Biology subjects

Richards, S. A.

Publications and source records attributed to Richards, S. A..

3 recordsLinked to original sources

bioRxiv2026

Decoupled seasonal effects of an environmentally transmitted wildlife disease

O_LISeasonal forcing is a dominant factor shaping host-pathogen interactions and disease dynamics across many wildlife systems, including species impacted by environmentally transmitted parasites. How seasonality in parasite dynamics translates to the host when the infection and disease impacts operate at different timescales, however, remains poorly understood. C_LIO_LIWe investigate how seasonality shapes sarcoptic mange in bare-nosed wombats, Vombatus ursinus, a disease caused by the environmentally transmitted parasitic mite Sarcoptes scabiei, causing a protracted clinical time-course in the host. Using an empirically informed state-based deterministic model we explore how wombat population trajectories are influenced by (i) seasonal constraints to mite survival and (ii) in context of host-pathogen encounter rates, as measured by the ratio of burrows to wombats. C_LIO_LIWe demonstrate three long-term outcomes of wombat-mange: host and parasite extinction, endemic disease, and disease-free. We find seasonal environments narrow the range of host-pathogen encounter rates that support S. scabiei persistence relative to stable environments, and prevalence and population sizes vary more in seasonal compared to stable environments except under moderate host-pathogen encounter rates when seasonal effects are less apparent. We also find that a protracted infectious period is essential for host-parasite coexistence in the wombat-mange system. C_LIO_LIOur seasonal model results are consistent with field observations, such that mange prevalence in natural populations increases during seasons of longer off-host mite survival. Application of these findings suggest management efforts could reduce host population impacts through disease management in seasons with longer off-host parasite survival or reduce the environmental reservoir through disease management in seasons with shorter off-host survival. C_LIO_LIWe provide novel, mechanistic explanations for distinctive population trajectories that arise from a seasonally forced wildlife disease, including climate factors that operate independently on parasites, host demography, and disparate timescales over which seasonality affects parasites and hosts. Broadly, linking seasonality to long-term population dynamics can improve the predictability and management of wildlife diseases, but requires an understanding of how local intrinsic factors interact with seasonal pressures over time. C_LI

ecology↗

bioRxiv2026

Thermally driven sex reversal reveals divergent sex determination dynamics in wild viviparous reptile populations

Climate change can threaten population viability by disrupting sex ratios in species whose sex is influenced by temperature. While species with sex chromosomes were historically considered immune, in some species, temperatures can override genetic sex determination via sex reversal, leaving them vulnerable to climate-driven sex ratio shifts. The Tasmanian spotted snow skink (Carinacincus ocellatus), a viviparous reptile with an XX/XY system, provides a compelling case study. While laboratory studies demonstrated that extreme thermal conditions induce female-to-male sex reversal (XX males), its occurrence in the wild remains unexplored, limiting our understanding of actual climate impacts. Integrating 23 years of phenotypic and genetic sexing data across two climatically distinct populations, we provide the first evidence of sex reversal in a wild viviparous reptile. XX reversal occurred in both populations, affecting up to 23.5% of XX births in the warmer population, and was associated with colder minimum daily temperatures. Despite high birth rates in some years, sex-reversed adults were rare. We also identified putative XY females, suggesting bidirectional sex reversal and reinforcing the extreme plasticity of reptilian sex determination. Ultimately, sex reversal could act as an evolutionary trap, potentially compromising population viability as climate instability increases.

evolutionary biology↗

bioRxiv2025

Robust Phylogenetics

We present a robust phylogenetic inference method, called the trimmed log-likelihood method, which effectively identifies fast-evolving, saturated, or erroneous sites in both simulated and empirical multiple sequence alignments. This method avoids circularity by dynamically identifying and removing sites without relying on an initial tree, allowing the specific sites removed to change as tree topology and branch lengths are estimated. Our analyses demonstrate that this method outperforms existing approaches, such as the Slow-Fast method, Tree Independent Generation of Evolutionary Rate approach, and Le Quesne Probability statistics, by removing fewer sites while still inferring phylogenies with comparable or greater accuracy. Implemented in IQ-TREE2, the trimmed log-likelihood method is user-friendly with a simple command-line interface. However, challenges remain in addressing heterogeneous evolutionary processes including compositional biases, such as GC bias. Despite these challenges, our approach offers a practical solution for improving phylogenetic inference by automatically and dynamically identifying sites to down-weight during phylogenetic analyses. We recommended that researchers compare trees inferred by varying the proportion of down-weighted sites to monitor changes in tree topology and to identify a set of candidate tree topologies for further consideration.

evolutionary biology↗