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The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south-eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high-coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes. The data are consistent with repeated ecological divergence in H. pusillum, uncovering up to five polytopic origins of one ecotype from the other. A complex evolutionary history is evidenced, with local isolation-with-migration in two population pairs and intra-ecotype migration in two others. In all cases, the time of divergence or secondary contact was inferred as postglacial. A metagenomic analysis on exogenous contaminant RAD sequences suggests divergent microbial communities between the ecotypes. The lack of shared genomic regions of high divergence across population pairs illustrates the action of drift and/or local selection in shaping genetic divergence across repeated cases of ecological divergence., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.

Repeated adaptation, also known as parallel or convergent evolution, occurs when different lineages successfully respond to similar environmental challenges. If the same genes are used by independent lineages during repeated adaptation ('gene reuse'), the genetic basis of adaptation might be predictable. Recent genomic studies have highlighted that there is variability in the extent of gene reuse among lineages experiencing repeated adaptation. Divergence time is a promising factor influencing variation in gene reuse in repeated adaptation, as it drives the diversification of shared genetic variation, genome structure, and gene functions among lineages. Genomic studies of repeated adaptation support the idea that gene reuse decreases with increasing divergence time. However, the relationship is complex, emphasizing the need for additional research to better understand evolutionary repeatability. When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability. [ABSTRACT FROM AUTHOR]

Understanding the molecular basis of repeated evolution improves our ability to predict evolution across the tree of life. Only since the last decade has high‐throughput sequencing enabled comparative genome scans to thoroughly examine the repeatability of genetic changes driving repeated phenotypic evolution. The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), and the European corn borer (ECB), Ostrinia nubilalis (Hübner), are two closely related moths displaying repeatable phenological adaptation to a wide range of climates on two separate continents, largely manifesting as changes in the timing of diapause induction and termination across latitude. Candidate genes underlying diapause variation in North American ECB have been previously identified. Here, we sampled seven ACB populations across 23 degrees of latitude in China to elucidate the genetic basis of diapause variation and evolutionary mechanisms driving parallel clinal responses in the two species. Using pooled whole‐genome sequencing (Pool‐seq) data, population genomic analyses revealed hundreds of single nucleotide polymorphisms (SNP) whose allele frequencies covaried with mean diapause phenotypes along the cline. Genes involved in circadian rhythm were over‐represented among candidate genes with strong signatures of spatially varying selection. Only one of two circadian clock genes associated with diapause evolution in ECB showed evidence of reuse in ACB (period [per]), but per alleles were not shared between species nor with their outgroup, implicating independent mutational paths. Nonetheless, evidence of adaptive introgression was discovered at putative diapause loci located elsewhere in the genome, suggesting that de novo mutations and introgression might both underlie the repeated phenological evolution. [ABSTRACT FROM AUTHOR]

Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological, or molecular level. Here, we show that the vertebral stripe, a cryptic color pattern, has evolved hundreds of times in the evolutionary history of anurans (frogs and toads) and is favored in terrestrial habitats. Using a genome-wide association study, we demonstrate that variation near the Agouti signaling protein gene (ASIP) is responsible for the different vertebral stripe phenotypes in the African grass frog Ptychadena robeensis. RNAseq and real-time quantitative PCR revealed that differential expression of the gene and an adjacent long non-coding RNA is linked to patterning in this species. Surprisingly, and although the stripe phenotypes are shared with closely related species, we found that the P. robeensis alleles are private to the species and unlikely to evolve under long-term balancing selection, thus indicating that the vertebral stripe phenotypes result from parallel evolution within the group. Our findings demonstrate that this cryptic color pattern evolved rapidly and recurrently in terrestrial anurans, and therefore constitutes an ideal system to study repeated evolution. [ABSTRACT FROM AUTHOR]

The multitude of herbicide resistance patterns that have evolved in different weed species is a remarkable example of the rapid adaptation to anthropogenic‐driven disturbance. Recently, resistance to glyphosate was identified in multiple populations of Lolium multiflorum in Oregon. We used phenotypic approaches, as well as population genomic and gene expression analyses, to determine whether known mechanisms were responsible for glyphosate resistance and whether resistance phenotypes evolved independently in different populations, and to identify potential loci contributing to resistance. We found no evidence of genetic alterations or expression changes at known target and non‐target‐site resistance mechanisms of glyphosate. Population genomic analyses indicated that resistant populations tended to have largely distinct ancestry from one another, suggesting that glyphosate resistance did not spread among populations by gene flow. Rather, resistance appears to have evolved independently on different genetic backgrounds. We also detected potential loci associated with the resistance phenotype, some of which encode proteins with potential effects on herbicide metabolism. Our results suggest that Oregon populations of L. multiflorum evolved resistance to glyphosate due to a novel mechanism. Future studies that characterize the gene or genes involved in resistance will be necessary to confirm this conclusion. [ABSTRACT FROM AUTHOR]

A major goal of evolutionary biology is to identify the genotypes and phenotypes that underlie adaptation to divergent environments. Stickleback fish, including the threespine stickleback (Gasterosteus aculeatus) and the ninespine stickleback (Pungitius pungitius), have been at the forefront of research to uncover the genetic and molecular architecture that underlies phenotypic diversity and adaptation. A wealth of quantitative trait locus (QTL) mapping studies in sticklebacks have provided insight into longstanding questions about the distribution of effect sizes during adaptation as well as the role of genetic linkage in facilitating adaptation. These QTL mapping studies have also provided a basis for the identification of the genes that underlie phenotypic diversity. These data have revealed that mutations in regulatory elements play an important role in the evolution of phenotypic diversity in sticklebacks. Genetic and molecular studies in sticklebacks have also led to new insights on the genetic basis of repeated evolution and suggest that the same loci are involved about half of the time when the same phenotypes evolve independently. When the same locus is involved, selection on standing variation and repeated mutation of the same genes have both contributed to the evolution of similar phenotypes in independent populations. This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. [ABSTRACT FROM AUTHOR]