"Phylogenetic trees are graphs representing evolutionary histories and ancestry, and are typically inferred from the genomic data. In genomic epidemiology, for example, DNA sequences of the same pathogen are collected from different hosts (for example, SARS-CoV-2 genomes collected from different patients) and compared with one another. Phylogenetic trees inferred from these genomes can reveal the emergence of drug resistance and new variants of concern, transmission between individuals and countries, and many other details of the evolution and spread of the pathogen4."
"This issue is typically addressed with additional methods such as Felsenstein's bootstrap2. For a given dataset, Felsenstein's bootstrap typically creates 100 or 1,000 replicates by randomly resampling the genetic data with replacement. Phylogenetic inference is performed on each to estimate replicate trees, and the support score of a clade (the set of taxa inferred to be all the descendants of one ancestor in the tree) is defined as the proportion of replicate trees containing that clade."
Phylogenetics underpins evolutionary biology by inferring evolutionary histories and ancestry through phylogenetic trees derived from genomic data. In genomic epidemiology, pathogen DNA sequences collected from different hosts are compared to trace emergence of drug resistance, new variants, and transmission patterns. Scalable phylogenetic methods often estimate a single tree without measuring uncertainty. Felsenstein's bootstrap generates many resampled datasets and computes clade support as the proportion of replicate trees containing the clade, which also serves as branch support. Felsenstein's bootstrap was developed for inter-species studies and faces computational and applicability limitations for closely related pandemic-scale datasets.
Read at Nature
Unable to calculate read time
Collection
[
|
...
]