bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440113; this version posted April 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Polygenic adaptation from standing genetic variation allows rapid ecotype formation Nico Fuhrmann, Celine Prakash, Tobias S. Kaiser* Max Planck Institute for Evolutionary Biology, Max Planck Research Group Biological Clocks, August-Thienemann-Strasse 2, 24306 Plön, Germany *
[email protected] Abstract Adaptive ecotype formation is the first step to speciation, but the genetic underpinnings of this process are poorly understood. While in marine midges of the genus Clunio (Diptera) re- production generally follows a lunar rhythm, we here characterize two lunar-arrhythmic eco- types. Analysis of 168 genomes reveals a recent establishment of these ecotypes, reflected in massive haplotype sharing between ecotypes, irrespective of whether there is ongoing gene flow or geographic isolation. Genetic analysis and genome screens reveal patterns of poly- genic adaptation from standing genetic variation. Ecotype-associated loci prominently include circadian clock genes, as well as genes affecting sensory perception and nervous system de- velopment, hinting to a central role of these processes in lunar time-keeping. Our data show that adaptive ecotype formation can occur rapidly, with ongoing gene flow and largely based on a re-assortment of existing and potentially co-adapted alleles. Keywords: Local adaptation, reproductive timing, lunar rhythm, biological clocks, sympat- ric speciation, gene flow, Chironomidae, marine ecology 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440113; this version posted April 18, 2021.