2024
Breeding phenology drives variation in reproductive output, reproductive costs, and offspring fitness in a viviparous ectotherm Journal Article
Bodineau, Théo; Villemereuil, Pierre; Agostini, Simon; Decencière, Beatriz; Galliard, Jean-François Le; Meylan, Sandrine
In: Journal of Evolutionary Biology, vol. 37, no. 9, pp. 1023–1034, 2024, ISSN: 1010-061X.
@article{bodineau_breeding_2024,
title = {Breeding phenology drives variation in reproductive output, reproductive costs, and offspring fitness in a viviparous ectotherm},
author = {Théo Bodineau and Pierre Villemereuil and Simon Agostini and Beatriz Decencière and Jean-François Le Galliard and Sandrine Meylan},
url = {https://doi.org/10.1093/jeb/voae086},
doi = {10.1093/jeb/voae086},
issn = {1010-061X},
year = {2024},
date = {2024-09-01},
urldate = {2024-10-16},
journal = {Journal of Evolutionary Biology},
volume = {37},
number = {9},
pages = {1023–1034},
abstract = {Phenological advances are a widespread response to global warming and can contribute to determine the climate vulnerability of organisms, particularly in ectothermic species, which are highly dependent on ambient temperatures to complete their life cycle. Yet, the relative contribution of breeding dates and temperature conditions during gestation on fitness of females and their offspring is poorly documented in reptiles. Here, we exposed females of the common lizard Zootoca vivipara to contrasting thermal scenarios (cold vs. hot treatment) during gestation and quantified effects of parturition dates and thermal treatment on life-history traits of females and their offspring for 1 year. Overall, our results suggest that parturition date has a greater impact than thermal conditions during gestation on life history strategies. In particular, we found positive effects of an earlier parturition date on juvenile survival, growth, and recruitment suggesting that environmental-dependent selection and/or differences in parental quality between early and late breeders underlie seasonal changes in offspring fitness. Yet, an earlier parturition date compromised the energetic condition of gravid females, which suggests the existence of a mother–offspring conflict regarding the optimization of parturition dates. While numerous studies focused on the direct effects of alterations in incubation temperatures on reptile life-history traits, our results highlight the importance of considering the role of breeding phenology in assessing the short- and long-term effects of thermal developmental plasticity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phenological advances are a widespread response to global warming and can contribute to determine the climate vulnerability of organisms, particularly in ectothermic species, which are highly dependent on ambient temperatures to complete their life cycle. Yet, the relative contribution of breeding dates and temperature conditions during gestation on fitness of females and their offspring is poorly documented in reptiles. Here, we exposed females of the common lizard Zootoca vivipara to contrasting thermal scenarios (cold vs. hot treatment) during gestation and quantified effects of parturition dates and thermal treatment on life-history traits of females and their offspring for 1 year. Overall, our results suggest that parturition date has a greater impact than thermal conditions during gestation on life history strategies. In particular, we found positive effects of an earlier parturition date on juvenile survival, growth, and recruitment suggesting that environmental-dependent selection and/or differences in parental quality between early and late breeders underlie seasonal changes in offspring fitness. Yet, an earlier parturition date compromised the energetic condition of gravid females, which suggests the existence of a mother–offspring conflict regarding the optimization of parturition dates. While numerous studies focused on the direct effects of alterations in incubation temperatures on reptile life-history traits, our results highlight the importance of considering the role of breeding phenology in assessing the short- and long-term effects of thermal developmental plasticity.
Reproductive aging weakens offspring survival and constrains the telomerase response to herpesvirus in Pacific oysters Journal Article
Dupoué, Andréaz; Koechlin, Hugo; Huber, Matthias; Merrien, Pauline; Grand, Jacqueline Le; Corporeau, Charlotte; Fleury, Elodie; Bernay, Benoît; Villemereuil, Pierre; Morga, Benjamin; Luyer, Jérémy Le
In: Science Advances, vol. 10, no. 37, pp. eadq2311, 2024, (Publisher: American Association for the Advancement of Science).
@article{dupoue_reproductive_2024,
title = {Reproductive aging weakens offspring survival and constrains the telomerase response to herpesvirus in Pacific oysters},
author = {Andréaz Dupoué and Hugo Koechlin and Matthias Huber and Pauline Merrien and Jacqueline Le Grand and Charlotte Corporeau and Elodie Fleury and Benoît Bernay and Pierre Villemereuil and Benjamin Morga and Jérémy Le Luyer},
url = {https://www.science.org/doi/full/10.1126/sciadv.adq2311},
doi = {10.1126/sciadv.adq2311},
year = {2024},
date = {2024-09-01},
urldate = {2024-10-16},
journal = {Science Advances},
volume = {10},
number = {37},
pages = {eadq2311},
abstract = {Telomere length (TL) is increasingly recognized as a molecular marker that reflects how reproductive aging affects intergenerational transmissions. Here, we investigated the effects of parental age on offspring survival and the regulation of TL by examining the telomere-elongating activity of telomerase in the Pacific oyster. We assessed the classical hallmarks of aging in parents at three age classes (young, middle-aged, and old) and crossbred them using a split-brood design to examine the consequences of the nine maternal-by-paternal age combinations on their offspring. Reproductive aging leads to increased larval mortality and accelerated telomere shortening in spats, rendering them more susceptible to infection by the Ostreid herpesvirus. Viral exposure stimulates telomerase activity, a response that we identified as adaptive, but weakened by parental aging. While telomerase lengthens a spat’s telomere, paradoxically, longer individual TL predicts higher mortality in adults. The telomerase-telomere complex appeared as a conservative biomarker for distinguishing survivors and losers upon exposure to polymicrobial diseases.},
note = {Publisher: American Association for the Advancement of Science},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Telomere length (TL) is increasingly recognized as a molecular marker that reflects how reproductive aging affects intergenerational transmissions. Here, we investigated the effects of parental age on offspring survival and the regulation of TL by examining the telomere-elongating activity of telomerase in the Pacific oyster. We assessed the classical hallmarks of aging in parents at three age classes (young, middle-aged, and old) and crossbred them using a split-brood design to examine the consequences of the nine maternal-by-paternal age combinations on their offspring. Reproductive aging leads to increased larval mortality and accelerated telomere shortening in spats, rendering them more susceptible to infection by the Ostreid herpesvirus. Viral exposure stimulates telomerase activity, a response that we identified as adaptive, but weakened by parental aging. While telomerase lengthens a spat’s telomere, paradoxically, longer individual TL predicts higher mortality in adults. The telomerase-telomere complex appeared as a conservative biomarker for distinguishing survivors and losers upon exposure to polymicrobial diseases.
2023
Shared heritability of blood pressure and pulse wave velocity: insights from the STANISLAS cohort Journal Article
Xhaard, Constance; Villemereuil, Pierre; Benetos, Athanase; Bozec, Erwan; Dandine-Roulland, Claire; Floch, Edith Le; Regnault, Véronique; Lacolley, Patrick; Zannad, Faiez; Rossignol, Patrick; Girerd, Nicolas
In: Hypertension, 2023, (Publisher: American Heart Association).
@article{xhaard_shared_2023,
title = {Shared heritability of blood pressure and pulse wave velocity: insights from the STANISLAS cohort},
author = {Constance Xhaard and Pierre Villemereuil and Athanase Benetos and Erwan Bozec and Claire Dandine-Roulland and Edith Le Floch and Véronique Regnault and Patrick Lacolley and Faiez Zannad and Patrick Rossignol and Nicolas Girerd},
url = {https://www.ahajournals.org/doi/abs/10.1161/HYPERTENSIONAHA.122.20740
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Xhaard-et-al.-2023-Shared-heritability-of-blood-pressure-and-pulse-wa.pdf},
doi = {10.1161/HYPERTENSIONAHA.122.20740},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Hypertension},
abstract = {Background:
Pulse wave velocity (PWV) is a marker of arterial stiffness, which is intrinsically highly correlated with blood pressure (BP). However, the interplay of PWV and BP heritability has not been extensively studied. This study aimed to estimate the heritability of PWV and BP and determine the genetic correlation between PWV and BP.
Methods:
The heritability of PWV and BP was estimated in 1080 subjects from the STANISLAS (Suivi Temporaire Annuel Non-Invasif de la Santé des Lorrains Assurés Sociaux) cohort with at least one relative using a linear mixed model within one frequentist and one Bayesian framework implemented, respectively, in the Gaston and MCMCglmm R packages. Then their genetic correlations were also estimated.
Results:
The heritability estimations for PWV were within the same range of the heritability of systolic BP and diastolic BP (23%, 19%, and 27%, respectively). Daytime heritability of BP was higher than nighttime BP. In addition, phenotypic correlations between PWV and systolic BP/diastolic BP were, respectively, 0.34 and 0.23, whereas nonsignificant genetic correlations were 0.08 and 0.22 respectively, indicating that PWV and diastolic BP shared more polygenic codeterminants than PWV and systolic BP.
