Biology subjects

Fraimout, A.

Publications and source records attributed to Fraimout, A..

15 recordsLinked to original sources

bioRxiv2026

Evolutionary and acclimatory shifts in ion transporter gene expression across salinity transitions in the copepod Eurytemora carolleeae

Many aquatic invaders are crossing biogeographic boundaries from saline to freshwater habitats. This transition often requires acclimation or evolution of physiological mechanisms to maintain internal ionic homeostasis. Populations of the copepod Eurytemora affinis complex have repeatedly invaded freshwater environments from saline habitats over the past century, providing an ideal model for investigating rapid adaptation to salinity change. Prior studies have found that ion transport-related genes form the largest functional categories of genes under selection and show evolutionary shifts in gene expression across saline to freshwater transitions in the E. affinis complex. In this study, focusing on the top targets of selection, we investigated evolutionary and acclimatory shifts in gene expression for 19 ion transport-related genes for populations of E. carolleeae (Atlantic clade of the E. affinis complex). Using a quantitative real-time PCR approach, we compared gene expression between ancestral saline and derived freshwater populations through a common garden reaction norm experiment and a laboratory natural selection experiment. We found that different ion transport-related gene paralogs within expanded gene families showed divergent patterns of expression in response to salinity change, consistent with specialization. For instance, Na+/K+-ATPase subunit paralog 1 (NKA--1) and Na+,K+,2Cl- cotransporter paralog 3 (NKCC-3) exhibited the evolution of increased expression in the freshwater population across all conditions, relative to the saline population. In contrast, Na+/H+ antiporter paralog 7 (NHA-7) and NHA-5 showed evolution of elevated expression in the saline population under low salinity relative to the freshwater population. Several genes also showed evolutionary differences in plasticity between saline and freshwater populations, such that saline populations retained phenotypic plasticity, whereas freshwater populations were comparatively canalized. In the laboratory natural selection experiment imposing salinity decline, evolutionary responses of the paralogs NKCC-3, NHA-5, and NHA-7 in the saline selection line largely recapitulated the evolutionary shifts observed in the natural populations. On the other hand, expression patterns of the ion transporters in the freshwater selection line showed little response during salinity increase, suggesting canalization. Together, these results reveal evolutionary and acclimatory divergence in gene expression among paralogs, suggesting the evolution of functional divergence among them.

evolutionary biology↗

bioRxiv2026

Genome-Environment Associations reveal shared and unique adaptive loci across multiple pollutants and populations of the eastern mosquitofish Gambusia holbrooki

Rapid adaptation to human-induced stressors is commonplace in the context of global change, including during biological invasions. Identifying the genomic bases and associated biological functions underlying such adaptation is hence crucial to understand and anticipate the response of populations and species to changing conditions. In particular, the extent to which genetic responses to multiple anthropogenic stressors vary between populations in the wild has been relatively unexplored. We addressed this question by leveraging whole-genome sequence data (both PoolSeq and IndSeq) in invasive populations of Gambusia holbrooki - a widespread invasive fish species - collected from 14 locations with different multi-pollutants exposure. We sought to identify adaptive loci associated with pollution tolerance by conducting Genome-Environment Association (GEA) analyses. Additionally, we investigated the degree of adaptive loci reuse between pollutants and their combinations as well as across populations. We found strong signals of association between allele frequency changes and pollutant exposure at several genomic locations, often overlapping with genes known for their functions in detoxification and immune response. We further showed that most adaptive loci are not shared among all populations, suggesting heterogeneous genomic response to each local selection. Interestingly, multiple tests looking for footprints of selection and association to pollutants yielded consistent results. Our results shed new light on the extent of genetic convergence in the genomic bases of rapid adaptation to different cocktails of human-induced pollution, and are important to our understanding of the fate of wild populations facing increasingly complex and stressful environments.

genomics↗

bioRxiv2025

Predictability of preference from acceptance: influence of visual and olfactory stimuli in the Mediterranean fruit fly

