Unravelling the sensory and genomic underpinnings of circalunar versus circasemilunar clocks in Clunio marinus
Over the last decades, advances in sequencing technologies have brought insights into the genomic architecture of adaptive traits. Structural variants (SVs) are large genetic variants including deletions, duplications and inversions. Although their role in adaptive evolution is becoming evident, it is still poorly understood. In-depth exploration of genomes of different species and traits is thus necessary. Clunio marinus is a marine midge that inhabits intertidal regions of the Atlantic coast, with populations showing local adaptations in their emergence timing to coincide with the local times of low tides. The timing of emergence is controlled by circadian and circalunar clocks, although the genetic basis of the latter remains unknown. In my thesis, I have studied the sensory and genomic underpinnings of the circalunar versus circasemilunar clocks of C. marinus.
Chapter I explores the mechanisms that mediate entrainment by moonlight. This project shed light on crucial aspects that set the phase of the circalunar and circasemilunar clocks and lays the foundation for dissecting the genetic basis of these clocks. In Chapter II, I focus on the genomic architecture of emergence phenotypes by characterizing the SV landscape of C. marinus and finding genomic variants associated with the circalunar and circadian phenotypes. I show that many of the candidate alleles fall within known circadian clock genes. In Chapter III, I focused on the role of inversions in local adaptation of C. marinus. This work revealed putative direct effects of inversion breakpoints and indirect effects, with frequencies of some inversions varying with latitude.
This thesis provides a characterization of 1) moonlight entrainment mechanisms, 2) the genomic architecture of circalunar vs. circasemilunar clocks, and 3) candidate genes, genomic regions and inversions that can be further validated for their role in local adaptation.
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