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Exciting New Y DNA Haplogroup D Discoveries!

Roberta Estes

Haplogroup D is a very old branch of Y-DNA that has remained rather mysterious. It has been uncertain where haplogroup D was born – in Africa, Asia or elsewhere – and when. It’s always fascinating when new research sheds light on the early history of humanity – discovered through people living and testing today.

In the current issue of Genetics, the article A Rare Deep-Rooting African Y-chromosomal Haplogroup and its Implications for the Expansion of Modern Humans Out of Africa by Haber et al appeared.

Their abstract:

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 re-investigate 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).

Haplogroup DE was and is very rare. Because of its rarity, and that it had initially been reported in one man from Guinea-Bissau in West Africa and two Tibetans, it was unclear where DE originated, or when.

This new paper sequenced three men from Africa and five from Tibet.

D Splits

The result of the paper is that the authors confirm that the DE lineage split consists of three branches:

To calibrate the branch length between any two samples when calculating split times, the authors multiplied the number of derived variants (mutations) found in the first sample but absent from the record, meaning previously unknown.

In supplementary table S2, they recalculate the splits between the various haplogroups. I found the table confusing to read, so I reached out to Goran Runfeldt who heads the scientific research team at Family Tree DNA to make this simpler.

I knew from previous discussions with the team that they had split the haplogroup D line internally to reflect a new branch at the time they named D-FT75 and subsequently D-FT76, and they were waiting for verification from multiple tests before splitting the line further.

On the Family Tree DNA block tree, above, you can see the D split between D-F974 which is the main haplogroup D root (navy blue) which then splits into D-M174 which is the old line referred to as Haplogroup D, and the new D0/D2/D-FT75 lineage, both in lighter blue. You can see the public tree, here.

Goran explained that Family Tree DNA has actually found multiple lineages in what the authors call D0, which ISOGG calls D2 and Family Tree DNA refers to by the defining SNP as D-FT75.

If you’re like me, looking at this information in pedigree format is easier to comprehend.

I asked Goran and Big Y haplotree guru, Michael Sager if they could create something easy to understand. You can see them working together in this photo. Thanks guys!

The Haplogroup D Tree

Note that the following graphic is NOT TO TIME SCALE. Currently tested, unplaced and and pending samples are at the bottom.

In the chart above, haplogroups in red at the top are the base haplogroups, not refined by the paper. Green is the already known upper structure of haplogroup D. Tan is the haplogroup D structure being refined by Family Tree DNA. The blue group is the Nigerian structure from the paper.

Divergence times as quoted in the paper are noted. For example, the time between the split between CT and BT, according to the paper, is approximately 101.1 thousand years ago. (kya means thousands of years ago)

How the D-FT75 Branch was Discovered

At the end of 2018, Family Tree DNA published the first SNPs from the new haplogroup D lineage to the ISOGG SNP index. During 2019, additional SNPs have been added, including the new haplogroup D lines of D-FT75 and D-FT76.

I asked Michael Sager how he made that discovery.

When a customer purchases an STR test, if Family Tree DNA cannot reliably predict a haplogroup, they will run a backbone test, at no additional charge to the customer, to test enough SNPs to at least call a base level haplogroup, such as R-M269.

In this case, Family Tree DNA ran a backbone test on a customer’s Y DNA and the result came back as something Michael had never seen before – haplogroup CT, but no subgroup. As you’ve already noticed, haplogroup CT is far up the tree and Michael needed more information.

Michael said that he knew the only possible options were:

After the backbone results were returned, Family Tree DNA contacted the customer and asked permission to run a Big Y test. The result was the discovery and naming of D-FT75 and D-FT76 which split D, twice, into new subgroups.

Further testing has verified the haplogroup D-FT76 finding in another Saudi Arabian male. Two additional haplogroup D males have results pending – one from Syria and one from another part of the world.

We now know that indeed the new branch of D, D0/D2/D-F75 has been found outside Africa, specifically in Saudi Arabia. It’s possible that there are more than two distinct lineages. We’ll know more as pending results come back from the lab.

However, what can be added is that according to the paper, the age of haplogroup D to the Nigerian samples is 71,400 years. The Family Tree DNA calculations based on the total number of 702 SNPs at 100 years per SNP suggest that the age is 70,200, which is very close to the 71,400 age in the paper. Additionally, because of the haplogroup FT75 and FT76 split, we can estimate the age of the divergence of those two lines with 261 SNPs between them at between 26,000 and 26,500 years, using these two calculation methods.

To quote Michael Sager, it’s “pretty neat to find a 20,000+-year-old NEW branch off of a 70,000+-year-old NEW branch.” I’d certainly agree!

Family Tree DNA would also like to place the Nigerian samples precisely on the tree.

In the supplemental data, the paper provided a list of the HG19 SNPs that are positive, including the positions for both D-FT75 and D-FT76, but did not list the SNPs that were negative. In order for Family Tree DNA to assign the Nigerian samples from the paper precisely to a branch, they need the BAM file because they need to see positive, negative and no-call SNPs. Family Tree DNA would also need to convert the results from build HG19, used by the authors, to current HG38.

What About You?

If you’re a male and have taken a Y STR test, meaning the 12, 25, 37, 67 or 111 marker test and you do not have a predicted haplogroup, please contact support at Family Tree DNA.

The best thing you can do, if you haven’t Y DNA tested, is to actually take a Y DNA test at Family Tree DNA. You can start out with the STR marker test which provides you with STR marker results, matching to other males and a haplogroup prediction.

Many individuals also purchase the Big Y-700 test which provides a very granular haplogroup – the most detailed possible, matching and at least 700 STR marker results – in addition to revealing never before discovered SNPs. Without the Big Y test, D-FT75 and D-FT76 and most of the 150,000 Y SNPs would not yet be discovered. This is the only test that can make new discoveries like this.

To summarize, you can be a part of scientific discovery if you’re a male (only males have Y chromosomes) by either:

You can click here to order or upgrade.

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