Mark Stoneking review on Human Origins

Nothing really new in this paper, but the figure of the different models of human evolution is interesting. I have issues with the model of Assimilation shown, however, since only Europeans are shown as assimilating pre-existing populations (Neanderthals). There have been suggestions in the past that other human populations may have interacted with their own local inhabitants, e.g., erecti in Asia.

I also have issues with Stoneking's caricature of Carleton Coon's "candelabra" model. Saying that this model is not tenable today is one thing, but ascribing racist motivations behind it is another:

The candelabra model was most prominently associated with the anthropologist Carleton Coon (1904–1981), and fell out of favour when he used it to promote racist views. According to Coon, the transformation to modern humans occurred first

in Europeans, and hence they have had the most time to evolve from their ‘primitive’ ancestry, whereas Africans were the last to transform into modern humans and therefore have had the least amount of time to shed their primitive ancestry—and in case you were wondering, Carleton Coon was of European ancestry.

There is actually no good reason to ascribe racist motivations to Coon's model of human origins. It was simply an interpretation of the evidence (such as it was in his day). Coon's suggestion that different races crossed the sapiens threshold at different times did not imply superiority and inferiority. While he almost certainly believed in inherent differences between the races (as most scientists in his day did, and many still do), his views were definitely not based on an idea of Africans as having less time to evolve.

EMBO Reports 9, S1, S46–S50 (2008)

Human origins. The molecular perspective

Mark Stoneking

Abstract

Link

The face of Dante Alighieri

Journal of Archaeological Science doi:10.1016/j.jas.2008.09.006

THE FACE OF THE POET DANTE ALIGHIERI RECONSTRUCTED BY
VIRTUAL MODELLING AND FORENSIC ANTHROPOLOGY TECHNIQUES

Stefano Benazzi et al.

Abstract

This paper describes the multi-disciplinary approach to reconstruct the face of Dante Alighieri (1265-1321). Since the Dante’s sepulchre will be opened in 2021, the reconstructive process is based on morphological and metric data collected on the poet’s cranium during the formal identification of his remains in 1921 by the anthropologist Fabio Frassetto, as well as on the resulting plaster model. Starting from this plaster model and a morphologically compatible reference mandible, since the original mandible was never found, a 3D digital model of the complete skull was obtained by reverse engineering and virtual modelling techniques. The most important aspect in this work was the method of virtual modelling proposed for the ex novo generation of the mandible. The physical model of the skull (cranium + mandible) was then produced by means of a rapid prototyping system. This model was finally used to recreate Dante’s face via traditional facial reconstruction techniques currently used in forensic anthropology.

Link

Support for "large" Troy at the time of the Trojan War

See also the Historicity of the Trojan War and The eclipse of 1178BC and the return of Odysseus to Ithaca

Discovery of Bronze-Age `Refrigerators' Expands Homer's Troy :

Sept. 17 (Bloomberg) -- The remains of two outsized earthenware pots, a ditch and evidence of a gate dating back more than 3,000 years are changing scholars' perceptions about the city of Troy at the time Homer's ``Iliad'' was set.

The discoveries this year show that Troy's lower town was much bigger in the late Bronze Age than previously thought, according to Ernst Pernicka, the University of Tubingen professor leading excavations on the site in northwestern Turkey.

His team has uncovered a trench 1.4 kilometers long, 4 meters wide and 2 meters deep. The full length of the trench, which probably encircled the city and served a defensive purpose, may be as much as 2.5 kilometers, Pernicka said in an interview in his office in Mannheim, Germany. Troy may have been as big as 40 hectares, with a population as high as 10,000, he estimates.

...

The discovery of the trench around the lower town vindicates Pernicka's predecessor, Manfred Korfmann, who faced accusations from a fellow German scholar that he was misleading the public in his interpretation of the ditch, which might have been for drainage. After Korfmann died in 2005, Pernicka took over his work and aims to publish the results of 20 years of digging and research.

...

What archaeology has shown is that Troy's golden era ended in 1180. Where preceding Trojans had used potters' wheels for about 1,000 years, ceramics found on the site show the technology was lost with the arrival of a new people, probably from the Balkans, who reverted to hand-made pots. The newcomers also built their houses in a completely different style.

Origins of Venice

How the barbarians drove Romans to build Venice:

Historians agree that the explanation is that Venice was founded on the islands by refugees from Roman cities such as Ravenna, Padua and Aquileia as they fled from invasions, first by Attila the Hun in the 5th century and then, a century later, by the Lombards, as the final remnants of the Roman Empire crumbled.

