Repeated evolution of circadian clock dysregulation in cavefish populations

Abstract

16Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for 17 survival in diverse environments. Organisms inhabiting environments with arrhythmic days, such 18 as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to 19 changing ecological pressures. Here we demonstrate that the cave environment has led to the 20 repeated disruption of the biological clock across multiple populations of Mexican cavefish, with 21 the circadian transcriptome showing widespread reductions in rhythmicity and changes to the 22 timing of the activation/repression of genes in the core pacemaker. Then, we investigate the 23 function of two genes with decreased rhythmic expression in cavefish. Mutants of these genes 24 phenocopy reductions in sleep seen in multiple cave populations, suggesting a link between 25 circadian dysregulation and sleep reduction. Altogether, our results reveal that evolution in an 26 arrhythmic environment has resulted in dysregulation to the biological clock across multiple 27 populations by diverse molecular mechanisms. 28 29 30 degenerate eyes 19-21 , reduced pigmentation 22-25 , and changes in metabolism and behavior 26-35 . 53 Circadian rhythms and sleep behavior are also substantially altered in cavefish 27,36-38 . While 54 cavefish largely maintain locomotor and physiological rhythms in light-dark conditions, many 55 populations show loss of these rhythms under constant darkness [36][37][38][39][40][41] . Cavefish populations have 56 also convergently evolved a drastic reduction in sleep compared to surface fish 27 . Alterations can 57 also be seen at the molecular level; an examination of clock genes (per1, per2, cry1a) in cave 58 and surface fish found changes in the expression level and timing of activation of these genes in 59 multiple cave populations. 36 Consequently, the Mexican tetra provides a unique opportunity to 60 4 study the evolutionary response of the biological clock and circadian rhythms to the arrhythmic 61 cave environment across multiple cave populations. 62 63 In vertebrates, circadian rhythms are regulated by transcriptional feedback loops, where clock 64 proteins directly or indirectly regulate the expression of the genes from which they are 65 transcribed. The feedback loops of the circadian clock result in oscillations of gene expression of 66 ~24 hours 42 . These oscillating transcripts make up the "circadian transcriptome" and are a 67 substantial source of rhythmic physiology and behavior 43-45 . The conserved nature of the 68 biological clock in vertebrates make comparative studies extremely powerful. Even across 69 evolutionary timescales, many clock genes and downstream regulators of circadian behavior 70 maintain similar functions. 45 While many species of cave-dwelling organisms show evidence of 71 weakened or absent locomotor rhythms 46-52 , no global analysis of transcriptional changes 72 associated with clock evolution has been performed in any cave species, including A. mexicanus. 73 Compari...

Enhanced lipogenesis through Pparγ helps cavefish adapt to food scarcity

“…Our finding of per2 nonsense mutations in cavefish populations is interesting in terms of previous observations on this gene and circadian rhythms in general in cavefish. In studies of circadian rhythm in A. mexicanus , it was found that the ability to entrain a circadian rhythm is not completely lost in cavefish, but that there are differences in magnitude and timing of the rhythm (Beale et al, 2013; Mack et al, 2020). It has been speculated that this could be in part due to increased basal levels of per2 (Beale et al, 2013; Froland Steindal et al, 2018).…”

CaveCrawler: An interactive analysis suite for cavefish bioinformatics

“…This analysis identified four genes that were significantly different. These genes represent strong candidate for functional regulators of evolved differences in circadian behavior that have been widely studied in A. mexicanus and other species of cavefish (14,(22)(23)(24)(25). The gene arpin, a negative regulator of actin is of particular interest because it is identified as harboring markers of selection and transcriptional dysregulation across all three cavefish populations.…”

“…CaveCrawler pools data from multiple publications and authors can request that their own data be integrated into CaveCrawler's repository. As of publication, CaveCrawler's data bank includes transcriptional datasets (14,15), population genetics datasets (10,15), GO data from UniProt and the Gene Ontology Consortium (16)(17)(18), and genome architecture data from Ensembl Genome Browser, release 104 (19).…”

“…By using the Gene Search module, we found that previous studies had measured the between-morph logFC values for 267 of the 1140 genes for which we had FST values. Pairwise FST measures how dissimilar a DNA sequence is between two groups relative to diversity within the groups, and logFC is the log fold change in mRNA transcription between two groups (14,21). Of the genes for which both FST and logFC had been calculated by previous studies, there were 72 for which FST outlier status had been determined by a previous study (10).…”

“…This dataset describes the log fold-change (logFC) and p-values for each of these genes in each A. mexicanus morph where the change in transcription was significant compared to controls of the same morph (20). As described in the Transcription module section of this paper, CaveCrawler can also access transcription data for genes whose transcription is significantly different between morphs (14). The Transcription module has enough flexibility that new transcriptional data can be integrated.…”