Misc. links

Genome-wide association studies: slightly breathless article from the AP; why they can fail at Genetic Future

Lebanese Christians and Muslims genetically differentiated: Dienekes links the paper (PDF); supplemental data (PDF); GENEALOGY-DNA posters question elements of the study

John Hawks: Schiller skull to be identified using DNA? On "Boskopoids":

This category became untenable as further information about the archaeology of South Africa came to light. Ronald Singer (1958) reviewed the "Boskop race" evidence as it existed by the 1950's. He concluded that there was no reason to maintain that any "big-headed, small-faced group" had existed in prehistory, separate from the current biological variability of "Bushman, Hottentot and Negro." But that view is unsupportable -- in fact, what happened is that a small set of large crania were taken from a much larger sample of varied crania, and given the name, "Boskopoid." This selection was initially done almost without any regard for archaeological or cultural associations -- any old, large skull was a "Boskop". Later, when a more systematic inventory of archaeological associations was entered into evidence, it became clear that the "Boskop race" was entirely a figment of anthropologists' imaginations. Instead, the MSA-to-LSA population of South Africa had a varied array of features, within the last 20,000 years trending toward those present in historic southern African peoples.

[. . .]

So, how did this idea of ancient Boskops make it into a book by two neuroscientists in 2008?

If not through science, then possibly from science fiction. The "Boskop race" was immortalized in popular writing by Loren Eiseley, who included an essay on Boskop Man in his collection, The Immense Journey, first published in 1958. As you can see, by this time the entire concept of a "Boskop race" had fallen into scientific disrepute. But Eiseley was undeterred: he conjured the idea that the Boskopoids were advanced in their large brains and small faces -- the apex of a trend toward paedomorphism, the retention of juvenile characteristics.

[. . .]

For Eiseley, Boskop served as a kind of memento mori -- the so-called advanced race had succumbed to "more prolific and aggressive stocks." A theme of the essay is that the entire idea of "Future Man" is anti-evolutionary -- there are no ineluctible trends of progress in evolution, because such progressive populations may always be endangered by their own direction of change.

I hate to think that the theme of a 2008 book was pulled straight from a 1958 essay, but I don't know where else they would have gotten the idea. No anthropologists have written much about the so-called "Boskopoids" since 1958. There is no such thing as an "IQ estimate" for a fossil human; that's entirely nonsensical. There's no question that there have been massive cultural changes in the last 10,000 years. But the idea that our brains' functions have atrophied from some Pleistocene state has been left long behind in the dust of nineteenth-century race studies.

(In that case, it would seem Carleton Coon was engaged in "nineteenth-century race studies" as late as 1981:

Those that stayed on in Europe and western Asia from Upper Paleolithic to modern times have lost an average of two inches (5 cm) of stature and 140 cc of cranial capacity [. . .] From Neolithic to modern times, stature remained about the same, while average cranial capacity fell, though it rallied a little during the Bronze Age when metal took over from stone and much skill was needed to go to the sources of copper and tin and to smelt and cast the metals. Iron was more abundant and easier to work. The dip to the modern level may reflect a division of labor in which the specialists are outnumbered by those whom they have domesticated or who have domesticated themselves.

Racial Adaptations. pp. 170-171.)

Egypt: Study shows life was tough for ancient Egyptians:

CAIRO (Reuters) - New evidence of a sick, deprived population working under harsh conditions contradicts earlier images of wealth and abundance from the art records of the ancient Egyptian city of Tell el-Amarna, a study has found.

[. . .]

Studies on the remains of ordinary ancient Egyptians in a cemetery in Tell el-Amarna showed that many of them suffered from anemia, fractured bones, stunted growth and high juvenile mortality rates, according to professors Barry Kemp and Jerome Rose, who led the research.

[. . .]

Paintings in the tombs of the nobles show an abundance of offerings, but the remains of ordinary people tell a different story.

Rose displayed pictures showing spinal injuries among teenagers, probably because of accidents during construction work to build the city.

The study showed that anemia ran at 74 percent among children and teenagers, and at 44 percent among adults, Rose said. The average height of men was 159 cm (5 feet 2 inches) and 153 cm among women.

"Adult heights are used as a proxy for overall standard of living," he said. "Short statures reflect a diet deficient in protein. ... People were not growing to their full potential."

[. . .]

"We are seeing a more realistic picture of what life was like," he told Reuters.

Altai: New tomb for 'Altai Princess' to be built in Siberia:

NOVOSIBIRSK, March 20 (RIA Novosti) - A tomb to house the remains of a woman found after being preserved in ice for 2,500 years will be built in Siberia's Altai Republic, the director of a local museum said on Thursday.

The well-preserved remains of the woman dubbed the Altai Princess were discovered in the region by a team led by a Novosibirsk archeologist in 1993 near the Mongolian border, and have been studied at the Archaeology and Ethnography Institute in Novosibirsk.

[. . .]

Scientists have no information on the actual history of the Altai Princess, but DNA tests and facial reconstruction have suggested she was ethnically European.

"Italian-American" myths, part 1: William Paca

Was William Paca (a signer of the Declaration of Independence) of Italian descent, as claimed by many "Italian-Americans" and Italian-American organizations?

No; no good evidence points in that direction. To give you a sense of the "debate":

An interesting situation arose when one of the sponsors of the Paca House project called me and urged that in my genealogical research it would be helpful if I found that William Paca had an Italian ancestry. This was because a grant of $10,000 would have been forthcoming if that wre proved to be the case. I had found, however that Paca's grandfather, Aquila Peaker, from England, in leaving property to his heirs, used "Paca," and it is in that document where the transition from Peaker to Paca is demonstrated (South 1967j:8). The rumor that the name was Italian came from a remark made in 1911 by Cardinal James Gibbons of Baltimore, who commented that he thought a relationship existed between Paca and the Italian family Pecci (South 1967j: 7). I was not able to say William Paca was of Italian ancestry, disappointing some who had hoped otherwise.

South, Stanley A. An Archaeological Evolution. New York: Springer, 2005. p. 202

All evidence suggests the immigrant Robert, a Quaker [1], was of normal English ancestry [2]:

…the suggestion that Robert Paca, the immigrant, was born in Italy or that his family had recently moved to England from that country cannot be substantiated and probably has no basis in fact.

But the National Italian American Foundation told me "[a] letter to the editor of the New York Times (July 18, 1937) by Paca's great, great, grandson should dispel any reservations as to Paca's ethnicity wherein he stated that some of his forbears named Pacci came from Italy."

Anyone who asserts that a 17th-century or earlier Italian origin for the Paca family can somehow be proven using an unsubstantiated 20th-century claim by a Paca descendant is throwing up a huge red flag that (a) he has no idea how good genealogical or historical research is conducted; and/or (b) he is probably less concerned with discovering the truth than with advancing a particular agenda. Myths concerning family origins are extremely common and frequently wrong.

In this case, it's easy to see how the myth may have arisen. In the 1937 letter, William S. Paca claims:

The ancestors of William Paca were of Italian and English origin. The name is said to have originally been spelled Pacci.

Said by whom?

Giovanni Schiavo writes that he interviewed W.S. Paca (the letter writer) in 1937 and mentions (while arguing in favor of an Italian origin) [3]:

I think it was [W.S. Paca] who told me that it was Cardinal Gibbons of Baltimore to suggest the name Pecci . . .

As we saw earlier, Stanley South also attributes the existence of the rumour to "a remark made in 1911 by Cardinal James Gibbons of Baltimore, who commented that he thought a relationship existed between Paca and the Italian family Pecci". Probably not coincidentally, Pecci "was obviously the name of Pope Leo XIII (1879-1903) whom Mr. Paca mentioned during our conversations" [3]. Naturally, Cardinal Gibbons would have been well-aware of Leo XIII's name.

Stiverson and Jacobsen report [2]:

The surname of Robert Paca, the immigrant, was spelled in several ways in contemporary documents, including Peaker, Pecker, Peaca, Peca, [and Paka]

Not Pacci. Not Pecci. Nor any variant thereof. It's easy to imagine "Peaker" becoming "Paca" in the mouth of a non-rhotic speaker. It's quite difficult to imagine "Pacci" or "Pecci" (or even "Pacca") becoming "Peaker".

But Robert Paca named his son "Aquila"!!! "Aquila" is Italian. That has to prove it.

And Alexander Hamilton was Greek. And John Adams was Hebrew. Off the top of my head, I can immediately name a colonial American ancestor of mine named Acquila. Shockingly, he was not Italian. Aquila/Aquilla is hardly an unusual or surprising name in 18th-century British North America. (Of course, even if it were, it would hardly constitute strong evidence in the Italianist's favor--I've seen some genuinely strange names bestowed on children of purely English parents in C17/C18 America.)


[1] Richardson, Hester Dorsey. 1967. Side-lights on Maryland history, with sketches of early Maryland families. Baltimore: Genealogical Pub. Co. p. 194.

[2] Stiverson, G. A., & Jacobsen, P. R. 1976. William Paca, a biography. Baltimore: Maryland Historical Society. pp. 25-26.

[3] Giovanni Ermenegildo Schiavo. 1976. The Italians in America Before the Revolution. New York: Vigo Press. p. 74.