However, Paolo Mozzi, a researcher at the University of Padua geography department, said high-definition satellite photographs had revealed the ruins of an extensive town much closer to present day Venice at Altino – known in Roman times as Altinum – a little more than seven miles north of the city, close to Marco Polo airport.

“The hypothesis is that as Altinum also succumbed to the Barbarian invasions, the inhabitants fled farther down to the lagoon to build Venice on the islands, using some of the stones from their city,” he said. At its height, he said, Altinum had been an important trading and seafaring centre on the Adriatic, before it was overrun by Attila in the mid-5th century.

Vikings abroad in search of women

Viking Age Triggered by Shortage of Wives?:

Sept. 17, 2008 -- During the Viking Age from the late eighth to the mid-eleventh centuries, Scandinavians tore across Europe attacking, robbing and terrorizing locals. According to a new study, the young warriors were driven to seek their fortunes to better their chances of finding wives.

The odd twist to the story, said researcher James Barrett, is that it was the selective killing of female newborns that led to a shortage of Scandinavian women in the first place, resulting later in intense competition over eligible women.

...

Soren Sindbaek, assistant professor of medieval and Renaissance archaeology at Denmark's University of Aarhus, told Discovery News that the new paper "is very right in pointing out the inadequacy" of former explanations for the Viking Age.

"We need indeed to seek for an individual, social motivation behind the fact that a large number of young men chose to set out on extremely risky voyages in hopes of acquiring wealth and esteem in foreign lands," Sindbaek said.

Erratum on my Y-STR variance work (which, surprisingly further supports its central thesis)

I realized today that there was a central error in my assumptions today on the entire Y-STR series. This error related to the condition I used to detect whether a man was also a Most Recent Common Ancestor:

Lineages start with one man, and over the generations grow (or shrink) in size as men have (or fail to have) sons. Previously, I considered that there was a new MRCA in the lineage if the number of descendants in one generation was reduced to 1 man.

So, for example let these be the number of patrilineal descendants in the first few generations:

Generation	# of descendants
0	1 (Patriarch)
1	3
2	4
3	6
4	3
5	1
6	3
7	2

I concluded that the "Patriarch" (at generation 0) was not the MRCA (correct) and that the new MRCA was the single surviving man in generation 5 (not necessarily correct).

It is true that at generation 5, the man becomes the new MRCA, since no other patrilineal cousins of his exist at that time.

BUT, it is also possible for e.g., one of the 3 men of generation 6 to be an MRCA. All it takes is for the next generation (7) to be produced entirely by him.

So: the single survivor at generation 5 has three sons in generation 6, thus he is temporarily the MRCA. However, only one of his three sons produces the two men of generation 7, and thus this son becomes the new MRCA.

In retrospect this is an obvious mistake to make, and is the result of using a sufficient condition for an MRCA (the lineage reduced to one man) which is not however necessary for a man to be an MRCA.

What are the consequences?

I will be issuing a bug fix for the Y-chromosome Microsatellite Genealogy Simulator over the next few days. But, it's interesting to see how this error affects the story I've been defending throughout the posts in the Y-STR series, namely that Y-STR variance accumulates at near the germline mutation rate for large observable present-day haplogroups.

For any particular lineage, the MRCA I calculated so far was no younger, and sometimes older than the real one. Consequently, Y-STR variance has accumulated at an even faster rate since the time of the real MRCA, even closer to the germline rate.

At this point I am not in a position of determining how big this effect will be, and I will repeat and report some of my earlier experiments. A few exploratory runs so far, have revealed a small but not insignificant increase in the effective mutation rate.

Stay tuned...

UPDATE #1

I carried out some experiments to see how different in age are the previously calculated "MRCA" and the real MRCA. To differentiate between the two, I will call the previous "MRCA" as a "Near Extinction" event, where a lineage is reduced to one man in one generation. The real MRCA is simply a man of the lineage who produces the entire next generation.

As I mentioned in the very first post of this series, at the MRCA, variance is reset to 0; thus variance is of no use to determine the length of time that has elapsed between the Patriarch and the MRCA. This time can be estimated, however, from demographic considerations.

g	m	TMRCA	s.d	TNearExtinct	s.d
50	1	40	16	43	13
50	1.05	44	10	46	9
100	1	86	26	91	22
100	1.05	95	10	97	7

It can be seen that (i) the TMRCA is fairly close to the TNearExtinct, and they are both fairly close to the Patriarch, whose time is g. This closeness (in relative terms) increases as both g and m (the average number of sons/man) increase. Both TMRCA and TNearExtinct can be quite variable, as evidenced by their respective s.d.'s, but this variability decreases as m increases.

