Y-Chromosome Haplogroup A00: Archaic Introgression or Deep Human Lineage?

TL;DR

• Haplogroup A00 is the oldest known human Y-chromosome lineage, splitting from other human lines around 200,000–300,000 years ago.
• Its discovery in 2013 dramatically pushed back the estimated age of our most recent common paternal ancestor (“Y-chromosomal Adam”).
• A00 is found today in a small number of individuals from the Mbo people of western Cameroon.
• Its extreme age has led to two main hypotheses:
  1. It’s a relic from an unknown “ghost” archaic hominin population that interbred with early Homo sapiens in Africa.
  2. It’s simply a very ancient lineage from a structured ancestral Homo sapiens population that remained isolated for a long period.
• While the “ghost population” idea is plausible and fits some other genetic evidence, most researchers currently lean toward A00 being an ancient but integral part of human diversity.

The Shocking Discovery of a Ghost Lineage#

The discovery of Y-chromosome haplogroup A00 sent shockwaves through the genetics community. Identified in 2013, this Y-DNA lineage turned out to be the oldest known branch on the human paternal family tree. Its extreme age and rarity have raised fascinating questions about early human origins.

Haplogroup A00 came to light thanks to a combination of genetic genealogy and academic research. In 2012, scientists led by Fernando Mendez and Michael F. Hammer analyzed the Y chromosome of an African American man (later traced to the Mbo ethnic group of western Cameroon) and found something unprecedented.¹ This Y chromosome carried none of the usual mutations that define known human Y haplogroups – in other words, it occupied the deepest node of the Y-chromosomal tree. Mendez et al. officially reported this “new lineage” in early 2013 and dubbed it haplogroup A00, indicating a branch even older than the prior “A0” root of the tree.¹

Researchers were astonished by A00’s age estimate. Based on DNA mutations (using a molecular clock), Mendez et al. calculated that A00 split off from all other living men’s Y-chromosomes around 338,000 years ago (with a confidence interval of ~237,000–581,000 years).¹ This timing is extraordinary – it predates the oldest known fossils of anatomically modern humans (~195–200 thousand years old) by over 100,000 years. As Dr. Hammer noted, “our analysis indicates this lineage diverged… at a time when anatomically modern humans had not yet evolved”.² This makes A00 a truly basal lineage in our species.

Importantly, haplogroup A00 was not identified in any ancient remains, but in living people. After the initial discovery, researchers found 11 men from a small region of western Cameroon (Mbo people) carrying Y-chromosomes belonging to A00.¹

A00 as the Oldest Basal Human Y Lineage#

Haplogroup A00’s position at the base of the Y-chromosome family tree means that it is the most distantly related to all other known Y lineages. All other men (whether in haplogroup A0, B, C, D, E, etc.) share mutations that A00 lacks, meaning they share a more recent common ancestor with each other than they do with A00.

Because of A00, estimates for the age of “Y-chromosomal Adam” (the most recent common ancestor of all living male lineages) had to be revised significantly. Subsequent research has converged on a still-ancient age of around 200,000–300,000 years ago, overlapping with the period when early Homo sapiens were emerging in Africa.³⁴ Even with these revised dates, A00 remains the oldest known Y-chromosome lineage by a wide margin.

Figure: Simplified Y-chromosome tree illustrating the deep divergence of haplogroup A00 from all other modern human Y lineages. The initial analysis suggested a split ~338kya, while later estimates revised this to ~200-300kya.¹³

The “Ghost Population” Hypothesis#

Could this Y-chromosome have originated outside of Homo sapiens? One provocative idea is that A00 might have entered our gene pool via interbreeding with an archaic, now-extinct hominin – a “ghost population” that split from our ancestors long ago. Mendez et al. explicitly raised this possibility.¹

The idea is analogous to how non-African people today carry small fractions of Neanderthal or Denisovan DNA. In this case, the interbreeding would have occurred in Africa between early modern humans and a mysterious archaic group that left no known fossils.

