url = {http://devillemereuil.legtux.org/publis/Salloum et al. - 2020 - Hitchhiking consequences for genetic and morpholog.pdf},
doi = {10.1093/biolinnean/blaa073},
abstract = {Abstract. Onithochiton neglectus is a morphologically variable, brooding chiton inhabiting coastal reefs throughout New Zealand and its Sub-Antarctic Islands.},
language = {en},
number = {4},
journal = {Biological Journal of the Linnean Society},
author = {Salloum, Priscila and de Villemereuil, Pierre and Santure, Anna W. and Waters, Jon M. and Lavery, Shane D.},
year = {2020},
note = {IF: 2.20, Q1},
keywords = {ephe},
pages = {756--770},
file = {Salloum et al. - 2020 - Hitchhiking consequences for genetic and morpholog.pdf:/home/pierre/Zotero/storage/WS2QJMR3/Salloum et al. - 2020 - Hitchhiking consequences for genetic and morpholog.pdf:application/pdf},
}

• Rutschmann, A., de Villemereuil, P., Brekke, P., Ewen, J. G., Anderson, N., & Santure, A. W.. (2020). Consequences of space sharing on individual phenotypes in the New Zealand hihi. Evolutionary Ecology, 34(5), 821–839. doi:10.1007/s10682-020-10063-z

In heterogeneous habitats, individuals sharing a larger part of their home-range are also likely to live in a very similar environment. This ‘common environment’ effect can generate phenotypic similarities between neighbours and lead to the structuring of phenotypes through the habitat. In this study, we used an intensely monitored population of hihi (or stitchbird, Notiomystis cincta) from New Zealand, to assess whether home-range overlap and genetic relatedness between birds could generate phenotypic resemblance for a wide panel of morphological and life-history traits. Using a multiple-matrix animal model approach to partition the phenotypic variance present in the population, we included a spatial matrix measuring home range overlap between birds and estimated the proportion of variance attributable to space sharing. We detected a clear contribution of space sharing to the overall phenotypic similarity for two traits: hatchling mass and laying date. We also confirmed the very low estimates of genetic heritability already found for this species. These results suggest that models including space sharing can offer further insight into the determinants of individual differences in phenotype. In particular, the spatial matrix helps to capture fine-scale variation of the environment that classic animal models would potentially miss or miss-assign. In this species, results also suggest that small but significant genetic heritability estimates are not upwardly biased by clustering of close relatives in space.

@article{rutschmann_consequences_2020-perso,
title = {Consequences of space sharing on individual phenotypes in the {New} {Zealand} hihi},
volume = {34},
issn = {1573-8477},
url = {http://devillemereuil.legtux.org/publis/Rutschmann et al. - 2020 - Consequences of space sharing on individual phenot.pdf},
doi = {10.1007/s10682-020-10063-z},
abstract = {In heterogeneous habitats, individuals sharing a larger part of their home-range are also likely to live in a very similar environment. This ‘common environment’ effect can generate phenotypic similarities between neighbours and lead to the structuring of phenotypes through the habitat. In this study, we used an intensely monitored population of hihi (or stitchbird, Notiomystis cincta) from New Zealand, to assess whether home-range overlap and genetic relatedness between birds could generate phenotypic resemblance for a wide panel of morphological and life-history traits. Using a multiple-matrix animal model approach to partition the phenotypic variance present in the population, we included a spatial matrix measuring home range overlap between birds and estimated the proportion of variance attributable to space sharing. We detected a clear contribution of space sharing to the overall phenotypic similarity for two traits: hatchling mass and laying date. We also confirmed the very low estimates of genetic heritability already found for this species. These results suggest that models including space sharing can offer further insight into the determinants of individual differences in phenotype. In particular, the spatial matrix helps to capture fine-scale variation of the environment that classic animal models would potentially miss or miss-assign. In this species, results also suggest that small but significant genetic heritability estimates are not upwardly biased by clustering of close relatives in space.},
language = {en},
number = {5},
journal = {Evolutionary Ecology},
author = {Rutschmann, Alexis and de Villemereuil, Pierre and Brekke, Patricia and Ewen, John G. and Anderson, Neil and Santure, Anna W.},
month = oct,
year = {2020},
note = {IF: 2.47, Q1},
pages = {821--839},
file = {Rutschmann et al. - 2020 - Consequences of space sharing on individual phenot.pdf:/home/pierre/Zotero/storage/TAEKXB8V/Rutschmann et al. - 2020 - Consequences of space sharing on individual phenot.pdf:application/pdf},
}

• Duntsch, L., Tomotani, B. M., de Villemereuil, P., Brekke, P., Lee, K. D., Ewen, J. G., & Santure, A. W.. (2020). Polygenic basis for adaptive morphological variation in a threatened Aotearoa \textbar New Zealand bird, the hihi (Notiomystis cincta). Proceedings of the Royal Society B: Biological Sciences, 287(1933), 20200948. doi:10.1098/rspb.2020.0948

To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head–bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head–bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.

@article{duntsch_polygenic_2020-perso,
title = {Polygenic basis for adaptive morphological variation in a threatened {Aotearoa} {\textbar} {New} {Zealand} bird, the hihi ({Notiomystis} cincta)},
volume = {287},
url = {http://devillemereuil.legtux.org/publis/Duntsch et al. - 2020 - Polygenic basis for adaptive morphological variati.pdf},
doi = {10.1098/rspb.2020.0948},
abstract = {To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. We estimated the heritability of three hihi (Notiomystis cincta) morphological traits known to be under selection (nestling tarsus length, body mass and head–bill length) using 523 individuals and 39 699 single nucleotide polymorphisms (SNPs) from a 50 K Affymetrix SNP chip. We then examined the genetic architecture of the traits via chromosome partitioning analyses and genome-wide association scans (GWAS). Heritabilities estimated using pedigree relatedness or genomic relatedness were low. For tarsus length, the proportion of genetic variance explained by each chromosome was positively correlated with its size, and more than one chromosome explained significant variation for body mass and head–bill length. Finally, GWAS analyses suggested many loci of small effect contributing to trait variation for all three traits, although one locus (an SNP within an intron of the transcription factor HEY2) was tentatively associated with tarsus length. Our findings suggest a polygenic nature for the morphological traits, with many small effect size loci contributing to the majority of the variation, similar to results from many other wild populations. However, the small effective population size, polygenic architecture and already low heritabilities suggest that both the total response and rate of response to selection are likely to be limited in hihi.},
number = {1933},
urldate = {2020-10-15},
journal = {Proceedings of the Royal Society B: Biological Sciences},
author = {Duntsch, Laura and Tomotani, Barbara M. and de Villemereuil, Pierre and Brekke, Patricia and Lee, Kate D. and Ewen, John G. and Santure, Anna W.},
year = {2020},
note = {IF: 4.30, Q1},
pages = {20200948},
file = {Duntsch et al. - 2020 - Polygenic basis for adaptive morphological variati.pdf:/home/pierre/Zotero/storage/9TXL7H7Y/Duntsch et al. - 2020 - Polygenic basis for adaptive morphological variati.pdf:application/pdf},
}

• de Villemereuil, P., Gaggiotti, O. E., & Goudet, J.. (2020). Common garden experiments to study local adaptation need to account for population structure. Journal of Ecology, n/a(n/a). doi:10.1111/1365-2745.13528

Common garden experiments are valuable to study adaptive phenomenon and adaptive potential, in that they allow to study local adaptation without the confounding effect of phenotypic plasticity. The QST−FST comparison framework, comparing genetic differentiation at the phenotypic and molecular level, is the usual way to test and measure whether local adaptation influences phenotypic divergence between populations. Here, we highlight that the assumptions behind the expected equality QST = FST under neutrality correspond to a very simple model of population genetics. While the equality might, on average, be robust to violation of such assumptions, more complex population structure can generate strong evolutionary noise. Synthesis: We highlight recent methodological developments aimed at overcoming this issue and at providing a more general framework to detect local adaptation, using less restrictive assumptions. We invite empiricists to look into these methods and theorists to continue developing even more general methods.