Conclusions:
Our results suggest that the heritability of PWV is >20% and within the same range as BP heritability. It also suggests that the link between PWV and BP goes beyond phenotypic association: PWV and BP (in particular diastolic BP) share common genetic determinants. This genetic interdependence of PWV and BP appears largely polygenic.},
note = {Publisher: American Heart Association},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background:
Pulse wave velocity (PWV) is a marker of arterial stiffness, which is intrinsically highly correlated with blood pressure (BP). However, the interplay of PWV and BP heritability has not been extensively studied. This study aimed to estimate the heritability of PWV and BP and determine the genetic correlation between PWV and BP.
Methods:
The heritability of PWV and BP was estimated in 1080 subjects from the STANISLAS (Suivi Temporaire Annuel Non-Invasif de la Santé des Lorrains Assurés Sociaux) cohort with at least one relative using a linear mixed model within one frequentist and one Bayesian framework implemented, respectively, in the Gaston and MCMCglmm R packages. Then their genetic correlations were also estimated.
Results:
The heritability estimations for PWV were within the same range of the heritability of systolic BP and diastolic BP (23%, 19%, and 27%, respectively). Daytime heritability of BP was higher than nighttime BP. In addition, phenotypic correlations between PWV and systolic BP/diastolic BP were, respectively, 0.34 and 0.23, whereas nonsignificant genetic correlations were 0.08 and 0.22 respectively, indicating that PWV and diastolic BP shared more polygenic codeterminants than PWV and systolic BP.
Conclusions:
Our results suggest that the heritability of PWV is >20% and within the same range as BP heritability. It also suggests that the link between PWV and BP goes beyond phenotypic association: PWV and BP (in particular diastolic BP) share common genetic determinants. This genetic interdependence of PWV and BP appears largely polygenic.
Pulse wave velocity (PWV) is a marker of arterial stiffness, which is intrinsically highly correlated with blood pressure (BP). However, the interplay of PWV and BP heritability has not been extensively studied. This study aimed to estimate the heritability of PWV and BP and determine the genetic correlation between PWV and BP.
Methods:
The heritability of PWV and BP was estimated in 1080 subjects from the STANISLAS (Suivi Temporaire Annuel Non-Invasif de la Santé des Lorrains Assurés Sociaux) cohort with at least one relative using a linear mixed model within one frequentist and one Bayesian framework implemented, respectively, in the Gaston and MCMCglmm R packages. Then their genetic correlations were also estimated.
Results:
The heritability estimations for PWV were within the same range of the heritability of systolic BP and diastolic BP (23%, 19%, and 27%, respectively). Daytime heritability of BP was higher than nighttime BP. In addition, phenotypic correlations between PWV and systolic BP/diastolic BP were, respectively, 0.34 and 0.23, whereas nonsignificant genetic correlations were 0.08 and 0.22 respectively, indicating that PWV and diastolic BP shared more polygenic codeterminants than PWV and systolic BP.
Conclusions:
Our results suggest that the heritability of PWV is >20% and within the same range as BP heritability. It also suggests that the link between PWV and BP goes beyond phenotypic association: PWV and BP (in particular diastolic BP) share common genetic determinants. This genetic interdependence of PWV and BP appears largely polygenic.
Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation Journal Article
Salloum, Priscila M.; Lavery, Shane D.; Villemereuil, Pierre; Santure, Anna W.
In: Evolution, vol. 77, no. 1, pp. 210–220, 2023, ISSN: 0014-3820, (tex.ids= salloum_local_2022).
@article{salloum_local_2023,
title = {Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation},
author = {Priscila M. Salloum and Shane D. Lavery and Pierre Villemereuil and Anna W. Santure},
url = {https://doi.org/10.1093/evolut/qpac011
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Salloum-et-al.-2023-Local-adaptation-in-shell-shape-traits-of-a-broodi.pdf},
doi = {10.1093/evolut/qpac011},
issn = {0014-3820},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Evolution},
volume = {77},
number = {1},
pages = {210–220},
abstract = {Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into 2 geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesized to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single-nucleotide polymorphisms (SNPs) across 15 populations and 3 clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades, and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.},
note = {tex.ids= salloum_local_2022},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into 2 geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesized to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single-nucleotide polymorphisms (SNPs) across 15 populations and 3 clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades, and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.
Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine Journal Article
Duntsch, Laura; Whibley, Annabel; Villemereuil, Pierre; Brekke, Patricia; Bailey, Sarah; Ewen, John G.; Santure, Anna W.
In: Molecular Ecology, vol. 32, no. 8, pp. 1893–1907, 2023, ISSN: 1365-294X.
@article{duntsch_genomic_2023,
title = {Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine},
author = {Laura Duntsch and Annabel Whibley and Pierre Villemereuil and Patricia Brekke and Sarah Bailey and John G. Ewen and Anna W. Santure},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16855
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Duntsch-et-al.-2023-Genomic-signatures-of-inbreeding-depression-for-a-.pdf},
doi = {10.1111/mec.16855},
issn = {1365-294X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Molecular Ecology},
volume = {32},
number = {8},
pages = {1893–1907},
abstract = {For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.
2022
Lizards from warm and declining populations are born with extremely short telomeres Journal Article
Dupoué, Andréaz; Blaimont, Pauline; Angelier, Frédéric; Ribout, Cécile; Rozen-Rechels, David; Richard, Murielle; Miles, Donald; Villemereuil, Pierre; Rutschmann, Alexis; Badiane, Arnaud; Aubret, Fabien; Lourdais, Olivier; Meylan, Sandrine; Cote, Julien; Clobert, Jean; Galliard, Jean-François Le
In: Proceedings of the National Academy of Sciences, vol. 119, no. 33, pp. e2201371119, 2022, ISSN: 0027-8424.
@article{dupoue_lizards_2022,
title = {Lizards from warm and declining populations are born with extremely short telomeres},
author = {Andréaz Dupoué and Pauline Blaimont and Frédéric Angelier and Cécile Ribout and David Rozen-Rechels and Murielle Richard and Donald Miles and Pierre Villemereuil and Alexis Rutschmann and Arnaud Badiane and Fabien Aubret and Olivier Lourdais and Sandrine Meylan and Julien Cote and Jean Clobert and Jean-François Le Galliard},
url = {https://pnas.org/doi/full/10.1073/pnas.2201371119
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Dupoue-et-al.-2022-Lizards-from-warm-and-declining-populations-are-bo.pdf},
doi = {10.1073/pnas.2201371119},
issn = {0027-8424},
year = {2022},
date = {2022-08-01},
urldate = {2022-08-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {119},
number = {33},
pages = {e2201371119},
abstract = {Aging is the price to pay for acquiring and processing energy through cellular activity and life history productivity. Climate warming can exacerbate the inherent pace of aging, as illustrated by a faster erosion of protective telomere DNA sequences. This biomarker integrates individual pace of life and parental effects through the germline, but whether intra- and intergenerational telomere dynamics underlies population trends remains an open question. Here, we investigated the covariation between life history, telomere length (TL), and extinction risk among three age classes in a cold-adapted ectotherm (
Zootoca vivipara
) facing warming-induced extirpations in its distribution limits. TL followed the same threshold relationships with population extinction risk at birth, maturity, and adulthood, suggesting intergenerational accumulation of accelerated aging rate in declining populations. In dwindling populations, most neonates inherited already short telomeres, suggesting they were born physiologically old and unlikely to reach recruitment. At adulthood, TL further explained females’ reproductive performance, switching from an index of individual quality in stable populations to a biomarker of reproductive costs in those close to extirpation. We compiled these results to propose the aging loop hypothesis and conceptualize how climate-driven telomere shortening in ectotherms may accumulate across generations and generate tipping points before local extirpation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Aging is the price to pay for acquiring and processing energy through cellular activity and life history productivity. Climate warming can exacerbate the inherent pace of aging, as illustrated by a faster erosion of protective telomere DNA sequences. This biomarker integrates individual pace of life and parental effects through the germline, but whether intra- and intergenerational telomere dynamics underlies population trends remains an open question. Here, we investigated the covariation between life history, telomere length (TL), and extinction risk among three age classes in a cold-adapted ectotherm (
Zootoca vivipara
) facing warming-induced extirpations in its distribution limits. TL followed the same threshold relationships with population extinction risk at birth, maturity, and adulthood, suggesting intergenerational accumulation of accelerated aging rate in declining populations. In dwindling populations, most neonates inherited already short telomeres, suggesting they were born physiologically old and unlikely to reach recruitment. At adulthood, TL further explained females’ reproductive performance, switching from an index of individual quality in stable populations to a biomarker of reproductive costs in those close to extirpation. We compiled these results to propose the aging loop hypothesis and conceptualize how climate-driven telomere shortening in ectotherms may accumulate across generations and generate tipping points before local extirpation.
Zootoca vivipara
) facing warming-induced extirpations in its distribution limits. TL followed the same threshold relationships with population extinction risk at birth, maturity, and adulthood, suggesting intergenerational accumulation of accelerated aging rate in declining populations. In dwindling populations, most neonates inherited already short telomeres, suggesting they were born physiologically old and unlikely to reach recruitment. At adulthood, TL further explained females’ reproductive performance, switching from an index of individual quality in stable populations to a biomarker of reproductive costs in those close to extirpation. We compiled these results to propose the aging loop hypothesis and conceptualize how climate-driven telomere shortening in ectotherms may accumulate across generations and generate tipping points before local extirpation.
Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals Journal Article
Bonnet, Timothée; Morrissey, Michael B.; Villemereuil, Pierre; Alberts, Susan C.; Arcese, Peter; Bailey, Liam D.; Boutin, Stan; Brekke, Patricia; Brent, Lauren J. N.; Camenisch, Glauco; Charmantier, Anne; Clutton-Brock, Tim H.; Cockburn, Andrew; Coltman, David W.; Courtiol, Alexandre; Davidian, Eve; Evans, Simon R.; Ewen, John G.; Festa-Bianchet, Marco; Franceschi, Christophe; Gustafsson, Lars; Höner, Oliver P.; Houslay, Thomas M.; Keller, Lukas F.; Manser, Marta; McAdam, Andrew G.; McLean, Emily; Nietlisbach, Pirmin; Osmond, Helen L.; Pemberton, Josephine M.; Postma, Erik; Reid, Jane M.; Rutschmann, Alexis; Santure, Anna W.; Sheldon, Ben C.; Slate, Jon; Teplitsky, Céline; Visser, Marcel E.; Wachter, Bettina; Kruuk, Loeske E. B.
In: Science, vol. 376, no. 6596, pp. 1012–1016, 2022.
@article{bonnet_genetic_2022,
title = {Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals},
author = {Timothée Bonnet and Michael B. Morrissey and Pierre Villemereuil and Susan C. Alberts and Peter Arcese and Liam D. Bailey and Stan Boutin and Patricia Brekke and Lauren J. N. Brent and Glauco Camenisch and Anne Charmantier and Tim H. Clutton-Brock and Andrew Cockburn and David W. Coltman and Alexandre Courtiol and Eve Davidian and Simon R. Evans and John G. Ewen and Marco Festa-Bianchet and Christophe Franceschi and Lars Gustafsson and Oliver P. Höner and Thomas M. Houslay and Lukas F. Keller and Marta Manser and Andrew G. McAdam and Emily McLean and Pirmin Nietlisbach and Helen L. Osmond and Josephine M. Pemberton and Erik Postma and Jane M. Reid and Alexis Rutschmann and Anna W. Santure and Ben C. Sheldon and Jon Slate and Céline Teplitsky and Marcel E. Visser and Bettina Wachter and Loeske E. B. Kruuk},
url = {https://www.science.org/doi/full/10.1126/science.abk0853
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Bonnet-et-al.-2022-Genetic-variance-in-fitness-indicates-rapid-contem.pdf},
doi = {10.1126/science.abk0853},
year = {2022},
date = {2022-05-01},
urldate = {2022-05-01},
journal = {Science},
volume = {376},
number = {6596},
pages = {1012–1016},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Disturbance and indirect effects of climate warming support a plant invader in mountains Journal Article
Haider, Sylvia; Palm, Sebastian; Bruelheide, Helge; Villemereuil, Pierre; Menzel, Annette; Lachmuth, Susanne
In: Oikos, vol. 2022, iss. 4, no. 4, pp. e08783, 2022, ISSN: 1600-0706.
@article{haider_disturbance_2022,
title = {Disturbance and indirect effects of climate warming support a plant invader in mountains},
author = {Sylvia Haider and Sebastian Palm and Helge Bruelheide and Pierre Villemereuil and Annette Menzel and Susanne Lachmuth},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/oik.08783
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Haider-et-al.-2022-Disturbance-and-indirect-effects-of-climate-warmin.pdf},
doi = {10.1111/oik.08783},
issn = {1600-0706},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Oikos},
volume = {2022},
number = {4},
issue = {4},
pages = {e08783},
abstract = {Climate warming and increased disturbance (resulting from intensified land use) are expected to enhance the invasibility of plant communities and the performance of exotic species also at high elevations, and thus pose additional threats to mountain ecosystems. The invasion success of introduced genotypes will also depend on their degree of pre-adaption to high elevation climatic conditions, which may vary intra-specifically across source populations. For populations currently spreading in the lowlands, climate warming might reduce the climatic distance to high-elevation sites and thus remove a barrier to upwards spread. Here, we investigated the various facets of mountain invasions in a single, integrative experimental study. We applied a community transplant approach between high- and low-elevation sites in the European Alps to address effects of climate warming and disturbance through land use on community invasibility and the performance of the exotic species Senecio inaequidens, a potential future plant invader in the Alps. Additionally, the transplant sites served as common gardens to test the influence of climatic pre-adaptation to current (high site) and future (low site) climatic conditions on the performance of S. inaequidens in the transplanted communities. The 16 invasive central and western European S. inaequidens source population locations covered a wide geographic range, and thus a wide amplitude of climatic distances and presumed pre-adaptation to our gardens. Our results attest to a strong effect of disturbance, which increased community invasibility, and promoted the performance of the exotic species. Contrary to our expectation, experimentally induced climate warming did not increase community invasibility. However, the performance of the S. inaequidens populations was positively related to their pre-adaptation to the climatic conditions of our common gardens. Climate warming might thus promote the invasion of exotic species by reducing the climatic distance between mountain ranges and locations of potential source populations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Climate warming and increased disturbance (resulting from intensified land use) are expected to enhance the invasibility of plant communities and the performance of exotic species also at high elevations, and thus pose additional threats to mountain ecosystems. The invasion success of introduced genotypes will also depend on their degree of pre-adaption to high elevation climatic conditions, which may vary intra-specifically across source populations. For populations currently spreading in the lowlands, climate warming might reduce the climatic distance to high-elevation sites and thus remove a barrier to upwards spread. Here, we investigated the various facets of mountain invasions in a single, integrative experimental study. We applied a community transplant approach between high- and low-elevation sites in the European Alps to address effects of climate warming and disturbance through land use on community invasibility and the performance of the exotic species Senecio inaequidens, a potential future plant invader in the Alps. Additionally, the transplant sites served as common gardens to test the influence of climatic pre-adaptation to current (high site) and future (low site) climatic conditions on the performance of S. inaequidens in the transplanted communities. The 16 invasive central and western European S. inaequidens source population locations covered a wide geographic range, and thus a wide amplitude of climatic distances and presumed pre-adaptation to our gardens. Our results attest to a strong effect of disturbance, which increased community invasibility, and promoted the performance of the exotic species. Contrary to our expectation, experimentally induced climate warming did not increase community invasibility. However, the performance of the S. inaequidens populations was positively related to their pre-adaptation to the climatic conditions of our common gardens. Climate warming might thus promote the invasion of exotic species by reducing the climatic distance between mountain ranges and locations of potential source populations.
Variation in shape and consistency of selection between populations of the threatened Hihi (textitNotiomystis cincta) Journal Article
Rutschmann, Alexis; Santure, Anna W.; Brekke, Patricia; Ewen, John G.; Shanahan, Danielle; Villemereuil, Pierre
In: Journal of Evolutionary Biology, vol. n/a, no. n/a, 2022, ISSN: 1420-9101.
@article{rutschmann_variation_2022,
title = {Variation in shape and consistency of selection between populations of the threatened Hihi (textitNotiomystis cincta)},
author = {Alexis Rutschmann and Anna W. Santure and Patricia Brekke and John G. Ewen and Danielle Shanahan and Pierre Villemereuil},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jeb.14088
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Rutschmann-et-al.-2022-Variation-in-shape-and-consistency-of-selection-be.pdf},
doi = {10.1111/jeb.14088},
issn = {1420-9101},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Journal of Evolutionary Biology},
volume = {n/a},
number = {n/a},
abstract = {The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a “lag load”). In endangered species, often characterized by small population size, the lack of genetic diversity is expected to limit the response to this constant need to adjust to fluctuating selection, increasing the fitness burden and thus the risk of extinction. Here, we use long-term monitoring data to assess whether the type of selection for a key fitness trait (i.e., lay date) differs between two reintroduced populations of a threatened passerine bird, the hihi (Notiomystis cincta). We apply recent statistical developments to test for the presence or absence of fluctuation in selection in both the Tiritiri Mātangi Island and the Kārori sanctuary populations. Our results support the presence of stabilizing selection in Tiritiri Mātangi with a potential moving optimum for lay date. In Kārori our results favour a regime of directional selection. Although the shape of selection may differ, for both populations an earlier lay date generally increases fitness in both environments. Further, the moving optimum models of lay date on Tiritiri Mātangi, suggesting that selection varies between years, imply a substantial lag load in addition to the fitness burden caused by the population laying too late. Our results highlight the importance of characterizing the form and temporal variation of selection for each population to predict the effects of environmental change and to inform management.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The shape and intensity of natural selection can vary between years, potentially resulting in a chronic reduction of fitness as individuals need to track a continually changing optimum of fitness (i.e., a “lag load”). In endangered species, often characterized by small population size, the lack of genetic diversity is expected to limit the response to this constant need to adjust to fluctuating selection, increasing the fitness burden and thus the risk of extinction. Here, we use long-term monitoring data to assess whether the type of selection for a key fitness trait (i.e., lay date) differs between two reintroduced populations of a threatened passerine bird, the hihi (Notiomystis cincta). We apply recent statistical developments to test for the presence or absence of fluctuation in selection in both the Tiritiri Mātangi Island and the Kārori sanctuary populations. Our results support the presence of stabilizing selection in Tiritiri Mātangi with a potential moving optimum for lay date. In Kārori our results favour a regime of directional selection. Although the shape of selection may differ, for both populations an earlier lay date generally increases fitness in both environments. Further, the moving optimum models of lay date on Tiritiri Mātangi, suggesting that selection varies between years, imply a substantial lag load in addition to the fitness burden caused by the population laying too late. Our results highlight the importance of characterizing the form and temporal variation of selection for each population to predict the effects of environmental change and to inform management.
