Meiotic, genomic and evolutionary properties of crossover distribution in Drosophila yakuba

Patterns of crossover distribution in Drosophila mauritiana necessitate a re-thinking of the centromere effect on crossing over

We present an SNP-based crossover map for Drosophila mauritiana. Using females derived by crossing 2 different strains of D. mauritiana, we analyzed crossing over on all 5 major chromosome arms. Analysis of 105 male progeny allowed us to identify 327 crossover chromatids bearing single, double, or triple crossover events, representing 398 crossover events. We mapped the crossovers along these 5 chromosome arms using a genome sequence map that includes the euchromatin-heterochromatin boundary. Confirming previous studies, we show that the overall crossover frequency in D. mauritiana is higher than is seen in Drosophila melanogaster. Much of the increase in exchange frequency in D. mauritiana is due to a greatly diminished centromere effect. Using larval neuroblast metaphases from D. mauritiana-D. melanogaster hybrids we show that the lengths of the pericentromeric heterochromatin do not differ substantially between the species, and thus cannot explain the observed differences in crossover distribution. Using a new and robust maximum likelihood estimation tool for obtaining Weinstein tetrad distributions, we observed an increase in bivalents with 2 or more crossovers when compared with D. melanogaster. This increase in crossing over along the arms of D. mauritiana likely reflects an expansion of the crossover-available euchromatin caused by a difference in the strength of the centromere effect. The crossover pattern in D. mauritiana conflicts with the commonly accepted view of centromeres as strong polar suppressors of exchange (whose intensity is buffered by sequence nonspecific heterochromatin) and demonstrates the importance of expanding such studies into other species of Drosophila.

Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape

During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 23 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twenty one GIDs (~99% of outlier windows) fell in low recombining regions or subspecies-specific inversions. However, only two GIDs were in collinear, normally recombining regions suggesting a signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni-specialist, is known to be homosequential with its generalist relatives. Thus, whereas structural variation may disproportionally shape GIDs in some species, striking parallel adaptations can occur between species despite distinct genomic architectures.

Clonal ants reveal a potentially hidden meiotic feature

Meiosis is essential for eukaryotic reproduction and provides the basis for Mendel's segregation laws. A recent study by Lacy et al. identified a significant deviation from these laws in a clonal ant, hinting at a potentially overlooked meiotic feature. This discovery may have broader implications for recombination in nonclonal eukaryotes.

Background selection under evolving recombination rates

Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.