@article{devillemereuil_common_2020-perso,
title = {Common garden experiments to study local adaptation need to account for population structure},
volume = {n/a},
issn = {1365-2745},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2020 - Common garden experiments to study local adaptatio.pdf},
doi = {10.1111/1365-2745.13528},
abstract = {Common garden experiments are valuable to study adaptive phenomenon and adaptive potential, in that they allow to study local adaptation without the confounding effect of phenotypic plasticity. The QST−FST comparison framework, comparing genetic differentiation at the phenotypic and molecular level, is the usual way to test and measure whether local adaptation influences phenotypic divergence between populations. Here, we highlight that the assumptions behind the expected equality QST = FST under neutrality correspond to a very simple model of population genetics. While the equality might, on average, be robust to violation of such assumptions, more complex population structure can generate strong evolutionary noise. Synthesis: We highlight recent methodological developments aimed at overcoming this issue and at providing a more general framework to detect local adaptation, using less restrictive assumptions. We invite empiricists to look into these methods and theorists to continue developing even more general methods.},
language = {en},
number = {n/a},
urldate = {2020-10-23},
journal = {Journal of Ecology},
author = {de Villemereuil, Pierre and Gaggiotti, Oscar E. and Goudet, Jérôme},
year = {2020},
keywords = {population genetics, population structure, quantitative genetics, common garden, Local adaptation, phenotypic divergence, QST − FST comparison},
file = {de Villemereuil et al. - 2020 - Common garden experiments to study local adaptatio.pdf:/home/pierre/Zotero/storage/VIEWSJHC/de Villemereuil et al. - 2020 - Common garden experiments to study local adaptatio.pdf:application/pdf},
}

### 2019

• de Villemereuil, P., Rutschmann, A., Lee, K. D., Ewen, J. G., Brekke, P., & Santure, A. W.. (2019). Little adaptive potential in a threatened passerine bird. Current Biology, 29(5), 889–894.e3. doi:10.1016/j.cub.2019.01.072

@article{devillemereuil_little_2019-perso,
title = {Little adaptive potential in a threatened passerine bird},
volume = {29},
issn = {0960-9822},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2019 - Little adaptive potential in a threatened passerin.pdf},
doi = {10.1016/j.cub.2019.01.072},
abstract = {Summary
number = {5},
urldate = {2019-03-14},
journal = {Current Biology},
author = {de Villemereuil, Pierre and Rutschmann, Alexis and Lee, Kate D. and Ewen, John G. and Brekke, Patricia and Santure, Anna W.},
year = {2019},
note = {IF: 9.25, Q1 (Cit : 17)},
keywords = {quantitative genetics, adaptation, conservation biology, conservation genetics, genetic variance of fitness, heritability, nucleotide diversity},
pages = {889--894.e3},
file = {de Villemereuil et al. - 2019 - Little adaptive potential in a threatened passerin.pdf:/home/pierre/Zotero/storage/RE6K3MZL/de Villemereuil et al. - 2019 - Little adaptive potential in a threatened passerin.pdf:application/pdf},
}

• Xhaard, C., Dandine-Roulland, C., de Villemereuil, P., Floch, E. L., Bacq-Daian, D., Machu, J., Ferreira, J. P., Deleuze, J., Zannad, F., Rossignol, P., & Girerd, N.. (2019). Heritability of a resting heart rate in a 20-year follow-up family cohort with GWAS data: Insights from the STANISLAS cohort:. European Journal of Preventive Cardiology. doi:10.1177/2047487319890763

Background The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR i…

@article{xhaard_heritability_2019-perso,
title = {Heritability of a resting heart rate in a 20-year follow-up family cohort with {GWAS} data: {Insights} from the {STANISLAS} cohort:},
shorttitle = {Heritability of a resting heart rate in a 20-year follow-up family cohort with {GWAS} data},
url = {https://journals.sagepub.com/doi/10.1177/2047487319890763},
doi = {10.1177/2047487319890763},
abstract = {Background The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR i...},
urldate = {2020-04-22},
journal = {European Journal of Preventive Cardiology},
author = {Xhaard, Constance and Dandine-Roulland, Claire and de Villemereuil, Pierre and Floch, Edith Le and Bacq-Daian, Delphine and Machu, Jean-Loup and Ferreira, Joao Pedro and Deleuze, Jean-François and Zannad, Faiez and Rossignol, Patrick and Girerd, Nicolas},
month = dec,
year = {2019},
note = {IF: 5.64, Q1 (Cit: 2)},
keywords = {ephe},
file = {Xhaard et al. - 2019 - Heritability of a resting heart rate in a 20-year .pdf:/home/pierre/Zotero/storage/HZ6MNI6A/Xhaard et al. - 2019 - Heritability of a resting heart rate in a 20-year .pdf:application/pdf},
}

• Nakagawa, S., & de Villemereuil, P.. (2019). A general method for simultaneously accounting for phylogenetic and species sampling uncertainty via Rubin’s rules in comparative analysis. Systematic Biology, 68(4), 632–641. doi:10.1093/sysbio/syy089

Abstract. Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution

@article{nakagawa_general_2019-perso,
title = {A general method for simultaneously accounting for phylogenetic and species sampling uncertainty via {Rubin}’s rules in comparative analysis},
volume = {68},
url = {http://devillemereuil.legtux.org/publis/Nakagawa et de Villemereuil - 2019 - A general method for simultaneously accounting for.pdf},
doi = {10.1093/sysbio/syy089},
abstract = {Abstract. Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species’ trait evolution},
number = {4},
journal = {Systematic Biology},
author = {Nakagawa, Shinichi and de Villemereuil, Pierre},
year = {2019},
note = {IF: 8.52, Q1 (Cit: 8)},
keywords = {cofirst},
pages = {632--641},
file = {Nakagawa et de Villemereuil - 2019 - A general method for simultaneously accounting for.pdf:/home/pierre/Zotero/storage/G7EP7YGF/Nakagawa et de Villemereuil - 2019 - A general method for simultaneously accounting for.pdf:application/pdf},
}

• de Villemereuil, P., Rutschmann, A., Ewen, J. G., Santure, A. W., & Brekke, P.. (2019). Can threatened species adapt in a restored habitat? No expected evolutionary response in lay date for the New Zealand hihi. Evolutionary Applications, 12(3), 482–497. doi:10.1111/eva.12727

@article{devillemereuil_can_2018-perso,
title = {Can threatened species adapt in a restored habitat? {No} expected evolutionary response in lay date for the {New} {Zealand} hihi},
volume = {12},
issn = {1752-4571},
shorttitle = {Can threatened species adapt in a restored habitat?},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2018 - Can threatened species adapt in a restored habitat.pdf},
doi = {10.1111/eva.12727},
number = {3},
urldate = {2018-12-13},
journal = {Evolutionary Applications},
author = {de Villemereuil, Pierre and Rutschmann, Alexis and Ewen, John G. and Santure, Anna W. and Brekke, Patricia},
year = {2019},
note = {IF: 4.69, Q1 (Cit: 7)},
keywords = {phenology, quantitative genetics, conservation biology, laying date, Notiomystis cincta},
pages = {482--497},
file = {de Villemereuil et al. - 2018 - Can threatened species adapt in a restored habitat.pdf:/home/pierre/Zotero/storage/YNPBD6RB/de Villemereuil et al. - 2018 - Can threatened species adapt in a restored habitat.pdf:application/pdf},
}