UPDATE #2

I have repeated my experiments on the effective mutation rate. You can compare the results directly, but it's obvious that the discrepancy exists somewhat only for m=1 and the results are almost identical otherwise. Thus, the problem identified in this erratum does not appear to affect by much all my past inferences about TMRCA and its relationship to Y-STR variance.

g	m	Size	Var	ASD	μ/wv	μ/wa
50	1.00	32	0.043	0.058	2.9	2.2
50	1.01	41	0.047	0.062	2.6	2.0
50	1.02	53	0.052	0.068	2.4	1.8
50	1.03	72	0.057	0.072	2.2	1.7
50	1.04	98	0.061	0.077	2.1	1.6
50	1.05	135	0.065	0.080	1.9	1.6
50	1.10	813	0.086	0.099	1.5	1.3
100	1.00	58	0.081	0.106	3.1	2.4
100	1.01	99	0.097	0.123	2.6	2.0
100	1.02	185	0.118	0.147	2.1	1.7
100	1.03	360	0.135	0.163	1.9	1.5
100	1.04	757	0.153	0.180	1.6	1.4
50	1.00	31	0.043	0.058	2.9	2.2
50	1.01	41	0.048	0.063	2.6	2.0
50	1.02	54	0.052	0.067	2.4	1.9
50	1.03	73	0.058	0.074	2.2	1.7
50	1.04	97	0.064	0.081	2.0	1.5
50	1.05	134	0.065	0.081	1.9	1.5
50	1.10	813	0.085	0.098	1.5	1.3
100	1.00	58	0.082	0.108	3.0	2.3
100	1.01	99	0.101	0.130	2.5	1.9
100	1.02	184	0.120	0.151	2.1	1.7
100	1.03	362	0.135	0.163	1.9	1.5
100	1.04	749	0.154	0.181	1.6	1.4
100	1.05	1593	0.168	0.193	1.5	1.3
200	1.00	111	0.162	0.208	3.1	2.4
200	1.01	347	0.228	0.280	2.2	1.8
200	1.02	1443	0.293	0.342	1.7	1.5
200	1.03	7132	0.350	0.391	1.4	1.3
200	1.04	38123	0.387	0.421	1.3	1.2
400	1.00	212	0.300	0.377	3.3	2.7
400	1.01	2767	0.589	0.670	1.7	1.5
400	1.02	78149	0.768	0.825	1.3	1.2

Reconstruction of female Neanderthal

This is a very early prototype of things that may be possible in the future. The DNA-based evidence was limited to pigmentation, as far as I can tell. Unfortunately, as with other complex traits, there has been a limited crop of useful genes identified for observable human traits.

No need for such DNA evidence is -of course- needed to reconstruct skeletal structure, since the skeletal structure is pretty much the only part of a person's appearance that survives along Paleolithic time scales.

However, there is wide room for progress in inferring both pigmentation (there have been successes here, but the problem is by no means completely solved), as well as non-surviving traits such as muscular development, hair texture, etc.

Apparently, there is also a National Geographic documentary to accompany this.

Off topic: doesn't she resemble somewhat Vincent from Beauty and the Beast?

PHOTO IN THE NEWS: DNA-Based Neanderthal Face Unveiled:

September 17, 2008—Meet Wilma—named for the redheaded Flintstones character—the first model of a Neanderthal based in part on ancient DNA evidence.

Artists and scientists created Wilma (shown in a photo released yesterday) using analysis of DNA from 43,000-year-old bones that had been cannibalized. Announced in October 2007, the findings had suggested that at least some Neanderthals would have had red hair, pale skin, and possibly freckles.

Lactase persistence allele is clinal in Great Britain

Lactase non-persistence seems to be more important in the south and east of Great Britain.

European Journal of Human Genetics doi: 10.1038/ejhg.2008.156

Lactase persistence-related genetic variant: population substructure and health outcomes

George Davey Smith et al.

