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.

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/

 

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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