Abstract

Circadian rhythms are self-sustaining, endogenous processes that align behaviour and physiology with daily environmental cycles. Rhythms are regulated by conserved genes forming transcriptional feedback loops and are entrained by environmental cues (e.g., light). Circadian systems are well studied in model organisms, their molecular evolution in squamates (lizards and snakes) remains less understood. Squamates represent the most species-rich reptile group with extensive ecological and sensory diversity, exhibiting multiple independent transitions across ecological niches, including repeated shifts into low-light environments (e.g., nocturnality, fossoriality), making them ideal for examining circadian and light-associated gene evolution. This study investigates how ecological transitions have influenced the evolution of circadian clock and light-sensitive opsin genes. We analysed 20 circadian and 15 visual/non-visual opsin genes across 65 squamate species and only extant sister lineage member, using genomic and transcriptomic data. Genes were identified using BLAST and verified via phylogenetic reconstruction. Selection patterns were assessed using PAML, applying codon-based models (site, branch, branch-site, clade) to estimate the ratio of nonsynonymous to synonymous substitution rates (ω), and RELAX (via Datamonkey) to test for shifts in selection intensity (K) across ecological contexts. Our results show most circadian, and opsin genes are under strong purifying selection, indicating evolutionary constraint. RELAX detected intensified selection in some non-visual opsins, suggesting ecological influences. Consistent with prior studies, major opsin losses occurred in low-light clades including lepidopsin was lost in geckos and snakes. Functional redundancy led to relaxed selection in some circadian genes. PER3 was absent from most snakes except Boidae and some Scolecophidia. Frequent opsin loss and pseudogenization in fossorial and nocturnal taxa reflect reduced reliance on vision. These findings demonstrate how ecological transitions shape the molecular evolution of circadian and light-detection systems in squamates, offering new insights into the link between environmental conditions, sensory adaptation, and gene conservation.

Awarding Institution(s)

University of Plymouth

Supervisor

Bruno Fonseca Simoes, Mairi Knight

Keywords

Circadian rhythms, Clock genes, Photoreceptors, Ecology, Evolution, Squamates, Pineal gland, Parietal eye

Document Type

Thesis

Publication Date

2026

Embargo Period

2026-04-15

Deposit Date

April 2026

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