Finding the adaptive needles in a population-structured haystack: A case study in a New Zealand mollusc Journal Article
Salloum, Priscila M.; Santure, Anna W.; Lavery, Shane D.; Villemereuil, Pierre
In: Journal of Animal Ecology, vol. 91, no. 6, pp. 1209–1221, 2022, ISSN: 1365-2656.
@article{salloum_finding_2022,
title = {Finding the adaptive needles in a population-structured haystack: A case study in a New Zealand mollusc},
author = {Priscila M. Salloum and Anna W. Santure and Shane D. Lavery and Pierre Villemereuil},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2656.13692
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Salloum-et-al.-2022-Finding-the-adaptive-needles-in-a-population-struc-1.pdf},
doi = {10.1111/1365-2656.13692},
issn = {1365-2656},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Journal of Animal Ecology},
volume = {91},
number = {6},
pages = {1209–1221},
abstract = {Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci. Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographical contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the subtropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations. We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype–environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q-values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low confidence or high confidence. Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high-confidence GEA loci were detected in the context of strong population structure. However, 86 high-confidence loci were associated predominantly with latitudinally varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp rafting over the southern scale may be insufficient to counteract local adaptation in this species. Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non-model species to adapt to future environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci. Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographical contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the subtropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations. We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype–environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q-values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low confidence or high confidence. Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high-confidence GEA loci were detected in the context of strong population structure. However, 86 high-confidence loci were associated predominantly with latitudinally varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp rafting over the southern scale may be insufficient to counteract local adaptation in this species. Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non-model species to adapt to future environments.
Do leaf nitrogen resorption dynamics align with the slow-fast continuum? A test at the intraspecific level Journal Article
Sartori, Kevin; Violle, Cyrille; Vile, Denis; Vasseur, François; Villemereuil, Pierre; Bresson, Justine; Gillespie, Lauren; Fletcher, Leila Rose; Sack, Lawren; Kazakou, Elena
In: Functional Ecology, vol. 36, no. 5, pp. 1315–1328, 2022, ISSN: 1365-2435.
@article{sartori_leaf_2022,
title = {Do leaf nitrogen resorption dynamics align with the slow-fast continuum? A test at the intraspecific level},
author = {Kevin Sartori and Cyrille Violle and Denis Vile and François Vasseur and Pierre Villemereuil and Justine Bresson and Lauren Gillespie and Leila Rose Fletcher and Lawren Sack and Elena Kazakou},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2435.14029
https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Sartori-et-al.-2022-Do-leaf-nitrogen-resorption-dynamics-align-with-th.pdf},
doi = {10.1111/1365-2435.14029},
issn = {1365-2435},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Functional Ecology},
volume = {36},
number = {5},
pages = {1315–1328},
abstract = {The links between internal nitrogen recycling through the process of resorption from senescing leaves, whole-plant resource-use strategies and performance remain elusive. Indeed, tests of such potential linkages are hampered by the classical evaluation of plant nitrogen resorption efficiency (REN) based on ‘snapshots’ of leaf nitrogen concentration from adult and senescent leaves. We significantly increased the resolution for measuring leaf nitrogen resorption by non-destructively tracking time courses of nitrogen concentration in leaves of 137 natural Arabidopsis thaliana genotypes native to a wide range of climates across Europe, grown in a greenhouse. In addition to the classical measurement of resorption efficiency, we computed the relative maximum resorption rate of nitrogen (RRN), that is, the amount of nitrogen remobilized by a leaf per unit time and per unit nitrogen, together with slow–fast syndrome traits at the leaf and whole-plant levels. Across genotypes, high rates and efficiencies of nitrogen resorption were associated with low specific leaf area and late flowering. The RRN showed significant heritability, genetic associations and was negatively correlated with the mean annual temperature of the native populations. By contrast, despite the evidence of a correlation with temperature, REN showed lower heritability and no evidence of genetic association, questioning the mechanisms of nitrogen resorption. Overall, our results suggest a much stronger adaptive role for leaf nitrogen resorption than previously uncovered. Read the free Plain Language Summary for this article on the Journal blog.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The links between internal nitrogen recycling through the process of resorption from senescing leaves, whole-plant resource-use strategies and performance remain elusive. Indeed, tests of such potential linkages are hampered by the classical evaluation of plant nitrogen resorption efficiency (REN) based on ‘snapshots’ of leaf nitrogen concentration from adult and senescent leaves. We significantly increased the resolution for measuring leaf nitrogen resorption by non-destructively tracking time courses of nitrogen concentration in leaves of 137 natural Arabidopsis thaliana genotypes native to a wide range of climates across Europe, grown in a greenhouse. In addition to the classical measurement of resorption efficiency, we computed the relative maximum resorption rate of nitrogen (RRN), that is, the amount of nitrogen remobilized by a leaf per unit time and per unit nitrogen, together with slow–fast syndrome traits at the leaf and whole-plant levels. Across genotypes, high rates and efficiencies of nitrogen resorption were associated with low specific leaf area and late flowering. The RRN showed significant heritability, genetic associations and was negatively correlated with the mean annual temperature of the native populations. By contrast, despite the evidence of a correlation with temperature, REN showed lower heritability and no evidence of genetic association, questioning the mechanisms of nitrogen resorption. Overall, our results suggest a much stronger adaptive role for leaf nitrogen resorption than previously uncovered. Read the free Plain Language Summary for this article on the Journal blog.
Common Garden Experiments to Study Local Adaptation Need to Account for Population Structure Journal Article
de Villemereuil, Pierre; Gaggiotti, Oscar E.; Goudet, Jérôme
In: Journal of Ecology, vol. 110, no. 5, pp. 1005–1009, 2022, ISSN: 1365-2745.
@article{devillemereuil_common_2022,
title = {Common Garden Experiments to Study Local Adaptation Need to Account for Population Structure},
author = {Pierre de Villemereuil and Oscar E. Gaggiotti and Jérôme Goudet},
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},
issn = {1365-2745},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Journal of Ecology},
volume = {110},
number = {5},
pages = {1005--1009},
abstract = {Common garden experiments are precious 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Common garden experiments are precious 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.
Phenotypic Plasticity Drives Phenological Changes in a Mediterranean Blue Tit Population Journal Article
Biquet, Juliette; Bonamour, Suzanne; de Villemereuil, Pierre; Franceschi, Christophe; Teplitsky, Céline
In: Journal of Evolutionary Biology, vol. 35, no. 2, pp. 347–359, 2022, ISSN: 1420-9101.
@article{biquet_phenotypic_2021,
title = {Phenotypic Plasticity Drives Phenological Changes in a Mediterranean Blue Tit Population},
author = {Juliette Biquet and Suzanne Bonamour and Pierre de Villemereuil and Christophe Franceschi and Céline Teplitsky},
url = {https://devillemereuil.legtux.org/wp-content/uploads/2022/09/Biquet-et-al.-2022-Phenotypic-plasticity-drives-phenological-changes-.pdf},
doi = {10.1111/jeb.13950},
issn = {1420-9101},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Journal of Evolutionary Biology},
volume = {35},
number = {2},
pages = {347--359},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2021
Predicting Population Genetic Change in an Autocorrelated Random Environment: Insights from a Large Automated Experiment Journal Article
Rescan, Marie; Grulois, Daphné; Aboud, Enrique Ortega; de Villemereuil, Pierre; Chevin, Luis-Miguel
In: PLOS Genetics, vol. 17, no. 6, pp. e1009611, 2021, ISSN: 1553-7404.
@article{rescan_predicting_2021,
title = {Predicting Population Genetic Change in an Autocorrelated Random Environment: Insights from a Large Automated Experiment},
author = {Marie Rescan and Daphné Grulois and Enrique Ortega Aboud and Pierre de Villemereuil and Luis-Miguel Chevin},
url = {http://devillemereuil.legtux.org/publis/Rescan et al. - 2021 - Predicting population genetic change in an autocor.pdf},
doi = {10.1371/journal.pgen.1009611},
issn = {1553-7404},
year = {2021},
date = {2021-06-01},
urldate = {2021-06-01},
journal = {PLOS Genetics},
volume = {17},
number = {6},
pages = {e1009611},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Denoyelle, Laure; de Villemereuil, Pierre; Boyer, Frédéric; Khelifi, Meidhi; Gaffet, Clément; Alberto, Florian; Benjelloun, Badr; Pompanon, François
In: Frontiers in Genetics, vol. 12, pp. 1809, 2021, ISSN: 1664-8021.