This idea is supported by other genetic evidence. For example, a 2020 study concluded that some West African populations inherited 2% to 19% of their DNA from a yet-undiscovered archaic hominin that diverged from the human lineage even before Neanderthals did.⁵ Haplogroup A00 is often mentioned as a potential case of such archaic admixture.⁶

So, could A00 be a non-Homo sapiens lineage? The short answer is maybe – but it remains unproven. We haven’t found an ancient DNA sample from a fossil archaic male that carries A00. All known examples come from living Homo sapiens.

Alternative: A Deeply-Structured Homo sapiens Past#

A more conservative interpretation is that haplogroup A00 simply represents an extremely ancient branch within Homo sapiens. Recent research suggests the ancestral African population was not a single cohesive unit, but a “metapopulation” with branches that split off and rejoined intermittently over hundreds of thousands of years.⁷

In this model, some genetic lineages could have become very deeply separated while still belonging to our species, and later got re-integrated when the subgroups fused. This would make A00 an indigenous Homo sapiens lineage that merely remained separate for longer than others. Researchers found this model could explain the presence of very old genetic differences “without invoking ghosts.”⁷

It’s also useful to remember that terms like “archaic” and “modern” human are somewhat fluid around the time A00 originated. The line between a late Homo heidelbergensis and an early Homo sapiens might not have been sharp.

Conclusion: A Window into Our Tangled Roots#

Haplogroup A00 is unequivocally the oldest Y-chromosome lineage found in living humans. The central question is why it is so divergent. Two broad interpretations exist:

• Basal Human Lineage: A00 is an early, isolated offshoot from our own species, reflecting a complex population structure in early Africa.
• “Ghost” Archaic Introgression: A00 is a genetic relic from an unknown archaic hominin that interbred with our ancestors.

At present, there is no definitive proof favoring one explanation. Many researchers lean toward the simpler interpretation that A00 is an unusually deep Homo sapiens lineage.³ However, the ghost population hypothesis cannot be ruled out. A00 remains a profound example of how much we still have to learn about our origins, reminding us that the roots of the human family tree are entangled and ancient.

FAQ#

Q1. What is Haplogroup A00? A. Haplogroup A00 is the oldest and most divergent branch of the human Y-chromosome family tree found in living people today. Its carriers are most distantly related in the male line to all other men on Earth.

Q2. How old is Haplogroup A00? A. The lineage is estimated to have split from all other human Y-chromosome lines around 200,000 to 300,000 years ago, pushing back the age of our paternal common ancestor significantly.

Q3. Where is Haplogroup A00 found? A. So far, it has only been identified in a small number of individuals from the Mbo ethnic group in western Cameroon and in some African Americans with ancestry from that region.

Q4. What is the “ghost population” theory for A00? A. This theory proposes that A00 did not originate in Homo sapiens, but was passed to our ancestors through interbreeding with a now-extinct, “ghost” archaic human species in Africa for which we have no fossil evidence.

Q5. Is it more likely that A00 is from a ghost population or just an old human lineage? A. While the ghost population idea is intriguing, many scientists believe it’s more likely that A00 is a very ancient lineage from within Homo sapiens that survived due to complex population structures and long-term isolation in early Africa.

Footnotes#

Sources#

1. Mendez, Fernando L. et al. “An African American Y Chromosome Cradles the Deepest Root of the Human Y Chromosome Phylogeny.” American Journal of Human Genetics 92.3 (2013): 454-459.
2. Elhaik, Eran et al. “The ‘Extremely Ancient’ Chromosome that Isn’t: A Forensic Bioinformatics Approach.” European Journal of Human Genetics 22.9 (2014): 1111-1116.
3. Karmin, Monika et al. “A Recent Bottleneck of Y chromosome Diversity Coincides with a Global Change in Culture.” Genome Research 25.4 (2015): 459-466.
4. Hawks, John. “A00 and the African ‘superarchaic’.” John Hawks Weblog, 2019.
5. Vernimmen, Tim. “A new origin story for our species.” National Geographic, 2023.
6. “Y-Chromosomal Adam, the Common Male Ancestor of All Living Men, Lived 338,000 Years Ago.” Sci-News, 2013.
7. “Ghost Archaic Hominin Lineage Contributed to Genomes of Modern West Africans, Study Suggests.” Sci-News, 2020.