A global survey of eco-evolutionary pressures acting on horizontal gene transfer

Dmitrijeva, Marija; Tackmann, Janko; Rodrigues, João M. O. S.; Huerta-Cepas, Jaime; Coelho, Luís Pedro; Mering, Christian von

doi:10.21203/rs.3.rs-3062985/v1

Cited by 2 publications

(1 citation statement)

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“…Long (almost) exact matches are often interpreted as horizontal transfers, [44, 53, 62, 63]. However, in the absence of a model, it is not clear what is the threshold that discriminates horizontally transferred and well conserved sequences, leading to false-negative or false-positive detection errors [64]. Detailed analysis of the MLD can help to minimize those errors: the presence of two clear regimes in the MLD suggests that sequences with exact matches shorter than the crossover between the two regimes are conserved, while longer ones most probably have been horizontally transferred.…”

Section: Discussion and Summarymentioning

confidence: 99%

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

Sheinman,

Arndt,

Massip

2023

Preprint

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The timing and phylogeny of bacterial evolution is difficult to reconstruct because of a scarce fossil record, deep genomic divergences and complexities associated with molecular clocks. Studying bacterial evolutionary history using rich and rapidly accumulating genomic data requires accurate modeling of genome evolution, taking into account that different parts of bacterial genomes have different history. In particular, along the genome, different loci are subject to different selective pressure. In addition, some are horizontally transferred from one bacterium to another, resulting in a mosaic-like genome structure. An important technical aspect is that loci with high effective mutation rates can diverge beyond the aligner detection limit, biasing the genome-wide divergence estimate towards more conserved loci. Therefore, the genome-wide molecular clock cannot be directly applied to study bacterial evolutionary history. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genomic sequences comparisons. The length distribution of the sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers and by the aligner sensitivity. Based on these inputs we build a model and demonstrate that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Using the model and the empirical data we fit the evolutionary parameters: time divergences and horizontal transfer rates. Based on the estimated time divergences we build a time-calibrated phylogenetic tree, demonstrating the accuracy of the method and its ability to unravel vertical and horizontal transfers in bacterial genomes.

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Section: Discussion and Summarymentioning

confidence: 99%

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

Sheinman,

Arndt,

Massip

2023

Preprint

View full text Add to dashboard Cite

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Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

Sheinman,

Arndt,

Massip

2024

Proc. Natl. Acad. Sci. U.S.A.

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The chronology and phylogeny of bacterial evolution are difficult to reconstruct due to a scarce fossil record. The analysis of bacterial genomes remains challenging because of large sequence divergence, the plasticity of bacterial genomes due to frequent gene loss, horizontal gene transfer, and differences in selective pressure from one locus to another. Therefore, taking advantage of the rich and rapidly accumulating genomic data requires accurate modeling of genome evolution. An important technical consideration is that loci with high effective mutation rates may diverge beyond the detection limit of the alignment algorithms used, biasing the genome-wide divergence estimates toward smaller divergences. In this article, we propose a novel method to gain insight into bacterial evolution based on statistical properties of genome comparisons. We find that the length distribution of sequence matches is shaped by the effective mutation rates of different loci, by the horizontal transfers, and by the aligner sensitivity. Based on these inputs, we build a model and show that it accounts for the empirically observed distributions, taking the Enterobacteriaceae family as an example. Our method allows to distinguish segments of vertical and horizontal origins and to estimate the time divergence and exchange rate between any pair of taxa from genome-wide alignments. Based on the estimated time divergences, we construct a time-calibrated phylogenetic tree to demonstrate the accuracy of the method.

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A global survey of eco-evolutionary pressures acting on horizontal gene transfer

Cited by 2 publications

References 50 publications

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

Modeling the mosaic structure of bacterial genomes to infer their evolutionary history

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