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

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:

  • C-M130 – exclusively non-African
  • DE-M145
  • FT-M89 – exclusively non-African (became F-M89)

Not long after, DE split into:

  • D-M174 – exclusively non-African
  • E-M96 – largely African

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:

  • D0 – exclusively African (became D2-FT75)
  • E – mainly African
  • D – exclusively non-African (became D1-M174)

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.

click to enlarge

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

You’ll note that:

  • Option B shows haplogroup CT exiting Africa as was originally believed, but with D0 and E back-migrating, and E-M35 eventually leaving again, with other E haplogroups remaining.
  • Option C shows CT splitting in Africa with C, DE and FT exiting Africa about the same time, with D0 and E back migrating and E-M35 leaving again.
  • Option D shows CT and DE both splitting in Africa, with only C, D and FT exiting out of Africa initially, together, in one single event, with E-M35 following later.

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.

  • Option E – Haplogroup CT splits into two branches CF and DE within Africa, then haplogroups D and E split followed by CF and D leaving Africa. However, this requires C and F to split after D and E have already split, which is not the current calculated sequence of events. This sequence would constitute a new Option E scenario, where haplogroups CF and D (or pre-D1) leave Africa, with E following later.

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

  1. Fascinating article! My Jewish father, as tested by my 1st cousin on his side of the family belongs to E-M35. Surprisingly, my cousin had only three Y-37 matches, all with different surnames. My male cousin on my mother’s side belongs to E-M34.

  2. 23andme is autosomal only now ? I remember when i got the health + genealogy package eight years ago, the haplogroup sections were about the only thing that interested me. Sucks if new customers wont have access to that.

    • They do provide a base haplogroup only, but no matching and no detailed results. So yes, that’s still there.

  3. First response: Cool. Cool. Cool.

    Second response. I had a similar ydna test experience at FTDNA. My 55 y-37 matches cover about a dozen surnames and my 33 y-67 test matches about 8 different surnames. Until my 3C1R got ydna tested, I didn’t have a yDNA match against my surname. Now I do have a ydna match, which is exciting because we have confirmed a 3rd great grandparent’s ydna.

    Third response – more of a observation and experience:

    My mother’s parents have these nice neatly organized (and documented ) family trees that just pop out when I research dna matches. Its …ridiculously simple to find the ancestors by family groups. One group on my mother’s side consists of over 300 dna matches and traces to a single family that got here in the early 1700s. Coincidentally, its the only immigration event of that name into Virginia. Unfortunately, its not so easy with other branches.

    Anyone doing basic ydna research who wants to find people really needs to test at FTDNA. They also need to encourage as many of the men in their family to do likewise. And they need to map out the different ydna groups with that surname, too. I manage a surname project at wikitree because I needed somewhere to consolidate the research and try share. I’ve learned there are a 13 or 14 possible maximum ydna groups for my surname that might be relative to my research. I’be only confirmed 6 of then as unique ydna lines. Its so helpful to have both the ydna and autosomal testing but you can never have enough.

    I think the other thing I’ve learned is that although a lot of dna matches will fit patterns, some do not. If you find 91 people that trace to the same family and many of your cousins match them too, but you don’t know how they fit in and you have gaps in your tree…that requires further research. Something is there. Other family trees will fall off the fruit tree and everything aligns and documents very easily. Sometimes it will be easy, sometimes hard, and sometimes you have a very long (very long) research road.

    I wish I had the capabilities of FTDNA and Gedmatch and all their data combined with Ancestry’s database and corresponding ydna testing for all the men.

  4. Got my maternal grandfather’s line, BIG Y results C-FT245596 (from C-M216/M130). I just paid for another BIG Y test on my maternal grandmother’s father’s line, also C-M216 (predicted) and results will be done by February.

    Then there is my maternal grandfather’s maternal grandfather’s line, still not sure if that will also be C-M216 or could be K-M9. We only have a couple of K-M9 in our project, thought one of them did a BIG Y but need to double check on that.

    My own BIG Y results is O-B157019. Would be cool if I could find other lines on my paternal side that could be a D.

  5. To think there is still so much to learn, even with these tens of thousand years old haplogroup! Thank you very much for this review!

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