Biology subjects

Mallard, F.

Publications and source records attributed to Mallard, F..

10 recordsLinked to original sources

bioRxiv2022

Variation in mutational (co)variances

1Because of pleiotropy, mutations affect the expression and inheritance of multiple traits and are expected to determine the structure of standing genetic variation and phenotypic evolution. It is thus important to find if the M matrix, describing mutational (co)variances between traits, varies between genotypes. We here estimate the M matrix for six locomotion behavior traits in two genotypes of the nematode Caenorhabditis elegans. We find significant mutational variance along at least one phenotypic dimension of the M matrix, but its size and orientation was similar between genotypes. We then tested if the M matrices were similar to one G matrix describing the standing genetic (co)variances of a domesticated population derived by the hybridization of several genotypes and adapted to a lab defined environment for 140 generations. M and G are different in part because the genetic covariances caused by mutational pleiotropy in the two genotypes are smaller than those caused by standing linkage disequilibrium in the lab population. If generalized to other genotypes, these observations indicate that selection is unlikely to shape the evolution of the M matrix for locomotion behavior and suggests that the genetic restructuring due to the hybridization of C. elegans genotypes allows for selection in the lab on new phenotypic dimensions of locomotion behavior, phenotypic dimensions which are inaccessible to natural populations.

evolutionary biology↗

bioRxiv2022

Selection and the direction of phenotypic evolution

1Predicting phenotypic evolution on the short-term of tens to hundreds of generations, particularly in changing environments and under finite population sizes, is an important theoretical goal. Because organisms are not simply collections of independent traits, making headway into this goal requires understanding if the phenotypic plasticity of ancestral populations aligns with the phenotypic dimensions that contain more genetic variation for selection to be effective and eventually feedback on the maintenance of genetic variation and promote adaptation or rescue from extinction. By performing 50 generations of experimental evolution in a changing environment we show that ancestral phenotypic plasticity for locomotion behavior in the partially-outcrossing nematode Caenorhabditis elegans is nonadaptive because it does not align with the phenotypic dimension encompassing most genetic variance in the ancestral population and is of no consequence to future phenotypic divergence. Despite evolution of the genetic structure of locomotion behavior we are able to predict the direction of phenotypic divergence, but not the magnitude, based on the genetic covariances between the component traits of locomotion behavior and fitness of the ancestral population. We further demonstrate that indirect selection on the component traits of locomotion behavior with unobserved trait(s) is responsible for the observed phenotypic divergence on them. Our findings indicate that selection theory can predict the direction of short-term adaptive phenotypic evolution.

evolutionary biology↗

bioRxiv2022

Phenotypic stasis with genetic divergence

1Whether or not genetic divergence on the short-term of tens to hundreds of generations is compatible with phenotypic stasis remains a relatively unexplored problem. We evolved predominantly outcrossing, genetically diverse populations of the nematode Caenorhabditis elegans under a constant and homogeneous environment for 240 generations, and followed individual locomotion behavior. Although founders of lab populations show highly diverse locomotion behavior, during lab evolution the component traits of locomotion behavior - defined as the transition rates in activity and direction - did not show divergence from the ancestral population. In contrast, transition rates genetic (co)variance structure showed a marked divergence from the ancestral state and differentiation among replicate populations during the final 100 generations and after most adaptation had been achieved. We observe that genetic differentiation is a transient pattern during the loss of genetic variance along phenotypic dimensions under drift during the last 100 generations of lab evolution. These results suggest that short-term stasis of locomotion behavior is maintained because of stabilizing selection, while the genetic structuring of component traits is contingent upon drift history.

evolutionary biology↗

bioRxiv2020

The evolution of phenotypic plasticity in response to temperature stress

Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on a Drosophila simulans population in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g. chitin metabolism, glycolysis and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.

evolutionary biology↗

bioRxiv2020

The adaptive architecture is shaped by population ancestry and not by selection regime

Understanding the genetic architecture of adaptive phenotypes is a key question in evolutionary biology. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. The recent analysis of replicate populations from two different Drosophila simulans founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of loci under strong selection (19 selected alleles, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations have a pronounced impact on our understanding of adaptation in natural populations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

evolutionary biology↗

bioRxiv2020

Temperature change has the same effect as genetic variation on a morphological trait involved in reproductive isolation between Drosophila sister species

Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and D. yakuba. We designed a semi-automatic measurement pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches in D. yakuba but that in D. santomea ventral branches tend to morph into a D. yakuba-like shape at lower temperature. Our results suggest that speciation of D. santomea and D. yakuba was associated with a change in genitalia plasticity.

