Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

Hedge, Jessica; Wilson, Daniel J.

doi:10.1128/mbio.02158-14

Cited by 110 publications

(106 citation statements)

References 25 publications

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“…It has previously been shown that in maximum likelihood analyses of concatenated alignments, HGT influences branch lengths but hardly affects the topology of the resulting tree2324. The resulting rooted tree topology thus represents vertical inheritance among the 53 E. coli strains.…”

Section: Resultsmentioning

confidence: 98%

Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

Pang

Lercher

2017

Sci Rep

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Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer.

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Section: Resultsmentioning

confidence: 98%

Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

Pang

Lercher

2017

Sci Rep

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“…Recombination has also long been known to occur in some large DNA viruses, such as poxviruses, and whole-genome sequencing is providing new opportunities to shed light on its frequency and genomic consequences [52]. Ignoring recombination when analysing measurably evolving pathogens can be misleading [53], but accounting for such a complex and variable process is difficult. If all the strains under study are closely related, for example when studying a local outbreak, then most recombination among them will have little effect compared to imported sequences from other lineages, which would introduce a relatively high number of nucleotide changes.…”

Section: Biological Complexitiesmentioning

confidence: 99%

Measurably evolving pathogens in the genomic era

Biek

Pybus

Lloyd‐Smith

et al. 2015

Trends in Ecology & Evolution

256

240

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Current sequencing technologies have created unprecedented opportunities for studying microbial populations. For pathogens with comparatively low per-site mutation rates, such as DNA viruses and bacteria, whole-genome sequencing can reveal the accumulation of novel genetic variation between population samples taken at different times. The concept of “measurably evolving populations” and related analytical approaches have provided powerful insights for fast-evolving RNA viruses, but their application to other pathogens is still in its infancy. Here we argue that previous distinctions between slow- and fast-evolving pathogens become blurred once evolution is assessed at a genome-wide scale and we highlight important analytical challenges to be overcome in order to infer pathogen population dynamics from genomic data.

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“…SNPs can be introduced into bacterial genomes individually via mutations or in clusters by recombination, a process that may bias demographic inferences and rate estimates (Hedge & Wilson, 2014;Lapierre et al, 2016). In particular, ignoring recombination can lead to incorrect estimates of branch lengths, which in turn results in an apparently overdispersed molecular clock, precluding accurate estimates of evolutionary rates and time-scales.…”

Section: Impact Statementmentioning

confidence: 99%

Genome-scale rates of evolutionary change in bacteria

Duchêne

Holt

Weill

et al. 2016

Preprint

133

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Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with 'ancient DNA' data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from approximately 10 À5 to 10 À8 nucleotide substitutions per site year À1 . This variation was negatively associated with sampling time, with this relationship best described by an exponential decay curve. To avoid potential estimation biases, such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

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Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

Cited by 110 publications

References 25 publications

Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

Measurably evolving pathogens in the genomic era

Genome-scale rates of evolutionary change in bacteria

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