Temporal genomics reveals rapid parallel adaptation in experimental populations of Trinidadian guppies (Poecilia reticulata)

Understanding the genomic basis of early adaptation is a central question in evolutionary biology. Although there is ongoing debate about whether early adaptation is more likely to be driven by polygenic responses or by loci of large effect, few studies of natural populations have been able to address this problem. Furthermore, early adaptation to a novel environment often coincides with founding events, making it difficult to disentangle neutral effects from adaptive genomic changes. Here we take advantage of the unique in situ guppy experimental system, in which we established replicate populations by translocating guppies from a high predation locality to four low predation localities. We present whole genome sequencing from the source population and the four experimental populations, sampled after [~]8-10 generations (first period), and again at [~]18-22 generations (second period). We find signatures of inbreeding only in the first period, despite documented population crashes in the second period. We show genome-wide dynamics of selection as well as selective change at single loci and uncover new targets of selection. Overall, we found signatures of selection at all levels; genome-wide, chromosome, and individual windows are more repeatable among replicates in the first period than in the second period.