@article{denoyelle_genetic_2021,
title = {Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats},
author = {Laure Denoyelle and Pierre de Villemereuil and Frédéric Boyer and Meidhi Khelifi and Clément Gaffet and Florian Alberto and Badr Benjelloun and François Pompanon},
url = {http://devillemereuil.legtux.org/publis/Denoyelle et al. - 2021 - Genetic variations and differential DNA methylatio.pdf},
doi = {10.3389/fgene.2021.745284},
issn = {1664-8021},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Frontiers in Genetics},
volume = {12},
pages = {1809},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2020
Consequences of Space Sharing on Individual Phenotypes in the New Zealand Hihi Journal Article
Rutschmann, Alexis; de Villemereuil, Pierre; Brekke, Patricia; Ewen, John G.; Anderson, Neil; Santure, Anna W.
In: Evolutionary Ecology, vol. 34, no. 5, pp. 821–839, 2020, ISSN: 1573-8477.
@article{rutschmann_consequences_2020,
title = {Consequences of Space Sharing on Individual Phenotypes in the New Zealand Hihi},
author = {Alexis Rutschmann and Pierre de Villemereuil and Patricia Brekke and John G. Ewen and Neil Anderson and Anna W. Santure},
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},
issn = {1573-8477},
year = {2020},
date = {2020-10-01},
urldate = {2020-10-01},
journal = {Evolutionary Ecology},
volume = {34},
number = {5},
pages = {821--839},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Accounting for Stochasticity in Demographic Compensation along the Elevational Range of an Alpine Plant Journal Article
Andrello, Marco; de Villemereuil, Pierre; Carboni, Marta; Busson, Delphine; Fortin, Marie-Josée; Gaggiotti, Oscar E.; Till-Bottraud, Irène
In: Ecology Letters, vol. 23, no. 5, pp. 870–880, 2020, ISSN: 1461-023X, 1461-0248.
@article{andrello_2020_accounting,
title = {Accounting for Stochasticity in Demographic Compensation along the Elevational Range of an Alpine Plant},
author = {Marco Andrello and Pierre de Villemereuil and Marta Carboni and Delphine Busson and Marie-Josée Fortin and Oscar E. Gaggiotti and Irène Till-Bottraud},
url = {http://devillemereuil.legtux.org/publis/Andrello et al. - 2020 - Accounting for stochasticity in demographic compen.pdf},
doi = {10.1111/ele.13488},
issn = {1461-023X, 1461-0248},
year = {2020},
date = {2020-05-01},
urldate = {2020-05-01},
journal = {Ecology Letters},
volume = {23},
number = {5},
pages = {870--880},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Polygenic Basis for Adaptive Morphological Variation in a Threatened Aotearoa | New Zealand Bird, the Hihi (Notiomystis Cincta) Journal Article
Duntsch, Laura; Tomotani, Barbara M.; de Villemereuil, Pierre; Brekke, Patricia; Lee, Kate D.; Ewen, John G.; Santure, Anna W.
In: Proceedings of the Royal Society B: Biological Sciences, vol. 287, no. 1933, pp. 20200948, 2020.
@article{duntsch_polygenic_2020,
title = {Polygenic Basis for Adaptive Morphological Variation in a Threatened Aotearoa | New Zealand Bird, the Hihi (Notiomystis Cincta)},
author = {Laura Duntsch and Barbara M. Tomotani and Pierre de Villemereuil and Patricia Brekke and Kate D. Lee and John G. Ewen and Anna W. Santure},
url = {http://devillemereuil.legtux.org/publis/Duntsch et al. - 2020 - Polygenic basis for adaptive morphological variati.pdf},
doi = {10.1098/rspb.2020.0948},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {287},
number = {1933},
pages = {20200948},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Climate dependent heating efficiency in the common lizard Journal Article
Rutschmann, Alexis; Rozen-Rechels, David; Dupoué, Andreaz; Blaimont, Pauline; Villemereuil, Pierre; Miles, Donald; Richard, Murielle; Clobert, Jean
In: Ecology and Evolution, vol. 10, no. 15, pp. 8007–8017, 2020, ISSN: 2045-7758.
@article{rutschmann_climate_2020,
title = {Climate dependent heating efficiency in the common lizard},
author = {Alexis Rutschmann and David Rozen-Rechels and Andreaz Dupoué and Pauline Blaimont and Pierre Villemereuil and Donald Miles and Murielle Richard and Jean Clobert},
url = {http://devillemereuil.legtux.org/publis/Rutschmann et al. - 2020 - Climate dependent heating efficiency in the common.pdf},
doi = {10.1002/ece3.6241},
issn = {2045-7758},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Ecology and Evolution},
volume = {10},
number = {15},
pages = {8007–8017},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Hitchhiking consequences for genetic and morphological patterns: the influence of kelp rafting on a brooding chiton Journal Article
Salloum, Priscila; Villemereuil, Pierre; Santure, Anna W.; Waters, Jon M.; Lavery, Shane D.
In: Biological Journal of the Linnean Society, vol. 130, no. 4, pp. 756–770, 2020, ISSN: 0024-4066.
@article{salloum_hitchhiking_2020,
title = {Hitchhiking consequences for genetic and morphological patterns: the influence of kelp rafting on a brooding chiton},
author = {Priscila Salloum and Pierre Villemereuil and Anna W. Santure and Jon M. Waters and Shane D. Lavery},
url = {http://devillemereuil.legtux.org/publis/Salloum et al. - 2020 - Hitchhiking consequences for genetic and morpholog.pdf},
doi = {10.1093/biolinnean/blaa073},
issn = {0024-4066},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Biological Journal of the Linnean Society},
volume = {130},
number = {4},
pages = {756–770},
abstract = {Abstract. Onithochiton neglectus is a morphologically variable, brooding chiton inhabiting coastal reefs throughout New Zealand and its Sub-Antarctic Islands.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract. Onithochiton neglectus is a morphologically variable, brooding chiton inhabiting coastal reefs throughout New Zealand and its Sub-Antarctic Islands.
Fluctuating Optimum and Temporally Variable Selection on Breeding Date in Birds and Mammals Journal Article
de Villemereuil, Pierre; Charmantier, Anne; Arlt, Debora; Bize, Pierre; Brekke, Patricia; Brouwer, Lyanne; Cockburn, A.; Côté, Steve D.; Dobson, F. Stephen; Evans, Simon R.; Festa-Bianchet, Marco; Gamelon, Marlène; Hamel, Sandra; Hegelbach, Johann; Jerstad, Kurt; Kempenaers, Bart; Kruuk, Loeske E. B.; Kumpula, Jouko; Kvalnes, Thomas; McAdam, Andrew G.; McFarlane, S. Eryn; Morrissey, Michael B.; Pärt, Tomas; Pemberton, Josephine M.; Qvarnström, Anna; Røstad, Ole-Wiggo; Schroeder, Julia; Senar, Juan Carlos; Sheldon, Ben C; Pol, Martijn; Visser, Marcel E.; Wheelwright, Nathaniel T.; Tufto, Jarle; Chevin, Luis-Miguel
In: Proceedings of the National Academy of Sciences, vol. 117, no. 50, pp. 31969–31978, 2020, ISSN: 0027-8424, 1091-6490.
@article{devillemereuil_fluctuating_2020,
title = {Fluctuating Optimum and Temporally Variable Selection on Breeding Date in Birds and Mammals},
author = {Pierre de Villemereuil and Anne Charmantier and Debora Arlt and Pierre Bize and Patricia Brekke and Lyanne Brouwer and A. Cockburn and Steve D. Côté and F. Stephen Dobson and Simon R. Evans and Marco Festa-Bianchet and Marlène Gamelon and Sandra Hamel and Johann Hegelbach and Kurt Jerstad and Bart Kempenaers and Loeske E. B. Kruuk and Jouko Kumpula and Thomas Kvalnes and Andrew G. McAdam and S. Eryn McFarlane and Michael B. Morrissey and Tomas Pärt and Josephine M. Pemberton and Anna Qvarnström and Ole-Wiggo Røstad and Julia Schroeder and Juan Carlos Senar and Ben C Sheldon and Martijn Pol and Marcel E. Visser and Nathaniel T. Wheelwright and Jarle Tufto and Luis-Miguel Chevin},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2020 - Fluctuating optimum and temporally variable select.pdf},
doi = {10.1073/pnas.2009003117},
issn = {0027-8424, 1091-6490},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {117},
number = {50},
pages = {31969--31978},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2019
Heritability of a Resting Heart Rate in a 20-Year Follow-up Family Cohort with GWAS Data: Insights from the STANISLAS Cohort: Journal Article
Xhaard, Constance; Dandine-Roulland, Claire; de Villemereuil, Pierre; Floch, Edith Le; Bacq-Daian, Delphine; Machu, Jean-Loup; Ferreira, Joao Pedro; cois Deleuze, Jean-Franc; Zannad, Faiez; Rossignol, Patrick; Girerd, Nicolas
In: European Journal of Preventive Cardiology, 2019.
