The asexual genome of Drosophila

TL;DR

This study reveals that the Drosophila genome exhibits two distinct evolutionary modes influenced by recombination rates, with low-recombining regions showing characteristics of asexual evolution, affecting gene function and genome architecture.

Contribution

It is the first systematic demonstration of clonal interference and asexual-like evolution within a multicellular eukaryote genome, linked to recombination rate variation.

Findings

Approximately 20% of the genome is in an asexual-like interference condensate.

Regions in the condensate show reduced efficacy of selection and higher genetic load.

The transition between evolutionary modes correlates with recombination rate thresholds.

Abstract

The rate of recombination affects the mode of molecular evolution. In high-recombining sequence, the targets of selection are individual genetic loci; under low recombination, selection collectively acts on large, genetically linked genomic segments. Selection under linkage can induce clonal interference, a specific mode of evolution by competition of genetic clades within a population. This mode is well known in asexually evolving microbes, but has not been traced systematically in an obligate sexual organism. Here we show that the Drosophila genome is partitioned into two modes of evolution: a local interference regime with limited effects of genetic linkage, and an interference condensate with clonal competition. We map these modes by differences in mutation frequency spectra, and we show that the transition between them occurs at a threshold recombination rate that is predictable from genomic summary statistics. We find the interference condensate in segments of low-recombining sequence that are located primarily in chromosomal regions flanking the centromeres and cover about 20% of the Drosophila genome. Condensate regions have characteristics of asexual evolution that impact gene function: the efficacy of selection and the speed of evolution are lower and the genetic load is higher than in regions of local interference. Our results suggest that multicellular eukaryotes can harbor heterogeneous modes and tempi of evolution within one genome. We argue that this variation generates selection on genome architecture.