Reticulation events caused by hybridization are common and important sources of novelty in angiosperm evolution (Wood et al., 2009;Palfalvi et al., 2020). The detection, investigation, and representation of hybridization remains a challenge in phylogenomics (Kellogg, 2016;Mallet et al., 2016;Spooner et al., 2020). The combination of divergent genomes in hybrids (herein used for any organism that contains divergent genomes due to a hybridization event, e.g., many polyploids) introduces conflicting phylogenetic signal and can lead to topologically incorrect or poorly resolved phylogenetic trees (McDade, 1992;Soltis et al., 2008). However, the advancement of target capture data and universal probe kits such as Angiosperms353 (Johnson et al., 2018) provides an opportunity to gain insight into historical reticulations in angiosperm evolution and reduce phylogenetic conflict, if ortholog (or homeolog in polyploids) gene variants can be identified and separated (phased).Previously, inclusion of phased gene variants in phylogenetic studies has been used to confirm hybrid status of organisms (Sang and Zhang, 1999), determine the origin of polyploids (Popp and Oxelman, 2001), reveal parental lineages (Triplett et al., 2012;Estep et al., 2014), enable reconstruction of past reticulations (Estep et al., 2014;Brassac and Blattner, 2015), and date ancient hybridization events (Marcussen et al., 2015). Using Sanger sequencing, single-gene studies generated sequences for each variant separately using cloning (Sang and Zhang, 1999;Popp and Oxelman, 2001), and multi-gene studies linked these gene variants using their phylogenetic association in single-gene
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.
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