• de Villemereuil, P.. (2019). On the relevance of Bayesian statistics and MCMC for animal models. Journal of Animal Breeding and Genetics, 136(5), 339–340. doi:10.1111/jbg.12426
@article{devillemereuil_relevance_2019-perso,
title = {On the relevance of {Bayesian} statistics and {MCMC} for animal models},
volume = {136},
copyright = {© 2019 Blackwell Verlag GmbH},
issn = {1439-0388},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil - 2019 - On the relevance of Bayesian statistics and MCMC f.pdf},
doi = {10.1111/jbg.12426},
language = {en},
number = {5},
urldate = {2019-08-27},
journal = {Journal of Animal Breeding and Genetics},
author = {de Villemereuil, Pierre},
year = {2019},
note = {IF: 1.63, Q1 (Cit : 0)},
pages = {339--340},
file = {de Villemereuil - 2019 - On the relevance of Bayesian statistics and MCMC f.pdf:/home/pierre/Zotero/storage/GC8N2ST6/de Villemereuil - 2019 - On the relevance of Bayesian statistics and MCMC f.pdf:application/pdf},
}

• LeGrice, R. J., Tezanos‐Pinto, G., de Villemereuil, P., Holwell, G. I., & Painting, C. J.. (2019). Directional selection on body size but no apparent survival cost to being large in wild New Zealand giraffe weevils. Evolution, 73(4), 762–776. doi:https://doi.org/10.1111/evo.13698

When an individual’s reproductive success relies on winning fights to secure mating opportunities, bearing larger weapons is advantageous. However, sexual selection can be extremely complex, and over an animal’s life the opportunity to mate is influenced by numerous factors. We studied a wild population of giraffe weevils (Lasiorhynchus barbicornis) that exhibit enormous intra and intersexual size variation. Males bear an elongated rostrum used as a weapon in fights for mating opportunities. However, small males also employ sneaking behavior as an alternative reproductive tactic. We investigated sexual selection on size by tracking individual males and females daily over two 30-day periods to measure long-term mating success. We also assessed how survival and recapture probabilities vary with sex and size to determine whether there might be a survival cost associated with size. We found evidence for directional selection on size through higher mating success, but no apparent survival trade-off. Instead, larger individuals mate more often and have a higher survival probability, suggesting an accumulation of benefits to bigger individuals. Furthermore, we found evidence of size assortative mating where males appear to selectively mate with bigger females. Larger and more competitive males secure matings with larger females more frequently than smaller males, which may further increase their fitness.

@article{legrice_directional_2019-perso,
title = {Directional selection on body size but no apparent survival cost to being large in wild {New} {Zealand} giraffe weevils},
volume = {73},
copyright = {© 2019 The Author(s). Evolution © 2019 The Society for the Study of Evolution.},
issn = {1558-5646},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/evo.13698},
doi = {https://doi.org/10.1111/evo.13698},
abstract = {When an individual's reproductive success relies on winning fights to secure mating opportunities, bearing larger weapons is advantageous. However, sexual selection can be extremely complex, and over an animal's life the opportunity to mate is influenced by numerous factors. We studied a wild population of giraffe weevils (Lasiorhynchus barbicornis) that exhibit enormous intra and intersexual size variation. Males bear an elongated rostrum used as a weapon in fights for mating opportunities. However, small males also employ sneaking behavior as an alternative reproductive tactic. We investigated sexual selection on size by tracking individual males and females daily over two 30-day periods to measure long-term mating success. We also assessed how survival and recapture probabilities vary with sex and size to determine whether there might be a survival cost associated with size. We found evidence for directional selection on size through higher mating success, but no apparent survival trade-off. Instead, larger individuals mate more often and have a higher survival probability, suggesting an accumulation of benefits to bigger individuals. Furthermore, we found evidence of size assortative mating where males appear to selectively mate with bigger females. Larger and more competitive males secure matings with larger females more frequently than smaller males, which may further increase their fitness.},
language = {en},
number = {4},
urldate = {2020-12-07},
journal = {Evolution},
author = {LeGrice, Rebecca J. and Tezanos‐Pinto, Gabriela and Villemereuil, Pierre de and Holwell, Gregory I. and Painting, Christina J.},
year = {2019},
note = {IF: 3.82, Q1 (Cit. : 0)
tex.ids: legrice\_directional\_2019-perso},
keywords = {sexual selection, mark-recapture, Alternative reproductive tactics, brentidae, exaggerated traits, size-assortative mating},
pages = {762--776},
file = {LeGrice et al. - 2019 - Directional selection on body size but no apparent.pdf:/home/pierre/Zotero/storage/8DWE79JH/LeGrice et al. - 2019 - Directional selection on body size but no apparent.pdf:application/pdf},
}

### 2018

• de Villemereuil, P., Mouterde, M., Gaggiotti, O. E., & Till-Bottraud, I.. (2018). Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant \textitArabis alpina. Journal of Ecology, 106(5), 1952–1971. doi:10.1111/1365-2745.12955

1. Local adaptation and phenotypic plasticity are two important characteristics of alpine plants to overcome the threats caused by global changes. Among alpine species, Arabis alpina is characterised by an unusually wide altitudinal amplitude, ranging from 800m to 3100m of elevation in the French Alps. Two non-exclusive hypotheses can explain the presence of A. alpina across this broad ecological gradient: adaptive phenotypic plasticity or local adaptation, making this species especially useful to better understand these phenomena in alpine plant species. 2. We carried out common garden experiments at two different elevations with maternal progenies from 6 sites that differed in altitude. We showed that (i) key phenotypic traits (morphotype, total fruit length, growth, height) display significant signs of local adaptation, (ii) most traits studied are characterised by a high phenotypic plasticity between the two experimental gardens, and (iii) the two populations from the highest elevations lacked morphological plasticity compared to the other populations. 3. By combining two genome scan approaches (detection of selection and association methods), we isolated a candidate gene (SPS1). This gene was associated with height and local average temperature in our studied populations, consistent with previous studies on this gene in A. thaliana. Synthesis Given the nature of the traits involved in the detected pattern of local adaptation and the relative lack of plasticity of the two most extreme populations, our findings are consistent with a scenario of a locally adaptive stress response syndrome in high elevation populations. Due to a reduced phenotypic plasticity, an overall low intra-population genetic diversity of the adaptive traits and weak gene flow, populations of high altitude might have difficulties to cope with e.g. a rise of temperature.

@article{devillemereuil_patterns_2018-perso,
title = {Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant \textit{{Arabis} alpina}},
volume = {106},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2018 - Patterns of phenotypic plasticity and local adapta.pdf},
doi = {10.1111/1365-2745.12955},
abstract = {1. Local adaptation and phenotypic plasticity are two important characteristics of alpine plants to overcome the threats
caused by global changes.
Among alpine species, Arabis alpina is characterised by an unusually wide altitudinal amplitude, ranging from 800m to 3100m of elevation in the French Alps.
Two non-exclusive hypotheses can explain the presence of A. alpina across this broad ecological gradient: adaptive phenotypic plasticity or local adaptation, making this species especially useful to better understand these phenomena in alpine plant species.
2. We carried out common garden experiments at two different elevations with maternal progenies from 6 sites that differed in altitude. We showed that (i) key phenotypic traits (morphotype, total fruit length, growth, height) display significant signs of local adaptation, (ii) most traits studied are characterised by a high phenotypic plasticity between the two experimental gardens, and (iii) the two populations from the highest elevations lacked morphological plasticity compared to the other populations.
3. By combining two genome scan approaches (detection of selection and association methods), we isolated a candidate gene (SPS1). This gene was associated with height and local average temperature in our studied populations, consistent with previous studies on this gene in A. thaliana.
Synthesis Given the nature of the traits involved in the detected pattern of local adaptation and the relative lack of plasticity of the two most extreme populations, our findings are consistent with a scenario of a locally adaptive stress response syndrome in high elevation populations.
Due to a reduced phenotypic plasticity, an overall low intra-population genetic diversity of the adaptive traits and weak gene flow, populations of high altitude might have difficulties to cope with e.g. a rise of temperature.},
number = {5},
journal = {Journal of Ecology},
author = {de Villemereuil, Pierre and Mouterde, Médéric and Gaggiotti, Oscar E. and Till-Bottraud, Irène},
year = {2018},
note = {IF: 5.17, Q1 (Cit: 13)},
pages = {1952--1971},
file = {de Villemereuil et al. - 2018 - Patterns of phenotypic plasticity and local adapta.pdf:/home/pierre/Zotero/storage/E4XVRA9L/de Villemereuil et al. - 2018 - Patterns of phenotypic plasticity and local adapta.pdf:application/pdf},
}

