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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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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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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Thomas Wilson – convict ancestor

After my previous slightly light-hearted post about Thomas Wilson ( an-odd-fellow ), I thought I should tell his real story, his transportation to Sydney in the Lady Nugent in 1835 and his later role in the Mona Vale Outrages.

The Lady Nugent on the high seas. Pencil drawing by George Richard Hilliard, 1840 (4).

The Lady Nugent on the high seas. Pencil drawing by George Richard Hilliard, 1840 (4).

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An odd fellow

Back in 2011, I discovered that one of my great-great- great-grandfathers (on grandpa Baker’s side) Thomas Wilson (1817-1890) had been transported to Australia in 1835 as a convict. He and two others had committed a highway robbery.

Just recently, I came across convict records that gave more information and a description of him. He was aged 21, single, a Protestant who could read and write. He came from Kent, and was a skinner and poulterer.  According to the convict records, he was 5 feet 4¾ inches tall, with ruddy and freckled complexion, brown hair and grey eyes, his eyebrows partially meeting. Among various marks and scars, he had (presumably tattooed) a sun, half moon, seven stars and a crucifix inside his lower left arm. At this point, I realized I was out of my depth, and called in the renowned symbologist, Professor Robert Langdon of Harvard, who told me that the sun, moon and seven stars were a set of symbols used by Freemasons and were also adopted by the Order of Oddfellows, founded in the eighteenth century. The Oddfellows modelled themselves on freemasons though were dedicated more to people of modest lifestyle, labourers and artisans. For the Oddfellows, the “sun, moon and stars” collectively might represent all God’s creation, all that is wonderful and admirable. The seven stars recalls The Pleaides constellation representing the “seven liberal arts”, and for a skinner and poulterer would probably translate to literacy and numeracy.

Langdon concluded that a literate 19 year old working class boy who was already a member of the Oddfellows and had a distinctive set of symbols tattooed on his arm was unlikely to have been a simple highway robber. Could he have deliberately set out on a course of action that would result in him being transported to NSW?  Was there any significance that after he was given his ticket of leave, he bought substantial land holdings in the Manly area in 1853? Land now worth $300 million. And in 1869 became tenants of the “Mona Vale” property belonging to William Charles Wentworth, one of the three explorers who found the first route across the Blue Mountains in 1813. Was it significant that when he arrived in Australia in 1835, Wilson was first sent to Paramatta to work for William Lawson one of the other three explorers. Could it be another coincidence that Thomas Wilson sold his land in 1877, exactly one year before the foundation stone was laid for the first Oddfellows Hall at Manly.

Langdon immediately flew to Geneva and interviewed Mathers, seeking any evidence of Oddfellows involvement in his life. Mathers was surprised at the turn this research had taken, and unwilling to believe that the location of the Oddfellows Hall in Casino just half a block from where he lived as a child was anything more than coincidence. Or that one of father’s close colleagues was the Warden of the local Oddfellows Lodge. And why did the Lodge reach out and offer Mathers a scholarship as a teenager that enabled him to visit New Zealand. Why did they try to bend his interest in astronomy towards astrology and more occult concerns? Clearly Langdon would have to follow the leads in New Zealand to see what connections were found.

Discussions with Mathers also revealed that in the 1940s, his grandfather had applied considerable pressure on his mother to get her to  visit two elderly women in Mosman, the granddaughers of Thomas Wilson. Why was it so important that this contact be made? Could the Oddfellows really have had a plan, a vision, reaching centuries ahead. And what could it possibly be?