Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

Cheng, Lei; Connor, Thomas R.; Sirén, Jukka; Aanensen, David M.; Corander, Jukka

doi:10.1093/molbev/mst028

Cited by 566 publications

(539 citation statements)

References 20 publications

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“…As well as modeling SNP evolution, ALF also allows for short insertions and deletions (INDELs), gene loss and horizontal gene transfer events which occur in real populations but are usually not included in phylogenetic models. We used a phylogeny ( Figure 1), originally produced by Kremer et al 11 from a core genome alignment of 96 Listeria monocytogenes genomes from patients with bacterial meningitis, possessing a number of qualities we wished to be able to reproduce: two distinct lineages (also making midpoint rooting suitable, and negating the strong dependence on correct rooting implicit in the Kendall and Colijn metric), several clonal groups within each lineage, long branches and a polyphyletic population cluster (population clusters were estimated from a core genome alignment using Bayesian Analysis of Population Structure v6.0 (BAPS) 12 ). We define N as the number of strains in the study and M as the number of aligned sites.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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“…Bayesian analysis of population structure (hierBAPS) (Corander et al 2008;Cheng et al 2013) was used to analyze the population structure. A core genome alignment was produced with Roary, and a SNP alignment was generated using SNP sites (Page et al 2016a) and used in hierBAPS, which was run five times with the prior upper bound for the number of clusters varying between 100 and 300.…”

Section: Sequence Data Analysismentioning

confidence: 99%

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

et al. 2017

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Escherichia coli associated with urinary tract infections and bacteremia has been intensively investigated, including recent work focusing on the virulent, globally disseminated, multidrug-resistant lineage ST131. To contextualize ST131 within the broader E. coli population associated with disease, we used genomics to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful lineages identified the emergence of ST131 and ST69 and their establishment as two of the five most common lineages along with ST73, ST95, and ST12. The most frequently identified lineage was ST73. Compared to ST131, ST73 was susceptible to most antibiotics, indicating that multidrug resistance was not the dominant reason for prevalence of E. coli lineages in this population. Temporal phylogenetic analysis of the emergence of ST69 and ST131 identified differences in the dynamics of emergence and showed that expansion of ST131 in this population was not driven by sequential emergence of increasingly resistant subclades. We showed that over time, the E. coli population was only transiently disturbed by the introduction of new lineages before a new equilibrium was rapidly achieved. Together, these findings suggest that the frequency of E. coli lineages in invasive disease is driven by negative frequency-dependent selection occurring outside of the hospital, most probably in the commensal niche, and that drug resistance is not a primary determinant of success in this niche.

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“…In practice, however, it may be simpler to use a genome-wide mutation rate average. Overestimation of mutation rate because of recombination can also be moderated by removal of recently recombined genes (Wilson et al 2009;Cheng et al 2013) or by constructing a tree that gives equal significance to individual point mutations and clusters of mutations that are likely to result from a single recombination event (Didelot and Falush 2007).…”

Section: The Timescale Of Campylobacter Evolutionmentioning

confidence: 99%

The Evolution ofCampylobacter jejuniandCampylobacter coli

Sheppard

Maiden

2015

Cold Spring Harb Perspect Biol

143

127

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The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.

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Hierarchical and Spatially Explicit Clustering of DNA Sequences with BAPS Software

Cited by 566 publications

References 20 publications

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

The Evolution ofCampylobacter jejuniandCampylobacter coli

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