Oviposition behavior in phytophagous insects is influenced by different stimuli and plays a key role in pest dynamics and crop loss. This study used 3D-printed artificial fruits varying in colour (yellow, blue, white) and odour (cherry, orange, banana) to test how visual and olfactory cues affect oviposition acceptance (no-choice) and preference (choice). In no-choice assays, the nine artificial fruits displayed sufficiently different visual and olfactory cues to trigger different egg-laying outputs (by a factor 1:3 between the least attractive fruit, white fruit with banana scent and the most attractive fruit, yellow fruit with cherry scent). While cues acted independently in no-choice settings, significant interactions were observed in choice conditions, highlighting multimodal sensory integration. In choice assays, the number of eggs laid and female preference depended on both the characteristics of fruits and their context. However a strong correlation was found between acceptance and preference. The relationship found between acceptance and preference implied that when a fruit seemed preferred in no-choice assays, it was even more preferred in one-choice assays. We finally discussed the practical implications for behavior-based pest management strategies.

animal behavior and cognition↗

bioRxiv2024

Evolution of genetic (co)variances during the worldwide invasion of Drosophila suzukii

The extent to which phenotypic evolution can be constrained by genetic correlations is an important question in evolutionary biology. To address this question, biological invasions are opportune models where derived, invasive populations can be compared to their extant ancestors, allowing to track the evolution of genetic correlations from the ancestor, throughout the invasion process. In this paper, we focused on the worldwide invasion of Drosophila suzukii (Matsumara, 1931), and investigated the evolution of the genetic covariance matrix G of wing shape between ancestral native, and derived invasive populations. Leveraging demographic history resolved by population genetics approaches, we tested whether G remained stable during the invasion. Using a multivariate QST-FST approach, we further tested whether or not the observed phenotypic divergence in wing shape aligned with a neutral scenario of evolution. Our results show moderate yet significant quantitative genetic differentiation of wing shape among D. suzukii populations and a relative stability in the structure of G, presenting a roughly spherical shape but slightly different volumes. These characteristics likely reflect the demographic history of populations and suggest a low level of genetic constraint on wing shape evolution. The divergence between populations was greater than expected under a purely neutral model of evolution, compatible with an effect of divergent selection among them. Overall, our study suggests that selection and drift, but not ancestral genetic constraints, affected the early stages of wing shape evolution during D. suzukii invasion.

evolutionary biology↗

bioRxiv2023

Divergent evolution of head morphology between marine and freshwater sticklebacks

AbstractIntraspecific phenotypic differentiation is of common place occurrence, but the degree to which it reflects phenotypic plasticity or local adaptation remains often unclear. To be considered as adaptive, the differentiation must be genetically based and exceed what could be expected by neutral processes only. Using laboratory reared full-sib family data from replicate nine-spined stickleback (Pungitius pungitius) populations, we show that freshwater and marine fish display genetically based adaptive differentiation in head size and shape. Utilising identity-by-descent relationships among full-sibs as estimated with the aid of molecular markers, we further show that the studied traits are also highly heritable in all populations indicating and that they can respond to future episodes of natural selection. The head shape and size of pond fish suggests that observed adaptive differentiation has been driven by selection favoring limnetic feeding strategy among the pond fish. Analyses of gill-raker morphology were less conclusive: genetic differentiation was found in gill-raker length (pond > marine) and number, but the degree of divergence in these traits did not exceed neutral expectations. Yet, the direction of divergence in gill raker traits are suggestive of the limnetic feeding mode of pond fish, aligning with the inference from the head morphology analyses.

evolutionary biology↗

bioRxiv2023

Heterogeneous genomic architecture of skeletal armour traits in sticklebacks

Whether populations adapt to similar selection pressures using the same underlying genetic variants depends on population history and the distribution of standing genetic variation at the metapopulation level. Studies of sticklebacks provide a case in point: when colonising and adapting to freshwater habitats, three-spined sticklebacks (Gasterosteus aculeatus; TSSs) with high gene flow tend to fix the same adaptive alleles in the same major loci, whereas nine-spined sticklebacks (Pungitius pungitius; NPSs) with limited gene flow tend to utilize a more heterogeneous set of loci. In accordance with this, we report results of quantitative trait locus (QTL) analyses using a F2 back-cross design showing that lateral plate number variation in the western European lineage of NPSs mapped to three moderate-effect QTL, contrary to one major QTL in TSSs and these QTL were different from the four previously identified QTL in the eastern European lineage of NPSs. Furthermore, several QTL were identified associated with variation in lateral plate size, and three moderate-effect QTL with body size. Together, these findings indicate that genetic underpinnings of skeletal armour variation in Pungitius sticklebacks are more polygenic and heterogenous than those in three-spined sticklebacks, indicating limited genetic parallelism underlying armour trait evolution in the family Gasterostidae.