23andMe's "Ancestry Painting"

23andMe has added a three-population (Europe/Asia/Africa) admixture analysis feature. According to a 23andMe employee, "[a] white paper with full details of our procedure [and plans to reduce statistical noise] is shortly to appear on the site for the motivated". Notably, 23andMe's scientific advisors include Jonathan Pritchard (of STRUCTURE fame) and Serafim Batzoglou.

It will be interesting to see how "Ancestry Painting" compares to deCODEme's current effort. David Faux has posted a compilation of deCODEme admixture results, and I am not impressed. Asian and African affiliations seem to be improbably high. I stand by my contentions that deCODEme is almost certainly already better than DNAprint/ABD, but evidently not good enough.

Update: Ann Turner posts a comparison of 23andMe and deCODEme
ancestry admixture graphs (DOC). deCODEme reports the individual is 88% European, 7% East Asian, and 4% African, while 23andMe calculates 99% European and 1% Asian. Naturally, 23andMe's numbers seem more plausible.

"Nordicism", racial preservationism, and ethnonationalism

In a comment at majorityrights.com, Guessedworker identifies what he claims are the "four possible positions for an ethnically- or racially-aware member of our people(s) in respect to European preservation", described in terms of two binary variables: does the individual belong to "[a single] one of the European ethnies" or not; and is the individual "concerned to preserve his ethny while desiring the preservation of Europe’s ethnies as a whole" or does he see "no intrinsic value in ethny at all, and desires only the preservation at a combinative level". GW claims the latter "is the position of the Nordicist and the pan-European." While I believe GW's entire schema here is off base (with, for example, the rather glaring omission of an "advance my ethny at the expense of other European ethnies" position, despite the fact that almost the entirety of Europe's history [and likely prehistory] has been characterized by intertribal and interethnic competition), I'm concerned here primarily with GW's claim that "Nordicists" deprecate "ethnies". I find the claim so bizarre and wrongheaded it's hard to know where to start in refuting it, but defining terms is as good a place as any.

"Nordicism", particularly as the term is thrown around by Rienzi- and diabloblanco-types, encompasses various distinct schools of thought with divergent purposes, emphases, and interpretations. Here, I'll simply define "Nordicist" as someone who recognizes the existence within Europe of racially distinct type(s) associated today primarily with Northern Europe and her offshoots and who favors the continued existence of these type(s).

I'll let Frank Salter--from whom GW borrowed the term--define "ethny":

ethny

A population sharing common descent. 'Ethny' is a preferable term to 'ethnic group' because members of such a category rarely form a group. Ethnies are usually concentric clusters of encompassing populations, such as tribe, regional population, and geographic race. The term 'ethny' used in this book usually means 'a named human population with myths of common ancestry, shared historical memories, one or more elements of common culture, a link with a homeland and a sense of solidarity among at least some of its members'.² However, it sometimes has a more general meaning, and thus corresponds most closely to the biological concept of the population.

[From On Genetic Interests, Appendix 2; my emphasis.]

What should be immediately clear is that not only is "Nordicism" compatible with the preservation of "ethnies", to the extent the Nordicist correctly discerns relative kinship, Nordicism is synonymous with a desire to preserve a particular ethny or ethnies.

I presume when GW writes "ethny" he has in mind traditionally-defined ethnicities or nationalities. Frank Salter, as we see above, sometimes uses "ethny" in a similar manner. And indeed we should expect present-day national and linguistic borders to play some role in structuring genetic variation in Europe; but it's an empirical question (yet to be investigated adequately) how large that role is. Sir Arthur Keith argued nations are "races in the making" and I agree--but that process of race formation is, I think, far from complete in most European polities. Some "Nordicists" have critiqued elements of nationalism (e.g. "fratricidal" wars), but none of the major Nordicist thinkers I'm aware of ever called for abolition of national borders, customs, languages, or so forth--nor are they desirous only of "preservation at a combinative level." In fact, the ethnonationalist is more like the "pan-Europeanist" in that respect. The "Nordicist" almost by definition recognizes and values the existence of racial variation within national borders. The single-minded nationalist, on the other hand, would seek to minimize regional and class differences to promote national unity (at the likely expense of regional genetic interests). The "Pan-Europeanist" merely expands that mindset to cover an entire continent.

GW's belief that America is not a "real" country is again on display. I'll probably have more to say about that later, but for now I'll note that the genetic distance between SW and NE Germans (F_ST = 0.00054) is five times that between Americans reporting "western European" ancestry and those reporting "central European" ancestry (F_ST = 0.0001). No doubt the "ancient" nation of Italy (est. 1861) is even more homogenous.

New program for analyzing individual admixture

The article is open-access:

Effect of genetic divergence in identifying ancestral origin using HAPAA

Andreas Sundquist, Eugene Fratkin, Chuong B. Do, and Serafim Batzoglou

The genome of an admixed individual with ancestors from isolated populations is a mosaic of chromosomal blocks, each following the statistical properties of variation seen in those populations. By analyzing polymorphisms in the admixed individual against those seen in representatives from the populations, we can infer the ancestral source of the individual’s haploblocks. In this paper we describe a novel approach for ancestry inference, HAPAA (HMM-based analysis of polymorphisms in admixed ancestries), that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy. We also introduce a methodology for evaluating the effect of genetic divergence between ancestral populations and time-to-admixture on inference accuracy. Using HAPAA, we explore the limits of ancestry inference in closely related populations.

[HAPAA is available at http://hapaa.stanford.edu.]

Press release:

Some people may know where their ancestors lived 10 or 20 generations ago, but the rest of us can learn our distant biological heritage only from our DNA. New genomics analysis software developed by computer scientists at Stanford appears far more adept than prior methods at unraveling the ancestry of individuals. A paper describing the HAPAA system, which takes its name from "hapa," the Hawaiian word for someone of mixed ancestry, appears online today and in the April printed issue of the journal Genome Research.

Going back 20 generations the software can identify what continent or broad global region an individual's ancestors were from. But going back about 10 generations the software can be much more precise, making distinctions as fine-grained as the traditional gene pools of nearby population groups—hypothetically differentiating Greek from Italian, or Russian from German.

Specifically what the software does is compare an individual to all those in the International HapMap database to see what distinct spans of genetic snippets, called haploblocks, they share in common.

"With very high accuracy, even for 20 generations, we can trace the populations of those individuals who are indeed represented in your genome," says Stanford computer science Assistant Professor Serafim Batzoglou, who led a team of graduate students to create HAPAA. They include co-lead authors Andreas Sundquist and Eugene Fratkin, as well as Chuong B. Do.

Batzoglou points out that because the HapMap database, a genetic record of 270 individuals of Western European, West African and East Asian ancestry, is very small, HAPAA now can only generate an ethnic profile in terms of these populations.

Fratkin himself was able to verify that he is of European ancestry, but not that he is 1/64th Polish. But more genomics data will become available, the researchers said, which will further expand the software's ability to help people discern their roots.

[. . .]

The team also compared HAPAA to the current state-of-the-art system known as SABER. Using the standard statistical measure of "mean-square" error, Batzoglou and his students found that HAPAA's error rates were between a half and a third as big as SABER's. The difference widened as the generations probed went further back—meaning that HAPAA's error rate remains consistently low, even back 15 or 20 generations.

An important advance that improves HAPAA's accuracy is its more accurate modeling of individual variation. The Stanford computer scientists created an algorithm efficient enough to compare the genetic information of the test individual to that of every individual in the database. Other systems, including SABER, rely on comparisons to a composite that represents an averaging of the data from many individuals. That methodology is easier to program and run on a computer, but the problem with averaging is that a lot of information is lost.

[. . .]

For now the HAPAA software provides proof of this concept but limited utility given the small size of the HapMap database. In the future the software will benefit not only from having more individuals available for comparison, Batzoglou said, but also more detailed data about each individual. Today's genome samples track about 500,000 markers, or common genetic differences, but there are about 10 million candidates. Most individuals have about 3 million such specific differences. As genomics technology improves, he says, so will HAPAA's ability to infer ancestry from the data.

