Nei critical of tests for detecting selection in humans

The paper isn't online yet (post will be updated when it is) so it's not clear which studies come under criticism. From the press release, it seems that there are at least two problems detected: tests using ratios of synonymous/nonsynonymous mutations, and small sample size numbers. As always, I am very fond of this type of whistle-blowing paper that examines a widely, but uncritically used technique which has formed the basis of numerous recent studies.

Nei said that for many years he has suspected that the statistical methods were faulty. "The methods assume that when natural selection occurs the number of nucleotide substitutions that lead to changes in amino acids is significantly higher than the number of nucleotide substitutions that do not result in amino acid changes," he said. "But this assumption may be wrong. Actually, the majority of amino acid substitutions do not lead to functional changes, and the adaptive change of a protein often occurs by a rare amino acid substitution. For this reason, statistical methods may give erroneous conclusions." Nei also believes that the methods are inaccurate when the number of nucleotide substitutions observed is small.

To demonstrate the faultiness of the statistical methods, Nei's team compiled data collected by their Emory University colleague, Shozo Yokoyama, on the genes that control the abilities of fish to see light at different water depths and on the genes that control color vision in a variety of animals. The team used these data to compare statistically predicted sites of natural selection with experimentally determined sites. They found that the statistical methods rarely predicted the actual sites of natural selection, which had been identified by Yokoyama through experiments. "In some cases, statistical method completely failed to identify the true sites where natural selection occurred," said Nei. "This particular exercise demonstrated the difficulty with which statistical methods are able to detect natural selection."

To demonstrate how small sample sizes can lead to incorrect results, the team used computer simulations to examine the evolution of genes in three primates: humans, chimpanzees, and macaques. The scientists mimicked the procedures used by the authors of a 2007 paper, which applied the branch-site method to 14,000 orthologous genes -- genes that are genealogically identical among different species -- and which found that the method predicted selection in 32 of the genes. Nei and his team also studied selection using Fisher's exact test, but this test did not detect any selection. "The results indicate that the number of nucleotide substitutions that occurred were too small to detect any selection; therefore, all of the 32 cases obtained by the branch-site method must be false positives," said Nozawa.

PNAS doi:10.1073/pnas.0901855106

Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

Masafumi Nozawa et al.

Abstract

Natural selection operating in protein-coding genes is often studied by examining the ratio (ω) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is ≈80 or smaller. Because the ω value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high ω values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high ω value. To understand adaptive evolution, some form of experimental confirmation is necessary.


Link

Quantifying the extent of possible Neandertal introgression

The absence of Neandertal mtDNA sequences in modern Europeans argues against large-scale admixture between Cro-Magnoids and Neandertals. On the other hand, this could be explained if there was a selective advantage of Cro-Magnoid mtDNA types. Thus, the survival of ancient Cro-Magnoid (but not Neanderthal) mtDNA into modern Europeans does not in itself demonstrate the absence of admixture, although it certainly makes it more likely.

mtDNA is implicated in energy production of the body, and a selective advantage is not inconceivable, perhaps associated with fluctuations in temperature that may have weeded out cold-adapted Neanderthal mitotypes.

Alternatively, Neanderthal mothers may have been at a disadvantage when it came to bearing offspring from Cro-Magnoid fathers, due to some incompatibility of the genomes (or body types) of the two species, a stronger version of what happens in modern humans of different races.

Ultimately, detecting Neandertal introgression will have to involve the detection of a genetic variant in Neandertal remains, that is not found in the earliest Cro-Magnoid remains, but is found in modern humans. Given the very small samples of both species, this may, in fact be quite difficult.

Thus, I don't anticipate the question of Neandertal introgression to be settled any time soon, although the continued absence of a "smoking gun" may ultimately lead scientists to accept the absence (or quantitative insignificance) of any such admixture event.

Heredity doi:10.1038/hdy.2008.103

Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations

E M S Belle et al.

