ClonalFrameML: accounting for recombination in bacterial phylogenies

Horizontal gene transfer in bacteria, mediated by transformation, transduction or conjugation, can result in gain, loss and replacement of genes. The replacement of horizontally transferred genes or gene fragments in a process known as homologous recombination has far-reaching effects on bacterial phylogenetics - the study of relatedness between bacteria. A new method published by Xavier Didelot and me last month in PLoS Computational Biology corrects for these distorting effects of homologous recombination on bacterial phylogenies.

Two forms of phylogenetic distortion are caused by recombination. The first affects the shape of the tree topology. Although this is a potentially serious difficulty, Jessica Hedge and I recently showed that phylogenies estimated from whole bacterial genomes are surprisingly robust to this problem. The second affects the lengths of the branches. When genetic material is replaced by a homologous but distantly related sequence, it gives the appearance of a cluster of substitutions in the genome, and this can exaggerate branch lengths. ClonalFrameML detects these clusters of substitutions, identifies them as recombination events, and corrects the branch lengths of the tree.

Correcting for recombination is important in a variety of settings. In transmission studies, recent transmission between patients can be detected by comparing the genomes of the infecting bacteria. As we show in the paper, ClonalFrameML improves detection of transmission events by accounting for the tendency of recombination to elevate the evolutionary distance between genomes. We also report the discovery of a remarkably large chromosomal replacement event spanning 310 kilobases that may have led to the evolution of the ST582 strain of Staphylococcus aureus, underlining the importance of recombination over short and long timescales.

ClonalFrameML is a much faster implementation of the popular ClonalFrame method by Xavier and Daniel Falush. It is based on the same underlying assumptions and the same explicit evolutionary model, so it provides interpretable estimates of rates of recombination, the length of DNA imported by recombination, and the relative impact of recombination versus mutation. However, it can now analyse thousands of whole bacterial genomes in a matter of hours, representing a substantial improvement over the earlier method.

New paper: bacterial phylogenetic inference is robust to recombination but demographic inference is not

Published this week in mBio, Jessica Hedge's new paper "Bacterial phylogenetic inference is robust to recombination but demographic inference is not" looks at a long-standing problem: why are phylogenetic trees so popular in bacterial genomics when everyone knows recombination (which is detectable in most species studied) leads to seriously misleading inference? A burst of research activity in the early 2000s showed that homologous recombination - which can result from various forms of horizontal gene transfer in bacteria - can distort phylogenetic trees and lead to false inference of positive selection and demographic growth in methods that rely on them.

In the intervening years there has been intense research in the field of population genetics into approaches that account for recombination, although the practically useful methods rely on approximations because of the inherent difficulties of learning about complex reticulated evolutionary networks that recombination generates. This has led many of my population genetics colleagues to regard - at least privately - the use of phylogenetic trees in recombining species as "bust", and the conclusions drawn from such studies as questionable. In this paper we show that this view is too simple.

New paper: Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

This week published in Nature Communications we have a new open access paper looking at what drives variability in rates of recombination (horizontal gene transfer, HGT) in the core genome of Staphylococcus aureus. HGT in the core genome is important for eliminating harmful mutations and promoting the spread of beneficial mutations, such as those that make the bacteria resistant to antibiotics.

Compared to recent work focusing on individual, highly-related strains of S. aureus, we found much higher rates of core HGT across the species as a whole. We saw that the frequency of HGT varies along the genome. At broad scales, core HGT is higher near the origin of replication, a pattern reminiscent of the one described by Eduardo Rocha and colleagues in E. coli, who hypothesized that the over-abundance of DNA near the origin during rapid growth could promote HGT.

At fine scales, we found more frequent HGT in regions of the core genome close to mobile elements. The hottest regions occurred near mobile regions called ICE6013, SCC and genomic island α. The insertion and excision of mobile elements from the genome represents a type of HGT, so our finding that nearby core regions also experience more HGT suggests there is some sort of "spill over". This idea is supported by work in Ashley Robinson's group that found similarities between ICE6013 and a class of mobile elements in Streptococcus agalactiae called TnGBS2. TnGBS2 was discovered by Phillipe Glaser's lab who showed it sometimes transfers large tracts of adjacent core material during conjugation.

Whether conjugation alone can explain the high levels of core HGT we saw in S. aureus is unclear - our results suggest there is detectable HGT even in core regions far from mobile elements. Transformation is another possible mechanism of core HGT, but S. aureus is generally thought to be naturally incapable of transformation. However, intriguing work published by Tarek Msadek and colleagues in 2012 indicates there may be cryptic mechanisms of transformation in S. aureus after all. It remains to be seen whether the relative contributions of transformation, transduction and conjugation to the long-term evolution of S. aureus can be disentangled.

omegaMap at BioHPC

All evolutionary biologists wishing to make use of omegaMap now have access to a high performance parallel computing cluster via the internet courtesy of Cornell's CBSU and Microsoft. The software, which allows the detection of selection and recombination in DNA or RNA sequences, can be run via the web interface at cbsuapps.tc.cornell.edu/omegamap.aspx, or downloaded as part of the BioHPC suite.

The web interface consists of a simple form where users can upload their configuration file and sequences in FASTA format. Completed jobs are notified by e-mail. To learn more about the project visit the CBSU home page.

Meanwhile, I am working on several major updates to omegaMap, the most interesting of which will probably be the development of a new model that allows for the joint analysis of natural selection acting on sequences from different populations or species. The aim is to integrate population genetic and phylogenetic models of selection in order to exploit the signal of selection contained both in polymorphism within populations (or species) and divergence between them. I will be presenting progress on this work, in the context of hominid evolution, at the 2009 SMBE meeting in Iowa City this June.

Inferring niche membership from genetic diversity

Each Wednesday the Ecology and Evolution department run a journal club called Noon Illumination, and this week I volunteered to lead discussion on a recent article titled Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton (Science 320: 1081-5), by Dana Hunt and colleagues based at MIT and Ghent. I originally prepared the presentation for a Bacterial Metagenomics workshop in Berlin this July, organized by Daniel Falush.

Of central interest in the paper is a novel methodology that infers habitat/niche based on ecological variables and DNA sequencing in the family of marine bacteria Vibrionaceae. That places it in the wider context of methods that attempt to predict phenotype (in this case niche) from genotype. Their approach is an elegant extension of familiar phylogenetic methods to model habitat switching over evolutionary time. Based on arguments put forward by Christophe Fraser and colleagues, the paper reasons that the ancestral habitat switches they detect are likely to be adaptive because the rate of recombination eclipses the mutation rate sufficiently to preclude the possibility of neutral genetic clustering.

However the high rate of recombination raises some difficulties of interpretation. The principal phylogenetic reconstruction was based on the hsp60 gene, but by sequencing other housekeeping genes, Hunt and colleagues found that in some cases, recombination between genes caused an artefactual habitat switch in the hsp60 ancestry that was not evident in the other genes. Using a permutation test, I found evidence for recombination within the vibrio hsp60 genes, which may confound the phylogenetic reconstruction of evolutionary relationships (Schierup and Hein 2000). On a more philosophical note, suppose you could directly observe ancestral habitat switches. Would that be strong evidence for adaptation? An association between habitat and genetic lineage is probably not sufficient to demonstrate the action of natural selection. On the other hand, frequent recombination could empower genome-wide scans for extreme association between genes and habitats, that would provide stronger support for adaptation.

You can view a PDF of the presentation of this stimulating article in our journal club here.