On April 14 , 2022 , Star Protocols , an academic journal of CellPressThe research results " Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.
0 " by Xu Shuhua's team from the School of Life Sciences of Fudan University were published online
This work provides the specific analysis process of ArchaicSeeker 2.
0 method .
The ArchaicSeeker 2.
0 method is mainly used to detect the fragments infiltrated by ancient humans in the modern human genome, and then reconstruct the analysis process of the historical model of population blending between modern humans and ancient humans (Figure1)
Figure 1 ArchaicSeeker 2.
0Analysis flow chart
In the long evolutionary history of modern humans and ancient humans, there is an intricate genetic exchange relationship
Due to factors such as the low proportion of genetic introgression retained in modern populations and the relatively long introgression time, most of the previous methods used to detect introgression fragments from ancient humans to modern humans have not achieved good results.
The historical model of genetic introgression between humans and ancient humans is also difficult
0 addresses these issues in a targeted manner, effectively detecting and quantifying gene communication in closely related species and reconstructing complex gene communication histories at a finer scale
The method is mainly composed of the following three functional modules: ( 1 ) searching for potential introgression fragments; ( 2 ) matching the introgressed fragments to the corresponding ancestral population; ( 3 ) constructing a genetic introgression history model
htm for an introduction to the previous paper on ArchaicSeeker 2.
The protocol in this article takes the data of chromosomes 21 and 22 of the Chinese Han population in the public open database as an example to demonstrate the use of ArchaicSeeker 2.
0Methods To detect and quantify the introgressed genomic fragments of ancient human Neanderthals and Denisovans, and then reconstruct the analysis process of the historical model of genetic introgression of the Chinese Han population by Denisovans, including the analysis process The input file format, precautions, code execution commands and corresponding output file formats that need to be prepared for each step
in In addition, the protocol also lists the code error messages or file format problems that users may encounter when installing and using the ArchaicSeeker 2.
0 method, and provides corresponding solutions, which provides certain convenience for users' analysis work
Doctoral student Zhang Rui is the first author, Professor Xu Shuhua is the corresponding author, and the School of Life Sciences of Fudan University is the first corresponding author
This work has been funded by the National Natural Science Foundation of China, the Pilot Project of the Chinese Academy of Sciences, the Newton Fund of the Royal Society, and the Shanghai Science and Technology Major Project "International Human Phenotyping Project (Phase I)" and other funds
Paper link: https://star-protocols.