Abstract

Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T-13910 variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60–79 years from 23 towns across Britain. We found an overall frequency of 0.253 for the C (lactase non-persistence) allele, but with considerable gradients of decreasing frequency from the south to the north and from the east to the west of Britain for this allele. Daily sunlight was positively related to C (non-persistence) allele prevalence. However, sunlight exposure and latitude are strongly correlated, and it was not possible to identify which is the primary factor statistically underlying the distribution of lactase persistence. The C/T-13910 variant (rs4988235) was not related to drinking milk or bone health (although drinking milk itself was protective of bone health), and was essentially unrelated to a wide range of other lifestyle, health and demographic characteristics. One exception was general health being rated as being poor or fair, for which there was an odds ratio of 1.38 (1.04, 1.84) for women homozygous for the C allele; on adjustment for latitude and longitude of place of birth, this attenuated to 1.19 (0.87, 1.64). The lactase persistence variant could contribute to the examination of data for the existence of, and then statistical control for, population substructure in genetic association studies.

Link

Three-stage colonization model for Americas reconsidered

I had blogged about this model before. From the earlier paper:

Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability.

This model was now criticized by Fagundes et al. who discovered that the early stage of the model was an artifact of the inclusion of mtDNA sequences of non-American origin:

Our results refute the specific details of the “three-stage model”, since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes.

This is acknowledged by the authors of the three-stage model in Mulligan et al:

We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. ~40,000 years ago) expansion signal we had proposed for the proto-Amerind population.

The authors do however claim that:

Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.

What's the lesson from all this? Many of the conclusions drawn by geneticists are very sensitive to data outliers: 9 out of 77 sequences that shouldn't have been included was enough to provide support for the 40kya stage of growth, which was now revealed to be spurious.

Clustering humans: on biological boundaries

From the paper:

Nevertheless beyond such a treacherous ideology, we need boundaries, since we need clusters both to achieve group-oriented diagnostics and therapeutics, and to grasp the evolution of Homo sapiens. Of course these clusters must be named in some way. To be honest nothing prevents us from continuing to use the word ‘race’ for them, especially now that we have understood the real epistemological status of this notion and the methodological path used to determine its content. Unfortunately ‘race’ is a too ideologically and historically committed term, and it would be wise not to use it. The history of human culture has showed us that even if words are not dangerous, the humans who use them can be extremely dangerous.

The problem with this view is that by not using the word "race", the wrong impression is given, namely that "races do not exist", rather than the intended one that "things that we could call races exist, but we prefer not to name them because some bad people do so, and have done so in the past".

A secondary consequence is that by avoiding the use of the word "race" and its terminology, or replacing it with "ethnic group", "continental population", or "cluster", we make communication more difficult, e.g., because "ethnic group" is a social-political-cultural as well as biological concept, races do not map perfectly to geographically circumscribed continents, and "clusters" can be defined in a number of different ways without necessarily the property of "exhibiting genetic similarity reflecting common descent" that is characteristic of biological race.

Thirdly, even if "race" is a dangerous word, does any one believe that people's attitudes towards each other will magically change if they stop using racial terminology? Will a person's prejudices evaporate into thin air if it becomes impolite to speak of human races? On the contrary, existing prejudices will most likely go underground, and all sorts of incorrect notions about it will proliferate as scientists refuse to acknowledge its existence.

If we look back to the age before the emergence of race classification in Homo sapiens in the 18th century, we will see that there was plenty of opportunity for prejudice and conflict. So, rather than thinking that the identification of human races leads to prejudice, we should think that prejudice leads to an abuse of the race concept, just as it leads to an abuse of other religious, linguistic, or social concepts to justify itself. Does the fact that dangerous people use religious differences suggest that we should abandon classification of mankind's religious belief systems?

Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Volume 39, Issue 1, March 2008, Pages 163-170

Clustering humans: on biological boundaries

Ludovica Lorussoa, and Giovanni Boniolo

Abstract

We inquire into the notions of ‘boundary’ and ‘cluster’ in the fields of medical genetics, pharmacogenetics, and population genetics. First we show that the two notions are not well discussed in literature. Then we propose a promising explication of them, in which we argue that clustering is always ‘property laden’, that is, fundamentally dependent on decisions about the properties to be taken into account. In particular we suggest three different kinds of properties (main properties, investigating properties, and catalyzing properties) that have a role in these decisions. That is, we conclude that boundaries and clusters among humans depend on our way of considering nature. Concepts of ‘race’ and ‘ethnic group’ are discussed too, since they are the most used clusters among humans.

Link

Genographic project paper on human mtDNA mutation rates

This is a fairly technical paper which should be of interest for those interested in uniparental markers and their age estimation.

Genetics doi: 10.1534/genetics.108.091116

Maximum Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA from Partial Phylogenetic Classification

Saharon Rosset et al.

