Recent progress on methods for estimating and updating large phylogenies

Abstract

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the past few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g. incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.

Target capture and genome skimming for plant diversity studies

“…Other efforts tackling larger taxonomic scales, such as the Angiosperm tree of life initiative (Baker et al, 2022 ), aim to sequence every angiosperm genus using a target capture bait set of 353 nuclear loci. These phylogenomic platforms might prove invaluable as a backbone to combine different sets of genomic data already available, for example using a phylogenetic placement approach (Ringelberg et al, 2022 ; Zaharias and Warnow, 2022 ).…”

“…One approach would be to independently build phylogenies from assemblies of each bait set and place the smaller‐scale studies (e.g., genus level) onto a larger‐scale (e.g., family level) backbone phylogeny based on overlapping taxa (Ringelberg et al, 2022 ). Other methods to deal with or update larger phylogenies have been developed recently (Zaharias and Warnow, 2022 ) using phylogenetic placement, i.e., updating an existing large tree with new sequences (Barbera et al, 2019 ; Balaban et al, 2022 ; Wedell et al, 2022 ).…”

Genomic population structures of microbial pathogens

“…Zaharias & Warnow [ 5 ] provide a broad overview of new methods that can generate highly accurate maximum likelihood (ML) trees from multiple sequence alignments containing 100 000 s of gene or genomic sequences. Many of these methods rely on divide-and-conquer techniques that can handle phylogenetic heterogeneity resulting from incomplete lineage sorting and/or gene duplication or loss.…”

Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent

“…Pairwise comparisons within collections of genomes are commonly integrated to establish phylogenies, providing insight into their shared evolutionary history. They are similarly used to position novel genomes within an established phylogeny [ 1 ]. Substitution distances can also be converted to genome-wide percentage identity to define taxonomic demarcations, such as the distance a novel genome must be from known genomes to establish it as a new species [ 2 ].…”