Atkins, H. | Search bioRxiv

bioRxiv2026

Selecting for lysis in a temperate phage population

Temperate phages represent an abundant source of phage diversity, but their capacity for lysogeny limits their therapeutic potential. Here, we asked whether repeated selection for lytic replication could drive a temperate phage toward an obligately lytic lifestyle. We serially propagated a cocktail of three temperate coliphages using a modified Appelmans protocol in which phage populations were independently passaged on eight E. coli hosts. Whole-genome sequencing revealed substantial changes in population composition and mutation frequencies. The Uetakevirus phage 1362 was undetectable after the first round, whereas the closely related P2-like phages in the cocktail dominated the evolving populations. Mutations repeatedly accumulated in lysis- and lysogeny-associated genes. Longitudinal genomic analysis revealed rapid fixation of mutations in the integrase coding region, while variants in lysA, lysB, and holin increased in frequency over successive rounds of selection. Protein structure modeling localized selected mutations to regions with potential functional significance. These include the DNA-binding domain of integrase and a surface-exposed region of LysA. Together, these results show that sustained selection for lytic replication can drive rapid and repeatable genomic adaptation in temperate phage populations.

evolutionary biology↗

bioRxiv2021

Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

Defining appropriate null expectations for species distribution hypotheses is important because sampling bias and spatial autocorrelation can produce realistic, but ecologically meaningless, geographic patterns. Generating null species occurrences with similar spatial structure to observed data can help overcome these problems, but existing methods focus on single or pairs of species and do not incorporate between-species spatial structure that may occlude comparative biogeographic analyses. Here, we describe an algorithm for generating randomised species occurrence points that mimic the within- and between-species spatial structure of real datasets and implement it in a new R package - fauxcurrence. The algorithm can be implemented on any geographic domain for any number of species, limited only by computing power. To demonstrate its utility, we apply the algorithm to two common analysis-types: testing the fit of species distribution models (SDMs) and evaluating niche-overlap. The method works well on all tested datasets within reasonable timescales. We found that many SDMs, despite a good fit to the data, were not significantly better than null expectations and identified only two cases (out of a possible 32) of significantly higher niche divergence than expected by chance. The package is user-friendly, flexible and has many potential applications beyond those tested here, such as joint SDM evaluation and species co-occurrence analysis, spanning the areas of ecology, evolutionary biology and biogeography.

ecology↗