My paternal ancestors – from Adam via ice age Siberia to the steppes of Europe

In earlier posts, I discussed how I have used an analysis of my Y chromosome DNA to identify my paternal ancestors all the way back to Y-chromosomal Adam, the most recent common ancestor of all men alive today. The following map summarizes my Y haplogroup ancestors from Y-chromosomal Adam down to those who left Africa around 70 thousand years ago (70 kya) and headed east through India and South East Asia and then up through China into ice age Siberia and then across to the Ukrainian steppeland north of the Black Sea.

I was originally going to continue this story all the way across Europe to the Iberian Peninsula and up to Ireland and Scotland, but I will keep that for a later post. I have discovered that there is an immense amount of recent research on European Bronze Age genetics and migrations and a very considerable unfinished debate on how to interpret the evidence. So it may take me a little while to come to grips with it.

The estimated dates for haplogroup founders shown on the map are mostly taken from the SNP Tracker [1] and are interpolated from the dates in the Y haplotree on Yfull.com. The latter use the updated method of Adamov et al [2] to estimate ages, based on the average SNP mutation rate parts of the Y chromosome expected to be stable in the mutation rate. The date for Y chromosomal Adam is estimated from recent studies cited in the post about him. Note that there is large uncertainty in age estimates and locations of Y haplogroups. The 95% uncertainty for dates ranges from ±10% for early haplogroups to ±20% for R1b. Some of the possible locations discussed below are speculative and will be revised as new data becomes available. The acronyms BCE and CE refer to “Before Current Era” and “Current Era” and correspond to BC and AD respectively.

The Y chromosome is substantially larger than mitochondrial DNA (56 million versus 16,600 base pairs). As a consequence there are more paternal haplogroups than maternal haplogroups. There are 36 paternal haplogroup founders between me and Y chromosomal Adam, compared to only 17 maternal haplogroup founders between me and mitochondrial Eve. In the story below of my paternal ancestors, I have focused on important haplogroup founders associated with key developments in human migration and culture.

Y-Chromosomal Adam

Y-chromosomal Adam, our great*8,870th grandfather [3], lived approximately 275,000 years ago in western Africa, likely in western Cameroon. His haplogroup A is ancestral to all Y-haplogroups found today. Y-chromosomal Adam was not the first Y-chromosomal Adam was not the first man, nor was he the only man alive at the time. His contemporaries could still have descendants, whose line zig-zagged back and forth between males and females, but Adam was the only one who had an unbroken line of sons, through thousands of generations, right down to the present time. He is the paternal ancestor of all humans alive today. In a previous post, I have told the story of the discovery around 2010 of a new haplogroup A00, which pushed the date of Y-chromosomal Adam from around 120-160 thousand years ago (kya) to 275 kya. This is somewhere around the time the first anatomically modern humans appeared.

Haplogroup A is restricted to Africa, where it is present in several populations at low frequency but is most commonly found in populations of the Koi and the San tribes of Southern Africa. Early sub-branches of A have been found in central Africa. My paternal lineage descended through haplogroups A0-T, A1, A1b and BT to haplogroup CT, whose founders progressively moved eastwards towards the horn of Africa.

Haplogroup CT – Out of Africa Adam

Haplogroup CT (CT-M168/PF1416) has been referred to as the lineage of “Eurasian Adam” or “Out of Africa Adam”; because, along with many African Y-lineages, all non-African Y-lineages descend from it. Recent dating of CT [4, 5] gives a date close to 100 kya, making the CT founder my great*3,160th grandfather (and yours if you are a non-African). He is thought to have lived in what is now Ethiopia.

In describing these haplogroups, I will note the key mutations (SNP) which define the haplogroup (or sometimes are a marker chosen from a larger group of SNPs defining the haplogroup. Thus CT is defined by the two SNPs M168 and PF1416.

There is some evidence that modern humans left Africa around 130 to 115 kya, and possibly in even earlier waves, but none of these survived or left any trace in the human genome. All modern non-African men (and women) descended from Eurasian Adam in their paternal line. This migration is thought to have occurred between about 70 to 50 kya, at a time when a period of warmer temperatures and moister climate in Africa changed the desert in north-east Africa to savannah. Parts of the inhospitable Sahara briefly became habitable. As the drought-ridden desert changed to a savanna, the animals hunted by our ancestors expanded their range and began moving through the newly emerging green corridor of grasslands.

