Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Abstract

Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster , in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

Immunity to infections in arboviral vectors by integrated viral sequences: an evolutionary perspective

“…aegypti is estimated between 52-67 Kb (Matthews et al, 2018). Windows in the top 15% most extreme G12 values were selected and analyzed for the presence of viral integrations (Rech et al, 2019).…”

“…Selection in fixed nrEVEs was also tested by calculating Tajima's D values (Tajima, 1989), a procedure previously applied to test for selection in fixed TEs (Kofler et al, 2012;Rech et al, 2019).…”

“…Tajima's D values were calculated in non-overlapping 500 bp windows using vcftools v.0.1.15 (Danecek et al, 2011). The approach of Rech et al, (2019) Supplementary Table 9). Finally, significant windows were screened for the presence of nrEVEs.…”

“…6C). Rha44 and Rha69 are fixed in the populations where hard sweep was predicted; Rha53 is close to fixation in American Samoa (Freq= 0.938), supporting the hypothesis that the increase in frequency of these three nrEVEs is likely due to positive selection.Adaptive evolution at viral integrations was also tested by estimating Tajima´s D statistics genomewide and verifying if nrEVEs map in windows with significantly negative Tajima´s D values(Koefler et al, 2012;Rech et al, 2019). Tajima's D compares the polymorphism and the segregating sites in a region under the premises of the neutral evolution theory: a low Tajima's D value occurs in presence of an excess of low frequency variants resulting from a bottleneck or a selective sweep; on the contrary a value of Tajima's D significantly higher than 0 indicates a scarcity of rare variants, interpreted as balancing selection or recent population admixture(Stephan, 2019).…”

RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements

“…For example, transposon-derived sequences contribute to the transcriptome by providing alternatively spliced exons [6,7]. By contributing transcription factor binding sites, promoters, and distal regulatory elements, co-opted transposons are involved in rewiring of regulatory networks and drive regulatory innovation [7][8][9][10][11][12][13][14][15]. Importantly, a sizeable portion of evolutionarily constrained regions arose from ancestral transposon sequences [16,17].…”