@article{xhaard_heritability_2019,
title = {Heritability of a Resting Heart Rate in a 20-Year Follow-up Family Cohort with GWAS Data: Insights from the STANISLAS Cohort:},
author = {Constance Xhaard and Claire Dandine-Roulland and Pierre de Villemereuil and Edith Le Floch and Delphine Bacq-Daian and Jean-Loup Machu and Joao Pedro Ferreira and Jean-Franc cois Deleuze and Faiez Zannad and Patrick Rossignol and Nicolas Girerd},
url = {https://devillemereuil.legtux.org/wp-content/uploads/2024/01/Xhaard-et-al.-2019-Heritability-of-a-resting-heart-rate-in-a-20-year-.pdf},
doi = {10.1177/2047487319890763},
year = {2019},
date = {2019-12-01},
urldate = {2019-12-01},
journal = {European Journal of Preventive Cardiology},
abstract = {Background The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR i...},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background The association between resting heart rate (HR) and cardiovascular outcomes, especially heart failure, is now well established. However, whether HR i...
On the Relevance of Bayesian Statistics and MCMC for Animal Models Journal Article
de Villemereuil, Pierre
In: Journal of Animal Breeding and Genetics, vol. 136, no. 5, pp. 339–340, 2019, ISSN: 1439-0388.
@article{devillemereuil_relevance_2019,
title = {On the Relevance of Bayesian Statistics and MCMC for Animal Models},
author = {Pierre de Villemereuil},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil - 2019 - On the relevance of Bayesian statistics and MCMC f.pdf},
doi = {10.1111/jbg.12426},
issn = {1439-0388},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Journal of Animal Breeding and Genetics},
volume = {136},
number = {5},
pages = {339--340},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Directional Selection on Body Size but No Apparent Survival Cost to Being Large in Wild New Zealand Giraffe Weevils Journal Article
LeGrice, Rebecca J.; Tezanos-Pinto, Gabriela; de Villemereuil, Pierre; Holwell, Gregory I.; Painting, Christina J.
In: Evolution, vol. 73, no. 4, pp. 762–776, 2019, ISSN: 1558-5646.
@article{legrice_directional_2019,
title = {Directional Selection on Body Size but No Apparent Survival Cost to Being Large in Wild New Zealand Giraffe Weevils},
author = {Rebecca J. LeGrice and Gabriela Tezanos-Pinto and Pierre de Villemereuil and Gregory I. Holwell and Christina J. Painting},
url = {https://devillemereuil.legtux.org/wp-content/uploads/2022/09/LeGrice-et-al.-2019-Directional-selection-on-body-size-but-no-apparent.pdf},
doi = {10.1111/evo.13698},
issn = {1558-5646},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Evolution},
volume = {73},
number = {4},
pages = {762--776},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
A General Method for Simultaneously Accounting for Phylogenetic and Species Sampling Uncertainty via Rubin's Rules in Comparative Analysis Journal Article
Nakagawa, Shinichi; de Villemereuil, Pierre
In: Systematic Biology, vol. 68, no. 4, pp. 632–641, 2019.
@article{nakagawa_general_2019,
title = {A General Method for Simultaneously Accounting for Phylogenetic and Species Sampling Uncertainty via Rubin's Rules in Comparative Analysis},
author = {Shinichi Nakagawa and Pierre de Villemereuil},
url = {http://devillemereuil.legtux.org/publis/Nakagawa et de Villemereuil - 2019 - A general method for simultaneously accounting for.pdf},
doi = {10.1093/sysbio/syy089},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Systematic Biology},
volume = {68},
number = {4},
pages = {632--641},
abstract = {Abstract. Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species' trait evolution},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract. Phylogenetic comparative methods (PCMs), especially ones based on linear models, have played a central role in understanding species' trait evolution
Little Adaptive Potential in a Threatened Passerine Bird Journal Article
de Villemereuil, Pierre; Rutschmann, Alexis; Lee, Kate D.; Ewen, John G.; Brekke, Patricia; Santure, Anna W.
In: Current Biology, vol. 29, no. 5, pp. 889-894.e3, 2019, ISSN: 0960-9822.
@article{devillemereuil_little_2019,
title = {Little Adaptive Potential in a Threatened Passerine Bird},
author = {Pierre de Villemereuil and Alexis Rutschmann and Kate D. Lee and John G. Ewen and Patricia Brekke and Anna W. Santure},
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},
issn = {0960-9822},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Current Biology},
volume = {29},
number = {5},
pages = {889-894.e3},
abstract = {Summary Threatened species face numerous threats, including future challenges triggered by global change. A possible way to cope with these challenges is through adaptive evolution, which requires adaptive potential. Adaptive potential is defined as the genetic variance needed to respond to selection and can be assessed either on adaptive traits or fitness [1]. However, a lack of high-quality data has made it difficult to rigorously test adaptive potential in threatened species, leading to controversy over its magnitude [1, 2, 3]. Here we assess the adaptive potential of a threatened New Zealand passerine (the hihi, Notiomystis cincta) based on two populations: (1) the sole remaining natural population, on the island of Te Hauturu-o-Toi, and (2) a reintroduced population with a long-term dataset (intensively monitored for 20 years) based on the island of Tiritiri Matangi. We use molecular information (reduced representation genome sequencing, on both populations), as well as long-term phenotypic and fitness data from the Tiritiri Matangi population, to find (1) a lack of molecular genetic diversity at a genome-wide level in both populations, (2) low heritability of traits under selection and (3) negligible additive genetic variance of fitness in the Tiritiri Matangi population. In combination, these results support a lack of adaptive potential in this threatened species. We discuss our findings within the context of other passerines and methods for assessing adaptive potential, as well as the impact of these results on conservation practice, for the hihi and species of conservation concern in general.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary Threatened species face numerous threats, including future challenges triggered by global change. A possible way to cope with these challenges is through adaptive evolution, which requires adaptive potential. Adaptive potential is defined as the genetic variance needed to respond to selection and can be assessed either on adaptive traits or fitness [1]. However, a lack of high-quality data has made it difficult to rigorously test adaptive potential in threatened species, leading to controversy over its magnitude [1, 2, 3]. Here we assess the adaptive potential of a threatened New Zealand passerine (the hihi, Notiomystis cincta) based on two populations: (1) the sole remaining natural population, on the island of Te Hauturu-o-Toi, and (2) a reintroduced population with a long-term dataset (intensively monitored for 20 years) based on the island of Tiritiri Matangi. We use molecular information (reduced representation genome sequencing, on both populations), as well as long-term phenotypic and fitness data from the Tiritiri Matangi population, to find (1) a lack of molecular genetic diversity at a genome-wide level in both populations, (2) low heritability of traits under selection and (3) negligible additive genetic variance of fitness in the Tiritiri Matangi population. In combination, these results support a lack of adaptive potential in this threatened species. We discuss our findings within the context of other passerines and methods for assessing adaptive potential, as well as the impact of these results on conservation practice, for the hihi and species of conservation concern in general.
Can Threatened Species Adapt in a Restored Habitat? No Expected Evolutionary Response in Lay Date for the New Zealand Hihi Journal Article
de Villemereuil, Pierre; Rutschmann, Alexis; Ewen, John G.; Santure, Anna W.; Brekke, Patricia
In: Evolutionary Applications, vol. 12, no. 3, pp. 482–497, 2019, ISSN: 1752-4571.
@article{devillemereuil_can_2018,
title = {Can Threatened Species Adapt in a Restored Habitat? No Expected Evolutionary Response in Lay Date for the New Zealand Hihi},
author = {Pierre de Villemereuil and Alexis Rutschmann and John G. Ewen and Anna W. Santure and Patricia Brekke},
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},
issn = {1752-4571},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Evolutionary Applications},
volume = {12},
number = {3},
pages = {482--497},
abstract = {Many bird species have been observed shifting their laying date to earlier in the year in response to climate change. However the vast majority of these studies were performed on non-threatened species, less impacted by reduced genetic diversity (which is expected to limit evolutionary response) as a consequence of genetic bottlenecks, drift and population isolation. Here we study the relationship between lay date and fitness, as well as its genetic basis, to understand the evolutionary constraints on phenology faced by threatened species using a recently reintroduced population of the endangered New Zealand passerine, the hihi (Notiomystis cincta). A large discrepancy between the optimal laying date and the mode of laying date creates a strong selection differential of -11.24. The impact of this discrepancy on fitness is principally mediated through survival of offspring from hatchling to fledgling. This discrepancy does not seem to arise from a difference in female quality or a trade-off with lifetime breeding success. We find that start of breeding season depends on female age and average temperature prior to the breeding season. Laying date is not found to be significantly heritable. Overall, our research suggests that this discrepancy is a burden on hihi fitness, which will not be resolved through evolution or phenotypic plasticity. More generally, these results show that threatened species introduced to restored habitats might lack adaptive potential and plasticity to adjust their phenology to their new environment. This constraint is also likely to limit their ability to face future challenges, including climate change. This article is protected by copyright. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Many bird species have been observed shifting their laying date to earlier in the year in response to climate change. However the vast majority of these studies were performed on non-threatened species, less impacted by reduced genetic diversity (which is expected to limit evolutionary response) as a consequence of genetic bottlenecks, drift and population isolation. Here we study the relationship between lay date and fitness, as well as its genetic basis, to understand the evolutionary constraints on phenology faced by threatened species using a recently reintroduced population of the endangered New Zealand passerine, the hihi (Notiomystis cincta). A large discrepancy between the optimal laying date and the mode of laying date creates a strong selection differential of -11.24. The impact of this discrepancy on fitness is principally mediated through survival of offspring from hatchling to fledgling. This discrepancy does not seem to arise from a difference in female quality or a trade-off with lifetime breeding success. We find that start of breeding season depends on female age and average temperature prior to the breeding season. Laying date is not found to be significantly heritable. Overall, our research suggests that this discrepancy is a burden on hihi fitness, which will not be resolved through evolution or phenotypic plasticity. More generally, these results show that threatened species introduced to restored habitats might lack adaptive potential and plasticity to adjust their phenology to their new environment. This constraint is also likely to limit their ability to face future challenges, including climate change. This article is protected by copyright. All rights reserved.