Abstract

Populations of anatomically archaic (Neandertal) and early modern (Cro-Magnoid) humans are jointly documented in the European fossil record, in the period between 40 000 and 25 000 years BP, but the large differences between their cultures, morphologies and DNAs suggest that the two groups were not close relatives. However, it is still unclear whether any genealogical continuity between them can be ruled out. Here, we simulated a broad range of demographic scenarios by means of a serial coalescence algorithm in which Neandertals, Cro-Magnoids and modern Europeans were either part of the same mitochondrial genealogy or of two separate genealogies. Mutation rates, population sizes, population structure and demographic growth rates varied across simulations. All models in which anatomically modern (that is, Cro-Magnoid and current) Europeans belong to a distinct genealogy performed better than any model in which the three groups were assigned to the same mitochondrial genealogy. The maximum admissible level of gene flow between Neandertals and the ancestors of current Europeans is 0.001% per generation, one order of magnitude lower than estimated in previous studies not considering genetic data on Cro-Magnoid people.

Link

Long Live the 25th of March 1821

Slavopaionian propaganda video + Stephen Miller's excellent letter to Archaeology magazine

Last year, when the "Macedonian issue" was in the news, due to FYROM's NATO candidacy I proposed that the issue could be resolved if FYROM accepted a compromise in the "name issue" that would qualify "Macedonia" with an appropriate geographical disambiguating adjective.

Events since that time have further strengthened my belief that no compromise is possible any more with our neighbors to the north, who refuse to budge even to the slightest degree in their stubborn adherence to their invented identity.

If you are in doubt of the degree of irrationality present in FYROM, this official video in state TV will change your mind:



The part at 04:25 is especially strange, where the narrator announces that one of the three races of mankind are the "Whites-Macedonoids" who spread to the "Sea of Japan", but the whole thing has a lunatic vibe to it.

On a more positive note, Prof. Stephen G. Miller's letter to Archaeology magazine is a welcome scholarly demolition of the Slavomacedonians' invented history.

I opened the January/February issue of Archaeology today and eagerly turned to “A Letter from Macedonia” only to discover that it was actually a letter from ancient Paionia – the land north of Mt. Barmous and Mt. Orbelos. Livy’s account of the creation of the Roman province of Macedonia (45.29.7 and 12) makes clear that the Paionians lived north of those mountains (which form today the geographically natural northern limits of Greece) and south of the Dardanians who were in today’s Kosovo. Strabo (7. frag 4) is even more succinct in saying that Paionia was north of Macedonia and the only connection from one to the other was (and is today) through the narrow gorge of the Axios (or Vardar) River. In other words, the land which is described by Matthew Brunwasser in his “Owning Alexander” was Paionia in antiquity.


While it is true that those people were subdued by Philip II, father of Alexander, in 359 B.C. (Diodorus Siculus 16.4.2), they were never Macedonians and never lived in Macedonia. Indeed, Demosthenes (Olynthian 1.23) tells us that they were “enslaved” by the Macedonian Philip and clearly, therefore, not Macedonians. Isokrates (5.23) makes the same point. Likewise, for example, the Egyptians who were subdued by Alexander may have been ruled by Macedonians, including the famous Cleopatra, but they were never Macedonians themselves, and Egypt was never called Macedonia (and so far as I can tell does not seek that name today).

Certainly, as Thucydides (2.99) tells us, the Macedonians had taken over “a narrow strip of Paionia extending along the Axios river from the interior to Pella and the sea”. One might therefore understand if the people in the modern republic centered at Skopje called themselves Paionians and claimed as theirs the land described by Thucydides.

But why, instead, would the modern people of ancient Paionia try to call themselves Macedonians and their land Macedonia? Mr. Brunwasser (p. 55) touches on the Greek claims “that it implies ambitions over Greek territory” and he notes that “the northern province of Greece is also called Macedonia.” Leaving aside the fact that the area of that northern province of modern Greece has been called Macedonia for more than 2,500 years (see, inter alios, Herodotus 5.17; 7.128, et alibi), more recent history shows that the Greek concerns are legitimate. For example, a map produced in Skopje in 1992 (Figure 1) shows clearly the claim that Macedonia extends from there to Mt. Olympus in the south; that is, combining the ancient regions of Paionia and Macedonia into a single entity. The same claim is explicit on a pseudo-bank note of the Republic of Macedonia which shows, as one of its monuments, the White Tower of Thessalonike, in Greece (Figure 2). There are many more examples of calendars, Christmas cards, bumper-stickers, etc., that all make the same claim.