Bab-el-Mandeb. Source: eol.jsc.nasa.gov

It has been estimated that from a population of less than 10,000 individuals in Africa, only a small group, possibly as few as 150 to 1,000 people, crossed the Red Sea around 70,000 years ago, and these were all members of haplogroup CT [4]. Today at the Bab-el-Mandeb straits, the Red Sea is about 20 kilometres wide, but 70,000 years ago sea levels were 70 meters lower (owing to glaciation) and the water was much narrower. Though the straits were never completely closed, there may have been islands in between which could be reached using simple rafts.

Haplogroup CF

The founder of haplogroup CF-P143/PF2587 probably lived in the Arabian Peninsula around 68 kya, making him my great*2,130th grandfather. Haber et al. [5] estimate the date is somewhat earlier at 75.6 kya. Over the next twenty thousand years, my paternal lineage descended through haplogroups F, G, H and I to K as humans numbering at most in a few tens of thousands, moved north along the Arabian Pensinsula through Iraq and Iran into India. This period was towards the beginning of the Upper Paelolithic or Late Stone Age. At this time, stone tools were still relatively unsophisticated, humans were hunter-gatherers with an increasing diversity of foods, including fish. Cave paintings and carvings became more common, and the first evidence has been found of organized settlements, in the form of campsites.

Haplogroup K

The founder of haplogroup K-M9/PF5506 probably lived in South Asia or South East Asia around 47 kya, making him my great*1,450th grandfather. His identifying SNP M9 marked a new lineage, the Eurasian Clan, which spent the next 30,000 years populating Europe, Asia and the Americas. One group of descendents in subclade K2, then K2b move down through South East asia.

Haplogroup P (or K2b2)

The founder of haplogroup P (or K2b2) is identified by the SNP P295. The basal P* haploclade is found at its highest rate in the Aeta (or Agta), a people indigenous to Luzon, in The Philippines. Luzon is also the only location where P*, P1* and rare P2 are now found together, along with significant levels of K2b1.[5] Even though P1 is now more common among individuals in Eastern Siberia and Central Asia, these distributions suggest that P* (P295) emerged in South East Asia, and I have shown its origin as Luzon.

Haplogroup P1 (or K2b2a)

Members of haplogroup P (P-M45 or K2b2a) migrated northwards from the Philippines through China and Haplogroup P1 probably arose in Siberia or in Kazakhstan in the Late Stone Age around 42,000 years ago. Around this period, the environment on the Eurasian steppes was becoming increasingly hostile as the glaciers of the ice age began to expand again. Reductions in rainfall may have induced desert-like conditions in the south and led members of ancestral haplogroup P to follow herds of game north. They developed smaller stone points and blades—microliths—that could be mounted to bone or wood handles and used effectively. Their tool kit also included bone needles for sewing animal-skin clothing that would both keep them warm and allow them the range of movement needed to hunt the reindeer and mammoth that kept them fed.

In 2001, Russian scientists discovered a 31,000-year-old site where ancient hunters lived on the Yana River in Siberia, 300 miles (480 kilometers) north of the Arctic Circle and not far from the Bering land bridge that then connected Asia with North America [6]. The researchers found stone tools, ivory weapons and the butchered bones of mammoths, bison, bear, lion and hare, all animals that would have been available to hunters during that Ice Age period. This age is twice that of other known human occupations in any Arctic region and shows that people adapted to this harsh, high-latitude, Late Pleistocene environment much earlier than previously thought.

The archaeological site where two 31,000-year-old milk teeth were found. Credit: Elena Pavlova

DNA analysis of two human milk teeth found at the site found that one of them (labelled Yana1) belonged to haplogroup P1 (P-M45) Yana2 had five additional SNPs that defined a new haplogroup P1a (P-P284) [7]. The earlier map shows the location of the Yana site.

Haplogroup P gave rise to haplogroup R, the ancestors of most European men, and also to haplogroup Q, to which most native Americans belong.

Haplogroup R

The founder of haplogroup R, identified by signature SNP M207, lived in southern Siberia around 31,000 years ago, making him my great*997th grandfather. At this time, glaciers were expanding over much of Europe and western Eurasia, and the estimated population of homo sapiens was approximately one hundred thousand.

The 24,000 year old remains of Mal’ta boy

Several thousand years later we have our first evidence of R-M207. The remains of a four year old boy was found in a hunter-gather group dated to 24 kya, near the village of Mal’ta in the Lake Baikal area of Central Siberia [8]. Descendants of the haplogroup R founder moved westward over the next twenty thousand years across the Eurasian steppes into Europe, another group of descendants turned south and eventually made it to India.

