Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0.

Area of Science:

• Paleogenetics
• Population Genetics
• Bioinformatics

Background:

• Understanding archaic hominin admixture is crucial for reconstructing human evolutionary history.
• Previous methods lacked comprehensive tools for identifying introgressed sequences and modeling complex gene flow patterns.

Purpose of the Study:

• To introduce ArchaicSeeker 2.0, a novel computational tool for detecting archaic hominin DNA and modeling admixture.
• To provide a protocol for applying ArchaicSeeker 2.0 to population genetic data.

Main Methods:

• ArchaicSeeker 2.0 employs functional modules to seek introgressed sequences.
• It determines the ancestry of these sequences.
• It reconstructs admixture history, including multiple gene flow events.

Main Results:

• The study demonstrates the application of ArchaicSeeker 2.0 on Han Chinese population data.
• The tool successfully identifies introgressed sequences and models admixture history.

Conclusions:

• ArchaicSeeker 2.0 is an effective tool for analyzing archaic hominin introgression and admixture.
• The protocol facilitates the application of ArchaicSeeker 2.0 in population genetic studies.