Lake sunset

Sitting by the lake at sunset.
Thoughts drop away as the light of the sun drops away,
the stillness of mind and the stillness of the lake here-now

Looking south across Lake Leman from Montreux, Switzerland.

Geneva hidden in a golden glow

Sunset behind the Intra-coastal water way, Ocean Isle, North Carolina

Swans on Lake Garda, northern Italy

Sunset reflected in a farm dam, Gloucester, New South Wales

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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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COVID-19: light at the end of the tunnel for some countries

Tomorrow, Switzerland will relax its social distancing regime. Classroom teaching at primary and lower secondary schools will again be permitted. Shops, markets, museums, libraries, gyms and restaurants will be able to reopen under strict compliance with precautionary measures. Switzerland has had the 10th highest death rate per million people but has been one of the few high death rate countries to successfully control the epidemic. See the plot for Switzerland below.

I just watched the UK’s Churchill tribute act, aka Boris, give a speech to the nation on the phased easing of restrictions, which is conditional on the reproduction rate R remaining below 1. It apparently is somewhere between 0.5 and 0.9, and even partial easing could easily kick it over 1 (restarting exponential growth). Apart from England, the other three governments are all maintaining current social isolation rules. From tomorrow, workers who cannot work from home should return to work, but try not to use public transport to get there. Primary schools won’t open until at least the beginning of June, and restaurants etc not till July. From the UK plot above, its clear that a much more cautious and conditional easing is definitely desirable.

I have to say that Boris, with his hair neatly combed (!!), actually made what I thought was a quite good speech, with strong emphasis that the government would be guided by data feedback and by the science, by a reasonably sincere expression of empathy for the sacrifices and difficulties of many, and by strong expression of the need for community solidarity. The contrast with the clown show across the Atlantic was quite marked.

The plots above separate New York and the rest of the USA. The timing and size of the epidemic is different in these, but more importantly, it shows the very different time trends. New York is past its (current) peak and on the way to controlling the epidemic. The rest of the USA has not peaked, and cases and deaths continue to rise. Absolutely not the time to start relaxing social distancing in New York, let alone the rest of the country.

Australia (and New Zealand) acted early to implement social distancing, and have done as well as China and South Korea in controlling their epidemics. And they are now relaxing social distancing rules as well.

My professional blog has a post with plots for more countries, and some further explanation of the plots and data.

Breathwork and altered states of consciousness

Until recently I had paid little attention to breathwork techniques for achieving non-ordinary states of consciousness.  I’ve done zen meditation for many years now, on and off, and spent quite a bit of time paying attention to the breath, counting the breath etc, but I had been somewhat sceptical of claims I had read that breathwork could induce psychedelic-like experiences.

Late last year I went to a 5 day retreat in the Netherlands which introduced me to a number of new (to me) practices aimed at personal transformation. Among these were breathwork sessions which introduced me to several forms of breathwork, including the form of energising breathwork taught by Wim Hof, the Iceman. Our facilitator was a trained Wim Hof instructor. He also taught us another form of breathwork, called transformational breathwork, and I will describe one of my transformational breathwork sessions at the retreat.

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COVID-19 short-run projections

Its now one month since my earlier post on the coronavirus pandemic    A lot has changed since then. We have gone from 24,392 deaths globally on March 26 to 206,915 on April 26th. And recent analysis of total registered deaths by week in February and March, compared to the same periods in the previous year, suggest that the reported deaths (mostly hospital deaths) are only about 70% of the actual deaths. The proportion of deaths reported in developing countries without good death registration (including most of Africa, and much of Asia) will be even lower.

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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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Buddhism without beliefs

My son has been reading the existentialists, starting with Camus (of course, The Plague is quite relevant for more than one reason now). He recently moved on to Kierkegaard, who took a form of Christianity as a solution to existential angst. I was reminded of a book I read probably 15 years ago, by Stephen Batchelor: Buddhism Without Beliefs (London: Bloomsbury 1997) which argued that the Buddha was concerned with addressing the existential issue of suffering not with metaphysics and beliefs.  I couldn’t find my copy of this, and bought another, which I enjoyed reading even more than the first time.

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