Y chromosomal Adam

Y-chromosomal Adam is the name given to the patrilineal most recent common ancestor (MRCA) of modern humans. In other words, he was the man from whom all living humans today descend, on their father’s side, and through the fathers of those fathers and so on, back until all lines converge on one person. He is the male counterpart of Mitochondrial Eve, who,lived in north-western Botwsana around 177,000 years ago (confidence interval ± 11,300 years).

When I did my first Y-DNA test in 2012 with the National Geographic’s  National Genographic Project, it gave a date of 60,000 years ago (60 kya) for Y-chromosomal Adam. This was already outdated, as other recent estimates around that time gave dates ranging from 120 to 160 kya. By definition, it is not necessary and highly unlikely that Y-chromosomal Adam and Mitochondrial Eve lived at the same time or in the same location.

However, in 2013 scientists announced the discovery of an extremely ancient Y DNA haplogroup from a sample submitted for an African-American man in the USA.  Y-chromosomal haplogroups are defined by mutations in the non-recombing portions of DNA from the Y chromosome. These mutations accumulate at the rate of roughly two per generation. The accumulation of mutations in the descendants of Y-chromosomal Adam allow us to map out the major branches of the family tree in terms of Y-haplogroups. This discovery adds a completely new branch to the Y-DNA family tree and pushes back the age of Y-chromosomal Adam to around 250 to 300 kya.

There are a number of inconsistent stories about this discovery in popular science magazines and online media, and I’ve relied on what seems to be an authoritative account by TL Dixon [1]. In 2008 an African-American family genealogist, Jacqueline Johnson, submitted samples for several male cousins to Family Tree DNA for Y DNA analysis. The Y DNA for one of these cousins (who has remained anonymous and died in 2013) had no matches in the database. Various genetic genealogists carried out further tests and concluded they had found a new haplogroup which had never been seen before. Jacqueline Johnson traced this cousin’s paternal line back to a former slave named Albert Perry (born between 1819 and 1827) who lived in South Carolina and first appeared on the 1870 census five years after the civil war and the emancipation of slaves.

The sample was then sent for deeper testing to a geneticist at the University of Arizona in Tucson, Professor Michael Hammer. He found similarities between the Perry sample and those from 11 West African Mbo men, from one village in Cameroon, who shared a recent ancestor about 500 years ago. This suggests that it was also home to Albert Perry’s male ancestors, before one of them was taken as a slave across the Atlantic. His team’s research also revealed the extraordinary fact that Perry did not descend from the then Y-chromosomal Adam, and they estimated that his lineage split from all the others about 338,000 years ago, before the emergence of anatomically modern humans [2].

There was speculation at the time that Perry’s Y-chromosome (but not all his DNA) may have been inherited from an archaic human population that has since gone extinct. Unlike the other chromosomes, the lack of recombination along most of the Y chromosome results in fairly stable mutations. Over the last 10 years, it has become understood that mutations occur at different average rates on different sections of the Y chromosome, and that some regions have especially stable average mutation rates. This has allowed much more accurate dating of Y-DNA haplogroups (defined by specific sets of mutations that are passed down from the haplogroup founder in which one or more of the mutations first occurred).

Recent dating analyses have revised the initial age of 338 kya for the new Y-chromosomal Adam, who is the most recent ancestor of Perry’s haplogroup (named A00) and the haplogroups of other living men. These dates have ranged between 160 and 300 kya [3-5]. The most recent of these papers dated Y-chromosomal Adam to 275 kya (95% CI: 241–305 kya). That would make him approximately the 11,065th great grandfather to every man and boy living today.

The most basal haplogroups have been detected in West, Northwest and Central Africa, and Perry’s A00 haplogroup has been found in Mbo men living in western Cameroon. This is all consistent with a location of Y-chromosomal Adam in the north-western quadrant of the African continent. In the migration map for my paternal ancestors which I am working on, I am choosing to locate Y-chromosomal Adam in western Cameroon at the Banyang-Mbo Wildlife Sanctuary, not far from the border with Nigeria.

The red marker shows the location of the Banyang-Mbo Wildlife Sanctuary in western Cameroon

Future discoveries of presently unknown archaic haplogroups in living people may well lead to further revisions in the age and location of a new Y-chromosomal Adam. In particular, because we now know humans interbred with Neanderthals, the discovery of Neanderthal DNA on the Y chromosome would immediately push back the time to the most recent common patrilineal ancestor to at least twice its current estimate.

In 2016, Mendez et al [5] analysed Y-chromosome DNA from a Neanderthal individual from El Sidron, Spain, and investigated its divergence from chimpanzee and modern human sequences. They estimated that the time to the most recent common ancestor of Neanderthal and modern human Y chromosomes is around 588 kya (95% confidence interval: 447–806 kya). However, they also identified protein-coding differences between Neandethal and modern human Y chromosomes, including potentially damaging changes to three genes that produce male-specific minor histocompatibility (H-Y) antigens. These antigens are thought to elicit a maternal immune response during gestation, somewhat like the Rhesus R+ and R- incompatility. It is possible that pregnancies resulting from a male Neanderthal and female human were not viable, and that Neanderthal genes were only passed down from human males mating with Neanderthal females. If that is the case, the Neanderthal Y-chromosome has not crossed to humans and is extinct.

