Biology subjects

Belcher, L. J.

Publications and source records attributed to Belcher, L. J..

3 recordsLinked to original sources

bioRxiv2025

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinders high accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specifically, we show that enhanced phylogenetic delineation of orthogroups provides a 7% relative increase in orthogroup inference accuracy. We further demonstrate that a new gene assignment method substantially reduces overall runtime RAM usage without compromising accuracy. The latest version of OrthoFinder is available at https://github.com/OrthoFinder/OrthoFinder.

bioinformatics↗

bioRxiv2024

Cooperation shapes bacterial niche breadth evolution and patterns of diversification

Bacteria exhibit varying niche breadths, with generalists thriving in diverse environments and specialists confined to specific habitats. This variability reflects the adaptability of bacteria to their environment and may influence their speciation and extinction rates. We used phylogenetic causal inference and diversification analysis techniques to investigate the influence of cooperation on bacterial niche breadth evolution and patterns of diversification across 25,785 species. We found: (1) a positive correlation between the proportion of genes for cooperation and niche breadth; (2) a decreased proportion of genes for cooperation promotes niche contraction; and (3) species with a higher proportion of genes for cooperation show increased speciation and extinction rates when their niche breadths are narrower. Our study highlights the role of genes for cooperation in shaping both niche breadth and diversification of bacteria, underscoring their critical function in maintaining the ecological versatility and diversity of bacteria.

evolutionary biology↗

bioRxiv2022

Signatures of kin selection in a natural population of the bacteria Bacillus subtilis

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviours, which are favoured because they are directed towards relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations, because theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns, and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest cooperation favoured by kin selection, with an average relatedness of r=0.77 between interacting individuals.

evolutionary biology↗