2018
Convergent Genomic Signatures of Domestication in Sheep and Goats Journal Article
Alberto, Florian J.; Boyer, Frédéric; Orozco-terWengel, Pablo; Streeter, Ian; Servin, Bertrand; de Villemereuil, Pierre; Benjelloun, Badr; Librado, Pablo; Biscarini, Filippo; Colli, Licia; Barbato, Mario; Zamani, Wahid; Alberti, Adriana; Engelen, Stefan; Stella, Alessandra; Joost, Stéphane; Ajmone-Marsan, Paolo; Negrini, Riccardo; Orlando, Ludovic; Rezaei, Hamid Reza; Naderi, Saeid; Clarke, Laura; Flicek, Paul; Wincker, Patrick; Coissac, Eric; Kijas, James; Tosser-Klopp, Gwenola; Chikhi, Abdelkader; Bruford, Michael W.; Taberlet, Pierre; Pompanon, François
In: Nature Communications, vol. 9, no. 1, pp. 813, 2018, ISSN: 2041-1723.
@article{alberto_convergent_2018,
title = {Convergent Genomic Signatures of Domestication in Sheep and Goats},
author = {Florian J. Alberto and Frédéric Boyer and Pablo Orozco-terWengel and Ian Streeter and Bertrand Servin and Pierre de Villemereuil and Badr Benjelloun and Pablo Librado and Filippo Biscarini and Licia Colli and Mario Barbato and Wahid Zamani and Adriana Alberti and Stefan Engelen and Alessandra Stella and Stéphane Joost and Paolo Ajmone-Marsan and Riccardo Negrini and Ludovic Orlando and Hamid Reza Rezaei and Saeid Naderi and Laura Clarke and Paul Flicek and Patrick Wincker and Eric Coissac and James Kijas and Gwenola Tosser-Klopp and Abdelkader Chikhi and Michael W. Bruford and Pierre Taberlet and François Pompanon},
url = {https://devillemereuil.legtux.org/wp-content/uploads/2022/09/Alberto-et-al.-2018-Convergent-genomic-signatures-of-domestication-in-.pdf},
doi = {10.1038/s41467-018-03206-y},
issn = {2041-1723},
year = {2018},
date = {2018-03-01},
urldate = {2018-03-01},
journal = {Nature Communications},
volume = {9},
number = {1},
pages = {813},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Patterns of Phenotypic Plasticity and Local Adaptation in the Wide Elevation Range of the Alpine Plant emphArabisemph Alpina Journal Article
de Villemereuil, Pierre; Mouterde, Médéric; Gaggiotti, Oscar E.; Till-Bottraud, Irène
In: Journal of Ecology, vol. 106, no. 5, pp. 1952–1971, 2018.
@article{devillemereuil_patterns_2018,
title = {Patterns of Phenotypic Plasticity and Local Adaptation in the Wide Elevation Range of the Alpine Plant emphArabisemph Alpina},
author = {Pierre de Villemereuil and Médéric Mouterde and Oscar E. Gaggiotti and Irène Till-Bottraud},
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},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {Journal of Ecology},
volume = {106},
number = {5},
pages = {1952--1971},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Quantitative Genetics Methods Depending on the Nature of the Phenotypic Trait Journal Article
de Villemereuil, Pierre
In: Annals of the New York Academy of Sciences, vol. 1422, no. 1, pp. 29–47, 2018.
@article{devillemereuil_quantitative_2018,
title = {Quantitative Genetics Methods Depending on the Nature of the Phenotypic Trait},
author = {Pierre de Villemereuil},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil - 2018 - Quantitative genetics methods depending on the nat.pdf},
doi = {10.1111/nyas.13571},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {Annals of the New York Academy of Sciences},
volume = {1422},
number = {1},
pages = {29--47},
series = {The Year in Evolutionary Biology},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Fixed-Effect Variance and the Estimation of Repeatabilities and Heritabilities: Issues and Solutions Journal Article
de Villemereuil, Pierre; Morrissey, Michael B.; Nakagawa, Shinichi; Schielzeth, Holger
In: Journal of Evolutionary Biology, vol. 31, no. 4, pp. 621–632, 2018, ISSN: 1420-9101.
@article{devillemereuil_fixed_2018,
title = {Fixed-Effect Variance and the Estimation of Repeatabilities and Heritabilities: Issues and Solutions},
author = {Pierre de Villemereuil and Michael B. Morrissey and Shinichi Nakagawa and Holger Schielzeth},
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},
issn = {1420-9101},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {Journal of Evolutionary Biology},
volume = {31},
number = {4},
pages = {621--632},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2017
Perturbations on the Uniform Distribution of P-Values Can Lead to Misleading Inferences from Null-Hypothesis Testing Journal Article
Garamszegi, László Zsolt; de Villemereuil, Pierre
In: Trends in Neuroscience and Education, vol. 8--9, pp. 18–27, 2017, ISSN: 2211-9493.
@article{garamszegi_perturbations_2017,
title = {Perturbations on the Uniform Distribution of P-Values Can Lead to Misleading Inferences from Null-Hypothesis Testing},
author = {László Zsolt Garamszegi and Pierre de Villemereuil},
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},
issn = {2211-9493},
year = {2017},
date = {2017-12-01},
urldate = {2017-12-01},
journal = {Trends in Neuroscience and Education},
volume = {8--9},
pages = {18--27},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2016
General Methods for Evolutionary Quantitative Genetic Inference from Generalised Mixed Models Journal Article
de Villemereuil, Pierre; Schielzeth, Holger; Nakagawa, Shinichi; Morrissey, Michael B.
In: Genetics, vol. 204, no. 3, pp. 1281–1294, 2016, ISSN: 0016-6731, 1943-2631.
@article{devillemereuil_general_2016,
title = {General Methods for Evolutionary Quantitative Genetic Inference from Generalised Mixed Models},
author = {Pierre de Villemereuil and Holger Schielzeth and Shinichi Nakagawa and Michael B. Morrissey},
url = {http://devillemereuil.legtux.org/publis/Villemereuil et al. - 2016 - General methods for evolutionary quantitative gene.pdf},
doi = {10.1534/genetics.115.186536},
issn = {0016-6731, 1943-2631},
year = {2016},
date = {2016-11-01},
urldate = {2016-11-01},
journal = {Genetics},
volume = {204},
number = {3},
pages = {1281--1294},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Common Garden Experiments in the Genomic Era: New Perspectives and Opportunities Journal Article
de Villemereuil, Pierre; Gaggiotti, Oscar E.; Mouterde, Médéric; Till-Bottraud, Irène
In: Heredity, vol. 116, no. 3, pp. 249–254, 2016, ISSN: 0018-067X.
@article{devillemereuil_common_2016,
title = {Common Garden Experiments in the Genomic Era: New Perspectives and Opportunities},
author = {Pierre de Villemereuil and Oscar E. Gaggiotti and Médéric Mouterde and Irène Till-Bottraud},
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},
issn = {0018-067X},
year = {2016},
date = {2016-03-01},
urldate = {2016-03-01},
journal = {Heredity},
volume = {116},
number = {3},
pages = {249--254},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Kin Recognition or Phenotype Matching? Journal Article
Till-Bottraud, Irène; de Villemereuil, Pierre
In: New Phytologist, vol. 209, no. 1, pp. 13–14, 2016, ISSN: 1469-8137.
@article{tillbottraud_kin_2016,
title = {Kin Recognition or Phenotype Matching?},
author = {Irène Till-Bottraud and Pierre de Villemereuil},
url = {http://devillemereuil.legtux.org/publis/Till-Bottraud et de Villemereuil - 2016 - Kin recognition or phenotype matching.pdf},
doi = {10.1111/nph.13554},
issn = {1469-8137},
year = {2016},
date = {2016-01-01},
urldate = {2016-01-01},
journal = {New Phytologist},
volume = {209},
number = {1},
pages = {13--14},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
A New FST-based Method to Uncover Local Adaptation Using Environmental Variables Journal Article
de Villemereuil, Pierre; Gaggiotti, Oscar E.
