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Phylogenetic coherence in microbiome composition across environmental gradients

Chakraverti-Wuerthwein, M. S.; Domenig, A.; Kuehn, S.

2026-06-11 ecology
10.64898/2026.06.07.730742 bioRxiv
Show abstract

Global surveys of microbial communities across biomes have shown that environmental variables such as depth and pH are strong determinants of community composition. However, we do not understand how the traits of individual taxa, and their evolutionary conservation, conspire to give rise to these patterns. Exploiting large-scale surveys of top soil and marine microbiomes, we use canonical correlation analysis (CCA) to concurrently infer directions of environmental variation and the associated compositional changes. We find that the primary canonical direction, capturing the dominant environmental gradient, exhibits a strong phylogenetic signal: individual species responses to environmental shifts along this direction are similar among taxa with shared evolutionary history. In contrast, secondary canonical directions show weak or no phylogenetic structure. Together, these results suggest a two-scale view of microbial community assembly. Deeply evolutionarily conserved traits govern community reorganization along the main environmental driver of community composition. Additional environmentally driven changes in community composition then reflect traits that are more evolutionarily labile.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.