Asian vs. African origin of Humans and the "inverted" phylogenetic tree of Shi Huang

I have mentioned Shi Huang in two previous posts (Out of China? in 2019 and On Neanderthals in America and the Out of China Hypothesis in 2025).

I love how he inverts the phylogenetic trees, from a root in Africa and youngest brances in East Asia, Europe, and America, to one rooted in Asia, with a youngest African branch, going against the consensus of the Out of Africa theory.

This posture is similar to what I suggested in a post nearly 8 years ago, "On the direction and root of phylogenetic trees" (April 2018): "When I see a phylogenetic tree (also known as an evolutionary tree), I always wonder why do we believe that those branches, trunk and the root which anchors it, are correct. I ask myself why is it assumed that the mutation took place in one direction and not the other. And this trivial question is fundamental because the branches open up from other branches based on the differences between the DNA as you move along them." (sorry for quoting myself). The post included the image below.

Two different trees built from the same genome samples. Copyright © 2018 by Austin Whittall

In today's post I mention another paper co-authored by Shi Huang: Ancient Y chromosomes confirm origin of modern human paternal lineages in Asia rather than Africa, Hongyao Chen, Ye Zhang, Shi Huang. bioRxiv 2020.03.10.986042; doi: https://doi.org/10.1101/2020.03.10.986042

The paper includes the following figure, which, as you can see, inverts the root of the Y-chromosome tree, from Africa to Asia, and places Africa in the newest branch.

Figure 1. Y chromosome phylogenetic trees of modern humans. Only major branches and representative SNPs are shown with branch lengths not to scale. The tree topology was built without making use of any ancient DNAs. A. The Out of East Asia model. B. The Out of Africa model.. Source

They argue in this paper that "The mutation pattern in the ancient Y chromosomes as revealed here confirms the expectation that ancient haplogroups should mutate in only a fraction of the sites that define a haplogroup they belonged to. Two observations here confirm the Asia model and invalidate the Africa model. First, only haplogroups specific to the Asia model showed the expected mutation pattern in ancient samples. Second, the genetic reality that a haplogroup, be it ancient or present, should not carry mutations found in basal haplogroups to which they do not belong is only met by the Asia model but not the Africa model."

Interesting and controversial, and also, not peer reviewed either.

By the way, Shi Huang expands this idea in a paper published one year ago: Examining models of modern human origins through the analysis of 43 fully sequenced human Y chromosomes, Shi Huang. bioRxiv 2023.11.09.566475; doi: https://doi.org/10.1101/2023.11.09.566475. In it he uses the same inverted trees to argue against the Out of Africa theory and support his Out of East Asia theory.

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