Bronze Age German DNA

Results of ancient DNA research on the 40 Bronze Age skeletons recovered from Lichtenstein cave in Lower Saxony have been trickling out for years. A 252-page doctoral dissertation which covers much of the work (in German) may be downloaded here (Felix Schilz: Molekulargenetische Verwandtschaftsanalysen am prähistorischen Skelettkollektiv der Lichtensteinhöhle, Dissertation, Göttingen 2006). An English summary is available at dna-forums (Post #44):

Archeological artefacts (pottery, bracelets, arrowheads, a polished dogtooth, a fibula…) date the remains as 1000 to 700 BC (= the Urnfieldsculture of the Late Bronze period).
In the bronze-age the family was the biological, social and economic centre. Communities consisted out of 5 to 8 families of 5 to 10 members. These extended families lived 3 to 5 generations in the same community/location. When the soil became exhausted the community had to look for new fertile grounds.
Possibly the Lichtenstein-people lived near a fortification (Burg) in Osterode: the Pipinburg. The cave is located along the road that connected the Pipinsburg with the Thüringer plain. The presence of a Burg indicates violent and turbulent times. On the other hand Burgs were also centres of commerce and craftmenship.
Culturally the archeological artefacts belong to the Unstrut-Group. This culture blossomed in between the Unstrut river and the Southern Harz mountains. The centre of the culture was the Thüringen-valley where the fertile löss-soil was used for agriculture and raising cattle. The disappearance of the culture coincidences the end of the usage of the Lichtenstein-cave as a burial chamber.
This Untstrut-group developed out of the Funnelbeaker-culture and developped later into the Jastorf-culture (that united all local cultures to a unified ‘German’ culture).
[. . .]
DNA-reserach, by the team of Dr. Susanne Hummel, showed that all skelettons belonged to one extended family of 4 or 5 generations. This found supports the theory that the cave was used as a burial chamber. It also indicates that the cremations of the Urnfieldculture weren’t that widespread as was thought.
Bones that were found in caves in the Thüringer neighbourhood are supposed to be of persons who were ritually killed (there is even some evidence of cannibalism). For this reason it was first thought that the Lichtenstein-people also were ritually killed. But:
- the bones showed no signs of violence or cutting
- it is unlikely that a whole family was sacrified (usually the sacrified young women)
[. . .]
MtDNA-analysis
The mitochondrionale haplogroups of 36 individuals (men and women) are:
· MtHG J: 5 individuals, 14%
· MtHG T: 5 individuals, 14%
· MtHG U: 9 individuals, 25%
· MtHG H: 17 individuals, 47%
The mitochondrional-DNA research showed that there are more female haplotypes (20) than male haplotypes (5). This supports the hypothesis that the Lichtensteiners belonged to a patrilocal culture, where women married into the clan of the men).

The poster above (hansdb) ran Y-STR profiles reported for the remains through White Athey's haplogroup predictor; he determined most of the males belonged to haplogroup I1b2, two were R1a, and one was R1b. Interestingly:

In 2006 reseachers took DNA-samples among 220 people who lived for at least 3 generations in the Sösethal.
Eleven people had STR-values matched those of Lichtensteiners. Five men belonged to the rare I1b2*-haplotypes; meaning this family-line strechtes beck forr 3000 years in the same region.

But keep in mind these are only 12-marker haplotypes.

Still waiting for the aDNA analysis of the Mycenaean shaft grave royalty, which Greeks have been promising for years. . .

A few abstracts

Eur J Hum Genet. 2008 Mar 5 [Epub ahead of print]

Quantifying the increase in average human heterozygosity due to urbanisation.

Rudan I, Carothers AD, Polasek O, Hayward C, Vitart V, Biloglav Z, Kolcic I, Zgaga L, Ivankovic D, Vorko-Jovic A, Wilson JF, Weber JL, Hastie N, Wright A, Campbell H.

[1] 1Department of Public Health Sciences, University of Edinburgh, Edinburgh, UK [2] 2Croatian Centre for Global Health, Split, Croatia.

The human population is undergoing a major transition from a historical metapopulation structure of relatively isolated small communities to an outbred structure. This process is predicted to increase average individual genome-wide heterozygosity (h) and could have effects on health. We attempted to quantify this increase in mean h. We initially sampled 1001 examinees from a metapopulation of nine isolated villages on five Dalmatian islands (Croatia). Village populations had high levels of genetic differentiation, endogamy and consanguinity. We then selected 166 individuals with highly specific personal genetic histories to form six subsamples, which could be ranked a priori by their predicted level of outbreeding. The measure h was then estimated in the 166 examinees by genotyping 1184 STR/indel markers and using two different computation methods. Compared to the value of mean h in the least outbred sample, values of h in the remaining samples increased successively with predicted outbreeding by 0.023, 0.038, 0.058, 0.067 and 0.079 (P<0.0001), where these values are measured on the same scale as the inbreeding coefficient (but opposite sign). We have shown that urbanisation was associated with an average increase in h of up to 0.08-0.10 in this Croatian metapopulation, regardless of the method used. Similar levels of differentiation have been described in many populations. Therefore, changes in the level of heterozygosity across the genome of this magnitude may be common during isolate break-up in humans and could have significant health effects through the established genetic mechanism of hybrid vigour/heterosis.European Journal of Human Genetics advance online publication, 5 March 2008; doi:10.1038/ejhg.2008.48.

PMID: 18322453 [PubMed - as supplied by publisher]


Coll Antropol. 2007 Dec;31(4):1135-41.

Anthropological analysis of neolithic and Early Bronze Age skeletons--a classical and molecular approach (East Slavonia, Croatia).

Hincak Z, Drmić-Hofman I, Mihelić D.

Institute for Mediterranean Heritage, Science and Research Center of Koper, University of Primorska, Koper, Slovenia. zdhincak@inet.hr

Theories about the first Indo-European migration are numerous. Significant contribution in attempt to resolve these theories is given by analysing skeletal material from two biggest prehistoric archaeological sites from N-E Croatia. Eight skeletons of Starcevo culture from sites "Nama" and "Hotel" at Vinkovci (6100-5500 BC) and seven skeletons of Vucedol culture from the site Vineyard Streim at Vucedol near Vukovar (3000-2500 BC) were analysed. Methods of classical anthropological analysis tried to distinguish the differences among members of both populations, while the methods of molecular genetics were used in defining possible genetic structure of both ancient populations. Established differences speak on the behalf of the theory of Maria Gimbutas about the first Indo-European migration with a cattle breeding population from the east around 3500 BC.

PMID: 18217472 [PubMed - indexed for MEDLINE]


BMC Evol Biol. 2008 Feb 29;8(1):75 [Epub ahead of print]

X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans).

Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Ben Dhiab M, Ramon M, Morling N.

ABSTRACT: BACKGROUND: Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. RESULTS: A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. CONCLUSIONS: Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.

PMID: 18312628 [PubMed - as supplied by publisher]

[Note: This last looks like a pretty weak study--only 25 SNPs are examined. The provisional PDF is freely available.]

Dupanloup et al. (2004): ridiculous study

It is beyond me how anyone could take seriously a study whose authors at one point estimate Finns are of >95% Neolithic Near Eastern origin.

Wasting my time refuting such a study should be unnecessary. Briefly, though, the Barbujani/Chikhi/Dupanloup method generally entails taking a sample of Basques and a sample of Near Easterners and using these as "parental populations" for calculating "Paleolithic" and "Neolithic" "admixture" in various European populations.

Any "admixture" estimate can make only as much sense as the choice of "parental populations". Given our knowledge of genetic variation in Europe, it is nonsensical to use Basques as stand-ins for Paleolithic Europeans in this sort of calculation. This is particularly obvious when we look at the uniparentally inherited loci, which feature prominently in this and other Barbujani/Chikhi papers. Basque men overwhelmingly belong to Y haplogroup R1b--but the phylogeographic evidence says R1b represents far from the totality of Paleolithic European Y chromosomes (which also include, most prominently, hgs R1a1 and I). Barbujani and Chikhi are aware of this evidence, but keep pushing their own bizarre estimates and insisting it is better to ignore phylogeography.

The Basque mtDNA pool seems to be highly fragmented (Alfonso-Sánchez 2008). It's unclear how representative the mtDNA haplogroup profile of a given sample of Basque mtDNA is for Basques in general, much less for all "Paleolithic Europeans".

In truth, the Basque are "little more of a Mesolithic relict than any other European population" (Richards 2003).

In the 2004 paper, Dupanloup et al. stretch a little and throw in a second European parental population for some of their calculations. Their choice: "North-Eastern Europe". Yep. Another set of genetic outliers, from the opposite corner of Europe, who we know from phylogeography are dissimilar from most other Europeans. Makes complete sense. Unsurprisingly, they find:

In general, the estimated contributions from North-Eastern Europe are higher than the African contributions, but they still represent a small component of genetic diversity, accounting for between 10.5% (molecular estimates) and 17.4% (frequency estimates) of the total. Variation among regions is high, and most groups show little or no North-Eastern Europe admixture. The exceptions are Finland and Eastern Europe, where roughly 95% and 50% of the gene pools, respectively, seem to come from North-Eastern European ancestors.

The lesson they take from this?

The main components in the European genomes appear to derive from ancestors whose features were similar to those of modern Basques and Near Easterners, with average values greater than 35% for both these parental populations, regardless of whether or not molecular information is taken into account. The lowest degree of both Basque and Near Eastern admixture is found in Finland, whereas the highest values are, respectively, 70% in Spain and more than 60% in the Balkans.

The authors then switch back to their favored two parental population (Basque / Near Eastern) model.

The Near Eastern contribution is generally high, with a mean of 49.4% across Europe (range: 20.8% in England, 79.0% in the Balkans) when considering molecular information and 54.5% (22.1% in England, 95.6% in Finland) when considering only the frequency of haplotypes. However, there is reason to mistrust the estimates obtained for Finland. Indeed, more than 90% of the alleles observed there seem to have come from North-Eastern Europe (table 3), so its population can by no means be regarded as a hybrid between Basques and Near Easterners (table 4).

You don't say? But the >50% Neolithic Near Eastern estimate for Scandinavia, on the other hand, makes perfect sense.