Abstract

The mitochondrial DNA hyper-variable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, such as haplogroup association. The resulting estimation problem is a generalized linear model, with a non-standard link function. We develop inference and bias correction tools for our estimates and a hypothesis testing approach for site independence. We demonstrate our methodology using 16,609 HVS-I samples from the Genographic Project. Our results suggest that mutation rates among nucleotide sites in HVS-I are highly variable. The 16,400--16,500 region exhibits significantly lower rates compared to other regions, suggesting potential functional constraints. Several loci identified in the literature as possible termination associated sequences (TAS) do not yield statistically slower rates than the rest of HVS-I, casting doubt on their functional importance. Our tests do not reject the null hypothesis of independent mutation rates among nucleotide sites, supporting the use of site-independence assumption for analyzing HVS-I. Potential extensions of our methodology include its application to estimation of mutation rates in other genetic regions, like Y-chromosome short tandem repeats.

Link

Why genome-wide association studies don't really work (and how human evolution really happens)

In case you are skeptical about my gloomy assessment of the power of genome-wide association studies, here is Nicholas Wade in today's New York Times, profiling David Goldstein (via john hawks):

This idea, called the common disease/common variant hypothesis, drove major developments in biology over the last five years. Washington financed the HapMap, a catalog of common genetic variation in the human population. Companies like Affymetrix and Illumina developed powerful gene chips for scanning the human genome. Medical statisticians designed the genomewide association study, a robust methodology for discovering true disease genes and sidestepping the many false positives that have plagued the field.

But David B. Goldstein of Duke University, a leading young population geneticist known partly for his research into the genetic roots of Jewish ancestry, says the effort to nail down the genetics of most common diseases is not working. “There is absolutely no question,” he said, “that for the whole hope of personalized medicine, the news has been just about as bleak as it could be.”

...

The reason for this disappointing outcome, in his view, is that natural selection has been far more efficient than many researchers expected at screening out disease-causing variants. The common disease/common variant idea is largely wrong. What has happened is that a multitude of rare variants lie at the root of most common diseases, being rigorously pruned away as soon as any starts to become widespread.

I would only add that the common variant idea is probably wrong for neutral or positive traits as well. While negative traits are culled from the gene pool by purifying selection, advantageous traits (muscularity, beauty, intelligence, etc.) are positively selected.

But, what is selected? Surely, "a multitude of rare variants" can't exist for positive traits: most mutation is deleterious; the good stuff doesn't appear de novo very often. In my opinion, by and large, it is not common variants behind these traits. Rather, it is fortuitous combinations of unexceptional alleles.

This Lego-block paradigm is based on the notion that most of our alleles are commodity"building blocks"; if they are brought together harmoneously, they produce positive results. The occasional allele may have a large effect, and some alleles fit better together than others. Yet, most of the success or failure of a construction depends on how the components fit together, and not what they are.

I had previously made the point that evolution doesn't require mutation, selection, or drift but can be effected by the self-segregation of individuals into geographical or social niches for which they are better adapted. Differential reproduction of the semi-segregated geographical or social groups (i.e. group selection) then ensues.

There has doubtlessly been recent selection in humans, particularly because of feedback from the changed environments humans created for ourselves.

But, individuals don't differ from each other primarily because of genes that have undergone population-wide selection. Rather, we differ from each other first because we belong to a specific hierarchy of groups (race, subrace, ethnic group, etc.) and foremost because we have inherited a particular combination of alleles, our "family lego shape" from our parents.

Why I won't be testing with 23andMe (yet)

Since the announcement of the price reduction of the 23andMe service, I had a couple of readers e-mail me, asking whether I thought it was worth it. My response was to do their own research to figure out whether the information they would learn would be worth the asking price.

Here is why, despite the much lowered price, I am not convinced.

What is a 23andMe test worth to you?

The 23andMe test gives you four types of information:

• The frivolous, e.g., Bitter Taste perception.
• The obvious, e.g., Hair Color.
• The medical, e.g., Type 2 Diabetes.
• The ancestral.

The frivolous kind is perhaps a good and safe topic for conversation (as opposed, e.g., to Schizophrenia) but its value is obviously not $400.

The obvious kind tells you something that you already know about yourself; it only confirms that you have the genes for your known phenotype. Again, this is not useful information, unless perhaps your spouse orders a test too: then, you could sometimes calculate the chances of your children presenting a phenotype for simple quasi-Mendelian traits. 

