Biology subjects

Knowles, S. C. L.

Publications and source records attributed to Knowles, S. C. L..

5 recordsLinked to original sources

bioRxiv2026

The Friendship Paradox across animal social systems is governed by network structure and biological features

A populations social structure, often represented as a social network, shapes fundamental biological processes including the spread of disease, information, and behaviour. The Friendship Paradox is a network phenomenon whereby the average individual has fewer friends than their friends do. This effect can be quantified as relationship disparity (the difference between an individuals connectedness and those they are connected to) which captures the local social environment. Previous work has shown that such relationship disparity can be exploited in effective outbreak monitoring, targeted health interventions and optimized contact tracing. Yet, how its magnitude varies across real-world social networks remains poorly understood. Here, we analyse relationship disparity across 391 empirical animal social networks to test how intrinsic network properties and biological attributes predict its extent. We find that smaller and sparser networks exhibit stronger relationship disparity, and it is further shaped by both species-specific differences and shared phylogenetic history. After controlling for variation in individual sociability, relationship disparity was more strongly accentuated in mammalian direct physical contact networks than indirect social association networks, whilst the corresponding finding was not detected among Sauropsids. Phylogenetic and species identity largely explained variation in relationship disparity indicating biological drivers. Together, these findings demonstrate that both network structure and biological attributes shape relationship disparity in animal social systems, providing a foundation for predicting how higher-order network architecture influences social processes such as contagion. Significance StatementIn natural populations, social connections are unevenly distributed, often resulting in a small subset of individuals that are highly connected while many are relatively peripheral. The Friendship Paradox is a measure of relationship disparity between individuals and their local social environment. Understanding how features of the social network and biological system are associated with relationship disparity can contribute to understanding what shapes social behaviour. Relationship disparity may not just be an emergent network property but could reflect a higher level of social structuring, and therefore shape processes that depend on social contacts. Our findings demonstrate the value of comparative network analysis for generating insights into fundamental principles structuring real-world societies.

animal behavior and cognition↗

bioRxiv2025

The gut microbiota of two rodents varies over fine spatial scales yet is minimally influenced by the environmental microbiota

The gut microbiota of animals varies considerably between individuals within the same population. Given the importance of gut microbiota composition for animal biology and ultimately fitness (e.g., via effects on physiology, immunity and even behaviour), there is considerable interest in understanding which factors shape its variation. Here, we tested whether local environments are an important source of microbial diversity for mammalian guts, by sampling the faecal microbiota of wood mice (Apodemus sylvaticus) and bank voles (Myodes glareolus), as well as environmental microbiotas, across Wytham Woods. We first find that both species share a low proportion of their microbiotas with local environments and that most shared microbes are aerotolerant. We then detect that microgeographic patterns (namely soil chemistry) are associated with variation in the microbiota of local environments but this does not translate to microbiota variation between animals. Nevertheless, between-individual gut microbiota variation is strongly associated with where animals are sampled, suggesting that other local factors (e.g., biotic environment, interactions between individuals) are much stronger predictors of microbiota composition than local abiotic factors. Finally, we find that wood mice (but not bank voles) are more likely to share microbes with local than non-local environments, but that local environments still contribute little to animal microbiotas. Our findings challenge the prevailing view that mammalian microbiotas are strongly affected by local soil chemistry or the abiotic environment, while further supporting the prediction that biotic and/or other intrinsic factors (which can also act on a local scale) contribute more to microbiota composition.

ecology↗

bioRxiv2023

Elevated epigenetic age in wild compared to lab-raised house mice

Age is a key parameter in population ecology, with a myriad of biological processes changing with age as organisms develop in early life then later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology, and are often developed or calibrated using captive animals of known age. However, studies typically rely on invasive blood or tissue samples, which limits their application in more sensitive or elusive species. Moreover, few studies have directly assessed how methylation patterns and epigenetic age estimates compare across environmental contexts (e.g., captive or lab-based vs. wild animals). Here, we built a targeted epigenetic clock from laboratory house mice (strain C57BL/6, Mus musculus) using DNA from non-invasive faecal samples, and then used it to estimate age in a population of wild mice (Mus musculus domesticus) of unknown age. This lab mouse-derived epigenetic clock accurately predicted adult wild mice to be older than juveniles, and showed that wild mice typically increased in epigenetic age over time, but with wide variation in epigenetic ageing rate among individuals. Our results also suggested that, for a given body mass, wild mice had higher methylation across targeted CpG sites than lab mice (and consistently higher epigenetic age estimates as a result), even among the smallest, juvenile mice. This suggests wild and lab mice may display different CpG methylation levels from very early in life, and indicates caution is needed when developing epigenetic clocks on lab animals and applying them in the wild.

molecular biology↗

bioRxiv2022

Seasonal dynamics of the wild rodent faecal virome

Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Leveraging non-invasive faecal samples from a long-term wild rodent study, we characterised viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis, and M. glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most abundant virus families, Picornaviruses, show pronounced temporal changes in viral richness and diversity, which were associated with concurrent and up to [~]3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.

ecology↗

bioRxiv2021

Synchronous seasonality in the gut microbiota of wild wood mouse populations

O_LIThe gut microbiome performs many important functions in mammalian hosts, with community composition shaping its functional role. However, what factors drive individual microbiota variation in wild animals and to what extent these are predictable or idiosyncratic across populations remains poorly understood. C_LIO_LIHere, we use a multi-population dataset from a common rodent species (the wood mouse, Apodemus sylvaticus), to test whether a consistent set of core gut microbes is identifiable in this species, and to what extent the predictors of microbiota variation are consistent across populations. C_LIO_LIBetween 2014 and 2018 we used capture-mark-recapture and 16S rRNA profiling to intensively monitor two wild UK mouse populations and their gut microbiota, as well as characterising the microbiota from a laboratory-housed colony of the same species. C_LIO_LIAlthough broadly similar at high taxonomic levels and despite being only 50km apart, the two wild populations did not share a single bacterial amplicon sequence variant (ASV). Meanwhile, the laboratory-housed colony shared many ASVs with one of the wild populations from which it is thought to have been founded decades ago. Despite strong taxonomic divergence in the microbiota, the factors predicting compositional variation in each wild population were remarkably similar. We identified a strong and consistent pattern of seasonal microbiota restructuring that occurred at both sites, in all years, and within individual mice. While the microbiota was highly individualised, seasonal convergence in the gut microbiota among individuals occurred in late winter/early spring. C_LIO_LIThese findings reveal highly repeatable seasonal gut microbiota dynamics across distinct populations of this species, despite divergent taxa being involved. Providing a platform for future work to understand the drivers and functional implications of such predictable seasonal microbiome restructuring, including whether it might provide the host with adaptive seasonal phenotypic plasticity. C_LI

ecology↗