2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2021

Rafal Mostowy, Nicholas J. Croucher, Cheryl P. Andam, Jukka Corander, William P. Hanage, Pekka Marttinen. Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations. Molecular biology and evolution, 34(5):1167-1182. 2017.

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Prokaryotic evolution is affected by horizontal transfer of genetic material
through recombination. Inference of an evolutionary tree of bacteria thus relies 
on accurate identification of the population genetic structure and
recombination-derived mosaicism. Rapidly growing databases represent a challenge 
for computational methods to detect recombinations in bacterial genomes. We
introduce a novel algorithm called fastGEAR which identifies lineages in diverse 
microbial alignments, and recombinations between them and from external origins. 
The algorithm detects both recent recombinations (affecting a few isolates) and
ancestral recombinations between detected lineages (affecting entire lineages),
thus providing insight into recombinations affecting deep branches of the
phylogenetic tree. In simulations, fastGEAR had comparable power to detect recent
recombinations and outstanding power to detect the ancestral ones, compared with 
state-of-the-art methods, often with a fraction of computational cost. We
demonstrate the utility of the method by analyzing a collection of 616
whole-genomes of a recombinogenic pathogen Streptococcus pneumoniae, for which
the method provided a high-resolution view of recombination across the genome. We
examined in detail the penicillin-binding genes across the Streptococcus genus,
demonstrating previously undetected genetic exchanges between different species
at these three loci. Hence, fastGEAR can be readily applied to investigate
mosaicism in bacterial genes across multiple species. Finally, fastGEAR correctly
identified many known recombination hotspots and pointed to potential new ones.
Matlab code and Linux/Windows executables are available at
https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).