The revised root of the Y-chromosome family tree is is shown in the following diagram. The basal haplogroup is labelled A. The dates shown in the figure for the split between humans and Denisovans, humans and Neanderthal, and Perry’s Y-haplogroup A00, are from a very recent paper which has been posted on bioRxiv [6] in preprint form, but not yet reviewed or published. The authors have carried out the sequencing of the first Denisovan Y chromosomes from two Denisovan specimens as well as the Y chromosomes of three late Neandethals and estimated the ages of the splits of these two species from the modern human line. Because the majority of archaic human specimens preserved well enough for genome sequencing have been female, an analysis of Denisovan and Neanderthal Y DNA has not previously been carried out.

The revised basal haplogroup A with dates from Petr et al 2020 [6].

The figure below shows the locations and ages of the two male Denisovans, Denisova 4 (55–84 ky old) and Denisova 8 (106–136 ky old), and three male late Neandertals, Spy 94a (38-39 ky old), Mezmaiskaya 2 (43-45 ky old) and El Sidrón 1253 (46-53 ky old). The last of these was the Neanderthal used by Mendez et al [4] to estimate the splot of Neanderthals and modern humans at 588 kya. The new paper [6] estimates a much younger split time for Neanderthals of 350 kya and a slightly younger split time for Perry’s Y chromosome (A00) of 250 kya (213-293 kya). The Denisovan split time is much earlier at 700 (607-833) kya.

Geographical locations and ages of the male archaic humans analyzed by Petr et al 2020 [6]

The sequencing of ancient DNA has hugely expanded our understanding of the evolutionary history of Homo sapiens and related human species. It is almost certain that new papers will continue to revise this understanding and the dating of human lineages over the coming years. And it is entirely possible that the discovery of another deep-rooting Y haplogroup could again dramatically change the age and location of our Y-chromosomal Adam.

References

[1] Dixon TL. A00 Cameroon Research Project and Albert Perry’s Y. Posted 15 January 2017 on TL Dixon’s blog “Roots and Recombinant DNA”. Available at https://www.rootsandrecombinantdna.com/2017/01/a00-cameroon-research-project-and.html

[2] Mendez FL, Krahn T, Schrack B, et al. An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree [published correction appears in Am J Hum Genet. 2013 Apr 4;92(4):637]. Am J Hum Genet. 2013;92(3):454-459.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591855/

[3] Elhaik E, Tatarinova TV, Klyosov AA, Graur D. The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome. Eur J Hum Genet. 2014;22(9):1111-1116. doi:10.1038/ejhg.2013.303

[4] Karmin M, Saag L, Vicente M, et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 2015;25(4):459-466. doi:10.1101/gr.186684.114

[5] Mendez FL, Poznik GD, Castellano S, Bustamante CD. The Divergence of Neandertal and Modern Human Y Chromosomes. Am J Hum Genet. 2016;98(4):728-734. doi:10.1016/j.ajhg.2016.02.023

[6] Petr M, Hajdinjak M, Fu Q, Essel E, Rougier H, Crevecoeur I, et al. The evolutionary history of Neandertal and Denisovan Y chromosomes. bioRxiv 2020.03.09.983445; doi: https://doi.org/10.1101/2020.03.09.983445
https://indo-european.eu/proto-indo-european/topic/the-evolutionary-history-of-neandertal-and-denisovan-y-chromosomes/

 

Becoming Human Part 2

This is the second part of a post summarizing current understanding of the evolution of humans. In the previous post, I outlined the evolution of pre-human species from the first monkeys around 35 million years ago (Mya) to the appearance of the first human species around 2 Mya. This post takes a look across the evolution of humans from the appearance of the first human species Homo habilis to the appearance of anatomically modern Homo sapiens sapiens around 250 thousand years ago. The following figure summarizes the evolution of humans over the last 2 million years, based on [1] with some modifications to take account of some recent discoveries.

The evolution of humans (the genus Homo) over the last 2 million years. Updated from Figure in Wikimedia. User:Conquistador, User:Dbachmann / CC BY-SA. (https://creativecommons.org/licenses/by-sa/4.0)- . The late survival of robust australopithecines (Paranthropus) alongside humans until about 1.2 Mya is indicated in purple. The rapid “Out of Africa” expansion of H. sapiens is indicated at the top of the diagram, with admixture indicated with Neanderthals, Denisovans, and unspecified archaic African hominins.

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Becoming Human Part 1

Our understanding of the evolution of us modern humans has changed dramatically in the last few years as ancient genomes are decoded and we discover that humans, Neanderthals and Denisovans interbred, and also in the remote past interbred with previously unknown “superarchaic” human groups.  Scientists are also discovering new species of extinct hominids, and no doubt will continue to shed further light on our origins. Just to try to sort out the big picture in my own mind and to put these various discoveries in context, I’ve tried to summarize what we think we know, or at least what the evidence available to date suggests. This will no doubt continue to change.