The authors have discovered that, stunningly, Spaniards tend to be similar to Basques, Finns tend to be similar to North-Eastern Europeans, and those from the Balkans tend to be similar to Near Easterners. Choose a parental population from Central or Northern Europe, and you will find, amazingly, that Central Europeans are most similar to Central Europeans and Northern Europeans are most similar to Northern Europeans. Apart from demonstrating the obvious, the calculations in this paper are meaningless.

Alfonso-Sánchez et al. 2008. Mitochondrial DNA haplogroup diversity in Basques: A reassessment based on HVI and HVII polymorphisms. Am J Hum Biol. Mar-Apr;20(2):154-64.

Dupanloup et al.. 2004. Estimating the impact of prehistoric admixture on the genome of Europeans. Mol Biol Evol. Jul;21(7):1361-72. Epub 2004 Mar 24.

Richards, Martin. 2003 The Neolithic invasion of. Europe. Annual Review of Anthropology. 32, 135-62.

Brief reply on European genetic substructure

Rienzi seems to want to simultaneously to argue:
(1) Genetic differences between Northern and Southern Europeans are of little importance.
(2) The existence of substructure within Northern Europe is of great significance.

I'm sure Rienzi will insist that's not what he wrote. But his thought process seems clear. (Or, alternatively, Rienzi would prefer to ignore genetic differences within Europe entirely, but believes he can play "gotcha" with those who would distinguish between N. and S. Euros by pointing out variation among N. Euros; Rienzi has openly admitted as much this in the past.) Needless to say, this sort of logic doesn't work.

Rienzi acknowledges "the major genetic clustering in Europe is along the North/South axis", but doesn't seem to grasp how "major" this axis is. To put some numbers on it, in Tian et al. (2008) PC1--the "North-South" PC--explains 42.42% of the total variance in the first 10 PCs. The next largest PC takes in 8.32% of the variance, with the remaining PCs each being responsible for less than 7%.

The historic/Neolithic/Paleolithic debate is a red herring. The question is simple: how closely are various populations related today. And what do the numbers say? Southern Europeans are more similar to Ashkenazi Jews than to the Northern Europeans. From Price et al. (2008):

We computed F_ST statistics between clusters 1 (mostly NW), 2 (mostly SE) and 3 (mostly AJ), restricting our analysis to individuals unambiguously located in the center of each cluster (Figure 2). We obtained F_ST(1,2) = 0.005, F_ST(2,3) = 0.004 and F_ST(1,3) = 0.009.

No one has ever argued the above indicates Southern Europeans "are Jews"--though, in terms of genetic distance, Southern Italians and Greeks are over half-way there.

Details on deCODEme admixture analysis

I queried deCODE about their methodology and future plans. Here are the key points from the reply I received:

• Admixture calculations are performed using Structure 2.2.
  
• The analysis involves upwards of 18,000 "hand-picked" markers.
  
• Parental populations are confirmed as HapMap samples (Utah whites, Yorubans, and Chinese/Japanese).
  
• Finally: "We are working on an improved alternative ancestry analysis that will use the entire collection of SNPs to segregate individuals into ancestral clusters (e.g. Northern vs. Southern European)."
  

In contrast, ABD/DNAprint uses 176 SNPs.

Trask's takedown of Forster's foray into historical linguistics

Apropos a discussion thread at a desi site which shall not be linked.

Back in 2003, geneticist Peter Forster came out with some outlandish claims about Celtic languages. This work was later incorporated into Stephen Oppenheimer's equally outlandish Origins of the British.

If you were ever tempted to take Forster seriously, you should probably read this very thorough dismantling by linguist Larry Trask. Trask demonstrates to my satisfaction the paper is a "disaster" that is not worth paying attention to. Small sample:

The authors claim to be able to assign moderately reliable absolute
dates to branching events in their tree, and they do this, producing the astoundingly early dates given earlier.

But it is clear that they have merely re-invented glottochronology They claim that the rate of replacements is approximately constant -- a position known to be false.

How did the paper get published?

. . . interestingly, PNAS is not peer-reviewed. Hmmm. This is not the first time that PNAS has published some extremely dubious work in historical linguistics.

HLA in Sicilians

Since HLA genes constitute a relatively tiny portion of the genome and are subject to strong selection pressure, I give comparatively little weight to population affinities derived from HLA haplotypes. The following study may be worth reading mainly for the historical overview. It would be useful to conduct a similar study using high-resolution SNP genotypes.

HLA Class I and Class II Polymorphism in Three Sicilian Populations

Two human leukocyte antigen (HLA) class I loci (HLA-A and HLA-B) and one class II locus (HLA-DR) were typed at the DNA level in the Sicilian population. Study participants were of Sicilian origin (183 for class I loci and 260 for class II loci) and live in three towns, chosen on the basis of geographic position and different historical events. These towns are Sciacca (southwest Sicily, located at sea level, conquered by Arabs in A.D. 814), Piana degli Albanesi (northwest Sicily, 720 m above sea level, has maintained religious, cultural, and linguistic peculiarities traced to Albanian settlement in 1488), and Troina (northeast Sicily, 1,120 m above sea level, known as the first settlement of Normans). The assumptions underlying the study of genetic structure, based on HLA allele polymorphism, are that these three towns are located in areas that can be distinguished according to historical criteria and that they are likely to have contributed to cultural and probably genetic differences. As such, the high frequency of some alleles in Sciacca and Troina seems to be correlated with Greek, Phoenician, North African, and Arab influence. In accordance with different human settlements in Sicily, we found that the HLA allele frequencies support the existence of genetic differentiation between the western and eastern sides of Sicily. This separation is attributed to Greek colonization in the east and to Phoenician-Carthaginian-Arab influence in the west. Moreover, the comparisons of all allele frequencies between Mediterranean and African populations show the same trend, highlighting in some cases European origin and in other cases non-European origin.

[. . .]

Sciacca is located on the southwestern side of Sicily and belongs to the province of Agrigento. Its origin has been traced as far back as 628 B.c. The mythical founder of the city is said to have been Kokalos, king of the Sicani. Sciacca is one of the most ancient thermal resorts in the Mediterranean. It was known in Siceliot times for its sweating caves and for its thermal waters, and the Romans gave it the name Thermae Selinuntinae, or Aquae Larodae. In A.D. 814 Arabs conquered Sciacca and called it as-Shaqqah (hence the current name Sciacca). Arab domination seems to have had a strong genetic impact, in that it modified the demographic distribution of the town. The urban structure also gives evidence of a later settlement of a large Jewish community inside the quarter of Cadda, which had a near monopoly on dyeing and silk weaving.

Hum Biol. 2007 Jun;79(3):339-54.

(full text)

Gotme? Nope.

Rienzi, you are grasping at straws.

I posted the abstract on the East/West European division in dental morphology close to two days ago, but I'll pretend you found it by downloading the pdf via Dienekes and reading through dozens of pages. The fact I posted it might have given you a hint I have no interest in minimizing East-West differences in Europe. I've consistently identified Northwestern Europeans (particularly those of long tenure in America) as my ingroup. One needs only one's eyes to see that Poles and Englishmen are genetically distinct.

The fact remains: the best evidence indicates the primary genetic division in Europe is between North/Central Europeans (including northern Slavs) and Southern Europeans. This doesn't mean there are no other distinctions to be made. It means those distinctions are relatively less important from the standpoint of EGI. And if you are concerned about EGI, you should probably be looking for a test that at minimum can make that primary intra-European distinction (i.e., N. vs. S.)--not pushing a crude "assay" of quad-continental affiliation.

Back to the study: before you get too excited, you might want to find out exactly which populations were studied. Were, e.g., samples from Greece and S. Italy included? Regardless, no, there's no basis for generalizing from tooth morphology to "functional genes" across board. If anything, we might expect that due to climate and disease the N-S division is stronger in the adaptive portion of the genome. To wildly speculate, I could imagine some of the genes that influence personality and national character might be a different matter. Are western Europeans better suited for self-government? If so, western Europe would seem to stop before Naples.

Reply to Rienzi on DNAprint, part 2

Rienzi takes issue with "unfavorable comparison" of DNAprint's efforts to higher-resolution exploration of genetic structure.

The issue is not up for debate.

As DNAprint themselves acknowledge, "increasing the number of AIMs is expected to increase the precision of the individual ancestry estimates". Whether we are dealing with personal genetic testing or academic studies using admixture mapping, more markers unquestionably are better (at least well into the hundreds of thousands--not hundreds--of SNPs). Compare the results Rosenberg et al. obtained in 2002 using 377 autosomal STRs and those of Stanford's more recent 650,000 SNP analysis. Intra-European structure is indistinct in the earlier analysis; at higher resolution, the same population samples are cleanly separable.

Rienzi conflates the general principal above with a debate on the merits of specific testing companies. Beyond pointing out that DNAprint has no utility for white Americans or Europeans (even if we are to trust DNAprint's own data, the "admixture" of the typical white American is well below the error thresholds DNAprint acknowledge are built into their tests, which if anything underestimate error), I have little interest in such a debate. And it wouldn't matter if there were no other options for testing--useless shit is useless shit. Still, I'll bite.