• de Villemereuil, P., Morrissey, M. B., Nakagawa, S., & Schielzeth, H.. (2018). Fixed-effect variance and the estimation of repeatabilities and heritabilities: issues and solutions. Journal of Evolutionary Biology, 31(4), 621–632. doi:10.1111/jeb.13232

Linear mixed-effects models are frequently used for estimating quantitative genetic parameters, including the heritability, as well as the repeatability, of traits. Heritability acts as a filter that determines how efficiently phenotypic selection translates into evolutionary change, whereas repeatability informs us about the individual consistency of phenotypic traits. As quantities of biological interest, it is important that the denominator, the phenotypic variance in both cases, reflects the amount of phenotypic variance in the relevant ecological setting. The current practice of quantifying heritabilities and repeatabilities from mixed-effects models frequently deprives their denominator of variance explained by fixed effects (often leading to upward bias of heritabilities and repeatabilities), and it has been suggested to omit fixed effects when estimating heritabilities in particular. We advocate an alternative option of fitting models incorporating all relevant effects, while including the variance explained by fixed effects into the estimation of the phenotypic variance. The approach is easily implemented and allows optimizing the estimation of phenotypic variance, for example by the exclusion of variance arising from experimental design effects while still including all biologically relevant sources of variation. We address the estimation and interpretation of heritabilities in situations in which potential covariates are themselves heritable traits of the organism. Furthermore, we discuss complications that arise in generalized and nonlinear mixed models with fixed effects. In these cases, the variance parameters on the data scale depend on the location of the intercept and hence on the scaling of the fixed effects. Integration over the biologically relevant range of fixed effects offers a preferred solution in those situations.

@article{devillemereuil_fixed_2018-perso,
title = {Fixed-effect variance and the estimation of repeatabilities and heritabilities: issues and solutions},
volume = {31},
issn = {1420-9101},
shorttitle = {Fixed-effect variance and the estimation of repeatabilities and heritabilities},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2017 - Fixed effect variance and the estimation of repeat.pdf},
doi = {10.1111/jeb.13232},
abstract = {Linear mixed-effects models are frequently used for estimating quantitative genetic parameters, including the heritability, as well as the repeatability, of traits. Heritability acts as a filter that determines how efficiently phenotypic selection translates into evolutionary change, whereas repeatability informs us about the individual consistency of phenotypic traits. As quantities of biological interest, it is important that the denominator, the phenotypic variance in both cases, reflects the amount of phenotypic variance in the relevant ecological setting. The current practice of quantifying heritabilities and repeatabilities from mixed-effects models frequently deprives their denominator of variance explained by fixed effects (often leading to upward bias of heritabilities and repeatabilities), and it has been suggested to omit fixed effects when estimating heritabilities in particular. We advocate an alternative option of fitting models incorporating all relevant effects, while including the variance explained by fixed effects into the estimation of the phenotypic variance. The approach is easily implemented and allows optimizing the estimation of phenotypic variance, for example by the exclusion of variance arising from experimental design effects while still including all biologically relevant sources of variation. We address the estimation and interpretation of heritabilities in situations in which potential covariates are themselves heritable traits of the organism. Furthermore, we discuss complications that arise in generalized and nonlinear mixed models with fixed effects. In these cases, the variance parameters on the data scale depend on the location of the intercept and hence on the scaling of the fixed effects. Integration over the biologically relevant range of fixed effects offers a preferred solution in those situations.},
language = {en},
number = {4},
urldate = {2017-07-06},
journal = {Journal of Evolutionary Biology},
author = {de Villemereuil, Pierre and Morrissey, Michael B. and Nakagawa, Shinichi and Schielzeth, Holger},
year = {2018},
note = {IF: 2.53, Q1 (Cit: 25)},
keywords = {quantitative genetics, heritability, fixed effects, generalised linear mixed modelling, linear mixed modelling, variance component analysis},
pages = {621--632},
file = {Full Text PDF:/home/pierre/Zotero/storage/CNPKDFUC/Villemereuil et al. - 2018 - Fixed-effect variance and the estimation of repeat.pdf:application/pdf;de Villemereuil et al. - 2018 - Fixed effect variance and the estimation of repeat.pdf:/home/pierre/Zotero/storage/DJR9GDWQ/de Villemereuil et al. - 2018 - Fixed effect variance and the estimation of repeat.pdf:application/pdf},
}

• de Villemereuil, P.. (2018). Quantitative genetics methods depending on the nature of the phenotypic trait. Annals of the New York Academy of Sciences, 1422(1), 29–47. doi:10.1111/nyas.13571

A consequence of the assumptions of the infinitesimal model, one of the most important theoretical foundations of quantitative genetics, is that phenotypic traits are predicted to be most often normally distributed (so-called Gaussian traits). But phenotypic traits, especially those interesting for evolutionary biology, might be shaped according to very diverse distributions. Here, I show how quantitative genetics tools have been extended to account for a wider diversity of phenotypic traits using first the threshold model and then more recently using generalized linear mixed models. I explore the assumptions behind these models and how they can be used to study the genetics of non-Gaussian complex traits. I also comment on three recent methodological advances in quantitative genetics that widen our ability to study new kinds of traits: the use of “modular” hierarchical modeling (e.g., to study survival in the context of capture–recapture approaches for wild populations); the use of aster models to study a set of traits with conditional relationships (e.g., life-history traits); and, finally, the study of high-dimensional traits, such as gene expression.

@article{devillemereuil_quantitative_2018-perso,
series = {The {Year} in {Evolutionary} {Biology}},
title = {Quantitative genetics methods depending on the nature of the phenotypic trait},
volume = {1422},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil - 2018 - Quantitative genetics methods depending on the nat.pdf},
doi = {10.1111/nyas.13571},
abstract = {A consequence of the assumptions of the infinitesimal model, one of the most important theoretical foundations of quantitative genetics, is that phenotypic traits are predicted to be most often normally distributed (so-called Gaussian traits). But phenotypic traits, especially those interesting for evolutionary biology, might be shaped according to very diverse distributions. Here, I show how quantitative genetics tools have been extended to account for a wider diversity of phenotypic traits using first the threshold model and then more recently using generalized linear mixed models. I explore the assumptions behind these models and how they can be used to study the genetics of non-Gaussian complex traits. I also comment on three recent methodological advances in quantitative genetics that widen our ability to study new kinds of traits: the use of “modular” hierarchical modeling (e.g., to study survival in the context of capture–recapture approaches for wild populations); the use of aster models to study a set of traits with conditional relationships (e.g., life-history traits); and, finally, the study of high-dimensional traits, such as gene expression.},
number = {1},
journal = {Annals of the New York Academy of Sciences},
author = {de Villemereuil, Pierre},
year = {2018},
note = {IF: 4.28, Q1 (Cit: 8)},
pages = {29--47},
file = {de Villemereuil - 2018 - Quantitative genetics methods depending on the nat.pdf:/home/pierre/Zotero/storage/TZNLGJ38/de Villemereuil - 2018 - Quantitative genetics methods depending on the nat.pdf:application/pdf},
}

• Alberto, F. J., Boyer, F., Orozco-terWengel, P., Streeter, I., Servin, B., de Villemereuil, P., Benjelloun, B., Librado, P., Biscarini, F., Colli, L., Barbato, M., Zamani, W., Alberti, A., Engelen, S., Stella, A., Joost, S., Ajmone-Marsan, P., Negrini, R., Orlando, L., Rezaei, H. R., Naderi, S., Clarke, L., Flicek, P., Wincker, P., Coissac, E., Kijas, J., Tosser-Klopp, G., Chikhi, A., Bruford, M. W., Taberlet, P., & Pompanon, F.. (2018). Convergent genomic signatures of domestication in sheep and goats. Nature Communications, 9(1), 813. doi:10.1038/s41467-018-03206-y

