A roadmap for understanding the evolutionary significance of structural genomic variation

Author's accepted manuscriptStructural genomic variants (SVs) take diverse forms and are ubiquitous drivers of ecological and evolutionary processes. Most studies of SVs focus on the adaptive significance of gene duplications and large inversions. Future studies should catalog SVs of all types and sizes and systematically test their evolutionary implications. We propose a roadmap and definitions for the study of SVs in ecological and evolutionary genomics. Best practices for SV detection are needed to facilitate comparisons across studies. Integrating population genomic, theoretical, and experimental approaches to SVs will more comprehensively characterize genomic variation, uncover the adaptive and neutral processes shaping the evolutionary trajectory of SVs, and identify the mechanisms by which SVs impact adaptation and speciation.acceptedVersio

Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation.

Natural selection leaves distinct signatures in the genome that can reveal the targets and history of adaptive evolution. By analysing high-coverage genome sequence data from 4 major colour pattern loci sampled from nearly 600 individuals in 53 populations, we show pervasive selection on wing patterns in the Heliconius adaptive radiation. The strongest signatures correspond to loci with the greatest phenotypic effects, consistent with visual selection by predators, and are found in colour patterns with geographically restricted distributions. These recent sweeps are similar between co-mimics and indicate colour pattern turn-over events despite strong stabilising selection. Using simulations, we compare sweep signatures expected under classic hard sweeps with those resulting from adaptive introgression, an important aspect of mimicry evolution in Heliconius butterflies. Simulated recipient populations show a distinct 'volcano' pattern with peaks of increased genetic diversity around the selected target, characteristic of sweeps of introgressed variation and consistent with diversity patterns found in some populations. Our genomic data reveal a surprisingly dynamic history of colour pattern selection and co-evolution in this adaptive radiation

Evolution: How important is the dimensionality of natural selection in local adaptation?

International audienceOrganisms adapt to their local environments, which may vary in one aspect, or many. A new study shows that such dimensionality matters, as it impacts the magnitude and dynamics of local adaptation, with broader ecological consequences, such as the evolution of generalists

The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838

International audienceWe present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length

Data from: Beyond magic traits: multimodal mating cues in Heliconius butterflies

Species coexistence involves the evolution of reproductive barriers opposing gene flow. Heliconius butterflies display colorful patterns affecting mate choice and survival through warning signaling and mimicry. These patterns are called “magic traits” for speciation because divergent natural selection may promote mimicry shifts in pattern whose role as mating cue facilitates reproductive isolation. By contrast, between comimetic species, natural selection promotes pattern convergence. We addressed whether visual convergence interferes with reproductive isolation by testing for sexual isolation between two closely related species with similar patterns, H. timareta thelxinoe and H. melpomene amaryllis. Experiments with models confirmed visual attraction based on wing phenotype, leading to indiscriminate approach. Nevertheless, mate choice experiments showed assortative mating. Monitoring male behavior toward live females revealed asymmetry in male preference, H. melpomene males courting both species equally while H. timareta males strongly preferred conspecifics. Experiments with hybrid males suggested an important genetic component for such asymmetry. Behavioral observations support a key role for short-distance cues in determining male choice in H. timareta. Scents extracts from wings and genitalia revealed interspecific divergence in chemical signatures, and hybrid female scent composition was significantly associated with courtship intensity by H. timareta males, providing candidate chemical mating cues involved in sexual isolation