To get this out of the way: I have never endorsed a testing company, nor do I advocate personal genetic testing, though it's fine when used by knowledgeable people with reasonable goals (e.g. supporting a paternal-line genealogy through Y-STR testing). Question for Rienzi: why do you keep pushing DNAprint products? I see much emotional reactivity and little practical advice in your DNAprint advocacy. Lay out some scenarios outlining exactly what actions you propose people take based on ABD results.

I'm already on record as stating ML individual admixture estimates without accompanying information on confidence intervals are all but useless. So, given that ABD is also useless, deCODEme and DNAprint are presently battling for last place in the admixture analysis arena. That said, under a reasonable set of assumptions deCODEme's analysis is likely already superior:

• More markers available.
  
• The quality of data from the Illumina BeadChips is comparable to or better than that coming off DNAprint's SNP typing platform.
  
• One assumes deCODE uses a similar or the same (relatively simple and old) algorithm used by DNAprint.
  
• Though unfortunate, I don't see the absence of an Amerindian parental population as that huge an issue at the moment--DNAprint seems to have trouble distinguishing IA and EA admixture anyway.

Unless deCODE screwed up their math or chose to analyze only a tiny fraction of the available SNPs when calculating admixture, their estimates are already more precise than those of DNAprint.

More significantly, there's nothing to stop the deCODEme customer from doing his own admixture analyses. He can:
(1) Download his own genotype data.
(2) Download reference data. In addition to HapMap samples, we now have access to the 650,000 SNP data sets for the HGDP samples. More data sets will likely become available in the future.
(3) Run analyses with freely available software (e.g. STRUCTURE, frappe, ADMIXMAP).

It's true that such analyses on large data sets are computationally intensive. I don't consider this a valid excuse for companies, but, regardless, it should not deter the individual. Moreover, processing costs continue to fall and a new approach claims better results with fewer computational resources:

LAMP computes the ancestry structure for overlapping windows of contiguous SNPs and combines the results with a majority vote. Our empirical results show that LAMP is significantly more accurate and more efficient than existing methods for inferrring locus-specific ancestries, enabling it to handle large-scale datasets. We further show that LAMP can be used to estimate the individual admixture of each individual. Our experimental evaluation indicates that this extension yields a considerably more accurate estimate of individual admixture than state-of-the-art methods such as STRUCTURE or EIGENSTRAT, which are frequently used for the correction of population stratification in association studies.
[. . .]
We tested LAMP extensively on various datasets of admixed populations generated from the HapMap resource. Our simulations show that LAMP is significantly more accurate than state-of-the-art methods such as SABER and STRUCTURE. In addition, LAMP is highly efficient, with a running time that is about 200 times faster than SABER and about 104 times faster than STRUCTURE. The efficiency of LAMP allows us to estimate ancestries across the genome in several hours on a single computer.
[. . .]
A number of recent studies have produced panels of AIMs in admixed populations;33, 34, 35, 36 AIMs are SNPs that have differing frequencies in the ancestral populations. It is possible that the AIMs might be used to improve the accuracy of individual admixture prediction done by STRUCTURE or other methods, including LAMP. However, the AIMs have disadvantages because there is a risk of over fitting, and the studied population might be somewhat different than the population for which the AIMs were found. As we show here, in an era where the genotyping technology is getting cheaper, it is useful to use the entire set of genotyped SNPs in the analysis of population stratification.

The Watson analysis speaks poorly for deCODE's ethics, but due to the data quality confound says little about the accuracy of their admixture estimates. (Watson's genome was sequenced by 454 at 6 times coverage. Which lengths of DNA got sequenced was up to chance, which means some segments weren't sequenced at all, and others were sequenced an inadequate number of times. This is not an issue with the BeadChip platform.)

Reply to Rienzi on DNAprint

Rienzi draws the attention of unnamed "phenotypists" (*) to the following passage from the latest DNAprint publication (text quoted by Rienzi in bold):

There are relatively few genomic regions that differ substantially among populations. Yet, based on continental origin and ethnogeographic affiliation, some phenotypes (e.g., skin color, height, facial features, and hair textures) exhibit substantial variation as a function, seemingly, of genetic ancestry. Given the substantial interindividual variability in admixture proportions within most historically intermixed populations, the relationship between overt phenotypes and genetic ancestry (or social constructs) is tenuous. For example, dark skin color imparted by eumelanin expression would not be a good indicator of West African ancestry, since many other populations such as Australian, Melanesian, and South Asians also express higher levels of eumelanin and exhibit darker skin color. In other cases, cryptic population structure contributed by recent ancestral admixture can be common for many populations, yet not always appreciable and certainly not quantifiable through self-assessment or visual cues. Hence, the practice of binning persons into single population groups can be inaccurate, and can confound genetic associations contributing to both type I and II errors.

Naturally, if Mark Shriver wrote it, it must be true. However, I'm unclear why the heavily-couched and citation-free assertion warrants my attention. The claim concerns "historically intermixed populations"--e.g. Aframs and mestizos--rather than white Americans.

The population structure of white Americans has been investigated at resolutions much higher any ever used by DNAprint. What (not so) cryptic population structure did researchers uncover? You should already know this:

European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. . . . components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure.
[Discerning the ancestry of European Americans in genetic association studies..]

Likewise for Europeans:

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations.
[Analysis and application of European genetic substructure using 300 K SNP information.]

Put it to sleep. White Americans are not "historically intermixed" with nonwhites to any significant degree, however much you might wish it to be so. Nor is there any evidence "ancient admixture" is an important source of genetic structure in Europe (at least within the major population blocs). The relevant distinction is not between those who have a Nigerian or Mongol in the woodpile and those who don't, but between those of Northern or Central European origin and those of Southern European origin. You know which you are. Your 100% IE certificate can't change that.

More later.

(*) I am the "phenotypists" (sic) in question. I recognize the existence of no such category. It is practically a tautology to note that the definitive answers to questions of genetic relatedness are to be found in the genome. But not quite yet and not by Rienzi's favorite company. ABD tests 176 SNPs. Out of about 10 million. (Then there's the other 2.99 billion base pairs.) For now, I'll trust my eyes, thanks. This man is not 21% East Asian, and telling him he is does not advance European interests--no, it led a white man to start speculating about descents from Attila.

Similar mtDNA coupling efficiencies for haplogroups H and T

doi:10.1016/j.gene.2008.01.007

Experimental assessment of bioenergetic differences caused by the common European mitochondrial DNA haplogroups H and T

Taku Amoa, Nagendra Yadavab, Richard Ohb, David G. Nichollsb and Martin D. Brand

Abstract

Studies of both survival after sepsis and sperm motility in human populations have shown significant associations with common European mitochondrial DNA haplogroups, and have led to proposals that mitochondria bearing haplogroup H have different bioenergetic capacities than those bearing haplogroup T. However, the validity of such associations assumes that there are no non-random influences of nuclear genes or other factors. Here, we removed the effect of any differences in nuclear genes by constructing transmitochondrial cybrids harbouring mitochondria with either haplogroup H or haplogroup T in cultured A549 human lung carcinoma cells with identical nuclear backgrounds. We compared the bioenergetic capacities and coupling efficiencies of mitochondria isolated from these cells, and of mitochondria retained within the cells, as a critical experimental test of the hypothesis that these haplogroups affect mitochondrial bioenergetics. We found that there were no functionally-important bioenergetic differences between mitochondria bearing these haplogroups, using either isolated mitochondria or mitochondria within cells.

4. Discussion

There are published associations between mitochondrial haplogroups H and T and phenotypes that might be expected to have a strong bioenergetic component. However, our results show no significant bioenergetic differences in mitochondria with H or T-haplogroup mtDNAs in a constant nuclear background, at either the mitochondrial or the cellular level. We have previously shown that our methodology can pick up 10% differences in respiratory chain activity (Amo and Brand, 2007), so if haplogroup does affect mitochondrial bioenergetics, any effects must be very small. The lack of effect of haplogroup on mitochondrial coupling efficiency in intact cybrids shows that even if haplogroup affects mitochondrial proliferation or retrograde signalling, such changes do not affect coupling efficiency in the cells under basal conditions.

[. . .]

Our results fail to provide support for the hypothesis that the common European mitochondrial haplogroups H and T have significant effects on bioenergetics that cause the associations with survival after sepsis and sperm motility that have been reported. If such associations stand up to further scrutiny, they presumably operate through more subtle mechanisms than respiratory rates, mitochondrial coupling efficiencies or ATP supply.

Population variation in endocrine function

I don't necessarily agree that it's "unlikely that population differences in reproductive endocrine function are the result of genetic polymorphisms". What is clear, however, is that (1) the role of genetics (if any) in population differences in sex hormone levels is far from being fully ascertained, and (2) the differences that exist do not consistently line up with Rushton's assumptions/predictions.

Richard Bribiescas [1]:

Medical literature focuses primarily on the physiology of individuals from industrial nations. this is especailly true in endocrinology since hormone measurements have typically involved costly tests that require careful treatment of perishable samples. However, recent advances in sample storage techniques and the advent of robust and more sensitive assays have resulted in significant growth in our knowledge of reproductive hormone physiology in nonwestern populations who are more representative of humans around the globe (Ellison 1994).

