HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets

Abstract

Premise of the study: Hybrids contain divergent alleles that can confound phylogenetic analyses but can provide insights into parental lineages when identified and phased. We developed HybPhaser to detect hybrids in target capture datasets and to phase reads according to haplotypes based on similarity and a phylogenetic framework. Methods and Results: HybPhaser is an extension to the HybPiper sequence assembly workflow. We used Angiosperms353 target capture data for Nepenthes including known hybrids to test the novel workflow. Reference mapping was used to record heterozygous sites and identify hybrid accessions that were phased by mapping sequence reads to multiple references. The parental lineages of known hybrids were confirmed and conflicting phylogenetic signal reduced, improving the outcomes of phylogenetic analysis. Conclusions: HybPhaser is a novel pipeline for summarizing and optimizing target capture datasets, detecting hybrid accessions as well as paralogous genes, and generating phased accessions that can provide insights into reticulated evolution.

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

“…We were motivated by the general premise of using phased data to infer reticulate evolutionary histories of polyploids based on the success of empirical studies where phasing was informative about hybridization or introgression events (e.g., Oberprieler et al 2017; Eriksson et al 2018). We were aware of few instances of phasing genomic or phylogenomic data in polyploids, except in cases where chromosome-level whole- genome assemblies have characterized subgenomes in allopolyploid crops (Yang et al 2017; Colle et al 2019) or emerging results that are dependent on the sampling of parental lineages (Freyman et al 2020; Nauheimer et al 2020). We designed PATÉ for target enrichment data because of the availability of such data for many of taxa, but it is applicable to other types of data with paired-end Illumina reads.…”

“…While this may complicate analyses of concatenated multi-locus datasets, it is ideal for the MSC that assumes free recombination between loci and can leverage multiple alleles per species for estimating θs . Those interested in concatenated analyses can use other recent approaches that assign gene copies to parental subgenomes (Freyman et al 2020; Nauheimer et al 2020).…”

HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets

“…All workflow scripts are available through the HybPhaser repository on GitHub (https://github.com/LarsN auhei mer/HybPh aser; Nauheimer, 2021). Sequence data are available through the National Center for Biotechnology Information (NCBI) (BioProjects: PRJNA706038 [this study] and PRJEB35235 [Murphy et al, 2020]).…”

Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics

“…Their approach is to improve the target file used to recover genes in HybPiper by selecting more appropriate orthologs of the Angiosperms353 genes. Nauheimer et al (2021) describe HybPhaser, a method for detecting hybrid taxa using HybPiper assemblies. Using an Angiosperms353 data set collected for Nepenthes, they employ an innovative two-step strategy in which an initial phylogeny is first used to identify representatives of different clades that have low heterozygosity (and are thus presumably not hybrids).…”