This is the first of two posts and summarizes the evolution of pre-human species from the first monkeys around 35 million years ago (Mya) to the appearance of the first human species around 2 Mya. A following post will summarize the evolution of humans from the appearance of the first human species Homo habilis 2 Mya to the appearance of anatomically modern Homo sapiens sapiens around 250 thousand years ago and  mitochondrial Eve, who lived around 178,000 years ago.

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My maternal ancestors – from Eve via ice age Europe to Victorian England

In an early post on this blog, I summarized my maternal-line ancestors and where and when they lived. In the last 6 years, there have been substantial revisions to estimates of the dates associated with these mitochondrial DNA (mtDNA) haplogroup founders, and revisions to the mtDNA haplogroup tree (deep-maternal-ancestry-and-mtdna) and this post provides an update. I am a member of mtDNA haplogroup U5, which is one of nine native European haplogroups stemming from haplogroup U which most likely arose in the Near East, and spread into Europe in a very early expansion. The presence of haplogroup U5 in Europe pre-dates the last ice age and the expansion of agriculture in Europe. Today, about 11% of modern Europeans are the direct maternal descendants of the founder U5 woman. They are particularly well represented in western Britain and Scandinavia. My more recent maternal ancestors were part of the population that tracked the retreat of ice sheets from Europe at the end of the last ice age and re-colonized Britain about 12,000 years ago.

The mtDNA sequence at the root of each haplogroup arose from one or more mutations in the mtDNA of just one woman, and the age of the associated haplogroup gives the time in the past when this specific woman lived. To emphasise that the maternal clan founders were real individuals, I have used the names given to them by Sykes [1] and Oppenheimer [2] and given my own names to the more recent subgroup founders. The Table below summarizes these founders, dates and locations and is followed by brief biographies. The haplogroups are identified by the labels used in Build 17 of the ISOGG mtDNA tree which can be accessed at http://phylotree.org/ [3]. Dates in the table below have been updated using most recent available dating estimates as described in my previous post deep-maternal-ancestry-and-mtdna.

The migration path out of Africa into Europe of the “grandmothers” linking mitochondrial Eve through to Ursula (U5) is shown on a map in my previous post deep-maternal-ancestry-and-mtdna. The subsequent migration from Europe to Britain is shown in the map below.

Figure 1. Migration path of my maternal ancestors from Ursula (U5) to Viviane (410 CE). A map of the earlier migration from mitochondrial Eve to U5 is included in an earlier post.

Updated biographies of my maternal haplogroup great* grandmothers follow below.

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Our Asgardian ancestors

I grew up reading northern European myths and legends, including tales of Odin, Thor, and the other gods of Asgard. I was largely unaware of the Marvel comics appropriation of Thor and other Asgardians as superheros until the Marvel cinematic universe started to hit the big screens in the last 12 years.

Loki, Thor and Odin (from the Marvel Cinematic Universe)

I have only recently come across the growing evidence that an Asgardian was one of our ancestors, way back near the beginning of the evolution of life, when the first eukaryotic cell appeared. Eukaryotes are organisms whose cells contain membrane-wrapped internal structures, such as a nucleus, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound internal structures.

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Deep maternal ancestry and mtDNA

In February 2014, I did a series of posts on my deep maternal ancestors, identified through a test of mutations on my mitochondrial DNA (mtDNA) which is inherited only from the mother. This test was carried out by Ancestry.com, who have since discontinued tests of mtDNA and Y-chromosome DNA. Costs of DNA tests have dropped dramatically since then, and late last year I ordered an mtDNA test from FamilyTreeDNA (www.familytreedna.com) which carried out a full sequencing of the mitochondrial DNA.

As well as the DNA that makes up the chromosomes in the nuclei of our cells, we also have another type of DNA called mitochondrial DNA (mtDNA). The mitochondria are organs located outside the cell nucleus which convert sugars into energy.  Mitochondria have a small circular loop of DNA, containing only approximately 16,569 base pairs in humans. The circular mtDNA is similar to the DNA of bacteria, and it is thought that mitochondia evolved from symbiotic bacteria that were once free living.

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Other worlds

As a teenager I was fascinated by astronomy and cosmology and read voraciously as well as spending many hours outside at night with my telescope and Norton’s Star Atlas. During my brief years as a physicist in the 1970s, I kept up with the literature and was aware that some astronomers were attempting to detect planets around other stars by detecting the gravitational jiggling of the star around which the planet was orbiting. But these movements were slightly beyond detection by the technology of the day.

Headlines with messages like “First Planet Found Outside Our Solar System” appeared in newspapers dozens of times, at least twice in the New York Times, and once on the front page. But all these announcements were subsequently found to be wrong. And in one notorious incident, it was later found that the astronomer had detected not movements in stars, but movements in the telescope itself. So I was stunned to discover on reading the book “The Stardust Revolution” that new detection methods combined with space-based telescopes had resulted in the proven discovery of nearly 2000 exoplanets.

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