Infectious Disease Responses Laboratory, Prince of Wales Clinical Sciences, Medicine, University of New South Wales, Sydney, New South Wales, Australia.
Mass Spectrom Rev. 2022 Jan;41(1):3-14. doi: 10.1002/mas.21658. Epub 2020 Nov 10.
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.
已经构思并实施了一种替代的、更快速的、无需序列的构建系统发育树的方法。分子系统发生学一直主要侧重于基于基因序列比对的树构建的改进。在这里，使用代表在质量映射实验中记录的肽段质量的数值数据集（“phylonumerics”）构建基于蛋白质的系统发育树。这种真正无需序列的方法不需要基因序列，也不需要对其进行比对，从而为传统的系统发生学方法节省了大量的时间和成本。该方法还可以从数据集中不同图谱的质量对比较中计算单点氨基酸突变，并在树的分支节点处显示这些突变及其频率。对质量树的相互连接的分支上连续的和近乎连续的祖先和后代突变的研究，可以识别出可能的适应性、上位性和补偿性突变，以研究与进化过程和途径相关的机制。讨论了这种无需序列的方法与传统基因序列系统发生学的并排比较。
