Monday, April 27, 2015

My Genome II

I'd previously discussed my ancestry results from 23 and me which can be summarized as follows:
Y-DNA haplogroup: E1b1b1a2* (E1b1b1 is also known as E-M35, E1b1b1a is E-M78 and my own haplogroup is E-V36/V13).

mtDNA haplogroup: H1b

Broad ancestry composition (out of 31 regional groupings including speculative estimates):
European 99.9%
*Northern European 94.8%
**Finnish 38.1%
**Scandinavian 16.4% (Sweden-Norway-Denmark)
**British and Irish 6.3% (UK and Ireland)
**French and German 1.1% (Germany, Netherlands, France, Switzerland, Austria, Belgium)
**Broadly Northern European 32.9%
*Broadly Southern European 2.6%
*Broadly European 2.6%
East Asian - Yakut 0.1%
Unassigned less than 0.1%
In due course, my children's results came in, and that substantially changed the result for me due to "phasing" associated with the link to a child.  It now reads (with changes in bold):

European 99.9%
*Northern European 95.4% (up 0.6)
**Finnish 43.4% (up 5.3)
**Scandinavian 3.0% (down 13.4)
**British and Irish 9.6% (up 3.3)
**French and German 5.2% (up 4.1)
**Broadly Northern European 34.2% (down 0.7)
*Broadly Southern European 1.9% (down 0.7)
*Broadly European 2.7% (up 0.1)
East Asian - Yakut 0.1%
Middle East & North African - North African less than 0.1% (new)
Unassigned less than 0.1%

Where it comes from

It is also possible to discern that a modest part of the British and Irish component, the about a third the "Southern European" component, and all of the "Yakut" ancestry are from my mother's side of chromosome 6, while the "North African" portion, a modest part of the British and Irish component, and about half of the "Scandinavian" component is from my father's side on chromosome 6.

The remainder of the "Southern European" component, the remainder of the "Scandinavian" component, more of the rest of the British and Irish component, and all of the "French and German" component, are on other chromosomes on my father's side, while a little bit of the British and Irish component is on another chromosome on my mother's side.

Broadly European and Broadly Northern European components are found on every chromosome.

Thus from my mother I receive 43.4% Finnish, perhaps 1.6% British and Irish, and perhaps 0.6% Southern European and 0.1% Yakut, and about 4.3% Broadly Northern European and Broadly European.

Meanwhile from my father, I receive perhaps 8.0% British and Irish, 5.2% French and German, 3.0% Scandinavian, 1.3% Broadly Southern European, less than 0.1% North African, and 32.4% Broadly Northern European and Broadly European.


It seems a bit odd that I have one chromosome, number six, that is much more cosmopolitan and well defined than the others.

The rephased results case my mother as even more pure-bloodedly Finnish than she had been before, while my father comes out again as a Northern European mutt.

Neither the trace Yakut on my mother's side, from a region that had trade ties to Finland, nor the trace North African ancestry on my father's side given that I have a Y-DNA haplogroup that is only about three mutations away from a common Berber Y-DNA haplogroup, is much of a surprise.  Indeed, I was surprised at the absence of even trace North African ancestry the first time around.

The fact that the British and Irish ancestry is greater than before and mostly on my father's side is unsurprising, given that I have known Irish ancestry on that side.  The only surprise about the French and German ancestry on my father's side is that it is so low relative to "Broadly Northern European" ancestry.

Trace Southern European and British and Irish ancestry on my mother's side is a bit of a surprise, but it is small enough in amount to have cryptic origins, although careful examination of my mother's side's well documented genealogy could probably ferret it out.

Sunday, April 26, 2015

Dark Photon Parameter Space Constrained

The two most viable dark matter models are those with a single keV mass dark matter particle (warm dark matter) and self-interacting dark matter models in which dark matter fermions interact with each other via a "dark photon" that could also potentially mix with ordinary photons.  A new study restricts the properties that the dark photon can have in a self-interacting dark matter model.

