The genomic basis of circadian and circalunar timing adaptations in a midge

Abstract

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. ...

Seasonal temperature, the lunar cycle and diurnal rhythms interact in a combinatorial manner to modulate genomic responses to the environment in a reef‐building coral

“…We propose that post‐transcriptional control may be a major theme in the regulation of rhythmic processes in coral, including long‐phase seasonal and lunar cycles. An example of post‐transcriptionally driven patterns of camkII activity over a lunar month has been reported (Kaiser et al, ) and camkII is also differentially expressed in our results (Figure ), indicating this kinase may be a broadly used factor in long‐phase timing systems. The fact that our top DEG showing interactions in expression to all three variables ( mef2 ) is itself known to be regulated by another top gene ( hnrnpa1 , expressed in antiphase to mef2 ) indicates our strongest response identified by RNA‐sequencing may be due to a post‐transcriptional rather than transcriptional mechanism.…”

“…The transcriptional profiles of both hnrnpa1 and hnrnpk can be observed to be approximately in antiphase to the expression of mef2 , and also differ in lunar/temperature responsivity; both hnrnpa1 and hnrnpk show the greatest temperature differences at the full moon phase, while mef2 shows the greatest difference at the new moon (Figure ). Interestingly, post‐transcriptional control in a long‐range rhythm has been described for calmodulin kinase 2 ( camkII ), which has been associated with changes in lunar emergence timing in a marine midge (Kaiser et al, ), Clunio marinus , and this mechanism may be broadly utilized in long‐range timing systems. Post‐transcriptional processes were also the dominant response to lunar phase/hour of the day interactions discussed above (Figure ; Table ).…”

“…These clocks correspond largely to the periodicity of the environmental patterns that entrain them. For example, circadian rhythms drive daily oscillations from sleep–wake cycles (Dijk & Czeisler, ) to mental acuity (Mallis & DeRoshia, ), while longer‐period circalunar and circannual cycles drive reproductive and seasonal patterns (Kaiser et al, ; Sáenz De Miera et al, ). Circadian clocks are well understood and are based on transcription‐initiated processes (Dunlap, ), but the molecular underpinnings of longer cycles remain elusive and much of our knowledge in this regard is limited to hormonal cycles that are probably the terminal mediators of these systems (e.g., Crowder, Meyer, Fan, & Weis, ; Kaniewska, Alon, Karako‐Lampert, Hoegh‐Guldberg, & Levy, ; Takeda et al, ; Tarrant, ; Thorndyke & Goldsworthy, ).…”

Two sides of a coin: ecological and chronobiological perspectives of timing in the wild

“…Consequently, ecologists are keen to quantify chronotype and its repeatability for individuals [93,100,101,[139][140][141][142]. Under strong directional environmental pressure, entire local populations can modify chronotype, as for example observed in marine midges exposed to different tidal regimes [50]. As explained above, a promising future development of studies of chronotype would also measure individual differences in plasticity (slope of the reaction norm), which depending on conditions can confer selective costs or benefits (e.g.…”

“…While the former employs the autoregulatory transcription-translation feedback loop, for the latter, intercellular coupling within the SCN neuronal network is reconfigured [49] (figure 2). Our understanding of interactions of circadian rhythms with rhythms on other time-scales is still in its infancy, but recent years have seen substantial progress [50][51][52]. In addition to circa-rhythms, which approximate geophysical time-scales, biological processes are organized by further internal rhythms with no counterparts in the environment [26].…”