The sheep and goat were domesticated {\textasciitilde}10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

@article{alberto_convergent_2018-perso,
title = {Convergent genomic signatures of domestication in sheep and goats},
volume = {9},
copyright = {2018 The Author(s)},
issn = {2041-1723},
url = {https://www.nature.com/articles/s41467-018-03206-y},
doi = {10.1038/s41467-018-03206-y},
abstract = {The sheep and goat were domesticated {\textasciitilde}10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.},
language = {en},
number = {1},
urldate = {2018-09-21},
journal = {Nature Communications},
author = {Alberto, Florian J. and Boyer, Frédéric and Orozco-terWengel, Pablo and Streeter, Ian and Servin, Bertrand and de Villemereuil, Pierre and Benjelloun, Badr and Librado, Pablo and Biscarini, Filippo and Colli, Licia and Barbato, Mario and Zamani, Wahid and Alberti, Adriana and Engelen, Stefan and Stella, Alessandra and Joost, Stéphane and Ajmone-Marsan, Paolo and Negrini, Riccardo and Orlando, Ludovic and Rezaei, Hamid Reza and Naderi, Saeid and Clarke, Laura and Flicek, Paul and Wincker, Patrick and Coissac, Eric and Kijas, James and Tosser-Klopp, Gwenola and Chikhi, Abdelkader and Bruford, Michael W. and Taberlet, Pierre and Pompanon, François},
month = mar,
year = {2018},
note = {IF: 12.35, Q1 (Cit: 63)},
pages = {813},
file = {Alberto et al. - 2018 - Convergent genomic signatures of domestication in .pdf:/home/pierre/Zotero/storage/3A677CBY/Alberto et al. - 2018 - Convergent genomic signatures of domestication in .pdf:application/pdf},
}

### 2017

• Garamszegi, L. Z., & de Villemereuil, P.. (2017). Perturbations on the uniform distribution of p-values can lead to misleading inferences from null-hypothesis testing. Trends in Neuroscience and Education, 8-9, 18–27. doi:10.1016/j.tine.2017.10.001

Null-hypothesis testing (NHT) based on statistical significance is the most conventional statistical framework, on which neuroscientists rely for the analysis of their data. However, this approach can provide misleading results if p-values are wrongly interpreted, as often done in practice. Misconceptions can arise, in particular, when i) wrong null-hypothesis is chosen for reference; ii) the assumptions of the statistical model are not met; iii) p-values are interpreted as the probability of the null- or alternative hypotheses or as the measure of the importance of findings; iv) statistical thresholds guide scientific conclusions and decision making; v) one applies multiple testing or p-hacking. In this commentary, we address these issues by bringing into the focus the uniform distribution of p-values with the hope of enhancing the appreciation and proper use of the NHT approach among neuroscientists. We propose guidelines for the correct interpretations of p-values that brain and behavioural scientists may adopt to improve both the transparency of statistical reports and the value of scientific conclusions drawn from them.

@article{garamszegi_perturbations_2017-perso,
title = {Perturbations on the uniform distribution of p-values can lead to misleading inferences from null-hypothesis testing},
volume = {8-9},
issn = {2211-9493},
url = {http://devillemereuil.legtux.org/publis/Zsolt Garamszegi and de Villemereuil - 2017 - Perturbations on the uniform distribution of p-val.pdf},
doi = {10.1016/j.tine.2017.10.001},
abstract = {Null-hypothesis testing (NHT) based on statistical significance is the most conventional statistical framework, on which neuroscientists rely for the analysis of their data. However, this approach can provide misleading results if p-values are wrongly interpreted, as often done in practice. Misconceptions can arise, in particular, when i) wrong null-hypothesis is chosen for reference; ii) the assumptions of the statistical model are not met; iii) p-values are interpreted as the probability of the null- or alternative hypotheses or as the measure of the importance of findings; iv) statistical thresholds guide scientific conclusions and decision making; v) one applies multiple testing or p-hacking. In this commentary, we address these issues by bringing into the focus the uniform distribution of p-values with the hope of enhancing the appreciation and proper use of the NHT approach among neuroscientists. We propose guidelines for the correct interpretations of p-values that brain and behavioural scientists may adopt to improve both the transparency of statistical reports and the value of scientific conclusions drawn from them.},
urldate = {2017-12-26},
journal = {Trends in Neuroscience and Education},
author = {Garamszegi, László Zsolt and de Villemereuil, Pierre},
month = dec,
year = {2017},
note = {IF: 3.20, Q1 (Cit: 1)},
keywords = {-hacking, -values, Null-hypothesis testing, p-hacking, p-values, Statistics},
pages = {18--27},
file = {Zsolt Garamszegi and de Villemereuil - 2017 - Perturbations on the uniform distribution of p-val.pdf:/home/pierre/Zotero/storage/TB6TKTTV/Zsolt Garamszegi and de Villemereuil - 2017 - Perturbations on the uniform distribution of p-val.pdf:application/pdf},
}

### 2016

• Till-Bottraud, I., & de Villemereuil, P.. (2016). Kin recognition or phenotype matching?. New Phytologist, 209(1), 13–14. doi:10.1111/nph.13554
@article{tillbottraud_kin_2016-perso,
title = {Kin recognition or phenotype matching?},
volume = {209},
issn = {1469-8137},
url = {http://devillemereuil.legtux.org/publis/Till-Bottraud et de Villemereuil - 2016 - Kin recognition or phenotype matching.pdf},
doi = {10.1111/nph.13554},
language = {en},
number = {1},
urldate = {2016-01-23},
journal = {New Phytologist},
author = {Till-Bottraud, Irène and de Villemereuil, Pierre},
month = jan,
year = {2016},
note = {IF: 7.43, Q1 (Cit: 8)},
keywords = {Arabidopsis thaliana, kin selection, light signal, neighbor recognition, phenotype matching, shade avoidance},
pages = {13--14},
file = {Till-Bottraud et de Villemereuil - 2016 - Kin recognition or phenotype matching.pdf:/home/pierre/Zotero/storage/QVMF9EJS/Till-Bottraud et de Villemereuil - 2016 - Kin recognition or phenotype matching.pdf:application/pdf},
}

• de Villemereuil, P., Schielzeth, H., Nakagawa, S., & Morrissey, M. B.. (2016). General methods for evolutionary quantitative genetic inference from generalised mixed models. Genetics, 204(3), 1281–1294. doi:10.1534/genetics.115.186536

Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population.

@article{devillemereuil_general_2016-perso,
title = {General methods for evolutionary quantitative genetic inference from generalised mixed models},
volume = {204},
issn = {0016-6731, 1943-2631},
url = {http://devillemereuil.legtux.org/publis/Villemereuil et al. - 2016 - General methods for evolutionary quantitative gene.pdf},
doi = {10.1534/genetics.115.186536},
abstract = {Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. We demonstrate that fixed effects have a strong impact on those parameters and show how to deal with this by averaging or integrating over fixed effects. The expressions require integration of quantities determined by the link function, over distributions of latent values. In general cases, the required integrals must be solved numerically, but efficient methods are available and we provide an implementation in an R package, QGglmm. We show that known formulas for quantities such as heritability of traits with binomial and Poisson distributions are special cases of our expressions. Additionally, we show how fitted GLMM can be incorporated into existing methods for predicting evolutionary trajectories. We demonstrate the accuracy of the resulting method for evolutionary prediction by simulation and apply our approach to data from a wild pedigreed vertebrate population.},
language = {en},
number = {3},
urldate = {2016-12-27},
journal = {Genetics},
author = {de Villemereuil, Pierre and Schielzeth, Holger and Nakagawa, Shinichi and Morrissey, Michael B.},
month = nov,
year = {2016},
note = {IF: 4.08, Q1 (Cit: 59)},
keywords = {Statistics, additive genetic variance, evolution, G matrix, generalised linear mixed model, Generalized linear model, Quantitative Genetics, theory},
pages = {1281--1294},
file = {Villemereuil et al. - 2016 - General methods for evolutionary quantitative gene.pdf:/home/pierre/Zotero/storage/VT9IFDR5/Villemereuil et al. - 2016 - General methods for evolutionary quantitative gene.pdf:application/pdf},
}

• de Villemereuil, P., Gaggiotti, O. E., Mouterde, M., & Till-Bottraud, I.. (2016). Common garden experiments in the genomic era: new perspectives and opportunities. Heredity, 116(3), 249–254. doi:10.1038/hdy.2015.93

The study of local adaptation is rendered difficult by many evolutionary confounding phenomena (for example, genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specifically designed to deal with phenotypic plasticity, has a clear role to play in the study of local adaptation, even (if not specifically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efficient, thorough and integrative study of local adaptation. Especially, evidence from genomic (for example, genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits.

