Mass-Based Protein Phylogenetic Approach to Identify Epistasis

Downard, Kevin M.

doi:10.1007/978-1-0716-0947-7_1

Cited by 2 publications

(1 citation statement)

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“…The phylonumeric mass tree approach has been applied to a variety of different organisms with a particular focus on the influenza virus given the research interests of this laboratory (Lun et al, 2013;Swaminathan & Downard, 2014;Akand & Downard, 2017, 2018a, 2018b, 2020Downard, 2020a). Both experimental and theoretical insilico generated peptide mass sets have been used in these studies, the latter where there is insufficient experimental mass map data in order to study evolutionary mechanisms.…”

Section: | Application Of Phylonumerics To Study Antiviral Resistance and Epistasismentioning

confidence: 99%

Sequence‐free Phylogenetics With Mass Spectrometry

Downard

2020

Mass Spectrometry Reviews

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An alternative, more rapid, sequence-free approach to build phylogenetic trees has been conceived and implemented. Molecular phylogenetics has continued to mostly focus on improvement in tree construction based on gene sequence alignments. Here protein-based phylogenies are constructed using numerical data sets ("phylonumerics") representing the masses of peptide segments recorded in a mass mapping experiment. This truly sequence-free method requires no gene sequences, nor their alignment, to build the trees affording a considerable time and cost-saving to conventional phylogenetics methods. The approach also calculates single point amino acid mutations from a comparison of mass pairs from different maps in the data set and displays these at branch nodes across the tree together with their frequency. Studies of the consecutive, and near-consecutive, ancestral and descendant mutations across interconnected branches of a mass tree allow putative adaptive, epistatic, and compensatory mutations to be identified in order to investigate mechanisms associated with evolutionary processes and pathways. A side-by-side comparison of this sequence-free approach and conventional gene sequence phylogenetics is discussed.

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