Further, Mr. Brunwasser has reported with approval (International Herald Tribune 10/1/08) the work of the “Macedonian Institute for Strategic Research 16:9”, the name of which refers “to Acts 16:9, a verse in the New Testament in which a Macedonian man appears to the Apostle Paul begging him: ‘Come over into Macedonia, and help us.’” But where did Paul go in Macedonia? Neapolis (Kavala), Philippi, Amphipolis, Apollonia, Thessaloniki, and Veroia (Acts 16:11-17:10) all of which are in the historic Macedonia, none in Paionia. What claim is being made by an Institute based in Skopje that names itself for a trip through what was Macedonia in antiquity and what is the northern province of Greece today?

I wonder what we would conclude if a certain large island off the southeast coast of the United States started to call itself Florida, and emblazoned its currency with images of Disney World and distributed maps showing the Greater Florida.
Certainly there was no doubt of the underlying point of “Macedonia” in the mind of U.S. Secretary of State Edward Stettinius on December 26, 1944, when he wrote:

“The Department [of State] has noted with considerable apprehension increasing propaganda rumors and semi-official statements in favor of an autonomous Macedonia, emanating principally from Bulgaria, but also from Yugoslav Partisan and other sources, with the implication that Greek territory would be included in the projected state. This government considers talk of Macedonian ”nation”, Macedonian “Fatherland”, or Macedonian “national consciousness” to be unjustified demagoguery representing no ethnic nor political reality, and sees in its present revival a possible cloak for aggressive intentions against Greece.”
[Source: U.S. State Department, Foreign Relations vol viii, Washington, D.C., Circular Airgram (868.014/26Dec1944)]

Mr. Brunwasser (a resident of Bulgaria), however, goes on to state, with apparent distain, that Greece claims “Alexander III of Macedon (Alexander the Great) . . . as Greek.”

This attitude mystifies me. What is there to “claim”? Alexander’s great-great-great grandfather, Alexander I, was certified as Greek at Olympia and, in the words of the father of history “I happen to know that [the forefathers of Alexander] are Greek” (Herodotus 5.22). Alexander’s father, Philip, won several equestrian victories at Olympia and Delphi (Plutarch, Alexander 4.9; Moralia 105A), the two most Hellenic of all the sanctuaries in ancient Greece where non-Greeks were not allowed to compete. If Philip was Greek, wasn’t his son also Greek?

When Euripides – who died and was buried in Macedonia (Thucydides apud Pal. Anth. 7.45; Pausanias 1.2.2; Diodorus Siculus 13.103) – wrote his play Archelaos in honor of the great-uncle of Alexander, did he write it in Slavic? When he wrote the Bacchai while at the court of Archelaos did he not write it in Greek even as it has survived to us? Or should we imagine that Euripides was a “Macedonian” who wrote in Slavic (at a date when that language is not attested) which was translated into Greek?

What was the language of instruction when Aristotle taught Alexander? What language was carried by Alexander with him on his expedition to the East? Why do we have ancient inscriptions in Greek in settlements established by Alexander as far away as Afghanistan, and none in Slavic? Why did Greek become the lingua franca in Alexander’s empire if he was actually a “Macedonian”? Why was the New Testament written in Greek rather than Slavic?

On page 57 of the so-called “Letter from Macedonia” there is a photograph of the author standing “before a bronze statue of Alexander the Great in the city of Prilep.” The statue is patently modern, but the question is whether the real historic Alexander could have read the Slavic inscription beneath his feet. Given the known historic posterity of Slavic to Greek, the answer is obvious.

