Around the new or full moon, during a few specific hours surrounding low tide, millions of non-biting midges of the species C. marinus emerge from the sea to perform their nuptial dance. Adults live for only a few hours, during which they mate and oviposit. They must therefore emerge synchronously and-given that embryonic, larval and pupal development take place in the sea-at a time when the most extreme tides reliably expose the larval habitat. The lowest low tides occur predictably during specific days of the lunar month at a specific time of day. Consequently, adult emergence in C. marinus is under the control of circalunar and circadian clocks 1,2 . Notably, although the lowest low tides recur invariably at a given location, their timing differs between geographic locations 3 . Consequently, C. marinus strains from different locations (Extended Data Fig. 1a) show local adaptation in circadian and circalunar emergence times (Extended Data Fig. 1b, c). Crosses between the Jean and Por strains showed that the differences in circadian and circalunar timing are genetically determined 4,5 and largely explained by two circadian and two circalunar quantitative trait loci (QTLs) 6 . Studies on timing variation or chronotypes in animals and humans have often focused on candidate genes from the circadian transcriptiontranslational oscillator. In D. melanogaster, polymorphisms in the core circadian clock genes period, timeless and cryptochrome are associated with adaptive differences in temperature compensation 7 , photo-responsiveness of the circadian clock 8 and emergence rhythms 9 . While these studies offer insights into the evolution of known circadianclock molecules, genome-wide association studies 10,11 and other forward genetic approaches (reviewed in ref. 12) are essential to provide a comprehensive, unbiased assessment of natural timing variation, for instance underlying human sleep-phase disorders. While the adaptive nature of human chronotypes remains unclear, the chronotypes of C. marinus represent evolutionary adaptations to their habitat.Our study aimed to identify the genetic basis of C. marinus adaptation to its specific ecological 'timing niche' . In addition, the genetic dissection of adaptive natural variants of non-circadian rhythms 13 , as also present in C. marinus, may provide an entry point into their unknown molecular mechanisms.As a starting point for these analyses, we sequenced, assembled, mapped and annotated a C. marinus reference genome. The Clunio genome and QTLs for timingOur reference genome CLUMA_1.0 of the Jean laboratory strain contained 85.6 Mb of sequence (Table 1), close to the previous flowcytometry-based estimate of 95 Mb 6 , underlining that chironomids generally have small genomes [14][15][16] . The final assembly has a scaffold N50 of 1.9 Mb. Genome-wide genotyping of a mapping family with restriction-site associated DNA sequencing allowed 92% of the reference sequence to be consistently anchored along a genetic linkage map (Fig. 1a and Extended Data Fig. 2 Table 2). The C. ...
Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.
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