It is widely documented that hybridisation occurs between many closely related species, but the importance of introgression in adaptive evolution remains unclear, especially animals. Here, we have examined role introgressive transferring adaptations mimetic Heliconius butterflies, taking advantage recent identification a gene regulating red wing patterns this genus. By sequencing regions both linked and unlinked to colour locus, found region displays an almost perfect genotype by phenotype...

Although single-nucleotide polymorphism (SNPs) were initially thought to make-up the majority of selectable variation (Morin, Luikart, & Wayne, 2004; Sachidanandam et al., 2001), it is becoming increasingly recognized that structural represents a significant, yet often poorly understood, source genetic variation. It only within past 10 years, aided by development genomic technologies such as high throughput and later third generation sequencing, extent intra- interspecific has been...

Abstract How natural diversity is maintained an evolutionary puzzle. Genetic variation can be eroded by drift and directional selection but some polymorphisms persist for long time periods, implicating a role balancing selection. Here, we investigate the maintenance of chromosomal inversion polymorphism in seaweed fly Coelopa frigida . Using experimental evolution quantifying fitness, show that underlies life-history trade-off, whereby each haplotype has opposing effects on larval survival...

Abstract Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge evolution has largely been acquired by means single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role structural (SVs) particularly that CNVs overlooked wild populations, partly due to their challenging identification. Here, we document usefulness Rapture, derived reduced‐representation shotgun sequencing approach, detect investigate...

Abstract Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning ecosystems. Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast comprehensive monitoring entire ecosystems, but widespread adoption this technique requires performance evaluations compare it conventional surveys. We compared eDNA trawling data evaluate their efficiency...

Natural selection leaves distinct signatures in the genome that can reveal targets and history of adaptive evolution. By analysing high-coverage sequence data from 4 major colour pattern loci sampled nearly 600 individuals 53 populations, we show pervasive on wing patterns Heliconius radiation. The strongest correspond to with greatest phenotypic effects, consistent visual by predators, are found geographically restricted distributions. These recent sweeps similar between co-mimics indicate...

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation reside in the heterogeneity recombination along genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci potentially massive scale. In this study, we examined how inversions...

Species coexistence involves the evolution of reproductive barriers opposing gene flow. Heliconius butterflies display colorful patterns affecting mate choice and survival through warning signaling mimicry. These are called "magic traits" for speciation because divergent natural selection may promote mimicry shifts in pattern whose role as mating cue facilitates isolation. By contrast, between comimetic species, promotes convergence. We addressed whether visual convergence interferes with...

Abstract Chromosomal inversions have been implicated in facilitating adaptation the face of high levels gene flow, but whether chromosomal fusions also similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not case for tributaries Miramichi River North America. To resolve genetic relationships between populations system and known to contribute adaptation, we genotyped 728 juvenile using a 50...

The process by which species evolve can be illuminated investigating barriers that limit gene flow between taxa. Recent radiations, such as Heliconius butterflies, offer the opportunity to compare isolation pairs of taxa at different stages ecological, geographical, and phylogenetic divergence. Here, we report a comparative analysis existing novel data in order quantify strength direction isolating within well-studied clade . Our results highlight increased divergence is associated with...

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding evolutionary mechanisms impending or favouring in presence is still limited to a restricted number study systems. In this study, we examined how demographic history, shared ancestral...

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture speciation. Of particular interest is our recent ability consider wider range genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into speciation how different types are involved in...

Emma L. Berdan1,2, Thomas G. Aubier3,4, Salvatore Cozzolino5, Rui Faria6,7, Jeffrey Feder8, Mabel D. Giménez9,10, Mathieu Joron11, Jeremy B. Searle12 and Claire Mérot13 1Department of Marine Sciences, Gothenburg University, 40530, Sweden 2Bioinformatics Core, Department Biostatistics, Harvard T.H. Chan School Public Health, Medical School, Boston, Massachusetts 02115, USA 3Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse,...

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and known to contribute evolutionary processes in various organisms. However, they inherently difficult detect genotype from readily available short-read sequencing data, therefore remain poorly documented wild populations. Salmonid species displaying strong interpopulation variability both life history traits habitat characteristics, such Atlantic salmon (

Large chromosomal rearrangements are thought to facilitate adaptation heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in along environmental clines and ecotype specialization. Here, we combine classical ecological studies population genetics investigate an inversion polymorphism previously documented Europe among natural populations of the seaweed fly Coelopa frigida a latitudinal cline North America. We test if is present America...

Abstract Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose CNVs could be used infer neutral adaptive population structure, whose study has been restricted microsatellites,...

The study of phylogeography has transitioned from mitochondrial haplotypes to genome-wide analyses, borrowing population genomics methods along the way. Whole-genome sequencing allows both and nuclear DNA provides density markers investigate recombination genome. This level resolution could unravel complex histories admixture between lineages, which are commonly observed in species evolving recently deglaciated habitats. In this study, we sequenced 1120 Arctic Char genomes 33 populations...

Butterflies in the genus Heliconius have undergone rapid adaptive radiation for warning patterns and mimicry, are excellent models to study mechanisms underlying diversification. In Heliconius, mimicry rings typically involve distantly related species, whereas closely species often join different rings. Genetic behavioural studies n how reproductive isolation many pairs of taxa is largely mediated by natural sexual selection on wing colour patterns. However, recent uncovered new cases which...

Mimetic resemblance in unpalatable butterflies has been studied by evolutionary biologists for over a century, but largely focused on the convergence wing color patterns. In Heliconius numata, discrete color-pattern morphs closely resemble comimics distantly related genus Melinaea. We examine possibility that shape of butterfly also shows adaptive convergence. First, simple measures forewing dimensions were taken individuals cross between H. numata morphs, and showed quantitative differences...

Abstract Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, complexity, resulting from structural variants, paralogous sequences, repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading SNPs that deviate Mendelian expected patterns of heterozygosity allelic ratio....

Brook trout (Salvelinus fontinalis) is a socioeconomically important fish species for fisheries, aquaculture and aquatic conservation. We produced 2.5 Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- long-read sequencing of fully homozygous mitotic gynogenic doubled haploid fish, which facilitates highly complex salmonid genomes. The has an N50 50.98 Mb 88.9% the total assembled sequence length anchored into 42 main chromosomes, 63.44%...

Chromosomal inversions which form blocks of linked genes are increasingly recognized for their role in maintaining intra-specific diversity. They predicted to be relevant genetic architectures local adaptation the face gene flow. However, pinpointing underlying traits and functional mechanisms under selection remains challenging. The seaweed fly Coelopa frigida harbors several large polymorphic inversions, one (Cf-Inv(4.1)) displays a latitudinal cline frequencies along North American...