Jester notes significant restrictions on dark photon parameter space from a variety of recent experiments.
[T]he mixing angle in the minimal model has to be less than 0.001 as long as the dark photon is lighter than 10 GeV. This is by itself not very revealing, because there is no theoretically preferred value of ε or mA'. However, one interesting consequence the . . . result is that it closes the window where the minimal model can explain the 3σ excess in the muon anomalous magnetic moment.
I would agree with Jester that there is no theoretically preferred value for ε, which is the parameter determining the extent to which dark photons and ordinary photons mix.

But, I would disagree with him that there is no theoretically preferred value for mA' which is the mass of the dark photon (hypothesized as a boson that carries a force by which dark matter interacts with other dark matter). Most studies I have seen have favored a dark photon mass in the MeV range and certainly a mass of less than 10 GeV.

The constraint on mixing between dark photons and ordinary photons is significantly tighter for dark photon masses of under 10 MeV, which is the preferred mass range for dark photons.

The mass of a dark photon impacts the effective range of the force it carries.  A dark photon with a mass of 80 Gev-90 GeV would have a range similar to that of the weak force bosons, i.e. on the order of the size of an atomic nucleus.  An MeV range dark photon, in contrast, would have a long enough range to produce meaningful interactions of dark matter particles that are near each other sufficiently to tweak the dark matter halo shape in galaxies and galactic clusters.

Thus, this data, collectively, and together with other data attempting to detect dark matter directly, further buttresses the idea that if dark matter exists, that it has almost no interactions with ordinary matter except via gravity.

Interactions between ordinary photons and dark photons aren't important to the overall character of self-interacting dark matter models, but these studies do strictly narrow the classes of self-interacting dark matter models that can be consistent with empirical evidence.

UPDATE:  A new study reanalyzes the estimates of the strength of dark matter self-interactions based upon the observations of a galaxy falling into a galactic cluster.  The value reached is similar to, but a bit higher than, that estimated from the Bullet Cluster.

Ancient DNA Confirms That Proto-Arignacian Was Human Not Neanderthal

An mtDNA sample from the tooth of a Proto-Arignacian individual whom radiocarbon data confirms died 40,170 to 35,650 years before present, was a modern human and not a Neanderthal.

This had been the prevailing opinion regarding the species identity of the Proto-Arignacians and is also consistent with the modern features of the tooth, but this hypothesis had not previously been confirmed with DNA evidence.  This mtDNA sample is quite similar to that of the Ust Ishim individual whose 45,000 year old DNA from Siberia was recently announced.

This discovery further advances a narrative in which the Proto-Arignacians, as the first wave of modern humans in Europe, are the proximate cause of the extinction of the Neanderthals.

Tuesday, April 21, 2015

Two Ho Hum mtDNA Studies

Eurogenes recounts a new study of South Asian mtDNA with a huge sample size.  Dienekes reports on a new study of mtDNA lineages in indigenous populations of Arctic North America.

Both studies attempt to frame their results within the existing historical paradigms for the regions.  Neither adds much other than some very fine detail to what we already know.

UPDATE May 3, 2015:  The main significance of the Arctic North American study is to demonstrate that all post-founding era migrations into the Americas have taken place from West to East, as widely assumed, thereby ruling out (again) the Solutrean hypothesis.

Tuesday, April 14, 2015

A New Study On Y-DNA G1

Map via Wikipedia (not the new study)

Dienekes' has a post on a new paper reviewing that range and phylogeny of Y-DNA haplogroup G1, a Y-DNA clade that seems to play an important role in Iranian population history.

While G1 is found near some proposed homelands for proto-Indo-Europeans, its narrow geographic distribution precludes it as an important component of the proto-Indo-European population.

