Avian circadian clock genes: ontogeny and role for adaptive programming in avian embryos

Abstract

Circadian clocks are ubiquitous across almost all organisms, from cyanobacteria to humans, due to a highly conserved mechanism involving a network of negative feedback loops. This molecular oscillator underpins rhythmic oscillations in physiology and behaviour at the organismal level. In vertebrates, both cellular processes and the sensory detection mechanisms underlying rhythmic physiology are relatively well understood. But how these processes develop to optimise tissue-specific rhythmic gene expression is much less understood. Birds possess an intricate, multi-oscillatory core circadian system that governs the biological rhythms of all other tissues. Avian studies document rhythmic expression of genes and hormone production prior to hatching, and yet the consequences of the onset of this process and the interactions with embryonic development have rarely been considered. In this review, we summarise the existing literature on clock gene ontogeny in birds and suggest how rhythmic expression of these genes may develop. Then, by also drawing upon evidence from non-mammalian oviparous taxa, we hypothesise how the development of rhythmic clock gene expression may interact with avian developmental processes and events. Specifically, we highlight how rhythmic clock gene expression may adaptively benefit embryos by phasing rhythms in metabolic and neuro-endocrine systems and we suggest that rhythmic gene expression may play a role in coordinating the physiological systems and behavioural outputs required to initiate hatching. Lastly, we highlight the critical avenues of research that will enhance our understanding of the role of clock genes in avian ontogeny and their ecological relevance, particularly in understanding the impacts of anthropogenic light pollution on developing avian clocks.

Keywords: ALAN; avian ontogeny; circadian; clock gene; hatching; melatonin; mitochondria.

FIGURE 1

Avian circadian rhythms are orchestrated through a hierarchical, multi-oscillatory system. Core pacemakers (pineal gland, SCN, and retinae) entrain to photic cues to phase their own biological rhythms whilst also influencing other core pacemakers. Through downstream processes (dashed arrows) core pacemakers govern the biological outputs of physiological systems such as in the diversity of the microbiome or at the tissue level such as rhythmicity in cardiac parameters. Additionally, rhythms within tissues may be governed through other zeitgebers such as liver function entraining to organismal feeding rhythms. Regardless of the tissue type, within every cell remains the molecular mechanism influencing circadian rhythms of birds. In the core loop, Bmal1 and Clock products are produced and bind to E-boxes present on gene promoters throughout the genome. Products of the negative elements (Pers and Crys) are produced and inhibit the transcriptional activity of BMAL1:CLOCK heterodimers. A stabilising loop based on the REV-ERBs and RORs nuclear receptors inhibit and stimulate, respectively, Bmal1 and Clock transcription (dashed lines). This self-sustaining feedback loop lasts for approximately 24 h and maintains rhythms within all tissues of birds. Created in BioRender. Wellard, C. (2025) https://BioRender.com/d62z641.

FIGURE 2

Rhythmic light cycles throughout incubation may drive the ontogeny of clock gene expression in avian embryonic development. Subsequently, the molecular clock in avian embryos may gradually develop and mature, though only a handful of studies have tested the effects of incubation conditions on rhythmic clock gene development (Table 1). From the literature, we predict that the onset of rhythmic gene expression will commence earlier in core pacemakers (red and black lines) than in peripheral organs (blue line), but also that the amplitude of expression will be greater. Light may synchronise rhythmic expression so that by hatch day clock gene expression is synchronised across cells/tissues. There is an indication that the avian clock may be autonomous, however, we speculate that rhythmic cycles of light may be important in synchronizing and entraining clock gene expression earlier than it would be in free-running conditions. Created in BioRender. Wellard, C. (2025) https://BioRender.com/v67e215.

FIGURE 3

Central to all biological rhythms are clock genes which rhythmically express and dynamically shape the rhythmicity of a range of biological outputs. The ontogeny of rhythmic clock gene expression (a) throughout avian embryonic development may adaptively benefit embryos by stimulating rhythmicity in biological outputs influencing embryonic development and developmental events. Development of rhythmic clock gene expression may allow avian embryos to phase whole organism metabolism (c) which inherently shapes metabolism at the cellular level (d), influencing rhythms important for phasing growth, yolk acquisition, and tissue-specific processes. Concurrently, rhythmicity in clock gene expression may shape cellular proliferation (b), not shaping the rate of embryonic development but rather appropriately phasing rhythmicity in tissue growth. This rhythmicity in tissue growth would be sustained through rhythmicity in ATP generation (d). Circadian entrainment by the embryo may also allow birds to time the various behavioural stages of hatching (e). This coupled with coordination in changes of physiological and metabolic pathways (c) important to hatching may allow avian embryos to time emergence from the egg. Subsequently, embryonic entrainment and the ensuing ontogeny of rhythmicity in clock gene expression may adaptively benefit avian embryos in timing important developmental processes and events. Created in BioRender and using images from Ooid. Wellard, C. (2025) https://BioRender.com/6r4jx4a.