Haplogroup R1

Haplogroup R1 (R-M173) is estimated to have arisen during the height of the Last Glacial Maximum (LGM), about 23,000 years ago, most likely on the Eurasian steppes (possibly in Kazakhstan). During this period, the Eurasian steppelands extended from present-day Germany, and possibly France, to Korea and China. The two most common descendant clades of haplogroup R1 are R1a and R1b.

Map of the Eurasian Steppes

Haplogroup R1b

The founder of haplogroup R1b (R-M343)  most probably was born around 20,000 years ago in Western Asia, at a time close to the peak extent of the European and Siberian ice sheets, which extended to the northern edge of the Eurasian steppe.  The steppe itself became much less hospitable tundra, and the steppeland people moved south down the eastern side of the Caspian, the likely location of the founder of the R1b haplogroup.

Map shows Palaeolithic Europe 18,000 years ago in the grip of the last ice age. Glacial ice 2km thick covers much of Northern Europe and the Alps. Sea levels are approx. 125m lower than today and the coastline differs slightly from the present day. The air would have been on average 10-12 degrees cooler and much more arid. In between the ice and the tree line, drought-tolerant grasses and dunes would have dominated the landscape.

Haplogroup R1b (R-M343) is the most frequently occurring paternal lineage in Western Europe, accounting for 50% or more of all paternal lineages in Europe. It peaks at the national level in Wales at a rate of 92%, at 82% in Ireland, 70% in Scotland, 68% in Spain, 60% in France (76% in Normandy), about 60% in Portugal,] 45% in Eastern England, 50% in Germany, 50% in the Netherlands, 42% in Iceland, and 43% in Denmark.

Haplogroups R1b-L754 / R1b-L388 / R1b-P297

Soon after the appearance of R1b, another marker, R-L754 (R1b1) appeared in an individual who probably lived somewhere around the southern shore of the Caspian Sea, possibly in Iran. Three thousand years later (17 kya), haplogroup R-L388 arose near the northern border of modern day Ajerbaijan, and another four thousand years later (13 kya), haplogroup R-P297 arose further north on the western steppeland of southern Russia.

Rock carvings of paleolithic hunters on the western shore of Lake Caspian

When I was in Azerbaijan in 2011, I visited a stone age rock shelter close the western shore of the Caspian Sea, about 65 km south of Baku. The earliest rock engravings date back to around 23 kya, and others date from the Mesolithic period around 10,000 kya. The migration route of my paternal ancestors (and quite possibly yours) would have passed by this site around 18 kya. I like to think that one of my paternal ancestors used this rock shelter around 18 kya, ie 16,000 BCE. Just to complete the sweep of history, there is also a carving of what appears to be a Viking longship, and it is known that a Viking trade route connected northern Europe and Russia with the Caspian Sea via the Volga River. And in a field a couple of kilometres away is a boulder with Roman graffiti in Latin that translated says “In the time of Emperor Domitian Caesar Augustus Germanicus, Lucius Julius Maximus, Centurion of the 12th “Thunderbolt” Legion [was here]”. This is the furthest east that a Roman inscription has been found and is dated to around 90 AD.

Haplogroup R1b-M269

Haplogroup R1b1a2 (R-M269) is observed most frequently in Europe, especially western Europe, but also with some frequency in southwest Asia. R1b1a2-M269 is estimated to have arisen approximately 13 kya on the European Western Steppes and to have spread into Europe from there. R-M269 is the most common European haplogroup, greatly increasing in frequency on an east to west gradient (its prevalence in Poland estimated at 22.7%, compared to around 60% in France, 70% in Spain and south-east England, 92% in Wales, and 98% in parts of north-west Ireland. It is carried by approximately 110 million European men.

R-M269 can be used to trace the Neolithic expansion into Europe as well as founder-effects within European populations due to later (Bronze Age and Iron Age) migrations. My R-M269 ancestors lived on the Western Steppes for at least 7,000 years until the appearance of the R-L23 founder 6,400 years ago.

Haplogroup R1b-L23

The founder of the R-L23 haplogroup was born on the Western Steppe (Pontic-Caspian Steppe) around 4,400 BC (6.4 kya). This was around 1,000 years before the appearance on the Pontic-Caspian Steppe of the Yamnaya culture. Genetic studies performed since 2015 have revealed that the Yamnaya culture, thought to have spoken some stage of the Proto-Indo-European language, predominantly carried R1b-L23.

