Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria
- 1Department of Applied Physics, Stanford University, Stanford, California, United States of America.
- 2Department of Biology, Stanford University, Stanford, California, United States of America.
- 3Biohub, San Francisco, California, United States of America.
Abstract
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein-coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations.
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about selection pressures. This study develops a model of dN/dS in recombining populations of bacteria, revealing that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint.
Related
- EV-B 3D polymerase remodels viral populations through 5′UTR recombination to subvert cardiac antiviral innate immunity
- Population density is a selective driver of urban soil microbiomes: evidence from bacteria, fungi and protozoan communities in a regional city
- Comparison of intracellular and encapsidated viral RNA reveals selective constraints on reovirus recombination
- Strong correlations between mutation rates and selective constraint in the human genome?
- Recombination rate and efficiency of linked selection in small and large stickleback populations
BibTeX
@article{liu2026recombination,
title = {{Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria}},
author = {Zhiru Liu and Benjamin H Good},
journal = {PLOS Biology},
year = {2026},
month = oct,
doi = {10.1371/journal.pbio.3004052},
url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004052},
note = {CC BY},
}
RIS
TY - JOUR
TI - Recombination shapes the dynamics of selective constraint in global populations of human gut bacteria
AU - Zhiru Liu
AU - Benjamin H Good
PY - 2026
DA - 2026/10/12
JO - PLOS Biology
DO - 10.1371/journal.pbio.3004052
UR - https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3004052
AB - The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein-coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations. The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about selection pressures. This study develops a model of dN/dS in recombining populations of bacteria, revealing that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint.
SN - 1545-7885
SN - 1544-9173
ER -