Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

By Frederic Bertels, O. Silander, Mikhail Pachkov, P. Rainey, E. van Nimwegen. Molecular biology and evolution, 2014

441 citations recorded by the source corpus.

Studies of microbial evolutionary dynamics are being transformed by the availability of affordable high-throughput sequencing technologies, which allow whole-genome sequencing of hundreds of related taxa in a single study. Reconstructing a phylogenetic tree of these taxa is generally a crucial step in any evolutionary analysis. Instead of constructing genome assemblies for all taxa, annotating these assemblies, and aligning orthologous genes, many recent studies 1) directly map raw sequencing reads to a single reference sequence, 2) extract single nucleotide polymorphisms (SNPs), and 3) infer the phylogenetic tree using maximum likelihood methods from the aligned SNP positions. However, here we show that, when using such methods to reconstruct phylogenies from sets of simulated sequences, both the exclusion of nonpolymorphic positions and the alignment to a single reference genome, introduce systematic biases and errors in phylogeny reconstruction. To address these problems, we developed a new method that combines alignments from mappings to multiple reference sequences and show that this successfully removes biases from the reconstructed phylogenies. We implemented this method as a web server named REALPHY (Reference sequence Alignment-based Phylogeny builder), which fully automates phylogenetic reconstruction from raw sequencing reads.

Subfields: Food Science, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1753b3719a25991f483c71917c203b3721761567

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Citations in the corpus

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “In addition, mapping can be sensitive to contaminant, overlook structural variation, misalign low-complexity and repetitive sequence, and introduce systematic bias in phylogenetic reconstruction [57-59].”
Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies (2015, methodology): “Users of software pipelines that automatically assemble RAD loci and generate phylogenies (Bertels et al. 2014; Lee et al. 2014) should be careful to verify that the proper models are being used for phylogeny estimation, since default settings may not be appropriate for data sets composed entirely…”