title: Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes.
abstract: Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK. caitlin.collins12@imperial.ac.uk.
authors.forename: Caitlin
authors.initials: C
authors.lastname: Collins
authors.affiliation: Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK. x.didelot@imperial.ac.uk.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001424:Bacterial Infections / Q000382:microbiology; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005828:Genetics, Population; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D015233:Models, Statistical; D010802:Phylogeny; D011995:Recombination, Genetic; D012984:Software; D064878:Web Browser
keywords: Ancestral inference; Bacterial recombination; Comparative genomics; Pathogen genomics; Phylogenetics; Population structure