The medical kind is potentially useful. It is for this kind of information that you should research the traits on offer, to see if (i) they interest you, and (ii) there are strong associations for them. The truth is, however, as I pointed out recently that for all their hype, genome-wide association studies have produced meagre results. Your family medical history and lifestyle are much more likely to affect your health than the common variants genotyped in the current generation of microarrays. But, by all means, do your own research, since a trait that interests you may be one for which strong associations have been found.

Finally, the ancestral information is potentially useful, since recent papers have shown that multi-100K SNP genome-wide testing can produce fine-scale ancestral inference, even in relative homogeneous populations such as Europeans. However, as of this writing, you won't get this type of information, but rather a simple 4-group global admixture estimate, as well as a measure of your similarity to the Human Genome Diversity Panel populations. For anyone whose known genealogical ancestry isn't complex, this information will not be novel.

23andMe have also apparently included some fairly detailed SNP typing that place you in the Y-chromosome (if you are male) and mtDNA phylogeny, giving you a detailed haplogroup assessment. Even if this information wasn't known to me, this part of the test would not be tempting, since haplogroup assignment reveals only very coarse information. Almost certainly, you would want to follow up with a Y-STR panel or mtDNA full-genome sequence, which would allow you to meaningfully compare yourself with the many others that have tested so far; but that is not an option with 23andMe.

What is a 23andMe test worth to 23andMe?

23andMe have definitely emphasized the "coolness" factor of getting DNA tested. It has definitely generated a lot of publicity, and getting tested is marketed as a social prestige marker. 

However, the "coolness" factor isn't enough to sell tests. It is not known how many have been sold so far, but there are indications that not many is close to the truth:

• No one cuts the price by 60% if there is solid demand for a product. Prices for Y-STR tests haven't dropped by nearly as much in 5+ years, since there is a real demand for them by genetic genealogists.
• People have a Gattaca-view of genetic testing, and are afraid of the information it may reveal. It has been said that 23andMe has downplayed the significance of the associations they report to keep regulators off their backs, but a more significant reason may be to entice reluctant consumers to test.

One would think that a company selling genetic tests would stress the importance of the genetic information, but this is clearly not the case. To its credit, 23andMe doesn't oversell the actual science, which as I mentioned above, isn't all that revealing. 

This NY Times story gives a useful hint:

Ms. Wojcicki and Linda Avey, the company’s other founder, say their chief goal is to advance science by compiling a database of genetic information that medical researchers can tap (while protecting customers’ anonymity). Customers cannot opt out of having their information anonymously shared, but they can refuse to participate in surveys focusing on specific traits.

This is also why the Coriell Institute is offering genotyping for free. 

It is simply a problem of body count. Progress has been hampered by small sample sizes. Collecting and genotyping large samples is hampered both by strict ethics rules that publically-funded medical researchers must adhere to, and also by the actual cost of sample-collection and genotyping.

23andMe's goal isn't to be a service provider to consumers. Their goal is to entice regular people to pay the cost of genotyping, while at the same time helping it build its huge "database of genetic information."

Just as a TV station doesn't exist for providing news and entertainment to an audience, but provides news and entertainment so it can sell ads and make money, so 23andMe doesn't exist to sell genetic information to consumers, but sells genetic information to build and exploit its genetic database.

What it would take to make me a customer

There is nothing wrong with 23andMe's strategy: its goal is to advance science (and make money doing it) by offering genetic information to consumers. This is a potentially win-win situation for both. However, as I explained above, the information one can expect from the test today isn't all that special.

Since I don't want to be a naysayer, here is what it would take to convince me to test with 23andMe:

-- Fine-scale ancestry analysis --

The science has progressed to a point where this is possible. We now know that distinct subgroups can be discerned within all the major continental races. The latest research revealed an additional insight: it doesn't take a large samples to place individuals on the map fairly accurately. Even countries with less than 5 sampled individuals found their way to the "correct" geographical spot. 

The corrolary of the above observation is that a global-level sampling of human genetic diversity can be done at a reasonable cost. Leveraging existing samples, and adding mini-samples from many unstudied locations can lead to powerful ancestry analysis, which can be gradually and continuously refined as more samples are collected (both on the "field" and using customers of unmixed localized heritage)

23andMe's partnership with ancestry.com suggests that they take this segment of their market seriously. So, when and if they offer a test which provides ancestral information beyond the obvious, I will be tempted to test with them.

