A quick review of using ARGweaver-D to map gene flow in ancient hominins
Having read the paper “Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph”, which used ARGweaver-D, I would like to explain some of the subjects discussed. I am an amateur in the field but find it fascinating.
The research performed in this paper took genetic information from other studies and ran the information through a new(ish) computer program to attempt to find the amount of genetic material that transferred from one human ancestral group to another. The groups that were investigated were homo sapiens (us), Neanderthals, Denisovans, and multiple unknown ancient ancestral groups (super-archaic humans). They used a new extension of a computer program, ARGweaver, called ARGweaver-D, using Bayesian algorithms. ARG stands for ancestral recombination graphs which is a way of saying there is a common ancestor, a number of generations pass, and some descendants of the common ancestor have children together. The genes of the descendants have re-combined to form a new set of genes. The difference is that the number of generations that pass can be counted over some number of millennia.
This study was intended to see if the new ARGWeaver-D computer model update will work as accurately as hoped. The mixing of the different species of human over the years is too complex for the old computer program to work with, so an update was installed. The update can handle more mixing and re-mixing of genetic material. Even though genetic scientists know there has been interbreeding amongst the groups, it is difficult for them to find exactly which region of each gene was influenced by which group. This is due in part to the little amount of information we have on Neanderthal and Denisovan genetics and the complete lack of genetic material from the super-archaic humans.
The computer models successfully predicted the crossbreeding outcomes of the samples showing it is worth using as an improvement over the previous version. And by using African genetic material, which has no Neanderthal or Denisovan genes in it, they were able to find chunks of genes that were introduced to the human species from even further back. They also found that about one percent of Denisovan DNA came from another ancient human ancestor and 15% of that DNA was passed forward through the Denisovans to Asian and Oceanian descendants living today. The authors suspect the ancient human ancestor is Homo Erectus, but since we have no DNA from any Homo Erectus as of yet, we have no way to be sure.
Citation: Hubisz MJ, Williams AL, Siepel A (2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16(8): e1008895. https://doi.org/10.1371/journal.pgen.1008895
Also see:
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. Melissa J. Hubisz, Amy L. Williams, Adam Siepel; bioRxiv 687368; doi: https://doi.org/10.1101/687368
