Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species

Abstract

Adaptive introgression is ubiquitous in animals but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during one year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes, and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after four years (~ 60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically-distinct and reproductively-isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step towards understanding the genome-wide dynamics of speciation-through-introgression.

Genomic islands of divergence betweenDrosophila yakubasubspecies predominantly overlap with chromosomal inversions

“…The Nanopore MinION run has generated 143 587 reads with a N50 of 33,25 kb and with the final assembly we had obtained 563 fragments with an N50 of 6,9Mb, and a BUSCOv5 score of 99,5% (Manni et al 2021). We aligned the D. y. mayottensis assembly on a novel assembly of the West-African reference D. y. yakuba strain that was assembled using the same hybrid Nanopore-Illumina approach (Miller et al 2018; David et al 2022) (Figure 2A). This new assembly corrects the order of genes falling between 8,586,415 and 11,101,068 on chromosomal arm 2L (Figure S1).…”

“…Alignment of Drosophila yakuba mayottensis genome on (A) Drosophila yakuba on a new assemby of the reference genome correcting previous early missassemblies (David et al 2022) and (B) D. y. yakuba from Kenya NY73PB (Assembly GCA_016746335.2). Each colour represents a scaffold obtained during D. y. mayottensis reconstruction.…”

“…DNA sequences, from Nanopore and Illumina technologies, were then assembled using MaSuRCA genome assembler software v3.4.0 (Zimin et al 2013). We aligned our newly constructed D. y. mayottensis genome using minimap2 software package to a newly assembled genome of the reference D. yakuba strain (David et al 2022) in order to correct for early missassemblies in the v.1.05 reference genome (Miller et al 2019). D. y. mayottensis scaffolds were then ordered and oriented according to the reference genome, and chromosomal rearrangements were visually detected from a dotplot constructed by R. The newly constructed D. y. mayottensis genome was also aligned, following the same methodology, with a genome of D. y. yakuba (strain NY73PB, NCBI Assembly GCA_016746335.2) from Kenya, which differs from the reference genome in two rearrangements, namely 2Ll and 2Rj , to highlight inversions specific to the population of the island of Mayotte from those that could be polymorphic in D. y. yakuba .…”

“…DNA sequences, from Nanopore and Illumina technologies, were then assembled using MaSuRCA genome assembler software v3.4.0 (Zimin et al 2013). We aligned our newly constructed D. y. mayottensis genome using minimap2 software package to a newly assembled genome of the reference D. yakuba strain (David et al 2022) in order to correct for early missassemblies in the v.1.05 reference genome (Miller et al 2019)…”

“…In the recent article by David et al (2022), the word “up‐regulation of Gug” should be replaced by "down‐regulation of Gug" in the fourth paragraph of Discussion section.…”