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New Discoveries Shed Light on Out of Africa Theory, and Beyond

Roberta Estes

For many years, the accepted out-of-Africa Y DNA tree branches and calibration, meaning when that exit occurred, have focused on the exit of a single African lineage, CT-M168 which then, after leaving Africa, was believed to have split into three distinct branches:

Not long after, DE split into:

Obviously, if CT-M168 exited Africa and then branched into the other branches after its exit, either some branches had to have migrated back to Africa, or, there was something we didn’t know.

Turns out, there were multiple “somethings” we didn’t know.

D Divides – Thanks to Men in Nigeria

In August 2019, the paper A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa was authored by Haber et al.

I wrote about the haplogroup D split in the article Exciting New Y DNA Haplogroup D Discoveries. 

Haber et al Paper

Abstract from the Haber paper:

Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa – earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.

In 2003, five Nigerian men were sequenced yielding haplogroup DE, but the sequencing technology since that time has improved dramatically. In 2019, those early samples were resequenced by Haber and analyzed in combination with information not available in 2003.

Resequencing yielded a new ancient clade, branching from the DE lineage close to the divergence of the D and E split. The lineage formed by the Nigerian sample was named D0 (D zero) by the authors to avoid needing to rename the downstream branches. It should be noted that the authors used the older letter-number-letter naming method coined as “nomenclature by lineage” from the first YCC paper, rather than the SNP naming method called “Nomenclature by mutation,” aks shorthand – hence their concern about renaming branches. Having said that, typically the base branch names are retained for reference, regardless, and D0 is clearly a base haplogroup.

The Nigerian samples were narrowed from 5 to 3 quality samples. Those three samples had been collected from unrelated men in different villages from different cultures who spoke different languages. Their Y DNA estimated date of convergence, meaning their most recent common ancestor (MRCA,) is about 2500 years ago.

The results of full genome sequencing are far more robust today and the theories about the exit of mankind from Africa are informed by Neanderthal genomic information. All people worldwide have about 2% Neanderthal genome, but African peoples do not – other than the North African region where back-migration has occurred.

This split in the tree increases the early lineages from 4 to 5 with DE now including the following three branches:

Out of Africa Theories

The three out of Africa theories proposed by Haber are illustrated below with Figure 2 from their paper. Please note that dates are estimates and different calculation methodologies produce different date ranges.

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Haber et al put forth the above three theories in their paper.

You’ll note that:

Option D, of the above options, is the most parsimonious model, meaning the fewest amount of complex items needs to occur and is, therefore, most likely to have actually happened. Option D does not include or require any back-migration to occur and accommodates all of the haplogroups found exclusively in Africa along with those found only outside of Africa.

Dr. Miguel Vilar, anthropologist and former Lead Scientist for National Geographic’s Genographic Project provides the following comment about Option D and introduces Option E.

Neanderthal

It turns out that the sequencing of the Neanderthal genome appears to be the tie-breaker between scenarios B, C, and D.

All non-Africans carry about 2% Neanderthal in their genomes, worldwide. This means that the Neanderthal had to have interbred with the migrants who left Africa before they dispersed widely. They carried that Neanderthal DNA with them as they dispersed throughout the world, indicating that the entire population that existed at that time, shortly after the exit from Africa, and survived, was intermixed between the two populations.

African peoples do not carry Neanderthal admixture. Therefore, had there been back-migration of haplogroups D0 and E, African peoples would also carry some Neanderthal, and they do not which effectively removes the options of B and C.

To date, scenario D, which also includes other archaeological evidence, is the best fit between the three Haber models, plus Dr. Vilar’s Option E. The Haber paper is short and a good read.

Y Haplotree Updates

FamilyTreeDNA included the changes to haplogroup D, incorporating their own findings.

Michael Sager, the phylogeneticist at Family Tree DNA who is responsible for the Y DNA tree gave a great presentation in early 2020 at Genetic Genealogy Ireland, which you can view here.

The latest tree at Family Tree DNA looks like this, with haplogroup D split into Asian and African lineages.

New Haplogroup F Lineages

So where did the haplogroup F lineage go after having left Africa? New discoveries at FamilyTreeDNA provide some clues.

Before the new haplogroup F branches were added, the haplogroup F tree looked like this. There were known basal F lineages, but FamilyTreeDNA did not have any Big Y testers that belonged to those branches of haplogroup F and were not at that time making use of NGS results from academic studies to define tree branches.

Since then, among the thousands of new Big Y test results, a few haplogroup F lineages have been identified.

click to enlarge

The view of the Y DNA tree at FamilyTreeDNA shows the locations of the various test results. Please note that people in the F-M89 haplogroup may simply have not tested beyond that level today, and would benefit from the Big Y test.

The Y tree now includes the new branch F-F15527 (F1) with four immediate subclades with samples from Indonesia, Malaysia, Vietnam, and the southern border of China, as shown on this map.

What Does This Mean???

Goran Runfeldt, the head of Research and Development at Family Tree DNA says:

Finding F1 exclusively in Southeast Asia is significant because it represents the first split of haplogroup F.

Additionally, it gives some clues about where haplogroup F was before it split between F1 and GHIJK, which represents all the haplogroups F through T.

It is also significant that they all belong to different branches, four immediate subclades of F1, dated to circa 48,000 years ago. This shows a rapid expansion where several lineages quickly diverged then and survived for tens of thousands of years until present day. It is very likely that we will discover other ancient lineages in this part of the tree as more people from this part of the world take a high coverage Y-DNA test.

Michael Sager adds:

We have many distinct lineages close to the root of F (F1a, F1b, F1c, F1d, G, H, IJK.) All of these (and more) arose within a couple thousand years. All of these descendants in conjunction provide excellent support for the theory that F was long out of Africa. We did not have that clear support for haplogroup D as we had a ~20ky bottleneck to account for as well as Ds closest relative, E, being in Africa.

I asked Dr. Vilar for his opinion about the expansion of haplogroup F.

The discovery of new F1 lineages in Southeast Asia suggests that there was both a rapid and a broad expansion of paternal lineages across Eurasia some 55,000 years ago. Rapid because we see F lineages in China and Southeast Asia shortly after modern humans leave Africa some 60,000 years ago.

The pattern in haplogroup F is similar to that of its “cousin lineages” in haplogroup C, which likely moved through South Asia to Southeast Asia and even Australia shortly after its exodus from Africa.

Unlike F, haplogroup C is also found in Central Asia and the Americas, so the two paths may not have been exactly the same.

However, the range of F was also broad, since it gave rise to an older son (GHIJK) years earlier, and much further west. GHIJK likely arose in western Asia, where descendants G, H, and IJ were all born in the following millennia.

Acknowledgments

Thank you to the following individuals for their review of and input to this article:

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