@article{devillemereuil_common_2016-perso,
title = {Common garden experiments in the genomic era: new perspectives and opportunities},
volume = {116},
copyright = {© 2015 Nature Publishing Group},
issn = {0018-067X},
shorttitle = {Common garden experiments in the genomic era},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2015 - Common garden experiments in the genomic era new.pdf},
doi = {10.1038/hdy.2015.93},
abstract = {The study of local adaptation is rendered difficult by many evolutionary confounding phenomena (for example, genetic drift and demographic history). When complex traits are involved in local adaptation, phenomena such as phenotypic plasticity further hamper evolutionary biologists to study the complex relationships between phenotype, genotype and environment. In this perspective paper, we suggest that the common garden experiment, specifically designed to deal with phenotypic plasticity, has a clear role to play in the study of local adaptation, even (if not specifically) in the genomic era. After a quick review of some high-throughput genotyping protocols relevant in the context of a common garden, we explore how to improve common garden analyses with dense marker panel data and recent statistical methods. We then show how combining approaches from population genomics and genome-wide association studies with the settings of a common garden can yield to a very efficient, thorough and integrative study of local adaptation. Especially, evidence from genomic (for example, genome scan) and phenotypic origins constitute independent insights into the possibility of local adaptation scenarios, and genome-wide association studies in the context of a common garden experiment allow to decipher the genetic bases of adaptive traits.},
language = {en},
number = {3},
urldate = {2016-04-08},
journal = {Heredity},
author = {de Villemereuil, Pierre and Gaggiotti, Oscar E. and Mouterde, Médéric and Till-Bottraud, Irène},
month = mar,
year = {2016},
note = {IF: 3.87, Q1 (Cit: 101)},
pages = {249--254},
file = {de Villemereuil et al. - 2015 - Common garden experiments in the genomic era new .pdf:/home/pierre/Zotero/storage/HKQMUCWI/de Villemereuil et al. - 2015 - Common garden experiments in the genomic era new .pdf:application/pdf},
}

### 2015

• Frichot, É., Schoville, S. D., de Villemereuil, P., Gaggiotti, O. E., & François, O.. (2015). Detecting adaptive evolution based on association with ecological gradients: Orientation matters!. Heredity, 115(1), 22–28. doi:10.1038/hdy.2015.7
[BibTeX] [Abstract]

Population genetic signatures of local adaptation are frequently investigated by identifying loci with allele frequencies that exhibit high correlation with ecological variables. One difficulty with this approach is that ecological associations might be confounded by geographic variation at selectively neutral loci. Here, we consider populations that underwent spatial expansion from their original range, and for which geographical variation of adaptive allele frequency coincides with habitat gradients. Using range expansion simulations, we asked whether our ability to detect genomic regions involved in adaptation could be impacted by the orientation of the ecological gradients. For three ecological association methods tested, we found, counter-intuitively, fewer false-positive associations when ecological gradients aligned along the main axis of expansion than when they aligned along any other direction. This result has important consequences for the analysis of genomic data under non-equilibrium population genetic models. Alignment of gradients with expansion axes is likely to be common in scenarios in which expanding species track their ecological niche during climate change while adapting to changing environments at their rear edge.

@article{frichot_detecting_2015-perso,
title = {Detecting adaptive evolution based on association with ecological gradients: {Orientation} matters!},
volume = {115},
copyright = {© 2015 Nature Publishing Group},
issn = {0018-067X},
shorttitle = {Detecting adaptive evolution based on association with ecological gradients},
doi = {10.1038/hdy.2015.7},
abstract = {Population genetic signatures of local adaptation are frequently investigated by identifying loci with allele frequencies that exhibit high correlation with ecological variables. One difficulty with this approach is that ecological associations might be confounded by geographic variation at selectively neutral loci. Here, we consider populations that underwent spatial expansion from their original range, and for which geographical variation of adaptive allele frequency coincides with habitat gradients. Using range expansion simulations, we asked whether our ability to detect genomic regions involved in adaptation could be impacted by the orientation of the ecological gradients. For three ecological association methods tested, we found, counter-intuitively, fewer false-positive associations when ecological gradients aligned along the main axis of expansion than when they aligned along any other direction. This result has important consequences for the analysis of genomic data under non-equilibrium population genetic models. Alignment of gradients with expansion axes is likely to be common in scenarios in which expanding species track their ecological niche during climate change while adapting to changing environments at their rear edge.},
language = {en},
number = {1},
urldate = {2015-06-15},
journal = {Heredity},
author = {Frichot, Éric and Schoville, Sean D. and de Villemereuil, Pierre and Gaggiotti, Oscar E. and François, Olivier},
month = jul,
year = {2015},
note = {IF: 3.87, Q1 (Cit: 48)},
pages = {22--28},
file = {Frichot et al. - 2015 - Detecting adaptive evolution based on association .pdf:/home/pierre/Zotero/storage/HZKXA6HA/Frichot et al. - 2015 - Detecting adaptive evolution based on association .pdf:application/pdf},
}

• de Villemereuil, P., & Gaggiotti, O. E.. (2015). A new FST-based method to uncover local adaptation using environmental variables. Methods in Ecology and Evolution, 6(11), 1248–1258. doi:10.1111/2041-210X.12418

@article{devillemereuil_new_2015-perso,
title = {A new {FST}-based method to uncover local adaptation using environmental variables},
volume = {6},
issn = {2041210X},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et Gaggiotti - 2015 - A new FST-based method to uncover local adaptation.pdf},
doi = {10.1111/2041-210X.12418},
language = {en},
number = {11},
urldate = {2015-07-13},
journal = {Methods in Ecology and Evolution},
author = {de Villemereuil, Pierre and Gaggiotti, Oscar E.},
month = nov,
year = {2015},
note = {IF: 6.36, Q1 (Cit: 100)},
keywords = {local adaptation, Bayesian methods, environment, F model, false discovery rate, genome-scan},
pages = {1248--1258},
file = {de Villemereuil et Gaggiotti - 2015 - A new FST-based method to uncover local adaptation.pdf:/home/pierre/Zotero/storage/58LUPIVX/de Villemereuil et Gaggiotti - 2015 - A new FST-based method to uncover local adaptation.pdf:application/pdf},
}

• Aguilée, R., de Villemereuil, P., & Guillon, J.. (2015). Dispersal evolution and resource matching in a spatially and temporally variable environment. Journal of Theoretical Biology, 370, 184–196. doi:10.1016/j.jtbi.2015.01.018

Metapopulations may consist of patches of different quality, and are often disturbed by extrinsic processes causing variation of patch quality. The persistence of such metapopulations then depends on the species׳ dispersal strategy. In a temporally constant environment, the evolution of dispersal rates follows the resource matching rule, i.e. at the evolutionarily stable dispersal strategy the number of competitors in each patch matches the resource availability in each patch. Here, we investigate how the distribution of individuals resulting from convergence stable dispersal strategies would match the distribution of resources in an environment which is temporally variable due to extrinsic disturbance. We develop an analytically tractable asexual model with two qualities of patches. We show that convergence stable dispersal rates are such that resource matching is predicted in expectation before habitat quality variation, and that the distribution of individuals undermatches resources after habitat quality variation. The overall flow of individuals between patches matches the overall flow of resources between patches resulting from environmental variation. We show that these conclusions can be generalized to organisms with sexual reproduction, and to a metapopulation with three qualities of patches when there is no mutational correlation between dispersal rates.