Yamnaya herders from western Asia, four of whom are buried in this grave, started mating with European farmers hundreds of years before launching a major migration into Europe.

The Yamnaya culture, or Ochre Grave culture, was a late Copper Age to early Bronze Age herding culture of the Pontic-Caspian steppe, dating to 3300–2600 BC. Its name derives from its characteristic burial tradition: these people used to bury their dead in tumuli (kurgans) containing simple pit chambers. They lived primarily as nomads, with a chiefdom system and wheeled carts that allowed them to manage large herds. Recent studies indicate that the Yamnaya people played a role in the domestication of the modern horse.

Examination of physical remains of the Yamnaya people has determined that they were tall and massively built, overwhelmingly with brown eyed, dark haired and had a skin colour moderately light, though darker than that of modern Europeans. The Yamnaya culture is identified with the late Proto-Indo-Europeans, and is the strongest candidate for the urheimat (original homeland) of the Proto-Indo-European language, the ancestor of most modern European languages.

The migrations of the Yamnaya and their impacts on the Bronze age cultures and languages of Europe are complex and our understanding is evolving rapidly with increased genetic information from modern cultures and ancient remains. I will try to make sense of the evidence on the likely migration path of my paternal ancestors from the Western Steppe in Ukraine, through Bronze and Iron Age Europe and into Britain in a future post.

Horsemen of the Western Steppes

References

  1. Rob Spencer. SNP Tracker. [INTERNET] http://scaledinnovation.com/gg/snpTracker.html?fbclid=IwAR0irzIVQiqVzLsWodhJfnA8h-fbxYlLaPllOYf6kEQ146Ba002sW8jxYok
  2. Adamov, Dmitry & Gurianov, Vladimir M. & Karzhavin, Sergey & Tagankin, Vladimir & Urasin, Vadim. (2015). Defining a New Rate Constant for Y-Chromosome SNPs based on Full Sequencing Data. Russian Journal of Genetic Genealogy. 7. 1920-2997.
  3. International Society of Genetic Genealogy (2015). Generation length. ISOGG Wiki https://isogg.org/wiki/Generation_length. For calculating approximate degree of great-grandfatherhood, I have assumed that my average paternal line generation length is 31 years prior to 1000 CE, and 32 years after that.
  4. Kamin M, Saag L, Vincente M, et al. (April 2015). “A recent bottleneck of Y chromosome diversity coincides with a global change in culture”. Genome Research. 25 (4): 459–466. doi:1101/gr.186684.114
  5. Haber M, Jones AL, Connel BA, Asan, Arciero E, Huanming Y, Thomas MG, Xue Y, Tyler-Smith C (June 2019). “A Rare Deep-Rooting D0 African Y-chromosomal Haplogroup and its Implications for the Expansion of Modern Humans Out of Africa”. Genetics. 212 (4): 1421–1428. doi:1534/genetics.119.302368.
  6. Pitulko VV, Nikolsky PA, Girya EYu, Basilyan AE, Tumskoy VE, Koulakov SA, Astakhov SN, Pavlova EYu, Anisimov MA. The Yana RHS Site: Humans in the Arctic Before the Last Glacial Maximum. Science 2004; 02 Jan: 52-56.
  7. Sikora M, Pitulko VV, Sousa VC et al. The population history of northeastern Siberia since the Pleistocene. Nature 2019; 570, 182–188. https://doi.org/10.1038/s41586-019-1279-z
  8. BBC News. Ancient DNA from Siberian boy links Europe and America. 2013; 20 Nov. https://www.bbc.com/news/science-environment-25020958
  9. Balaresque P, Bowden GR, Adams SM, et al. A Predominantly Neolithic Origin for European Paternal Lineages. PLoS Biol 2010;8(1): e1000285. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000285

 

Tracing my paternal ancestors through Y DNA

The human Y chromosome is a male-specific sex chromosome. When mutations (errors in the copying process) arise in the Y chromosome, they are passed down directly from father to son in a direct male line of descent and define a tree of Y “haplogroups”. The mutations on the Y chromosome can thus be used to trace our paternal ancestors all the way back to the most recent common paternal ancestor of all men alive today, Y chromosomal Adam.