The abstract notes that (paragraph breaks mine):
Y-chromosomal haplogroup G1 is a minor component of the overall gene pool of South-West and Central Asia but reaches up to 80% frequency in some populations scattered within this area. 
We have genotyped the G1-defining marker M285 in 27 Eurasian populations (n= 5,346), analyzed 367 M285-positive samples using 17 Y-STRs, and sequenced ~11 Mb of the Y-chromosome in 20 of these samples to an average coverage of 67X. This allowed detailed phylogenetic reconstruction. 
We identified five branches, all with high geographical specificity: G1-L1323 in Kazakhs, the closely related G1-GG1 in Mongols, G1-GG265 in Armenians and its distant brother clade G1-GG162 in Bashkirs, and G1-GG362 in West Indians. 
The haplotype diversity, which decreased from West Iran to Central Asia, allows us to hypothesize that this rare haplogroup could have been carried by the expansion of Iranic speakers northwards to the Eurasian steppe and via founder effects became a predominant genetic component of some populations, including the Argyn tribe of the Kazakhs.
The study is also notable for its "clan" level genetic analysis, which is midway between geneology based studies and studies looking at large national or ethnic populations, and for its use of that method to more precisely pin down Y-DNA mutation rates in human populations.

Y-DNA G was the plurality haplogroup for men in the first wave of the Neolithic revolution, but then faded to a minor component of the European gene pool in most areas outside Sardinia, Tuscany, the Caucasus and West Asia.  But, G2 played a larger role than G1 in the Neolithic and in European populations traceable to that migration.

The geography of G1 and G2 respectively, suggest an origin for the most basal branch of Y-DNA haplogroup G in central to Western Iran.

Monday, April 13, 2015

Major Systematic Error In Dark Energy Estimates Discovered

It turns out that there are two different subtypes of type 1a supernovas, with one more common in the early universe, and the other more common recently.  They are very hard to distinguish in the visible light spectrum, but have clear differences in the UV spectrum.  As a result, the rate at which the universe is expanding, if indeed it is expanding, and the amount of dark energy in the universe, are systemically overestimated by a significant amount.

Less dark energy may, however, mean that another cosmology mystery is more profound.  This could bring the relative amounts of dark matter and dark energy in the universe closer together, something that is already called the cosmic coincidence problem because there is no obvious theoretical reason for the two dark components of cosmology to be so similar in aggregate amount.

A (Probably) Final Tevatron Top Quark Mass Measurement

The final Tevatron mass measurement for the top quark is 174.34±0.64 GeV.  This is the most accurate single measurement of this fundamental standard model mass parameter to date.

This compares to the latest top quark mass estimate from ATLAS of 172.99 +/- 0.91 GeV. The latest combined mass estimate of the top quark (excluding the latest top quark mass measurement estimate from ATLAS) is 173.34 +/- 0.76 GeV.

The Tevatron measurement pulls the LHC estimates to a higher value, which is a good fit for some theoretical expectations for it. The overlap of the combined one sigma experimentally measured ranges for the top quark mass at Tevatron and the LHC is 173.70 to 174.10 GeV with an average of 173.90 GeV.  Weighting the Tevatron results slightly more heavily than the LHC combined result since it has a smaller margin of error, only slightly increases the average since the margins of error are still quite similar.

The expected value of the top mass from the formula that the sum of the square of each of the fundamental particle masses equals the square of the Higgs vaccum expectation value, given the state of the art Higgs boson mass measurement (using a global fit value of 80.376 GeV for the W boson rather than the PDG value) is 173.73 GeV (173.39 to 174.07 GeV within the plus or minus one sigma band of the current Higgs boson measurement).

If the the sum of the square of the boson masses equals the sum of the square of the fermion masses the implied top quark mass is 174.03 GeV if pole masses of the quarks are used, and 174.05 GeV if MS masses at typical scales are used.

The experimental measurements are perfectly consistent with any of these theoretical expectations.

Tuesday, April 7, 2015

Planck Data Bounds On Dark Matter

A new preprint sets bounds on the minimum dark matter mean lifetime of 3.57*10^24 seconds, and also establishes a minimum value for cross-section of interaction divided by dark matter mass, based on the Planck data.  This is roughly 10^17 years.

By comparison the age of the universe is roughly 1.38 * 10^9 years.  This means that dark matter (if it exists) is at least as stable as anything other than a proton, which has an experimentally determined mean lifetime of at least 10^33 years.

