PT  - JOURNAL ARTICLE
AU  - Ya Hu
AU  - Qiliang Ding
AU  - Yi Wang
AU  - Shuhua Xu
AU  - Yungang He
AU  - Minxian Wang
AU  - Jiucun Wang
AU  - Li Jin
TI  - Investigating the Evolutionary Importance of Denisovan Introgressions in Papua New Guineans and Australians
AID  - 10.1101/022632
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022632
4099  - http://biorxiv.org/content/early/2015/07/15/022632.short
4100  - http://biorxiv.org/content/early/2015/07/15/022632.full
AB  - Previous research reported that Papua New Guineans (PNG) and Australians contain introgressions from Denisovans. Here we present a genome-wide analysis of Denisovan introgressions in PNG and Australians. We firstly developed a two-phase method to detect Denisovan introgressions from whole-genome sequencing data. This method has relatively high detection power (79.74%) and low false positive rate (2.44%) based on simulations. Using this method, we identified 1.34 Gb of Denisovan introgressions from sixteen PNG and four Australian genomes, in which we identified 38,877 Denisovan introgressive alleles (DIAs). We found that 78 Denisovan introgressions were under positive selection. Genes located in the 78 introgressions are related to evolutionarily important functions, such as spermatogenesis, fertilization, cold acclimation, circadian rhythm, development of brain, neural tube, face, and olfactory pit, immunity, etc. We also found that 121 DIAs are missense. Genes harboring the 121 missense DIAs are also related to evolutionarily important functions, such as female pregnancy, development of face, lung, heart, skin, nervous system, and male gonad, visual and smell perception, response to heat, pain, hypoxia, and UV, lipid transport, metabolism, blood coagulation, wound healing, aging, etc. Taken together, this study suggests that Denisovan introgressions in PNG and Australians are evolutionarily important, and may help PNG and Australians in local adaptation. In this study, we also proposed a method that could efficiently identify archaic hominin introgressions in modern non-African genomes.