HybridCheck

HybridCheck analyzes recombination and introgression signals in large DNA sequence datasets (including multi-kilobase contigs and whole-genome sequences from three or more individuals) to detect hybridization, genetic introgression, and horizontal gene transfer.

Key Features:

• Visualization: Generates high-density graphics that illustrate mosaic-like genome structures resulting from recombination and hybridization.
• ABBA-BABA Tests: Implements several ABBA-BABA tests for detecting introgression and distinguishing hybridization from incomplete lineage sorting.
• Detailed Reporting: Reports breakpoint positions, mutation counts per introgressed block, probabilities that regions are not caused by recombination, and estimated ages of recombination events.
• Divergence Time Calculation: Calculates divergence times between donor and recombinant sequences using correction models JC, K80, F81, HKY, and GTR with a fast dating algorithm.
• Coalescence Time Estimation: Estimates coalescence times of introgressed blocks to aid differentiation between hybridization and incomplete lineage sorting.

Scientific Applications:

• Recombination Detection: Detects and localizes recombination signals in DNA sequence datasets.
• Introgression and Hybridization Analysis: Identifies introgressed genomic regions and assesses hybridization among individuals.
• Horizontal Gene Transfer Identification: Assists in identifying horizontal gene transfer events.
• Temporal Analysis: Estimates ages of recombination events and divergence times between donor and recombinant sequences.
• Distinguishing Hybridization vs ILS: Differentiates hybridization from incomplete lineage sorting using ABBA-BABA tests and coalescence time estimates.
• Genome-scale Analyses: Applicable to analyses of large contigs and whole-genome sequences from three or more individuals.

Methodology:

Implemented in R; implements ABBA-BABA tests; calculates divergence times using JC, K80, F81, HKY, and GTR correction models; estimates coalescence times and ages of recombination events; reports breakpoint positions and mutation counts; and generates high-density graphics.