  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.
