Saturday, August 08, 2020

Another Mystery Ancestor Joins The Group

Science Daily has a story on genetic work done by researchers at Cornell University and Cold Spring Harbor Laboratory that suggests that there is, as yet, another unnamed ancestor to the modern human line. They write:

In the new paper, the researchers developed an algorithm for analyzing genomes that can identify segments of DNA that came from other species, even if that gene flow occurred thousands of years ago and came from an unknown source. They used the algorithm to look at genomes from two Neanderthals, a Denisovan and two African humans. The researchers found evidence that 3 percent of the Neanderthal genome came from ancient humans, and estimate that the interbreeding occurred between 200,000 and 300,000 years ago. Furthermore, 1 percent of the Denisovan genome likely came from an unknown and more distant relative, possibly Homo erectus, and about 15% of these "super-archaic" regions may have been passed down to modern humans who are alive today.
The paper is available in PLoS Genetics, which means that it is free to the public.  The above-description makes it sound like bootstrapping on stilts.  Here is a paragraph from the paper, itself, that describes the process:
In this paper, we describe a powerful and highly general new method, called ARGweaver-D, that samples ancestral recombination graphs (ARGs) [18–20] conditional on a generic demographic model, including population divergence times, size changes, and migration events. After introducing ARGweaver-D, we present simulation studies showing it can successfully detect Nea→Hum introgression, even when using a limited number of genomes, and that it also has power for older migration events, including Hum→Nea, Sup→Den, and Sup→Afr events. Finally, we apply this method to modern-day Africans and ancient hominins, and characterize both new and previously reported cases of introgression between humans and archaic hominins.
Okay, it still sounds like bootstrapping on stilts.  I am not sure how you can do a simulation to detect older migration events when that is what you are looking for in the first place.  What exactly is an ancestral recombination graph, you ask?  From a previous paper on this subject:
It is possible to capture these complex relationships using a representation called the ancestral recombination graph (ARG), which provides a complete description of coalescence and recombination events in the history of the sample. However, previous methods for ARG inference have not been adequately fast and accurate for practical use with large-scale genomic sequence data. In this article, we introduce a new algorithm for ARG inference that has vastly improved scaling properties. Our algorithm is implemented in a computer program called ARGweaver, which is fast enough to be applied to sequences megabases in length. With the aid of a large computer cluster, ARGweaver can be used to sample full ARGs for entire mammalian genome sequences.

The best data we have suggests that Neandertals and African archaics split some 600 ky ago when a group of Homo ergaster migrated out of Africa and took up residence in western Europe, leading to branching events that eventually included H. antecessor and the Neandertals.  This is supported by this research, which found about 7% introgression into the Neandertal genome of archaic H. sapiens.  The surprise was that 1% of the Denisovan genome likely came from an, as yet, undiscovered hominin.  

Increasingly, there is evidence that considerable interbreeding occurred throughout the middle to late Pleistocene, continuing through the interbreeding that occurred in China and Europe.  As I wrote about the 105-130 ky old Chinese Xuchang skulls:

These two Chinese skulls stand at the crossroads of these population movements. While showing clear Neandertal characteristics, they also express modern traits, possibly reflecting mixing with the late, modern human arrivals represented by the recent modern human finds at Daoxian. Yet they also express a clear link to ancient East Asian populations. The implications of these skulls are stark: there has been widespread population mixing and regional continuity in Europe and Asia for at least 400 thousand years. Not only did the Neandertals feel enough cultural kinship to mate and have children with these East Asian people, the early modern humans coming out of Africa did, as well. As Chris Davis of China Daily News put it: “One big happy family.”
This likely represents only a small part of the vast scope of population mixing. I will be curious to see where the ARG research leads.

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