Ideal craniofacial height / standing height = 1/7-1/8.5, (plus instructions to test your own)

Here is how to test your own craniofacial height / standing height ratio. Take a picture of yourself facing the camera, looking forward. A good rule of thumb is for the bottom of your eye socket to align with your earhole; you can use a side mirror to practice your posture before you take the shot. Obviously, you shouldn't wear shoes, and you should arrange your hair in a way that it doesn't "stand up". Your mouth shouldn't be open or your jaw loose; just have a natural expression. Also, make sure that the camera is a few meters away from you; the more, the better (as long as you can produce a picture with enough resolution for measurement). Use a self-timer or have your friend take the picture.

Once you have the picture in your computer, measure:

• craniofacial height CFH: from top of your head to bottom of your chin.
  
• standing height SH: from top of your head to the point on the floor where your heels touch.
  

Now divide CFH/SH and you have your own ratio: congrats! You can take SH/CFH to see how this is expressed as a fraction.

What is your craniofacial height / standing height
	Less than 1/8
	Between 1/8 and 1/7.5
	More than 1/7.5
Free polls from Pollhost.com

From the paper:

It is generally acknowledged that the work of Polycleitus in the fifth century BC was used by other sculptors as demonstrating the ‘ideal’ proportions of a man. The craniofacial height to standing height proportion of the available marble copies of the Doryphorus is 1/7.5.

In the late fourth century BC, the prolific sculptor Lysippos is thought to have established a new canon using eight heads to standing height. This is evident from inspection of the Roman marble copy of the Apollo Belvedere in the Vatican Museum.

The Roman architect Vitruvius based his guidelines on the Classical Greek sculptors. He described the facial height to standing height proportion of 1/10, which corresponds to a craniofacial height to standing height proportion of 1/8.

The scientifically enquiring minds of the Renaissance were no longer interested in blindly following the Classical ‘ideal’, and began to study human anatomy and record human proportions. Adapting the work of Vitruvius with his own research, Leonardo da Vinci provided the Renaissance canons of proportion. He described the ‘ideal’ craniofacial height to standing height proportion as 1/8. Durer later described the ‘ideal’ man of ‘Eight head-lengths’.

The results of this study lend support to the use of a proportional ratio between the Classical ideal of 1/7.5 and the Renaissance ideal of 1/8.

...

The craniofacial height to standing height proportion may be calculated from the original anthropometric data provided by Farkas2. From this original anthropometric data, the craniofacial height to standing height proportion in young adult males (age range 19–25 years) was found to be 1/7.7 (range 1/7.4 to 1/8.1), and in young adult females (age range 19–25 years) was found to be 1/7.6 (range 1/7.2 to 1/7.9) (Table 1).

The results of this study, based on lay and clinician judgements of attractiveness, generally validate the anthropometric data. In this study it was found that a proportion of 1/7.5 was perceived as the most attractive, with 1/8 a close second. The images regarded as most attractive by the participants had a mean craniofacial height to standing height proportion of 1/7.8 (min=1/7 and max=1/8.5). The mean rank preference score was found to be minimal for a craniofacial height to standing height proportion of 1/8 and increased when the craniofacial height to standing height proportion moved away from 1/8 in either direction (Table 8).

Int J Oral Maxillofac Surg. 2008 Sep 6. [Epub ahead of print]

The influence of craniofacial to standing height proportion on perceived attractiveness.

Naini FB, Cobourne MT, McDonald F, Donaldson AN.

Department of Orthodontics, St George's Hospital, United Kingdom.

An idealised male image, based on Vitruvian Man, was created. The craniofacial height was altered from a proportion of 1/6 to 1/10 of standing height, creating 10 images shown in random order to 89 observers (74 lay people; 15 clinicians), who ranked the images from the most to the least attractive. The main outcome was the preference ranks of image attractiveness given by the observers. Linear regressions were used to assess what influences the choice for the most and the least attractive images, followed by a multivariate rank ordinal logistic regression to test the influence of age, gender, ethnicity and professional status of the observer. A craniofacial height to standing height proportion of 1/7.5 was perceived as the most attractive (36%), followed by a proportion of 1/8 (26%). The images chosen as most attractive by more than 10% of observers had a mean proportion of 1/7.8(min=1/7; max=1/8.5). The images perceived as most unattractive had a proportion of 1/6 and 1/10. The choice of images was not influenced by the age, gender, ethnicity or professional status of the observers. The ideal craniofacial height to standing height proportion is in the range 1/7 to 1/8.5. This finding should be considered when planning treatment to alter craniofacial or facial height.