@article{aguilee_dispersal_2015-perso,
title = {Dispersal evolution and resource matching in a spatially and temporally variable environment},
volume = {370},
issn = {0022-5193},
url = {http://devillemereuil.legtux.org/publis/Aguil%C3%A9e%20et%20al.%20-%202015%20-%20Dispersal%20evolution%20and%20resource%20matching%20in%20a%20spa.pdf},
doi = {10.1016/j.jtbi.2015.01.018},
abstract = {Metapopulations may consist of patches of different quality, and are often disturbed by extrinsic processes causing variation of patch quality. The persistence of such metapopulations then depends on the species׳ dispersal strategy. In a temporally constant environment, the evolution of dispersal rates follows the resource matching rule, i.e. at the evolutionarily stable dispersal strategy the number of competitors in each patch matches the resource availability in each patch. Here, we investigate how the distribution of individuals resulting from convergence stable dispersal strategies would match the distribution of resources in an environment which is temporally variable due to extrinsic disturbance. We develop an analytically tractable asexual model with two qualities of patches. We show that convergence stable dispersal rates are such that resource matching is predicted in expectation before habitat quality variation, and that the distribution of individuals undermatches resources after habitat quality variation. The overall flow of individuals between patches matches the overall flow of resources between patches resulting from environmental variation. We show that these conclusions can be generalized to organisms with sexual reproduction, and to a metapopulation with three qualities of patches when there is no mutational correlation between dispersal rates.},
urldate = {2015-02-25},
journal = {Journal of Theoretical Biology},
author = {Aguilée, Robin and de Villemereuil, Pierre and Guillon, Jean-Michel},
year = {2015},
note = {IF: 1.83, Q1 (Cit: 2)},
pages = {184--196},
file = {Aguilée et al. - 2015 - Dispersal evolution and resource matching in a spa.pdf:/home/pierre/Zotero/storage/FDGSMM6P/Aguilée et al. - 2015 - Dispersal evolution and resource matching in a spa.pdf:application/pdf},
}

### 2014

• Morrissey, M. B., de Villemereuil, P., Doligez, B., & Gimenez, O.. (2014). Bayesian approaches to the quantitative genetic analysis of natural populations. In Charmantier, A., Garant, D., & Kruuk, L. E. B. (Eds.), In Quantitative Genetics in the Wild (, pp. 228–253). Oxford (UK): Oxford University Press.
[BibTeX]
@incollection{morrissey_bayesian_2014-perso,
address = {Oxford (UK)},
title = {Bayesian approaches to the quantitative genetic analysis of natural populations},
isbn = {978-0-19-165595-1},
language = {en},
booktitle = {Quantitative {Genetics} in the {Wild}},
publisher = {Oxford University Press},
author = {Morrissey, Michael B. and de Villemereuil, Pierre and Doligez, Blandine and Gimenez, Olivier},
editor = {Charmantier, Anne and Garant, Dany and Kruuk, Loeske E.B.},
month = apr,
year = {2014},
note = {(Cit: 29)},
pages = {228--253},
file = {Morrissey et al. - 2014 - Bayesian approaches to the quantitative genetic an.pdf:/home/pierre/Zotero/storage/8DKX8JG9/Morrissey et al. - 2014 - Bayesian approaches to the quantitative genetic an.pdf:application/pdf},
}

• de Villemereuil, P., & Nakagawa, S.. (2014). General Quantitative Genetic Methods for Comparative Biology. In Garamszegi, L. Z. (Ed.), In Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology (, pp. 287–303). Berlin, Heidelberg: Springer Berlin Heidelberg.
@incollection{devillemereuil_general_2014-perso,
address = {Berlin, Heidelberg},
title = {General {Quantitative} {Genetic} {Methods} for {Comparative} {Biology}},
isbn = {978-3-662-43550-2},
language = {en},
urldate = {2014-08-14},
booktitle = {Modern {Phylogenetic} {Comparative} {Methods} and {Their} {Application} in {Evolutionary} {Biology}},
publisher = {Springer Berlin Heidelberg},
author = {de Villemereuil, Pierre and Nakagawa, Shinichi},
editor = {Garamszegi, László Zsolt},
year = {2014},
note = {(Cit: 41)},
pages = {287--303},
file = {de Villemereuil et Nakagawa - 2014 - General Quantitative Genetic Methods for Comparati.pdf:/home/pierre/Zotero/storage/UIU9TSZK/de Villemereuil et Nakagawa - 2014 - General Quantitative Genetic Methods for Comparati.pdf:application/pdf},
}

• de Villemereuil, P., Frichot, É., Bazin, É., François, O., & Gaggiotti, O. E.. (2014). Genome scan methods against more complex models: when and how much should we trust them?. Molecular Ecology, 23(8), 2006–2019. doi:10.1111/mec.12705

The recent availability of next-generation sequencing (NGS) has made possible the use of dense genetic markers to identify regions of the genome that may be under the influence of selection. Several statistical methods have been developed recently for this purpose. Here, we present the results of an individual-based simulation study investigating the power and error rate of popular or recent genome scan methods: linear regression, Bayescan, BayEnv and LFMM. Contrary to previous studies, we focus on complex, hierarchical population structure and on polygenic selection. Additionally, we use a false discovery rate (FDR)-based framework, which provides an unified testing framework across frequentist and Bayesian methods. Finally, we investigate the influence of population allele frequencies versus individual genotype data specification for LFMM and the linear regression. The relative ranking between the methods is impacted by the consideration of polygenic selection, compared to a monogenic scenario. For strongly hierarchical scenarios with confounding effects between demography and environmental variables, the power of the methods can be very low. Except for one scenario, Bayescan exhibited moderate power and error rate. BayEnv performance was good under nonhierarchical scenarios, while LFMM provided the best compromise between power and error rate across scenarios. We found that it is possible to greatly reduce error rates by considering the results of all three methods when identifying outlier loci.

@article{devillemereuil_genome_2014-perso,
title = {Genome scan methods against more complex models: when and how much should we trust them?},
volume = {23},
copyright = {© 2014 John Wiley \& Sons Ltd},
issn = {1365-294X},
shorttitle = {Genome scan methods against more complex models},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2014 - Genome scan methods against more complex models w.pdf},
doi = {10.1111/mec.12705},
abstract = {The recent availability of next-generation sequencing (NGS) has made possible the use of dense genetic markers to identify regions of the genome that may be under the influence of selection. Several statistical methods have been developed recently for this purpose. Here, we present the results of an individual-based simulation study investigating the power and error rate of popular or recent genome scan methods: linear regression, Bayescan, BayEnv and LFMM. Contrary to previous studies, we focus on complex, hierarchical population structure and on polygenic selection. Additionally, we use a false discovery rate (FDR)-based framework, which provides an unified testing framework across frequentist and Bayesian methods. Finally, we investigate the influence of population allele frequencies versus individual genotype data specification for LFMM and the linear regression. The relative ranking between the methods is impacted by the consideration of polygenic selection, compared to a monogenic scenario. For strongly hierarchical scenarios with confounding effects between demography and environmental variables, the power of the methods can be very low. Except for one scenario, Bayescan exhibited moderate power and error rate. BayEnv performance was good under nonhierarchical scenarios, while LFMM provided the best compromise between power and error rate across scenarios. We found that it is possible to greatly reduce error rates by considering the results of all three methods when identifying outlier loci.},
language = {en},
number = {8},
urldate = {2014-04-09},
journal = {Molecular Ecology},
author = {de Villemereuil, Pierre and Frichot, Éric and Bazin, Éric and François, Olivier and Gaggiotti, Oscar E.},
year = {2014},
note = {IF: 6.13, Q1 (Cit: 202)},
keywords = {Bayesian methods, false discovery rate, Adaptation, genome scan, Genome scan, power simulation study},
pages = {2006--2019},
file = {de Villemereuil et al. - 2014 - Genome scan methods against more complex models w.pdf:/home/pierre/Zotero/storage/X4E5F8MS/de Villemereuil et al. - 2014 - Genome scan methods against more complex models w.pdf:application/pdf},
}

