Biology subjects

Nichols, A. L. A.

Publications and source records attributed to Nichols, A. L. A..

5 recordsLinked to original sources

bioRxiv2026

Social and environmental cues mask circadian activity patterns in a highly social shell-dwelling cichlid fish

Species exhibit variation in their circadian activity rhythms, including being active during the day (diurnal), the night (nocturnal), or the twilight periods (crepuscular). While the influence of environmental factors such as light on entraining and controlling activity patterns is well known, it is unclear how social and abiotic factors affect circadian behaviors. The daily activity patterns of Lake Tanganyikan cichlid fish are diverse, and may be associated with species diversification. Intriguingly, some shell-dwelling cichlid species, which anecdotal observation suggests are diurnal, displayed strong nocturnal activity when assayed in a "common garden" lab setup. Here, by integrating field and lab-based studies, we provide three lines of evidence that social and environmental cues mask underlying circadian rhythms in shell-dwelling cichlids. First, we demonstrate that shell-dwelling cichlids are diurnal in their natural habitat, but convert to nocturnal activity when assayed alone in a common garden. Second, we identify that in the presence of a shell and conspecifics the highly social N. multifasciatus becomes diurnal. In contrast, the circadian activity pattern of a closely related, but sub-social species, N. brevis, is masked only by a shell, and unaffected by the presence of conspecifics. Third, we demonstrate that the masking effect of shells and conspecifics is circadian and continues in the absence of light. Fourth, we identify that the response to these cues is influenced by sex, with greater effects in female fish, and by pedigree, with stronger effects in individuals bred and raised in captivity compared to those captured in the wild. Together, these experiments reveal new relationships between circadian rhythms and sociality in these fishes, offering broader insights into the ecological and evolutionary drivers of these behaviours.

animal behavior and cognition↗

bioRxiv2024

Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes

The partitioning of ecological niches is a fundamental component of species diversification in adaptive radiations. However, it is presently unknown if and how such bursts of organismal diversity are influenced by temporal niche partitioning, wherein species avoid competition by being active during different time windows. Here, we address this question through profiling temporal activity patterns in the exceptionally diverse fauna of cichlid fishes from African Lake Tanganyika. By integrating week-long longitudinal behavioural recordings of over 500 individuals from 60 species with eco-morphological and genomic information, we provide two lines of evidence that temporal niche partitioning facilitated this massive adaptive radiation. First, Tanganyikan cichlids exhibit all known circadian temporal activity patterns (diurnal, nocturnal, crepuscular, and cathemeral) and display substantial inter-specific variation in daily amounts of locomotion. Second, many species with similar habitat and diet niches occupy distinct temporal niches. Moreover, our results suggest that shifts between diurnal and nocturnal activity patterns are facilitated by a crepuscular intermediate state. In addition, genome-wide association studies indicate that the genetics underlying activity patterns is complex, with different clades associated with different combinations of variants. The identified variants were not associated with core circadian clock genes but with genes implicated in synapse function. These observations indicate that temporal niche partitioning contributed to adaptive radiation in cichlids and that many genes are associated with the diversity and evolution of temporal activity patterns.

evolutionary biology↗

bioRxiv2023

Frequent transitions from night-to-day activity after mass extinctions

Why certain species survive large-scale extinction events while others do not is poorly understood. While the fossil record can provide insights into morphological adaptations that increase survival probabilities, it provides limited information regarding behavioural traits. Here we integrate behavioural data with phylogenetic comparative models to study the evolution of day-night activity patterns (nocturnality and diurnality) in bony fishes, which have persisted through the last four mass extinction events. Our findings in fish, combined with data across all other clades of vertebrates, provide four lines of evidence that nocturnality conferred an evolutionary advantage during mass extinctions, and that frequent nocturnal-to-diurnal transitions facilitated post-extinction diversification: First, phylogenetic reconstruction indicates that the last common ancestors of all vertebrates and of clades of bony vertebrates were nocturnal. Second, in the lineage of bony fishes, which contains over half of all vertebrate species, twice as many transitions between nocturnal and diurnal activity patterns have occurred compared to tetrapods. Third, within a specific ecological niche, different species exhibit distinct temporal activity patterns, suggesting widespread temporal niche partitioning. Fourth, independent bursts in night-to-day transitions followed large-scale extinction events during the last two geological eras in all four major bony vertebrate groups. These observations suggest that ancestral nocturnality and frequent transitions to diurnality helped vertebrates survive and diversify in the face of extinction events, such as those expected during the current "6th mass extinction" event caused by anthropogenic climate change.

evolutionary biology↗

bioRxiv2022

Expanded olfactory system in fishes capable of terrestrial exploration

Smell abilities differ greatly among vertebrate species, as reflected by the exceptional size variability of gene families and brain regions involved in odour detection. However, key environmental factors shaping the molecular and phenotypic evolution of the olfactory sensory system remain mostly unknown. Here, we investigate the association between diverse ecological traits and the number of olfactory chemoreceptors in the genomes of more than two hundred ray-finned fishes. We found independent expansions producing large gene repertoires in nocturnal amphibious fishes, generally able to perform active terrestrial exploration. Furthermore, we reinforced this finding with an additional analysis of a clariid species (Channallabes apus), a fish lineage with chemosensory-based aerial orientation. Importantly, we also detected an augmented information-processing capacity in the olfactory bulb of examined nocturnal amphibious species. Overall, we report a convergent magnification of the olfactory system in amphibious fishes potentially enhancing terrestrial orientation, revealing the likelihood of an analogous event in tetrapod ancestors during the water-to-land transition.

evolutionary biology↗

bioRxiv2019

Hierarchical recurrent state space models reveal discrete and continuous dynamics of neural activity in C. elegans

Modern recording techniques enable large-scale measurements of neural activity in a variety of model organisms. The dynamics of neural activity shed light on how organisms process sensory information and generate motor behavior. Here, we study these dynamics using optical recordings of neural activity in the nematode C. elegans. To understand these data, we develop state space models that decompose neural time-series into segments with simple, linear dynamics. We incorporate these models into a hierarchical framework that combines partial recordings from many worms to learn shared structure, while still allowing for individual variability. This framework reveals latent states of population neural activity, along with the discrete behavioral states that govern dynamics in this state space. We find stochastic transition patterns between discrete states and see that transition probabilities are determined by both current brain activity and sensory cues. Our methods automatically recover transition times that closely match manual labels of different behaviors, such as forward crawling, reversals, and turns. Finally, the resulting model can simulate neural data, faithfully capturing salient patterns of whole brain dynamics seen in real data.

neuroscience↗