homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes

Abstract

Organisms such as allopolyploids and F1 hybrids contain multiple subgenomes, each potentially with its own evolutionary history. These organisms present a challenge for multilocus phylogenetic inference and other analyses since it is not apparent which gene copies from different loci are from the same subgenome. Here we introduce homologizer, a flexible Bayesian approach that uses a phylogenetic framework to infer the phasing of gene copies across loci into polyploid subgenomes. Through the use of simulation tests we demonstrate that homologizer is robust to a wide range of factors, such as the phylogenetic informativeness of loci and incomplete lineage sorting. Furthermore, we establish the utility of homologizer on real data, by analyzing a multilocus dataset consisting of nine diploids and 19 tetraploids from the fern family Cystopteridaceae. Finally, we describe how homologizer may potentially be used beyond its core phasing functionality to identify non-homologous sequences, such as hidden paralogs, contaminants, or allelic variation that was erroneously modelled as homeologous.

Polyploid phylogenetics

“…The outcome of incorrect phasing in either situation is the same: an accession (a tip on a phylogeny) becomes a chimeric mix of multiple distinct evolutionary histories. Such an amalgam violates the bifurcating model underlying both standard and coalescent models of phylogenetic inference—the phylogenetic position inferred for such a sample is, at best, unreliable (Oxelman et al ., 2017; Freyman et al ., 2020).…”

“…Most recently, Freyman et al . (2020) developed a method – ' homologizer ' – to infer the phasing of multiple loci in a Bayesian framework. Implemented in RevBayes (Höhna et al ., 2016), and able to analyse similarly sized datasets as in ‘regular’ Bayesian phylogenetic analysis, homologizer takes as input the individual‐locus alignments.…”

“…Kao et al ., 2019). Historically, polyploids were often dropped from such analyses, and polyploidy‐rich groups were avoided for phylogenetic study altogether (Freyman et al ., 2020). This tendency resulted in a body of literature that is based on a biased set of study groups and, within those groups that were studied, on a biased sample of included species.…”

Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies

“…Perityleae occupies a highly nested position within the Compositae, wherein a history of whole-genome duplication and parallel retention of duplicate genes is likely to contribute to widespread paralogy (Barker et al, 2008). Improved bioinformatic procedures that effectively separate and subset or phase paralogous gene regions (Gardner et al, 2019;Freyman et al, 2020), rather than excluding them, could be useful both for increasing statistical support as well as understanding the hybrid origins of putatively allopolyploid taxa (e.g., Brandrud et al, 2020).…”

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events inAlchemillas.l. (Rosaceae)

“…Paralog merger should be more problematic in cases of recent allopolyploidy or neo-allopolyploidy taxa. To this end, recently developed tools have been designed to phase gene copies into polyploid subgenomes using phylogenetic and similarity approaches (e.g., Freyman et al 2020, Nauheimer et al 2020.…”