HybPhaser

HybPhaser detects and phases hybrid organisms in target capture sequencing datasets to resolve divergent alleles and support phylogenetic inference of reticulated evolution.

Key Features:

• Reference mapping and heterozygosity assessment: Assesses heterozygous sites across target capture datasets via reference mapping to identify candidate hybrid accessions.
• Hybrid detection and paralog identification: Identifies hybrid accessions and detects paralogous genes through analysis of heterozygous sites and mapping results.
• Similarity-based read phasing: Phases reads by mapping hybrid-sample reads to multiple references and sorting reads according to similarity to parental lineages.
• Separation of divergent haplotypes: Sorts and phases reads to separate divergent haplotypes representing parental lineages.
• Phylogenetic integration: Incorporates phased accessions into phylogenetic frameworks to reduce conflicting signals and improve clade support.

Scientific Applications:

• Reticulate evolution analysis: Clarifies patterns of reticulated evolution by detecting and phasing hybrid lineages in target capture datasets.
• Phylogenetic accuracy improvement: Reduces conflicting signals in phylogenetic trees and increases clade support through phased accession inclusion.
• Parental lineage confirmation: Confirms parental lineages of hybrids to inform studies of speciation and genetic diversity.
• Target capture dataset applications: Applied to target capture data such as Angiosperms353 and demonstrated on plant groups like Nepenthes using known hybrid samples.

Methodology:

Uses target capture data (e.g., Angiosperms353) and known hybrid samples; performs reference mapping to assess heterozygous sites; maps reads from hybrid samples to multiple references and sorts them by similarity for similarity-based phasing; includes phased accessions in phylogenetic analyses to evaluate clade support and validate parental origins.