evolutionary biology↗

bioRxiv2023

De novo mutation rates in sticklebacks

Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what is the expected level of genetic diversity in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates ({micro}) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50x) whole genome re-sequencing and a high-quality reference genome. After stringent filtering, we discovered 295 germline mutations from 106 offspring translating to {micro} = 4.64 x 10-9 and {micro} = 4.08 x 10-9 per base, per generation, in the two populations, respectively. Twenty percent of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated {micro} was 3.2 times smaller than the commonly used substitution rate, recalibration with {micro} led to substantial increase in estimated divergence times between different stickleback species. Our estimates of de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

genomics↗

bioRxiv2022

Low heritability of crossover rate in wild sticklebacks

Crossover rate is mostly studied with domesticated or lab-reared populations and little is known about its genetic variation in the wild. We studied the variation and genetic underpinnings of crossover rate in outbred wild nine- (Pungitius pungitius) and three-spined (Gasterosteus aculeatus) sticklebacks. In both species, the crossover rate of females exceeded that of males as did also its repeatability (RFemales =0.21-0.33, RMales=0.026-0.11), implying individual differences of crossover rate in females, but no or less so in males. However, in both species and sexes additive genetic variance and heritability of crossover rate were effectively zero. A review of the previously reported repeatability and heritability estimates revealed that the repeatabilities in stickleback females were moderately high, whereas those in males were very low. Genome-wide association analyses recovered a few candidate regions possibly involved with control of crossover rate. The low additive genetic variance of crossover rate in wild sticklebacks suggest limited evolvability of crossover rate.

evolutionary biology↗

bioRxiv2022

Inbreeding depression in an outbred nine-spined stickleback (Pungitius pungitius) population

Inbreeding depression refers to the reduced fitness of offspring produced by related individuals and is expected to be rare in large outbred populations. When it occurs, marked fitness loss is possible as large populations can carry large loads of recessive harmful mutations which are normally sheltered at the heterozygous state. Using experimental cross data and genome-wide identity-by-descent (IBD) relationships from an outbred marine nine-spined stickleback (Pungitius pungitius) population, we documented a significant decrease in offspring survival probability with increasing parental IBD sharing associated with an average inbreeding load (B) of 15.896. Interestingly, we found that this relationship was also underlined by a positive effect of paternal inbreeding coefficient on offspring survival, suggesting that certain combinations of parental inbreeding and genetic relatedness among mates may promote offspring survival. Apart from demonstrating substantial inbreeding load in an outbred population, the results also highlight the potential caveat associated with artificial establishment of families in experimental studies: wild founder individuals are often - and perhaps mistakenly - assumed to be unrelated.

evolutionary biology↗

bioRxiv2022

Relaxed risk of predation drives parallel evolution of stickleback behaviour

The occurrence of similar phenotypes in multiple independent populations (viz. parallel evolution) is a testimony of evolution by natural selection. Parallel evolution implies that populations share a common phenotypic response to a common selection pressure associated with habitat similarity. Examples of parallel evolution at the genetic and phenotypic levels are fairly common, but the driving selective agents often remain elusive. Similarly, the role of phenotypic plasticity in facilitating early stages of parallel evolution is unclear. We investigated whether the relaxation of predation pressure associated with the colonization of freshwater ponds by nine-spined sticklebacks (Pungitius pungitius) likely explains the divergence in complex behaviours between marine and pond populations, and whether this divergence is parallel. Using laboratory-raised individuals exposed to different levels of perceived predation risk, we calculated vectors of phenotypic divergence for four behavioural traits between habitats and predation risk treatments. We found a significant correlation between the directions of evolutionary divergence and phenotypic plasticity, suggesting that habitat divergence in behaviour is aligned with the response to relaxation of predation pressure. Finally, we show that this alignment is found across multiple pairs of populations, and that the relaxation of predation pressure has likely driven parallel evolution of behaviour in this species.

evolutionary biology↗

bioRxiv2021

Age-dependent genetic architecture underlines similar heritability of body size in sticklebacks