In: Methods in Ecology and Evolution, vol. 6, no. 11, pp. 1248–1258, 2015, ISSN: 2041210X.
@article{devillemereuil_new_2015,
title = {A New FST-based Method to Uncover Local Adaptation Using Environmental Variables},
author = {Pierre de Villemereuil and Oscar E. Gaggiotti},
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},
issn = {2041210X},
year = {2015},
date = {2015-11-01},
urldate = {2015-11-01},
journal = {Methods in Ecology and Evolution},
volume = {6},
number = {11},
pages = {1248--1258},
abstract = {Genome-scan methods are used for screening genome-wide patterns of DNA polymorphism to detect signatures of positive selection. There are two main types of methods: (i) ``outlier'' detection methods based on FST that detect loci with high differentiation compared to the rest of the genome, and (ii) environmental association methods that test the association between allele frequencies and environmental variables. We present a new FST-based genome-scan method, BayeScEnv, which incorporates environmental information in the form of ``environmental differentiation''. It is based on the F model, but, as opposed to existing approaches, it considers two locus-specific effects; one due to divergent selection, and another due to various other processes different from local adaptation (e.g. range expansions, differences in mutation rates across loci or background selection). The method was developped in C++ and is avaible at http://github.com/devillemereuil/bayescenv. A simulation study shows that our method has a much lower false positive rate than an existing FST-based method, BayeScan, under a wide range of demographic scenarios. Although it has lower power, it leads to a better compromise between power and false positive rate. We apply our method to a human dataset and show that it can be used successfully to study local adaptation. We discuss its scope and compare it to other existing methods. This article is protected by copyright. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Genome-scan methods are used for screening genome-wide patterns of DNA polymorphism to detect signatures of positive selection. There are two main types of methods: (i) ``outlier'' detection methods based on FST that detect loci with high differentiation compared to the rest of the genome, and (ii) environmental association methods that test the association between allele frequencies and environmental variables. We present a new FST-based genome-scan method, BayeScEnv, which incorporates environmental information in the form of ``environmental differentiation''. It is based on the F model, but, as opposed to existing approaches, it considers two locus-specific effects; one due to divergent selection, and another due to various other processes different from local adaptation (e.g. range expansions, differences in mutation rates across loci or background selection). The method was developped in C++ and is avaible at http://github.com/devillemereuil/bayescenv. A simulation study shows that our method has a much lower false positive rate than an existing FST-based method, BayeScan, under a wide range of demographic scenarios. Although it has lower power, it leads to a better compromise between power and false positive rate. We apply our method to a human dataset and show that it can be used successfully to study local adaptation. We discuss its scope and compare it to other existing methods. This article is protected by copyright. All rights reserved.
Detecting Adaptive Evolution Based on Association with Ecological Gradients: Orientation Matters! Journal Article
Frichot, Éric; Schoville, Sean D.; de Villemereuil, Pierre; Gaggiotti, Oscar E.; François, Olivier
In: Heredity, vol. 115, no. 1, pp. 22–28, 2015, ISSN: 0018-067X.
@article{frichot_detecting_2015,
title = {Detecting Adaptive Evolution Based on Association with Ecological Gradients: Orientation Matters!},
author = {Éric Frichot and Sean D. Schoville and Pierre de Villemereuil and Oscar E. Gaggiotti and Olivier François},
url = {https://devillemereuil.legtux.org/wp-content/uploads/2022/09/Frichot-et-al.-2015-Detecting-adaptive-evolution-based-on-association-.pdf},
doi = {10.1038/hdy.2015.7},
issn = {0018-067X},
year = {2015},
date = {2015-07-01},
urldate = {2015-07-01},
journal = {Heredity},
volume = {115},
number = {1},
pages = {22--28},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Dispersal Evolution and Resource Matching in a Spatially and Temporally Variable Environment Journal Article
Aguilée, Robin; de Villemereuil, Pierre; Guillon, Jean-Michel
In: Journal of Theoretical Biology, vol. 370, pp. 184–196, 2015, ISSN: 0022-5193.
@article{aguilee_dispersal_2015,
title = {Dispersal Evolution and Resource Matching in a Spatially and Temporally Variable Environment},
author = {Robin Aguilée and Pierre de Villemereuil and Jean-Michel Guillon},
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},
issn = {0022-5193},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {Journal of Theoretical Biology},
volume = {370},
pages = {184--196},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2014
Bayesian Approaches to the Quantitative Genetic Analysis of Natural Populations Book Section
Morrissey, Michael B.; de Villemereuil, Pierre; Doligez, Blandine; Gimenez, Olivier
In: Charmantier, Anne; Garant, Dany; Kruuk, Loeske E. B. (Ed.): Quantitative Genetics in the Wild, pp. 228–253, Oxford University Press, Oxford (UK), 2014, ISBN: 978-0-19-165595-1.
@incollection{morrissey_bayesian_2014,
title = {Bayesian Approaches to the Quantitative Genetic Analysis of Natural Populations},
author = {Michael B. Morrissey and Pierre de Villemereuil and Blandine Doligez and Olivier Gimenez},
editor = {Anne Charmantier and Dany Garant and Loeske E. B. Kruuk},
isbn = {978-0-19-165595-1},
year = {2014},
date = {2014-04-01},
urldate = {2014-04-01},
booktitle = {Quantitative Genetics in the Wild},
pages = {228--253},
publisher = {Oxford University Press},
address = {Oxford (UK)},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
General Quantitative Genetic Methods for Comparative Biology Book Section
de Villemereuil, Pierre; Nakagawa, Shinichi
In: Garamszegi, László Zsolt (Ed.): Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology, pp. 287–303, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, ISBN: 978-3-662-43550-2.
@incollection{devillemereuil_general_2014,
title = {General Quantitative Genetic Methods for Comparative Biology},
author = {Pierre de Villemereuil and Shinichi Nakagawa},
editor = {László Zsolt Garamszegi},
isbn = {978-3-662-43550-2},
year = {2014},
date = {2014-01-01},
urldate = {2014-01-01},
booktitle = {Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology},
pages = {287--303},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Genome Scan Methods against More Complex Models: When and How Much Should We Trust Them? Journal Article
de Villemereuil, Pierre; Frichot, Éric; Bazin, Éric; François, Olivier; Gaggiotti, Oscar E.
In: Molecular Ecology, vol. 23, no. 8, pp. 2006–2019, 2014, ISSN: 1365-294X.
@article{devillemereuil_genome_2014,
title = {Genome Scan Methods against More Complex Models: When and How Much Should We Trust Them?},
author = {Pierre de Villemereuil and Éric Frichot and Éric Bazin and Olivier François and Oscar E. Gaggiotti},
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},
issn = {1365-294X},
year = {2014},
date = {2014-01-01},
urldate = {2014-01-01},
journal = {Molecular Ecology},
volume = {23},
number = {8},
pages = {2006--2019},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2013
de Villemereuil, Pierre; Gimenez, Olivier; Doligez, Blandine
In: Methods in Ecology and Evolution, vol. 4, no. 3, pp. 260–275, 2013, ISSN: 2041-210X.
@article{devillemereuil_comparing_2013,
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},
author = {Pierre de Villemereuil and Olivier Gimenez and Blandine Doligez},
url = {http://devillemereuil.legtux.org/publis/de Villemereuil et al. - 2013 - Comparing parent–offspring regression with frequen.pdf},
doi = {10.1111/2041-210X.12011},
issn = {2041-210X},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {Methods in Ecology and Evolution},
volume = {4},
number = {3},
pages = {260--275},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
* 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.
2012
Bayesian Models for Comparative Analysis Integrating Phylogenetic Uncertainty Journal Article
de Villemereuil, Pierre; Wells, Jessie A.; Edwards, Robert D.; Blomberg, Simon P.
In: BMC Evolutionary Biology, vol. 12, no. 1, pp. 102, 2012, ISSN: 1471-2148.
@article{devillemereuil_bayesian_2012,
title = {Bayesian Models for Comparative Analysis Integrating Phylogenetic Uncertainty},
author = {Pierre de Villemereuil and Jessie A. Wells and Robert D. Edwards and Simon P. Blomberg},
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},
issn = {1471-2148},
year = {2012},
date = {2012-06-01},
urldate = {2012-06-01},
journal = {BMC Evolutionary Biology},
volume = {12},
number = {1},
pages = {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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
2011
Consumer Functional Responses under Intra- and Inter-Specific Interference Competition Journal Article
de Villemereuil, Pierre; López-Sepulcre, Andrés
In: Ecological Modelling, vol. 222, no. 3, pp. 419–426, 2011, ISSN: 03043800.
@article{devillemereuil_consumer_2011,
title = {Consumer Functional Responses under Intra- and Inter-Specific Interference Competition},
author = {Pierre de Villemereuil and Andrés López-Sepulcre},
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},
issn = {03043800},
year = {2011},
date = {2011-02-01},
urldate = {2011-02-01},
journal = {Ecological Modelling},
volume = {222},
number = {3},
pages = {419--426},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
