Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster.
Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host-microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.
['Rudman|Seth M|SM|0000-0001-5816-2801', 'Greenblum|Sharon|S|', 'Hughes|Rachel C|RC|', 'Rajpurohit|Subhash|S|', 'Kiratli|Ozan|O|', 'Lowder|Dallin B|DB|', 'Lemmon|Skyler G|SG|', 'Petrov|Dmitri A|DA|', 'Chaston|John M|JM|0000-0002-2625-6413', 'Schmidt|Paul|P|']
D000220:Adaptation, Biological D000818:Animals D005075:Biological Evolution D004331:Drosophila melanogaster D005787:Gene Frequency D005828:Genetics, Population D016678:Genome D023281:Genomics D064307:Microbiota D011156:Population Density D012641:Selection, Genetic
microbiome Drosophila melanogaster genomics of adaptation rapid evolution