When I first got interested in genetic genealogy around 2010, I had my DNA tested by the National Genographic Project, funded by the National Geographic to collect over a million DNA samples to map the patterns of human migration across the world. This project measured mutations known as short tandem repeats (STRs) at 12 sites, and gave a statistical prediction of my Y-haplogroup, R1b (M343) and subclade R-M269. A year later I upgraded my Y-DNA analysis to 44 STRs with Ancestry.com. At the time, I decided that I would wait for the technology to improve and the cost to drop and do a more comprehensive test which would definitively determine my Y haplogroup.

And so last year I did the Big Y-700 test with FamilyTreeDNA which examines 700 short tandem repeats, and over 200,000 single-nucleotide polymorphisms(SNPs) identifying known haplogroups as well as millions of locations where there may be new branch markers on the Y chromosome. This company claims to have the world’s largest genealogical YDNA database with over 2 million people included.

A single-nucleotide polymorphism (SNP, pronounced snip) is a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G) in the genome differs between individuals. For example, two sequenced DNA fragments from different individuals, AAGCCTA to AAGCTTA, contain a difference in a single nucleotide. In this case we say that there are two alleles: C and T. Almost all common SNPs have only two alleles.

Although it contains ~1% of the genome length in a human male cell, the lack of recombination along most of the Y chromosome makes it relatively easy to construct the evolutionary relationships among the Y haplogroups, known as a phylogenetic tree. The most recent version of the Y chromosome phylogenetic tree is maintained by the International Society of Genetic Genealogy (https://isogg.org/tree/index.html). The human Y chromosome contains about 56 million positions or base pairs. Of them, roughly 23 million base pairs (40%) are useful for phylogenetic analysis and FamilyTree DNA has identified over 500,000 unique mutations in the Y chromosomes of their testers.

Figure 1. Migration routes of Y haplogroups dating back to Y-DNA Adam (denoted by capital Y) in West Africa around 275,000 years ago. All humans originated in Africa and migrated out, branching into the main out of Africa haplogroups, including haplogroup R predominant in Western Europe. Details of Eurasian haplogroup locations and migrations have changed somewhat from those shown on this 2010 map from Wikimedia. (Source: Chakazul Wikimedia Commons 18 Sep 2013)

The Y chromosome has regions of fast mutating STRs and stable regions with for which bias-free estimates of SNP mutations rates have been obtained. This allows relatively reliable dating of haplogroups. Additionally, increased levels of Y DNA testing along with substantial increases in sequenced Y DNA for ancient samples, has allowed major advances in understanding the origin, dispersal, and geographic spread of many haplogroups. Given the likely increase in dated ancient haplogroup samples, the detailed places and times of my paternal ancestral migration path from Y-chromosomal Adam onwards is likely to be revised in the future.

My Y DNA results show that I am a member of haplogroup R1b descended from Y-chromosomal Adam 275,000 years ago through haplogroups A1b, BT, CT, F-K, and P. The following diagram is an interesting visualization of the Y haplogroup tree with all its major branches from FamilyTree DNA.

World’s largest Y-DNA Haplotree from FamilyTreeDNA (Image generated using iTOL) (FamilyTree DNA 2020 https://blog.familytreedna.com/human-y-chromosome-testing-milestones/)

In May 2019, the Y-DNA Haplotree passed 20,000 branches, defining over 150,000 unique haplogroups. This makes the FamilyTreeDNA Haplotree the largest and most detailed phylogenetic tree of mankind in the world. The brown area is haplogroup R, R1b is most of R so you can see R1b is a good 40-45% of the tree. This is because the majority of testers to date have European ancestry, not that R1b is the largest haplogroup in the world.

There are at least 13,267 branches on the R1b tree. My Y haplogroup is at the end of one of the branches in the group that meets the circumference where the R1 of R1b is placed. Haplogroup R1b is the most frequently occurring paternal lineage in Western Europe, accounting for 50% or more of all paternal lineages in Europe. It peaks at the national level in Wales at a rate of 92%, at 82% in Ireland, 70% in Scotland, 68% in Spain, 60% in France (76% in Normandy), about 60% in Portugal,] 45% in Eastern England, 50% in Germany, 50% in the Netherlands, 42% in Iceland, and 43% in Denmark.

In a following post, I will summarize the migration path and time line of my paternal ancestors from Y chromosomal Adam down to my most recent haplogroup-defining mutation dated to 510 AD and figure out which wave of migrants into Europe my paternal great-grandfathers were part of and where they were during the ice age.

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.

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