evolutionary biology↗

bioRxiv2019

Selection and drift determine phenotypic stasis despite genetic divergence

1Evolutionary theory suggests that phenotypic stasis is explained by natural selection and genetic drift, or by constraints imposed by mutation and recombination of standing genetic variation. We performed experimental evolution from standing genetic variation with the nematode Caenorhabditis elegans, measuring individual locomotion in outcrossing populations for 240 generations. We find that, in our constant environment, locomotion bias shows no directional divergence, due to both stabilizing and disruptive selection on specific combinations of component traits. Despite phenotypic stasis, the genetic variance-covariance structure between component traits shows clear divergence from the ancestral state and extensive differentiation among replicated populations facing the same environment. Analysis of mutation accumulation experiments and genome-sequenced recombinant inbred lines from the experimental populations indicates that the evolution of the genetic variance-covariance structure is independent of de novo mutation or major effect QTL; being instead explained by the joint action of selection and drift in generating subtle linkage disequilibrium differences between small effect QTL among replicate populations. These findings indicate that phenotypic evolution is repeatable because of selection, even if the genetic structuring of component traits within lineages is mostly contingent upon drift history.

evolutionary biology↗

bioRxiv2019

From individuals to populations: How intraspecific competition shapes thermal reaction norms

O_LIMost ectotherms follow the temperature-size rule (TSR): in cold environments individuals grow slowly but reach a large asymptotic length. Intraspecific competition can induce plastic changes of growth rate and asymptotic length and competition may itself be modulated by temperature.\nC_LIO_LIOur aim is to disentangle the joint effects of temperature and intraspecific competition on growth rate and asymptotic length.\nC_LIO_LIWe used two distinct clonal lineages of the Collembola Folsomia candida, to describe thermal reaction norms of growth rate, asymptotic length and reproduction over 6 temperatures between 6{degrees}C and 29{degrees}C. In parallel, we measured the long-term size-structure and dynamics of populations reared under the same temperatures to measure growth rates and asymptotic lengths in populations and to quantify the joint effects of competition and temperature on these traits.\nC_LIO_LIWe show that intraspecific competition modulates the temperature-size rule. In dense populations there is a direct negative effect of temperature on asymptotic length, but there is no temperature dependence of the growth rate, the dominant factor regulating growth being competition. We fail to demonstrate that the strength of competition varies with temperature except at the lowest temperature where competition is minimal. The two lineages responded differently to the joint effects of temperature and competition and these genetic differences have marked effects on population dynamics along our temperature gradient.\nC_LIO_LIOur results reinforce the idea that the TSR response of ectotherms can be modulated by biotic and abiotic stressors when studied in non-optimal laboratory experiments. Untangling complex interactions between environment and demography will help understanding how size will respond to environmental change and how climate change may influence population dynamics.\nC_LI

ecology↗

bioRxiv2018

Polygenic adaptation fuels genetic redundancy in Drosophila

The genetic architecture of adaptive traits is of key importance to predict evolutionary responses. Most adaptive traits are polygenic - i.e. result from selection on a large number of genetic loci - but most molecularly characterized traits have a simple genetic basis. This discrepancy is best explained by the difficulty in detecting small allele frequency changes across many contributing loci. To resolve this, we use laboratory natural selection, a framework that is powerful enough to detect signatures for selective sweeps and polygenic adaptation. We exposed 10 replicates of a Drosophila simulans population to a new temperature regime and uncovered a polygenic architecture of an adaptive trait with high genetic redundancy among adaptive alleles. We observed convergent phenotypic responses, e.g. fitness, metabolic rate and fat content, and a strong polygenic response (99 selected alleles; mean s=0.061). However, each of these selected alleles increased in frequency only in a subset of the evolving replicates. Our results show that natural D. simulans populations harbor a vast reservoir of adaptive variation facilitating rapid evolutionary responses. The observed genetic redundancy potentiates this genotypic variation through multiple genetic pathways leading to phenotypic convergence. This key property of adaptive alleles requires the modification of testing strategies in natural populations beyond the search for convergence on the molecular level.

evolutionary biology↗

bioRxiv2017

A simple genetic basis of adaptation to a novel thermal environment results in complex metabolic rewiring in Drosophila

Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. To investigate the genetic architecture of thermal adaptation - a highly complex trait - we performed experimental evolution on a natural Drosophila simulans population. Transcriptome and respiration measurements revealed extensive metabolic rewiring after only [~]60 generations in a hot environment. Analysis of genome-wide polymorphisms identified two interacting selection targets, Sestrin and SNF4A{gamma}, pointing to AMPK, a central metabolic switch, as a key factor for thermal adaptation. Our results demonstrate that large-effect loci segregating at intermediate allele frequencies can allow natural populations to rapidly respond to selection. Because SNF4A{gamma} also exhibits clinal variation in various Drosophila species, we suggest that this large effect polymorphism is maintained by temporal and spatial temperature variation in natural environments.

evolutionary biology↗