The earliest endocrinological studies of male reproductive function consistently suggested that interpopulation variation may be related to ecological factors. In the 1940s, Africans were reported to exhibit what was then called "estrinization," that is, elevated levels of estrogens (Davies 1949). Other researchers echoed these results, suggesting that indigenous Africans had higher levels of estrogens than did Europeans (Bersohn and Oelofse 1957). However, no explanatory mechanism was ever found.

With the advent of salivary steroid assays, data from remote populations grew steadily (Figure 5.1). The ability to store salivary samples at ambient temperatures without refrigeration as well as the reflection of only free bioactive steroid in circulation makes this methodology ideal for biological anthropologists (Ellison 1988; Lipson and Ellison 1989). In addition to finding significantly lower progesterone levels in Lese women (Ellison et al. 1989b), researchers note that Efe and Lese men exhibit significantly lower salivary testosterone levels compared to Boston men (Bently et al. 1993; Ellison et al. 1989a). other African populations such as the !Kung (Christiansen 1991b) and Namibians (Christiansen 1991a) presented salivary testosterone levels significantly lower than western samples. Interestingly, Turkana males of Kenya exhibit testosterone levels that are not different from those of western populations despite their extreme leanness (Campbell et al. 1995).

Other nonwestern populations also exhibited significant variation. Urinary testosterone levels were shown to differ between Bolivian men living at high altitude and men at sea level (Guerra-Garcia et al. 1969). Moreover, undernourished Indian men exhibited blunted testosterone response to hCG stimulation, suggesting that developmental processes underlie adult Leydig cell insensitivity (Smith et al. 1975). Among New World populations presenting lower salivary testosterone levels compared with those of American males are the Ache of Paraguay (Bribiescas 1996, 1997) and the Aymara of Bolivia (Beall et al. 1992), although there is no evidence to suggest that low salivary testosterone levels among these populations are indicative of subfecundity (Galard at al. 1987). The Gainj of New Guinea manifest high FSH levels in otherwise healthy mean, a reflection of possible Sertoli cell insensitivity. The investigators suggest that this may indicate male subfecundity, although sperm couns were not available (Campbell 1994).

Salivary testosterone measurements of healthy urban men in Venezuela, Poland, Zimbabwe, and Japan have shown that the distinction between American and non-American populations is even more profound than previously suspected. Salivary testosterone levels from these urban populations, with the exception of Polish men, were lower than those for Americans. Moreover, modest age-related declines in salivary testosterone were noted relative to Americans (Campbell et al. 2000; Ellison et al. 1998).

It is unlikely that population differences in reproductive endocrine function are the result of genetic polymorphisms. With the exception of extremely rare gonadotropin transcription mutations that may be inherent to specific communities (Tapanainen et al. 1997), and perhaps testosterone hormone binding globulin (TeBG) (Larrea et al. 1995), there is little evidence to suggest that genetic population differences in gonadotropin production or transcription underlie population variation (Jameson 1996). Genetic differences in receptor affinities area possibility, but evidence is lacking. Most likely, chronic dietary intake and activity patterns during development are at the core of population variation. For example, poor urban youths in Kenya revealed significantly lower FSH levels in urinary gonadotropins compared with economically privileged Kenyan adolescents (Kulin et al. 1984).

Sperm count. Sperm counts have been reported to vary between populations (Fisch et al. 1996), although the differences do not suggest any differences in fecundability (Cooper et al. 1991). Longitudinal studies of nonwestern populations are few; however, available evidence does not indicate any significant temporal changes in sperm counts or semen quality (Seo et al. 2000; Tortolero et al. 1999).

Prostate cancer risk. Steroid-sensitive cancers vary significantly across populations (Rose et al. 1986). Although caution is merited when attempting to examine the etiology of disease by race owing to the ambiguous and often misleading nature of this classification (Lewontin 1972), certain communities do exhibit differential rates of prostate disease. African-American males have a twofold higher risk of contracting prostate cancer compared with non-African-American males and present significantly higher androgen levels (Ross et al. 1986). Given the central role of androgens in promoting prostate carcinomas (Henderson et al. 1982), differences in community steroid levels are noteworthy, although the relationship between individual lifetime androgen levels and prostate cancer risk remains unclear (Carter et al. 1995).

Environmental factors such as diet and activity patters warrant close attention because of their impact on the neuroendocrine system (Key 1995). Nigerian males exhibit less aggressive bouts of prostate cancer as well as lower androgen levels than do urban African-American males, suggesting that lifestyle differences before and after adolescence, such as diet, stress, and activity, may influence population risk (Jackson et al. 1977; Sminzu et al. 1991).

Data from nonwestern populations as well as ethnic differences in prostate cancer risk imply that population variation in testosterone levels reflects hormonal release in American populations rather than hormonal suppression among nonwestern populations. Ethnic differences in cancer risk and androgen levels also underscore the importance of developing an increased awareness of population variation in neuroendocrine function as well as the central role of environmental factors such as diet, activity, and stress. As suggested in reference to female reproductive endocrine function (Ellison 1994), clinical research on American male population must be viewed as representative of the extreme range of human variability and not the common or "healthiest" representation of Homo sapiens.

[1] pp. 116-119. "Reproductive Physiology of the Human Male: An Evolutionary and Life History Perspective". In Reproductive Ecology and Human Evolution. Evolutionary foundations of human behavior. New York: Aldine de Gruyter, 2001.

More AAPA 2008 asbtracts

Selected abstracts from 2008 AAPA meeting:

Interaction in pigmentation genes creates variation in brown irises.
E.E. Quillen1, S. Beleza2, E.J. Parra3, R.W. Pereira4, M.D. Shriver1. 1Department of Anthropology, Pennsylvania State University, 2Institute of Molecular Pathology and Immunology, University of Porto, 3Department of Anthropology, University of Toronto, 4Department of Genomics and Biotechnology, Catholic University of Brasília
Iris pigmentation varies substantially in humans and may have been under either natural or sexual selection at different times during our evolutionary history. While less than 10% of the people today have blue eyes, previous analyses have focused on the genetic basis of the differences between blue and brown iris pigmentation or between blue and green as light eyes and brown as dark eyes while neglecting the variation within brown eyes. In a heterogeneous brown-eyed Brazilian population, both iris and skin pigmentation vary widely and are significantly correlated (r2=0.39), suggesting that the same or linked genes are determining these two traits. However, an alternate explanation for this correlation between skin and eye pigmentation is admixture stratification which can lead to similarly high correlations among unlinked markers or traits. The history of tripartite admixture (European, West African, and Indigenous American) investigated using Ancestry Informative Markers, makes Brazil the ideal population to study the interaction between genes related to pigmentation of the eye and skin. Polymorphism previously associated with skin pigmentation differences in the parental populations, including SLC24A5, KITLG, MATP, OCA2, and TYRP1, were investigated to uncover the magnitude of their influence on pigmentation variation in brown irises.

Bringing the Stone Age into the Information Age: introducing the Paleoanthropology Database.
Z.J. Throckmorton. Department of Anthropology, University of Wisconsin, Madison. Online databases and datasets have become indispensable tools for modern scientists.
A number of such databases relevant to paleoanthropology are currently in development; many of these can be accessed through Paleoanthportal.org. These databases are thus far narrow in their scope and detailed in their content. I present here the Paleoanthropology Database (PADB), the first broad and general database designed to be useful to both researchers and students of human evolution. The database contains 40 types of basic data categories filled with information culled from the published literature. These data categories include, for example, age of the site, skeletal elements present, taxonomic affinities, archeological and behavioral evidence, and associated faunal remains, all fully referenced to an extensive source list (over 4,000 references in total for Europe). Here I present the first phase of the database, 300 European sites. An additional 900 African and Asian sites, as well as Miocene hominoid sites, will be added in the future. The primary goal of PADB is the facilitation of access to the evidence of human evolution through its open access status (anyone with a computer that is online may use it). Its secondary goal is to be a continuously updated source of paleoanthropological data through a streamlined updating protocol (utilizing the familiar Excel spreadsheet). At the heart of PADB’s ease of use and updateability are its straightforward database structure (two MySQL tables) and flexible, simple, yet powerful search functions (written largely in Perl). The database can be accessed through Johnhawks.net.

Reconstruction of the Early Neolithic/Bronze Age Population Diversity of the Lake Baikal Region Using mtDNA Polymorphism from Shamanka II Cemetery
H. Vahdati Nasab1, 2, T. A. Thomson1, F. J. Bamforth2, and V. I. Bazaliiski3. 1Department of Anthropology, University of Alberta, 2Human Identification Lab for Archaeology, Department of Laboratory Medicine and Pathology, University of Alberta, 3Department of Archaeology and Ethnography, Irkutsk State University.
This research examines the mtDNA polymorphism among individuals buried at a Neolithic (ca. 5000-4000 BC) hunter-gatherer cemetery, Shamanka II (field season 2002), located on the southwestern tip of Lake Baikal, Siberia. The present study principal research objective aims to compare the mtDNA polymorphism observed at Shamanka II cemetery to the mtDNA results of a previous study (Mooder, 2004), which includes Lokomotiv and Ust’Ida. Like Shamanka II, Lokomotiv is representative of the same culture group (Kitoi) and is contemporaneous in age (5000-4000 BC) while Ust’Ida is representative of a Bronze Age culture group (Serovo-Glazkovo, 1000 BC). There is a pronounced hiatus in radiocarbon dates stretching between the Neolithic and Bronze Age (4900-4200 BC) cultures around Lake Baikal region (Weber, 2002). Mooder’s (2004) results revealed disparate mtDNA distribution between preand post-hiatus groups. Our results indicate although the Neolithic Kitoi (Shamanka II and Lokomotiv) share the identical haplogroups with the Bronze Age Serovo-Glazkovo, the frequency distributions between pre- and post-hiatus cemetery groups are very different. Thus the general model for biological discontinuity between the pre- and post-hiatus Cis-Baikal populations is not disputed.