Genealogy v Genetics

Genealogy still towers over genetics in establishing family relationships.  23andMe located just under a thousand second and more distant cousins and relatives.  But, a genealogy website used in Finland has located approximately 350,000 of my closest relatives on my mother's side!  The Finns love their family histories, apparently.

Seriously, more than 6% of the population of Finland has a publicly documented family relationship to me.

I've met about half a dozen of my Finnish relatives and one stayed with my family for a summer after I had left for college.  The most illustrious of them was awarded a knighthood for his service to Finland by revolutionizing their waste treatment system, banishing diseases that would have otherwise afflicted Finland's people.

Monday, April 6, 2015

My Genome (An Executive Summary)

My 23 and Me personal genome testing preliminary results are in (much more promptly than advertised, for what it is worth):


Y-DNA haplogroup: E1b1b1a2* (E1b1b1 is also known as E-M35, E1b1b1a is E-M78 and my own haplogroup is E-V36/V13).

mtDNA haplogroup: H1b

Broad ancestry composition (out of 31 regional groupings including speculative estimates):
European 99.9%
*Northern European 94.8%
**Finnish 38.1%
**Scandinavian 16.4% (Sweden-Norway-Denmark)
**British and Irish 6.3% (UK and Ireland)
**French and German 1.1% (Germany, Netherlands, France, Switzerland, Austria, Belgium)
**Broadly Northern European 32.9%
*Broadly Southern European 2.6%
*Broadly European 2.6%
East Asian - Yakut 0.1%
Unassigned < 0.1%

Neanderthal Ancestry 2.9% (79th percentile; 82nd percentile for Europeans).

Feel-Good Gene: AC (mixed ancestral "C" and feel-good "A" type)


My Y-DNA haplogroup, which is most common in Greece and Albania, is surprising as it is rare in the places that are home to my ancestors (Protestant Germany near the former West German-East German border), but not shocking.  It could have been a part of either a first wave early European farmer migration, or a Bronze Age migration, to the north and west from the Balkans.  The source of this Y-DNA was probably not recent as my genome lacks any East European and only a very modest amount of Southern European ancestry, and no Near Eastern ancestry.

My combined Y-DNA and mtDNA haplogroups, while not terribly remarkable for someone of my ancestry, would also be quite normal for a man of Berber origin, until one gets to the very last couple of mutations in the Y-DNA haplogroup that are European specific.

I was surprised to be more Finnish than Scandinavian.  My Finnish ancestors are Swedish language speaking Finns and I'd expected the Scandinavian component to be half or more of the total.  But, apparently, Swede-Finns absorbed more native Finnish ancestry than I'd expected, although the possibility that Swedish ancestry which due to founder's effects is most common in Finland counts as Finnish could also be a factor.

The trace Yakut ancestry isn't too surprising given my substantial Finnish heritage, with a presumed cryptic circumpolar migration producing an ancestor hundreds of years ago.  This trace, which appears only on one of my chromosomes in a single bunch, also highlights the fact that you can have ancestry which is not reflected in either of your uniparental haplogroups.

The higher than average Neanderthal ancestry was also expected as Finns have above average hunter-gatherer ancestry in Europe and European hunter-gathers had higher levels of Neanderthal ancestry than post-Last Glacial Maximum migrants from the Near East.

There is less specifically British and Irish ancestry than I'd expected and less German ancestry than I'd expected, and I hadn't expected any Southern European ancestry.  But, as most of my father's ancestry is ascribed to "Broadly Northern European", it is fair to say that he's pretty much a Northern European mutt.

The "Feel-Good Gene" is one where I'd thought it was likely that I'd have a mixed or completely derived type, as this gene is particularly common in Finns and is associated with phenotypes that fit my personality.

Some spot checking has revealed that there are a not insignificant number of SNPs for which no result was obtained, although they are clearly a small minority and I don't expect 100% reads on everything in a mailed in spit test analyzed for an average price of less than $99 per genome.