Beyond magic traits: multimodal mating cues in <em>Heliconius</em> butterflies

International audienceSpecies coexistence involves the evolution of reproductive barriers opposing gene flow. Heliconius butterflies display colorful patterns affecting mate choice and survival through warning signaling and mimicry. These patterns are called "magic traits" for speciation because divergent natural selection may promote mimicry shifts in pattern whose role as mating cue facilitates reproductive isolation. By contrast, between comimetic species, natural selection promotes pattern convergence. We addressed whether visual convergence interferes with reproductive isolation by testing for sexual isolation between two closely related species with similar patterns, H. timareta thelxinoe and H. melpomene amaryllis. Experiments with models confirmed visual attraction based on wing phenotype, leading to indiscriminate approach. Nevertheless, mate choice experiments showed assortative mating. Monitoring male behavior toward live females revealed asymmetry in male preference, H. melpomene males courting both species equally while H. timareta males strongly preferred conspecifics. Experiments with hybrid males suggested an important genetic component for such asymmetry. Behavioral observations support a key role for short-distance cues in determining male choice in H. timareta. Scents extracts from wings and genitalia revealed interspecific divergence in chemical signatures, and hybrid female scent composition was significantly associated with courtship intensity by H. timareta males, providing candidate chemical mating cues involved in sexual isolation

Searching for intra-locus sexual conflicts in the three-spined stickleback (Gasterosteus aculeatus) genome

International audienceDifferences between sexes in trait fitness optima can generate intra-locus sexual conflicts that have the potential to maintain genetic diversity through balancing selection. However, these differences are unlikely to be associated with strong selective coefficients and are challenging to detect. Additionally, recent studies have highlighted that duplications on sexual chromosomes can create artefactual signals of intra-locus sexual conflicts. Thus, testing the relationship between intra-locus sexual conflicts and balancing selection requires stringent filtering of duplicated regions, and dedicated methods to detect loci with low levels of intersex differentiation. In this study, we investigated intra-locus sexual conflicts in the three-spined stickleback using whole genome sequencing (mean coverage = 12X) of 50 females and 49 males from an anadromous population in the St. Lawrence River, Québec, Canada. After stringent filtering of duplications from the sex chromosomes, we compared three methods to detect intra-locus sexual conflicts. We found only two genomic regions under potential intra-locus sexual conflict that also showed signals of balancing selection. Overall, our results suggest that most intra-locus sexual conflicts do not drive long-term balancing selection and are most likely transient

A roadmap for understanding the evolutionary significance of structural genomic variation

Structural genomic variants (SVs) are ubiquitous and play a major role in adaptation and speciation. Yet, comparative and population genomics have focused predominantly on gene duplications and large-effect inversions. The lack of a common framework for studying all SVs is hampering progress towards a more systematic assessment of their evolutionary significance. Here we (i) review how different types of SVs affect ecological and evolutionary processes; (ii) suggest unifying definitions and recommendations for future studies; and (iii) provide a roadmap for the integration of SVs in ecoevolutionary studies. In doing so, we lay the foundation for population genomics, theoretical, and experimental approaches to understand how the full spectrum of SVs impacts ecological and evolutionary processes

Data from: Mimicry refinement: Phenotypic variations tracking the local optimum

1. Müllerian mimicry between chemically defended preys is a textbook example of natural selection favouring phenotypic convergence onto a shared warning signal. Studies of mimicry have concentrated on deciphering the ecological and genetic underpinnings of dramatic switches in mimicry association, producing a well-known mosaic distribution of mimicry patterns across geography. However, little is known about the accuracy of resemblance between natural co-mimics when the local phenotypic optimum varies. 2. In this study, using analyses of wing shape, pattern and hue, we quantify multimodal phenotypic similarity between butterfly co-mimics sharing the so-called postman pattern in different localities with varying species composition. 3. We show that subtle but consistent variation between populations of the localised species, Heliconius timareta thelxinoe, enhance resemblance to the abundant co-mimics which drive the mimicry in each locality. 4. Those results suggest that rarer co-mimics track the changes in the phenotypic optimum caused by gradual changes in the composition of the mimicry community, providing insights into the process by which intra-specific diversity of mimetic pattern may arise. Furthermore, our results suggest a multimodal evolution of similarity, with coordinated convergence in different features of the phenotype such as wing outline, pattern and hue. 5. Finally, multilocus genotyping allows estimating local hybridization rates between H. timareta and co-mimic H. melpomene in different populations, raising the hypothesis that mimicry refinement between closely-related co-mimics may be enhanced by adaptive introgression at loci modifying the accuracy of resemblance

Adh_unphased_Dryad_march18

Sequences of Adh locus aligned and unphase