Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin’s finches, suggesting that similar features are important for evolution across diverse taxa.

Co-option of transposable elements (TEs) to become part of existing or new enhancers is an important mechanism for evolution of gene regulation. However, contributions of lineage-specific TE insertions to recent regulatory adaptations remain poorly understood. Gibbons present a suitable model to study these contributions as they have evolved a lineage-specific TE called LAVA (LINE-AluSz-VNTR-AluLIKE), which is still active in the gibbon genome. The LAVA retrotransposon is thought to have played a role in the emergence of the highly rearranged structure of the gibbon genome by disrupting transcription of cell cycle genes. In this study, we investigated whether LAVA may have also contributed to the evolution of gene regulation by adopting enhancer function. We characterized fixed and polymorphic LAVA insertions across multiple gibbons and found 96 LAVA elements overlapping enhancer chromatin states. Moreover, LAVA was enriched in multiple transcription factor binding motifs, was bound by an important transcription factor (PU.1), and was associated with higher levels of gene expression in cis. We found gibbon-specific signatures of purifying/positive selection at 27 LAVA insertions. Two of these insertions were fixed in the gibbon lineage and overlapped with enhancer chromatin states, representing putative co-opted LAVA enhancers. These putative enhancers were located within genes encoding SETD2 and RAD9A, two proteins that facilitate accurate repair of DNA double-strand breaks and prevent chromosomal rearrangement mutations. Co-option of LAVA in these genes may have influenced regulation of processes that preserve genome integrity. Our findings highlight the importance of considering lineage-specific TEs in studying evolution of gene regulatory elements.

High-throughput sequencing data enables the comprehensive study of genomes and the variation therein. Essential for the interpretation of this genomic data is a thorough understanding of the computational methods used for processing and analysis. Whereas “gold-standard” empirical datasets exist for this purpose in humans, synthetic (i.e., simulated) sequencing data can offer important insights into the capabilities and limitations of computational pipelines for any arbitrary species and/or study design—yet, the ability of read simulator software to emulate genomic characteristics of empirical datasets remains poorly understood. We here compare the performance of six popular short-read simulators—ART, DWGSIM, InSilicoSeq, Mason, NEAT, and wgsim—and discuss important considerations for selecting suitable models for benchmarking.

Transposable elements (TEs) can shape gene regulation networks by being co-opted as enhancers.However, the contribution of lineage-specific TE insertions to recent adaptations remains poorly understood. Gibbons present a suitable model to study these contributions, as they have evolved many distinct traits, including heavily rearranged genomes and a novel TE called LAVA. The LAVA retrotransposon is still active in the gibbon genome and is thought to have contributed to evolution of gibbon-specific traits. In this study, we characterized fixed and polymorphic LAVA insertions across multiple gibbon genomes and found that 10% of all LAVA elements overlap chromatin states associated with enhancer function. Moreover, LAVA was enriched in multiple transcription factor motifs, was bound by the important lymphoid transcription factor PU.1, and was associated with higher levels of gene expression in cis. Interestingly, despite the highly similar genomic distribution and epigenetic characteristics of fixed and polymorphic LAVA, only fixed LAVA insertions showed strong signatures of positive selection, and were enriched near genes implicated in DNA repair. Altogether, our population genetics, epigenetics, and evolutionary analyses indicate that several LAVA insertions have been coopted in the gibbon genome as cis-regulatory elements. Specifically, a subset of the fixed LAVA insertions appear to have been co-opted to enhance regulation of DNA repair genes, likely as an adaptive mechanism to improve genome integrity in response to the genomic rearrangements occurring in the gibbon lineage. evolution of gene-regulatory adaptations remains poorly understood, especially in non-human primates.Among primates, the endangered gibbons (Hylobatidae) present an attractive model for exploring functional contributions of a lineage-specific TE. Gibbons (or small apes) have an intriguing evolutionary history, and have evolved many unique traits [e.g. locomotion via brachiating, monogamy, etc. (9)]. Most notably, the gibbon lineage has experienced drastic genomic rearrangements since its divergence from the common Hominidae ancestor ~17 million years ago (mya) (10). These evolutionary rearrangements are not only evident through comparisons with great ape genomes, but also in the vastly different karyotypes of the four extant gibbon genera: Nomascus (2n=52), Hylobates (2n=44), Hoolock (2n=38) and Siamang (2n=50), which split only 5 mya. The factors leading to these evolutionary genome reorganizations are not fully understood, but a gibbon-specific retrotransposon, called LAVA (Fig. 1A), may have played a role (11).The LAVA element is a non-autonomous composite retrotransposon consisting of portions of repeats found in most primate genomes (CT-rich, Alu-like, a truncated SVA element, and portions of AluSz and L1ME5 elements), but the fully assembled element is only found among gibbons (12, 13). In the original analysis of the reference gibbon genome, which was derived from a northern white-cheeked gibbon (Nomascus leucogenys), nearly half of ...