Biology subjects

Stephenson, N. P.

Publications and source records attributed to Stephenson, N. P..

3 recordsLinked to original sources

bioRxiv2025

Community ecology dynamics on reefs in Fiji are dependent on soft coral density and depth

Some soft corals (order Alcyonacea) have the potential to increase in prevalence on tropical coral reefs as the severity of anthropogenic climate change increases. While soft corals are therefore an increasingly important component of reef ecosystems, little is known about their ecological role on coral reefs and their influence on community dynamics and diversity. We used Bayesian Network Inference to identify the relationships among benthic taxa across sites with varying degrees of soft coral dominance on the Great White Wall, Fiji, and then employed spatial point process analysis to reveal the ecological processes behind these associations. We found that depth was the dominant driver of community dynamics, and that white Nephtheidae soft corals were negatively associated with scleractinian corals and positively associated with algae due to a facilitative mutualism - possibly due to soft corals reducing grazing pressure. Our results show distinctions in reef benthos and ecological dynamics between scleractinian- and soft coral-dominated reefs. We found that diversity levels were significantly lower on soft coral than scleractinian reefs, potentially highlighting the risk of a loss in benthic diversity on reefs where soft corals replace scleractinians.

ecology↗

bioRxiv2025

tidygenclust: Clustering for Population Genetics in R

BackgroundPopulation structure analysis is crucial for evolutionary research and medical genomics. Clustering methods, broadly categorized as model-based (e.g. ADMIXTURE) or non-model-based (e.g. SCOPE), differ in their methodology and computational efficiency. Recently, fastmixture, a model-based approach, has improved scalability and performance, while replicate alignment tools, such as Clumppling, extend previous methods by also aligning the modes across K values. However, all the existing tools are standalone and generate numerous untracked text files, as well as offering limited plot customisability. ResultsWe introduce an R package, tidygenclust, which brings the functionalities of the original ADMIXTURE, fastmixture and Clumppling software into R, enabling a streamlined and integrated workflow. By integrating with tidypopgen, a package designed to handle large SNP datasets, these new tools maintain metadata, simplify data handling, and produce results as customisable ggplot2 objects for flexible visualisation. ConclusionsThe R package tidygenclust advances population genetic analysis by combining computational efficiency with reproducible workflows and user-friendly plotting. The source code and instructions can be accessed on https://github.com/EvolEcolGroup/tidygenclust.

bioinformatics↗

bioRxiv2025

Recolonisation strategies of early animals in the Avalon (Ediacaran 574 - 560 Ma)

The first geographically widespread metazoans are found in the Avalon assemblage (Ediacaran; 574 - 560 Ma). These early animals were regularly disturbed by sedimentation events such as ash flows and turbidites, leading to an apparent "resetting" of communities. However, it is not clear how biological legacies - remains or survivors of disturbance events - influenced community ecology in the Avalon. Here, we use spatial point process analysis on 19 Avalon palaeocommunities to test whether two forms of biological legacy (fragmentary remains of Fractofusus and surviving frondomorphs) impacted the recolonisation dynamics of Avalon palaeocommunities. We found that densities of Fractofusus were increased around the Fractofusus fragments, suggesting that they helped to recolonise the post-disturbance substrate, potentially contributing to the Fractofusus dominance found in 8 of the 19 palaeocommunities. However, we found no such effects for survivor fronds. Our results suggest that the evolution of height was for long-distance dispersal rather than local recolonisation. In modern deep-sea environments, there is a trade-off between local and long-distance dispersal, and our work demonstrates that this differentiation of reproductive strategies had already developed in the early animals of the Avalon.

ecology↗