Metric and non-metric trait variation in the dentition of Holocene Khoesan populations.
W. Black, R.R. Ackermann, J. Sealy. Department of Archaeology, University of Cape Town.
There have been many studies of dental variation in Holocene populations of Europe and the Americas, but few of African populations. Here, we present preliminary work on dental variation in the Khoesan, an African people who have received considerable attention from archaeologists and physical anthropologists. Recent research on well-dated Khoesan skeletal material has revealed general cranial size and stature fluctuations during the past 12,000 years, which appear to result from intrinsic factors affecting the populations, rather than gene flow from outlying areas. These results are consistent with hypotheses of morphological and genetic continuity in Southern African populations during this time. Most previous work has, however, focused on the second half of the Holocene. Here, we add to this body of work by examining dental variation among the Khoesan, extending back into the early Holocene. Metric and non-metric data were collected from >500 adult individuals. When possible, standard dental measurements were taken on all teeth. Cervical measurements, which are less affected by heavy wear, were also taken on all molars. Additionally, dentition was scored for a suite of dental morphological attributes, including 40 crown, root and intraoral osseous traits. Results demonstrate fluctuations in tooth size that generally conform with the mid- to late Holocene size variations observed in cranial and postcranial material. Teeth, during this time period, appear to be smaller than Early Holocene counterparts and discernible reductions are identified through most measurements. Qualitative trait variation is largely consistent throughout sample, supporting the hypothesis of population continuity throughout the Holocene.

Modern European population affinities: a dental study.
S.T. Price. Dept. of Anthropology, New York University, New York Consortium in Evolutionary Primatology (NYCEP).
European population history has been investigated largely through genetics and archaeological research, and has revealed a complex history for this region. Dental morphology is genetically controlled and only marginally influenced by environment. In addition, dental remains are the most common and often best-preserved remains from past populations, and have been shown to be good indicators of biological affinity. For these reasons, dental analyses will add important evidence to debates regarding European population history. Metric and nonmetric data were collected on 160 modern human individuals curated in the Natural History Museum, London and the American Museum of Natural History. Dental morphology was scored according to the Arizona State University Dental Anthropology System (ASUDAS). Statistical analyses including mean measure of divergence indicate important population differences as well as affinities between some groups. The current study is a pilot project as part of a larger investigation into European population history, but preliminary analyses of dental morphology indicate at least one division in Europe. This division seems to correspond to geographic location, and can broadly be categorized as an east-west separation of populations. More eastern populations not only have higher frequencies of certain dental traits, such as shoveling and double shoveling, but also show a tendency toward higher levels of expression of those traits as well. Overall, these analyses indicate different recent population histories for Eastern and Western Europe. Future research will examine more individuals over more time periods to understand this complex history.

Is there a biological rationale to the Frankfurt horizontal plane?
A. Barash, A. Marom. Department of Anatomy and Anthropology, Sackler School of Medicine, Tel Aviv University, Israel
The Frankfurt horizontal plane (FHP) is one of the most frequently used reference planes in morphological sciences, cranial surgery and dental medicine. The biological basis for this plane is that in humans it puts the line of vision parallel to the ground, perpendicular to earth’s gravitational field. Over the years several authors have criticized the use of this plane. While some doubted the spatial stability of the reference points, others claimed that, as intended by its original proponents, the plane should only be used in humans, since most other animals, including non-human primates, do not hold their head in the same manner as humans. The object of this study was to asses the nature of the FHP in human and non-human primates. This was done by defining a new plane, an optic plane (OP), using the orientation of the medial rectus (MR) muscle. The rationale behind this new plane was the assumption that humans and most primates, gaze habitually parallel to the ground, and that the medial recti muscles only rotate the eyes about the vertical axis. Three points- the origin of the left MR and the insertion of the left and right MR where digitized from CT scans. This new plane was compared with the FHP. The results indicate that in humans the two planes are almost parallel, demonstrating that the FHP indeed applies to human studies. Additionally discussed are the nature of the plane in non-human primates and its possible role as cross species plane.

Modern human limb proportions follow Allen’s rule predictions and reflect long term climate adaptations rather than short term epigenetic influences.
R.W. Higgins. Dept. Anthropology, George Washington University.
Distal limb segment length, relative to proximal limb segment length, is found to correlate with climate in modern human populations. The question remains whether this trait is determined by adaptation or epigenetic influences. Experiments on lab animals support the hypothesis that cold temperature influences limb development by reducing growth plate kinetics and/or vascular supply. Reduction in vascular supply would theoretically have a more pronounced effect on the smaller distal limb segments. This study uses a natural experiment, the migration of two modern human populations to North America, to examine the role of natural selection on human limb proportions. The hypotheses to be tested are: (1) If relative distal limb length is largely an inherited trait shaped over long periods of time by natural selection, then the trait should persist several generations after a population enters a new climate and (2) if limb proportions are largely a product of epigenetic influences, then limb proportions should not differ between populations living in the same environment. European American and African American long bones from the Terry Collection were measured (N = 80). Statistical analysis shows that (1) distal segments differed more between populations than did proximal segments with European Americans exhibiting relatively shorter distal segments, and (2) crural (p < .01) and brachial (p < .01) indices differed significantly between the two populations. These results suggest that European and African American limb proportions largely reflect ancestral climate adaptations rather than epigenetic influences.

A phylogenetically controlled analysis of the relationship between temperature and modern human limb length variation.
M. Dembo, A. Cross and M. Collard. Department of Archaeology, Simon Fraser University.
Several studies have found that modern human limb length variation is consistent with Allen’s Rule, which holds that there is a positive correlation between peripheral body part length and temperature in homeothermic species. However, none of these studies has controlled for the phylogenetic relationships among populations. This is potentially problematic because such relationships render taxa nonindependent, and data point independence is a key assumption of correlation analysis. To investigate this issue, anthropometric and temperature data were collected from the literature for indigenous populations from five continents. Next, the impact of mean annual temperature on limb segment length was investigated by analyzing subsamples stratified in such a way as to counter the over representation of warm climate populations in the complete sample. Subsequently, subsamples that returned significant correlations were subjected to phylogenetically controlled correlation analysis in CAIC. CAIC calculates correlation coefficients from “independent contrasts”, which estimate the amount of change in variables since taxa last shared a common ancestor. The phylogenetic trees used in CAIC were generated from published genetic distance data. To produce fully resolved trees, modifications were made to the genetic trees based on the linguistic affiliations of the populations. When the issue of over representation was addressed, only two limb segment lengths were significantly correlated with mean annual temperature: lower arm and foot. Only two of the 10 subsamples for these segments returned statistically significant correlations in CAIC. Thus, the analyses do not support the hypothesis that modern human limb length variation is consistent with Allen’s Rule.

Ecological and life course effects on mid upper arm somatic muscle allocation and skeletal stature among Bangladeshi male migrants to the UK.
K.S. Magid1, F.U. Ahamed2, G.R. Bentley3. 1Department of Anthropology, University College London, UK, 2Department of Anthropology, University of Chittagong, Bangladesh 3Department of Anthropology, Durham University, UK.
Life history theory predicts that selection will favour physiological mechanisms that efficiently regulate the allocation of energy and time between competing functions: reproduction, maintenance, storage and growth. Environmental conditions that lead to increased energetic availability will result in enhanced testosterone levels and anabolic muscle tissue in human males. While apportionment of somatic muscle tissue remains plastic throughout the human male life course, the effects of increased energy availability on muscle allocation are expected to be more pronounced in younger males compared with older males. In our previous study, we demonstrated increased free testosterone among young male migrants from Bangladesh to the UK. In the present study we assess the effects of changes in energetic availability on morphology through measures of mid-upper arm muscle tissue in human males. Anthropometric measures of bone stature (standing height and arm length) and proxies of soft tissue somatic allocation (BMI, midupper arm area, mid upper arm muscle + bone area) were collected on adults aged >40 (n=28) and <40 (n=29) who migrated from Bangladesh to the UK aged 1 to 57 years. A group of sedentee males who have remained in Sylhet, Bangladesh all their lives (n=76) were used as a reference. In line with our hypothesis, our results show that age at migration significantly predicted an increase in mid upper arm muscle tissue for males under the age of 40 years, but was not a significant predictor for males over the age of 40. These findings suggest the allocation of male anabolic muscle tissue is responsive to changes in energetic availability subject to age at migration.

Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa.
B.M. Henn1, P.A. Underhill2, A.A. Lin2, P.J. Oefner3, S.A. Tishkoff4, F. Cruciani5, P. Shen6, C. Gignoux1, and J.L. Mountain1,2. Departments of 1Anthropology and 2Genetics, Stanford University, 3Institute of Functional Genomics, University of Regensburg, 4Department of Biology, University of Maryland, 5Dipartmento di Genetica e Biologia Molecolare, Università “La Sapienza”, 6Stanford Genome Technology Center, Stanford University.
The initial origin and mode of diffusion of pastoralism into southern Africa about 2,000 years ago continues to be debated among anthropologists. Were early instances of sheep, pottery and other traits of the pastoralist package transmitted to southerncentral Africa by demic or cultural diffusion? Here we present a novel Y-chromosome specific mutation, E3b1f-M293, which is at high frequencies in pastoralist and huntergatherer groups across eastern and southern Africa, and now links the majority of haplotypes of the previously paraphyletic clade E3b1-M35*. Phylogeographic patterns of the E3b1f frequency distribution and associated microsatellite diversity are consistent with an migration through Tanzania to southern-central Africa. Our Ychromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa, possibly involving a Southern Nilotic-speaking population. The genetic distribution suggests that this dispersal was distinct from the later migration of Bantu-speaking peoples along a similar route. Instead, the expansion time of the E3b1f lineage correlates with archaeological evidence for the arrival of the pastoralist economy in southern Africa about 2,000 years ago.

Geometric Morphometrics Craniofacial Analysis of early Bronze Age Austrian Populations
A. Pellegrini1,2, M. Teschler-Nicola1, P. Mitteröcker2,3, F. Bookstein2,4.1Department of Anthropology, Natural History Museum Vienna, Austria, 2Department of Anthropology, University of Vienna, 3Konrad Lorenz Institute for Evolution & Cognition Research, Altenberg, Austria, 4Department of Psychiatry & Behavioral Sciences, University of Washington, USA.
Archeological data indicate that early Bronze Age populations in lower Austrian do not present a cultural unity, they differ in three regional manifestations: North of the Danube was the area of the Aunjetitz culture, south of the Danube the Unterwölbling (west of Vienna wood) and the Wieselburg culture (east of Vienna wood). In this study the craniofacial morphology of these populations was analyzed with Geometric Morphometrics methods. 58 threedimensional landmarks were measured in 171 adult individuals. We carried out a permutation test MANOVA of the Procrustes coordinates, which yields highly significant differences between the culturally separated populations; moreover a Principal Component Analysis in size-shape space has been carried out, which shows conspicuous differences between the Wieselburg and the Aunjetitz groups, while the (heterogenous) Unterwölblig group overlapps with both of them. A PCA of our sample divided by males and females provided evidence for a more heterogenous cranial morphology in males (length and breath) due to a prolonged cranial growth of males as indicated by an allometric analysis. In contrast, females of the three cultural groups differ in some morphological details (e.g., occipital region) substantiating a partial or total isolation. However, further analysis (e.g., TPS) have been carried out as well, which contribute considerably to our knowledge on mobility and population dynamics in early Bronze Age Austria. As the populations investigated are contemporary, inhabited a small geographic area and share a similar ecological environment, their phenotypic differences will be discussed in terms of genetic differences due to partial or total endogamy.

A comparison of craniofacial secular trends during the 19th and 20th centuries in the U.S. and Portugal.
K.E. Weisensee and R.L. Jantz, Department of Anthropology, University of Tennessee, Knoxville, TN 37996
Craniofacial secular changes over the past two hundred years have been observed in several worldwide populations. This project addresses the question of whether the pattern of change is similar across different populations experiencing the unique 20th century environment. Several studies have documented secular changes in modern populations using anthropometrics on living people, this study, however uses large, welldocumented skeletal samples to compare secular trends across different populations experiencing similar environmental conditions. Both American Black and White populations have been shown to be experiencing a similar pattern of change over time. The Portuguese have also been shown to have experienced significant changes in cranial morphology over the past two hundred years. This study seeks to determine if the pattern of change seen in the American population is the same as that observed in the Portuguese sample from the same time period. Lisbon, Portugal experienced typical changing environmental conditions as in much of the U.S. and Europe whereby urban density increased and mortality patterns were dramatically changed. Unlike the American sample, the Portuguese sample is taken from a single urban population which experienced little immigration. Because of the more tightly controlled Portuguese sample, it is possible to determine if these changes in environmental conditions impacted cranial shape in a similar manner across populations or if the American experience is unique compared to other populations which were not impacted by large immigrate populations. The study uses both interlandmark distances and 3d landmark coordinate data to compare changes between populations from 1820 to 1950.

Detecting natural selection in modern human skulls.
N. Martínez-Abadías1, M. Esparza1, T. Sjøvold2, R. González-José3, M. Santos4, M. Hernández1 and C.P. Klingenberg5. 1Unitat d’Antropologia, Dept. de Biologia Animal, Universitat de Barcelona,2Osteologiska enheten, Stockholms Universitet, 3Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, 4Dept. de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 5Faculty of Life Sciences, University of Manchester.
In human evolution selection is implicitly assumed to be one of the main forces driving evolutionary change and adaptation, but direct evidence of this is rarely available, especially for morphological traits such as skull shape. The main goal of this study is to assess how life-history and fitness measures relate to skull morphological variation, which is the most direct evidence of natural selection. To do this, we use a unique large collection of modern human skulls with genealogical associated data from Hallstatt (Austria). We combine morphological and demographical data and apply multivariate quantitative genetic methods to estimate selection on a three dimensional reconstruction of the skull morphology. Then, we compare the obtained selected pattern with the secular changes observed in this population over a period of almost 200 years. Our results show that selection significantly acted on the evolutionary changes observed in the skull morphology of the Hallstatt’s population during the 18th and the 19th centuries. Indeed, we detect relatively strong directional selection on skull shape and weak stabilizing selection on skull size. However, we find that the expected responses to these selection regimes do not correspond to the actual evolutionary patterns of skull morphology. Therefore, these results emphasize the major role of selective forces both in human skull size and shape, but suggests that microevolutionary factors other than natural selection are also contributing to the evolution of the skull in the Hallstatt’s population and these are obscuring the effects of natural selection.

Chin size and its relationship to facial prognathism in humans.
D. Durand1, D.R. Hunt2. 1Department of Anthropology, The George Washington University, 2Department of Anthropology, Smithsonian Institution.
The presence of a mental eminence has been identified as a trait unique to Homo sapiens. Hypotheses to account for its presence have ranged from a functional adaptation to a byproduct of morphological changes in the skull. The absence of a chin in Homo floresiensis has been used by some scientists to argue that it was not human. Other researchers regard it as a rare trait shared with modern day Australomelanesians, who also lack an apparent chin. In response to this, it has been suggested that there is no such thing as a chinless human, but rather that increased facial prognathism may deemphasize the expression of the chin. The present study tests whether modern humans with greater prognathic faces have smaller chins. Cranial and mandibular measurements were taken from forty-three European- American and African-American individuals and a ratio of facial prognathism to chin size was calculated. Results indicate there is a moderate inverse relationship between chin size and facial prognathism in humans. While these finding do not resolve the debate of adaptation versus a morphological byproduct of change, it appears that the morphological changes producing contraction of the lower face influence an increase in chin size. With this continuum of chin expression in the human species, it is apparent that this trait is not an accurate feature for species identification.

Allelic variability and tests for natural selection at the human ALDH2 locus.: J.C. Long1, C. Lewis4, J. Li1, R. Malhi2, K. Hunley3. 1Dept Human Genetics, Univ Michigan Medical Sch, Ann Arbor, MI; 2Dept Anthropology, University of Illinois, Urbana, IL; 3Dept Anthropology, University of New Mexico, Albuquerque, NM. 4Dept Anthropology, Oklahoma, Norman, OK. This research tests the hypothesis that natural selection has shaped variation at the human ALDH2 gene locus. The enzyme product of this locus catalyzes aldehyde oxidation and is important in alcohol metabolism. ALDH2 shows unusually high allelic differentiation among human populations. A deficiency variant, ALDH2-2, is common in Asians but absent in other populations. This observation implicates the action of natural selection. To test the neutral null hypothesis, we compare the ALDH2-2 allele frequency to the extent of intraallelic variability. We have sequenced 5 kb of DNA flanking the functional ALDH2-2 substitution in a total of 123 people. These people represent sixteen populations, including four indigenous populations from each of four continental regions: Africa, Europe, Asia, and the Americas. We see ALDH2-2 allele only Asians, and not on any other continent. We observe a common background substitution on ALDH2-2. This suggests an old age for ALDH2-2. An old age for the allele is consistent with its high frequency in Asians. However, it is important to examine variability at the locus in the context of the geographic structure of our species. To do this, we established neutral baselines for ALDH2 sequence diversity in our world-wide sample by fitting nested population structure models to the CEPH microsatellite diversity data. In this light, the presence of intraallelic variability and a high allele frequency is inconsistent with the restriction of ALDH2-2 to the Asian continent. Neutral evolution for ALDH2-2 is unlikely.