Heritable variation in traits under natural selection is a prerequisite for evolutionary response. While it is recognised that trait heritability may vary spatially and temporally depending under which environmental conditions traits are expressed, less is known about the possibility that genetic variance contributing to the expected selection response in a given trait may vary at different stages of ontogeny. Specifically, whether different loci underlie the expression of a trait throughout development - thus providing an additional source of variation for selection to act on - is unclear. Here we show that the heritability (h2) of body size, an important life history trait, remains constant across ontogeny in a stickleback fish. Nevertheless, both analyses of quantitative trait loci (QTL) and genetic correlations across ages show that different chromosomes/loci contribute to this heritability in different ontogenic time-points. This suggests that body size can respond to selection at different stages of ontogeny but that this response is determined by different loci at different points of development. Hence, this illustrates the notion that diverse genetic architectures may underline similar (expected) phenotypic outcomes, and that similar selection pressures may lead to genetically heterogeneous responses depending on what life stage selection is acting on.

evolutionary biology↗

bioRxiv2021

Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing among full-sibs

Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild outbred populations with high migration rate can impair the estimation of quantitative genetic parameters and bias heritability estimates downwards. On the other hand, the use of a half-sib/full-sib design allowed precise estimation of genetic variance components, and revealed significant additive variance and heritability for all measured traits, with negligible dominance contributions. Genome-partitioning and QTL mapping analyses revealed that most traits had a polygenic basis and were controlled by genes at multiple chromosomes. Furthermore, different QTL contributed to variation in the same traits in different populations suggesting heterogenous underpinnings of parallel evolution at the phenotypic level. Our results provide important guidelines for future studies aimed at estimating adaptive potential in the wild, particularly for those conducted in outbred large-sized populations.

evolutionary biology↗

bioRxiv2019

A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BO_SCPLOWAYC_SCPLOWPO_SCPLOWASSC_SCPLOW. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genes RhoGEF64C and cpo, the latter contributing to natural variation in several life-history traits (including diapause) in Drosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

evolutionary biology↗

bioRxiv2019

Limited plasticity of Drosophila suzukii wing spot size in response to developmental temperature

Phenotypic plasticity is an important mechanism allowing adaptation to new environments and as such it has been suggested to facilitate biological invasions. Under this assumption, invasive populations are predicted to exhibit stronger plastic responses than native populations. Drosophila suzukii is an invasive species whose males harbor a spot on the wing tip. In this study, by manipulating developmental temperature, we compare the phenotypic plasticity of wing spot size of two invasive populations with that of a native population. We then compare the results with data obtained from wild-caught flies from different natural populations. While both wing size and spot size are plastic to temperature, no difference in plasticity was detected between native and invasive populations, rejecting the hypothesis of a role of the wing-spot plasticity in the invasion success. In contrast we observed a remarkable stability in the spot-to-wing ratio across temperatures, as well as among geographic populations. This stability suggests either that the spot relative size is under stabilizing selection, or that its variation might be constrained by a tight developmental correlation between spot size and wing size. Our data show that this correlation was lost at high temperature, leading to an increased variation in the relative spot size, particularly marked in the two invasive populations. This suggests (i) that D. suzukiis development is impaired by hot temperatures, in agreement with the cold-adapted status of this species; (ii) that the spot size can be decoupled from wing size, rejecting the hypothesis of an absolute constraint and suggesting that the wing color pattern might be under stabilizing (sexual) selection; (iii) that such sexual selection might be relaxed in the invasive populations. Finally, a subtle but consistent directional asymmetry in spot size was detected in favor of the right side in all populations and temperatures, possibly indicative of a lateralized sexual behavior.

ecology↗

bioRxiv2019

Limited thermal plasticity and geographic divergence in the ovipositor of Drosophila suzukii

Phenotypic plasticity has been repeatedly suggested to facilitate adaptation to new environmental conditions, as in invasions. Here we investigate this possibility by focusing on the worldwide invasion of Drosophila suzukii: an invasive species that has rapidly colonized all continents over the last decade. This species is characterized by a highly developed ovipositor, allowing females to lay eggs through the skin of ripe fruits. Using a novel approach based on the combined use of SEM and photogrammetry, we quantified the ovipositor size and 3D shape, contrasting invasive and native populations raised at three different developmental temperatures. We found a small but significant effect of temperature and geographic origin on the ovipositor shape, showing the occurrence of both geographic differentiation and plasticity to temperature. The shape reaction norms are in turn strikingly similar among populations, suggesting very little difference in shape plasticity among invasive and native populations, and therefore rejecting the hypothesis of a particular role for plasticity of the ovipositor in the invasion success. Overall, the ovipositor shape seems to be a fairly robust trait, indicative of stabilizing selection. The large performance spectrum rather than the flexibility of the ovipositor would thus contribute to the success of D. suzukii worldwide invasion.

developmental biology↗