### 2013

• de Villemereuil, P., Gimenez, O., & Doligez, B.. (2013). Comparing parent–offspring regression with frequentist and Bayesian animal models to estimate heritability in wild populations: a simulation study for Gaussian and binary traits. Methods in Ecology and Evolution, 4(3), 260–275. doi:10.1111/2041-210X.12011

* Estimating heritability of traits in wild populations is a major prerequisite to understand their evolution. Until recently, most heritability estimates had been obtained using parent-offspring regressions. However, the popularity of animal models, that is, (generalized) linear mixed models assessing the genetic variance component based on population pedigree information, has markedly increased in the past few years. Animal models are claimed to perform better than parent–offspring regressions mainly because they use full between-individual relatedness information and they allow explicit modelling of the environmental effects shared by individuals. However, the differences between heritability estimates obtained using both approaches are not straight forward, and the factors influencing these differences remain unclear. * We performed a simulation study to evaluate and compare the accuracy and precision of estimates obtained from parent–offspring regressions and animal models using both Frequentist (REML, PQL) and Bayesian (MCMC) estimation methods. We explored the influence of (i) the presence and type of shared environmental effects (non-transgenerational or transgenerational), (ii) the distribution of the phenotypic trait considered (Gaussian or binary trait) and (iii) data quantity and quality (sample size, pedigree connectivity) on heritability estimates obtained from the two approaches for different levels of true heritability. * In the absence of shared environmental effects, the animal model using the REML method performed best for a Gaussian trait, while the animal model using MCMC was more appropriate for a binary trait. For low quantity and quality data, and a binary trait, the parent–offspring regression yielded very imprecise estimates. * Estimates from the parent–offspring regression were not influenced by a non-transgenerational shared environmental effect, whereas estimates from animal models in which environmental effects are ignored were affected by both non-transgenerational and transgenerational effects. * We discuss the relevance of each approach and estimation method for estimating heritability in wild populations. Importantly, because most effects fitted in animal models are, in fact, non-transgenerational (including environmental maternal effects), we advocate a systematic comparison between parent–offspring regression and animal model estimates to detect potentially missing non-transgenerational environmental effects.

@article{devillemereuil_comparing_2013-perso,
title = {Comparing parent–offspring regression with frequentist and {Bayesian} animal models to estimate heritability in wild populations: a simulation study for {Gaussian} and binary traits},
volume = {4},
issn = {2041-210X},
shorttitle = {Comparing parent–offspring regression with frequentist and {Bayesian} animal models to estimate heritability in wild populations},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2013 - Comparing parent–offspring regression with frequen.pdf},
doi = {10.1111/2041-210X.12011},
abstract = {* Estimating heritability of traits in wild populations is a major prerequisite to understand their evolution. Until recently, most heritability estimates had been obtained using parent-offspring regressions. However, the popularity of animal models, that is, (generalized) linear mixed models assessing the genetic variance component based on population pedigree information, has markedly increased in the past few years. Animal models are claimed to perform better than parent–offspring regressions mainly because they use full between-individual relatedness information and they allow explicit modelling of the environmental effects shared by individuals. However, the differences between heritability estimates obtained using both approaches are not straight forward, and the factors influencing these differences remain unclear. * We performed a simulation study to evaluate and compare the accuracy and precision of estimates obtained from parent–offspring regressions and animal models using both Frequentist (REML, PQL) and Bayesian (MCMC) estimation methods. We explored the influence of (i) the presence and type of shared environmental effects (non-transgenerational or transgenerational), (ii) the distribution of the phenotypic trait considered (Gaussian or binary trait) and (iii) data quantity and quality (sample size, pedigree connectivity) on heritability estimates obtained from the two approaches for different levels of true heritability. * In the absence of shared environmental effects, the animal model using the REML method performed best for a Gaussian trait, while the animal model using MCMC was more appropriate for a binary trait. For low quantity and quality data, and a binary trait, the parent–offspring regression yielded very imprecise estimates. * Estimates from the parent–offspring regression were not influenced by a non-transgenerational shared environmental effect, whereas estimates from animal models in which environmental effects are ignored were affected by both non-transgenerational and transgenerational effects. * We discuss the relevance of each approach and estimation method for estimating heritability in wild populations. Importantly, because most effects fitted in animal models are, in fact, non-transgenerational (including environmental maternal effects), we advocate a systematic comparison between parent–offspring regression and animal model estimates to detect potentially missing non-transgenerational environmental effects.},
language = {en},
number = {3},
urldate = {2013-03-15},
journal = {Methods in Ecology and Evolution},
author = {de Villemereuil, Pierre and Gimenez, Olivier and Doligez, Blandine},
year = {2013},
note = {IF: 6.36, Q1 (Cit: 92)},
keywords = {Statistics, Bayesian methods {\textbackslash}textless Statistics, Quantitative genetics {\textbackslash}textless Population Genetics},
pages = {260--275},
file = {de Villemereuil et al. - 2013 - Comparing parent–offspring regression with frequen.pdf:/home/pierre/Zotero/storage/ITH4ZWVP/de Villemereuil et al. - 2013 - Comparing parent–offspring regression with frequen.pdf:application/pdf},
}

### 2012

• de Villemereuil, P., Wells, J. A., Edwards, R. D., & Blomberg, S. P.. (2012). Bayesian models for comparative analysis integrating phylogenetic uncertainty. BMC Evolutionary Biology, 12(1), 102. doi:10.1186/1471-2148-12-102

Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable.

@article{devillemereuil_bayesian_2012-perso,
title = {Bayesian models for comparative analysis integrating phylogenetic uncertainty},
volume = {12},
issn = {1471-2148},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2012 - Bayesian models for comparative analysis integrati.pdf},
doi = {10.1186/1471-2148-12-102},
abstract = {Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable.},
language = {en},
number = {1},
urldate = {2013-02-27},
journal = {BMC Evolutionary Biology},
author = {de Villemereuil, Pierre and Wells, Jessie A. and Edwards, Robert D. and Blomberg, Simon P.},
month = jun,
year = {2012},
note = {IF: 3.03, Q1 (Cit: 77)},
pages = {102},
file = {de Villemereuil et al. - 2012 - Bayesian models for comparative analysis integrati.pdf:/home/pierre/Zotero/storage/QUBVS2JU/de Villemereuil et al. - 2012 - Bayesian models for comparative analysis integrati.pdf:application/pdf},
}

### 2011

• de Villemereuil, P., & López-Sepulcre, A.. (2011). Consumer functional responses under intra- and inter-specific interference competition. Ecological Modelling, 222(3), 419–426. doi:10.1016/j.ecolmodel.2010.10.011
@article{devillemereuil_consumer_2011-perso,
title = {Consumer functional responses under intra- and inter-specific interference competition},
volume = {222},
issn = {03043800},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et López-Sepulcre - 2011 - Consumer functional responses under intra- and int.pdf},
doi = {10.1016/j.ecolmodel.2010.10.011},
number = {3},
urldate = {2011-02-23},
journal = {Ecological Modelling},
author = {de Villemereuil, Pierre and López-Sepulcre, Andrés},
month = feb,
year = {2011},
note = {IF: 2.5, Q2 (Cit: 40)},
pages = {419--426},
file = {de Villemereuil et López-Sepulcre - 2011 - Consumer functional responses under intra- and int.pdf:/home/pierre/Zotero/storage/T4GGW89J/de Villemereuil et López-Sepulcre - 2011 - Consumer functional responses under intra- and int.pdf:application/pdf},
}