Ethics and Motivation

I'm aware that by posting this information, I am also posting without their consent, by inference, information about the uniparental genetics of my father, one my two children, my brother, my uncle, my male paternal first cousin, two maternal uncles, a maternal aunt, four maternal first cousins, and two children of one of my maternal first cousins, for a total of at least fourteen people, in addition to large numbers of deceased people (e.g. my grandparents and mother) and many more distant relatives.

On the other hand, the information is intrinsically a part of me and hence morally belongs to me to use as I see fit, anyone using it has to tease out the family relationships to do so, and there is not strong stereotypes attached to Y-DNA and mtDNA haplogroups at this point, although there is arguably mild anti-Neanderthal stigma that this post my help to dissolve (or enhance, depending upon what you think about me).  And, I think it is worthwhile for someone who blogs a great deal about genetics to disclose his own, after benefiting so much from the disclosures of others.

Moreover, the kind of information that I have disclosed already really provides very little information that couldn't be inferred from publicly available information on my family tree, ancestry, appearance, and demeanor.  I would think twice before posting my whole genome, or portions of it with greater medical significance.

I also think it is important for the public to put a face on genetic information, and make my own contribution here.

Also, knowledge of your own genes inevitably colors your interest in our research, something which I should disclose to my readers.

For example, Maju just blogged on mtDNA H1 in Cantabria from 19,000 years ago, something that it had previously not been clear existed.  This area in Northern Spain was a refuge in which modern humans survived the deepest part of the last Ice Age, with glaciers that reached their greatest extent around 20,000 years ago.  So, this find disproves the hypothesis that everyone in Europe who survived the last Ice Age was mtDNA U with all other haplogroups arriving more recently from the Near East, which had been the prevailing paradigm based upon ancient DNA findings to date, before this discovery.

Knowing that I bear this mtDNA haplogroup makes that discovery one of more personal significance than it otherwise would have been, although it was surely noteworthy in any case.

Wednesday, April 1, 2015

Blue Police Box Found In Precolumbian Peruvian Tomb

This morning, a police box resembling the one above was found in a tomb of the pre-Columbian Peruvian pyramid from the Norte Chico civilization shown below.

The artifact was apparently constructed on site near the Huaynaputina volcano, as it is much larger than any of the entrances to the chamber where it was found, which appears to have been hewn from solid bedrock by hand with stone chisels.  Radioactive isotype and material composition tests to determine if the materials in the artifact were locally sourced or obtained through trade have not yet been completed.  Researchers noted that the color of the artifact shows some similarity to Maya Blue which originates in the Yucatan Peninsula of Mexico.

Experts argue that this artifact demonstrates the high level of civility demonstrated by a people whose prehistoric culture is often demeaned merely because they sacrificed live (but humanely drugged) children to a volcano God from the Underworld (Uku Pacha) in order to further the greater good of the society, a practice that Jeremy Bentham himself surely would have approved of, if asked.  

In fact, these signs of respect for authority merely show that the Incas were among the most civilized prehistoric peoples of the Americas.  While the barbaric and rebellious United States of America was founded on the right to Life, Liberty and the Pursuit of Happiness, apparently the Incas, like the people of Australia, Canada, New Zealand, and South Africa, favored a society based upon Peace, Order and Good Government.

Some researchers have suggested that the inscription on the artifact found in the tomb may indicate that there were pre-Columbian links between the English government and Peru, although Scotland Yard adamantly denies any such connection and claims that this is a case of a pure chance similarity between languages.  Other researchers at the London School of Economics, cognizant of the long standing immigration history linking the two countries and London, in particular, whose immigrant narratives dating back to ancient times and before that into European prehistory are not always well known to non-specialists in the field, however, were not so quick to dismiss this hypothesis.  

While pre-Columbian contacts between South America and the Old World were extremely rare, they are not entirely without precedent, although not all such claims are plausible.

Lead investigator Dr. Who from the Perimeter Institute of Waterloo, Canada, was not available for comment on this report.