Link

Social perception of obesity

Caption for figure:

1. Lean (L - narrow shoulders, thin torso and extremities, knee and elbow joints thicker than thy and arm diameter). 2. Muscular (M – Broad shoulders, curved extremities, chest and abdominal muscles shown, thy and arm diameters greater than knee and elbow joints). 3. Slightly fat and feminine (F – rounded shoulders, cylindrical extremities). Each of the three body forms was represented with (designated by +) and without (−) abdominal obesity as shown in rows. The sequence of these figures was randomized during the test and the figures were labeled serially by alphabets.

From the paper:

hysical characters were associated with the appropriate body forms as expected. The physical traits strong, rough and tough and physically aggressive were associated with the muscular non-obese [M−] figure. Lethargic was associated with F+. Disease prone was significantly associated with L− on the one hand and F+ on the other indicating that people negatively associate both the extremes with health. The trait swift was also strongly associated with L−. The traits that are not obviously physical were also strongly associated with certain body forms. Brave, conscious about looks, influential, dominating, status conscious, modern and confident were associated with M−; physical risk avoider, money minded, political, rich, stupid, selfish and greedy were associated most strongly with F+; friendly, intelligent, methodical, business risk avoider, successful, loving, kind, and honest were associated with F−; and L− was the commonest choice for swift, physical risk avoider, talkative and the trait depressed was associated with L+ [table 1].

Link to Table 1.

PLoS ONE doi: 10.1371/journal.pone.0003187

Obesity as a Perceived Social Signal

Manasee Mankar et al.

Abstract

Fat accumulation has been classically considered as a means of energy storage. Obese people are theorized as metabolically ‘thrifty’, saving energy during times of food abundance. However, recent research has highlighted many neuro-behavioral and social aspects of obesity, with a suggestion that obesity, abdominal obesity in particular, may have evolved as a social signal. We tested here whether body proportions, and abdominal obesity in particular, are perceived as signals revealing personality traits. Faceless drawings of three male body forms namely lean, muscular and feminine, each with and without abdominal obesity were shown in a randomized order to a group of 222 respondents. A list of 30 different adjectives or short descriptions of personality traits was given to each respondent and they were asked to allocate the most appropriate figure to each of them independently. The traits included those directly related to physique, those related to nature, attitude and moral character and also those related to social status. For 29 out of the 30 adjectives people consistently attributed specific body forms. Based on common choices, the 30 traits could be clustered into distinct ‘personalities’ which were strongly associated with particular body forms. A centrally obese figure was perceived as “lethargic, greedy, political, money-minded, selfish and rich”. The results show that body proportions are perceived to reflect personality traits and this raises the possibility that in addition to energy storage, social selection may have played some role in shaping the biology of obesity.

Link

Y chromosomes of Bayash Romani

Once again, the 0.00069/locus/generation rate is used in this paper, and hence its estimated ages are wrong. The given Y-STR variance for haplogroup H1a in Table 2 is 0.06, which corresponds to an age of ~800 years.

It's interesting though, that Zhivotovsky is a co-author of this paper which states that:

A recent refinement of E1b1b1a-M78 by novel biallelic markers indicates that its subhaplogroup E1b1b1a2-V13 is the most common in Europe (Cruciani et al., 2007). In fact, E1b1b1a2-V13 originated in Western Asia about 11 KYA and expanded in Southeastern Europe about 4.5 KYA, not in connection with the spread of agriculture as traditionally assumed, but rather at the beginning of the Balkan Bronze age, as a consequence of the in situ population increase in the already populated territory (Cruciani et al., 2007).

and he was a co-author of King et al. (2008) which stated that:

The calculated expansion time of haplogroup E3b1a2-V13 in mainland Greece is 8,600 y BP at Nea Nikomedeia and 9,200 y BP at Lerna/Franchthi Cave and is consistent with the late Mesolithic/initial Neolithic horizon. These dates exceed those reported previously for Europe (Cruciani et al., 2007) that date to the Bronze Age. This discrepancy arises mainly because of differences in the choice of mutation rate used.

Peter Underhill was also a co-author of the latter study, and also of the recent paper on Sicily which used germline mutation rates and:

The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era.

Mesolithic - Early Bronze Age - classical Greek. Three completely different ages using three different mutation rates: a mutation rate 3.6x slower than the germline rate => Mesolithic. A mutation rate 2.4 to 2.8x slower => Early Bronze Age. A germline mutation rate => classical Greek.

My most recent take. I'll be much surprised if E-V13 turns out to be anything other than 2nd millennium BC in the Balkans.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20933

Dissecting the molecular architecture and origin of Bayash Romani patrilineages: Genetic influences from South-Asia and the Balkans

Irena Martinovi Klari et al.

Abstract

The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift.

Link