Xu Shuhua’s team developed a new method ArchaicSeeker 2.0: Reshaping the prehistoric human gene communication and evolution model

On October 29, 2021, Nature Communications published online the research results "Refining models of archaic admixture in Eurasia with ArchaicSeeker2.
0 " by the Shanghai Institute of Nutrition and Health of the Chinese Academy of Sciences and the Xu Shuhua team of Fudan University
.

This work proposes a new computational analysis method ArchaicSeeker 2.

As a species that appeared very late in the evolution of life on earth, human beings have a short history, but the process is complicated
.

Research in recent years has found that the ancestors of modern humans may have contacted and coexisted with ancient humans who arrived earlier on their journey to "out of Africa" ​​and explored the world for a long period of time, during which genetic exchanges occurred

1) Gene exchanges that occurred in prehistoric times, from the standpoint of modern humans, can be regarded as genetic introgression or genetic introgression of ancient humans into modern humans
.

Due to the relatively long time of gene infiltration events (30,000 to 100,000 years ago), the gene fragments of ancient humans were often fragmented into DNA sequences with an average length of only tens of thousands of nucleotides due to genetic recombination (human genome is 30 Billion nucleotides in length), and are extremely dispersed in the modern human genome

Figure 1.

Schematic diagram of ArchaicSeeker 2.

2) Earlier studies have shown that there are a small number of infiltrating gene sequences from ancient humans such as Neanderthals and Denisovans in the modern human genome outside of Africa
.

However, many key issues, such as when, where, and through which ancient humans these gene fragments infiltrated the modern human genome, are still controversial

3) Previous studies on the genetic mixing of ancient humans and modern humans are mostly based on the model of "single trip out of Africa" ​​by modern humans
.

However, the research team found that the "single trip out of Africa" ​​model contradicts the mixing time and frequency of modern human prehistoric and other ancient humans such as Neanderthals and Denisovans

Figure 2.

A schematic diagram of the prehistoric migration route of modern humans and their gene exchange patterns with ancient humans

Figure 3.

Schematic diagram of the evolution of modern humans and their genetic integration with ancient humans

　　4) Based on ArchaicSeeker 2.
0 's accurate and efficient evaluation of ancient human gene infiltration fragments, the research team analyzed the functions and distribution characteristics of ancient human gene infiltration sequences in nearly 300 modern populations around the world, and found that they are enriched in immunity, body weight ( ZNF169 ), Cardiopulmonary function ( HHAT ), ultraviolet response and carbohydrate metabolism ( HYAL1 , HYAL2 , HYAL3 ) and other related functional gene regions
.

Excluding these ancient human infiltrating fragment-enriched regions, the research team also detected 84 "introgressive desert" regions that completely lack ancient human gene fragments

　　The work was undertaken by Dr.
Yuan Kai, Dr.
Ni Xumin (Beijing Jiaotong University), Liu Chang, Pan Yuwen, Deng Lian Youth Researcher (Fudan University), Zhang Rui, Gao Yang (Shanghai University of Science and Technology), Ge Xueyan, Postdoctoral Fellow Liu Jiaojiao (Fudan University), Postdoctoral Ma Xixian, Young Researcher Lou Haiyi (Fudan University), Dr.
Wu Taoyang (University of East Anglia, UK), etc.
were completed under the leadership of Dr.
Xu Shuhua
.
This work has been funded by a number of funds from the Chinese Academy of Sciences, the National Natural Science Foundation of China, the Shanghai Municipal Science and Technology Commission, the National Key Research and Development Program, and the Royal Society Newton Fund.
At the same time, it has also obtained the outstanding innovation of the frontier of animal evolution and genetics of the Chinese Academy of Sciences.
Supported by the Center and the National Genetic and Developmental Collaborative Innovation Center
.

　　Link to the paper: https://