While Mr. Brunwasser’s reporting of the archaeological work in Paionia is welcome, his adoption and promotion of the modern political stance of its people about the use of the name Macedonia is not only unwelcome, it is a disservice to the readers of Archaeology who are, I imagine, interested in historic fact. But then, the decision to propagate this historical nonsense by Archaeology – a publication of the Archaeological Institute of America - is a disservice to its own reputation.

Let it be said once more: the region of ancient Paionia was a part of the Macedonian empire. So were Ephesos and Tyre and Palestine and Memphis and Babylon and Taxila and dozens more. They may thus have become “Macedonian” temporarily, but none was ever “Macedonia”.

Allow me to end this exegesis by making a suggestion to resolve the question of the modern use of the name “Macedonia.” Greece should annex Paionia – that is what Philip II did in 359 B.C. And that would appear to be acceptable to the modern residents of that area since they claim to be Greek by appropriating the name Macedonia and its most famous man. Then the modern people of this new Greek province could work on learning to speak and read and write Greek, hopefully even as well as Alexander did.


Sincerely,

Stephen G. Miller

Professor Emeritus,
University of California, Berkeley

PS: For a more complete examination of the ancient evidence regarding Paionia, see I. L. Merker,“The Ancient Kingdom of Paionia,” Balkan Studies 6 (1965) 35-54

My only disagreement with the good professor, is that the Slavs of FYROM do not merit either the name of Macedonians or of Paionians, since they have no ethnic link to either ancient people. They are in fact, largely Bulgarians, but since some of them don't like (or are afraid) to be called such, they should be called Slavopaionians, as is appropriate for Slavs inhabiting the ancient region of Paionia.

Selection in the human genome with HGDP samples

Genetic Future points me to a new paper on signatures of selection in the human genome. Also Gene Expression and John Hawks on the subject, in which he responds to criticism in the paper about his accelerated evolution theory. Go ahead and read these sources for commentary on the paper (which is open view anyway).

I would like to comment on this interesting bit:

In general, we find the evidence for selection on disease risk is not as conclusive as that for selection on pigmentation traits. One parsimonious explanation for this is that However, the role of the genetic architecture of a trait (the number of loci underlying a trait and their effect sizes and frequencies) in how it responds to selection remains largely unexplored. Since the genetic architecture of pigmentation is relatively simple (compared with other complex traits), perhaps a selection signal on this trait is more readily detected because it is selection on disease risk, assuming disease risk is under selection at all, is much weaker than selection on pigmentation.spread across fewer loci. On the other hand, this explanation may confuse cause and effect. Perhaps skin pigmentation has a simpler genetic architecture than other complex traits because it has been subject to recent strong selection—the first moves to a new phenotypic optimum are predicted to be on mutations of large fitness
effect (Orr 2002). So assuming a positive correlation between the effects of an allele on fitness and on a trait, it is also plausible that the relatively simple genetic architecture of skin pigmentation is actually a consequence of the strong selection that has acted on this phenotype. Further work on the interplay between genetic architecture and natural selection is needed to clarify these issues.

In my opinion, there is a fairly clear dependence of pigmentation with environment (exposure to solar radiation) and with geographical latitude. While disease load varied with time and social organization, natural selection for skin pigmentation has been fairly constant: it has always been "better" to possess a dark phenotype in Africa than it is in Europe or Asia.

Depigmentation of Caucasoids and Mongoloids was thus -in all likelihood- a continuous process which invariably resulted in lighter phenotypes compared to the original dark standard. This process initially involved response to reduced solar radiation, but may have been shaped at a later stage by other factors, such as ready access to vitamin D from milk products, or sexual selection for rare phenotypes that seems to have taken hold in northern Europe.

Genome Research doi:10.1101/gr.087577.108

Signals of recent positive selection in a worldwide sample of human populations

Joseph K. Pickrell et al.

Abstract

Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel. We refine the geographic distributions of known selective sweeps, and find extensive overlap between these distributions for populations in the same continental region but limited overlap between populations outside these groupings. We present several examples of previously unrecognized candidate targets of selection, including signals at a number of genes in the NRG–ERBB4 developmental pathway in non-African populations. Analysis of recently identified genes involved in complex diseases suggests that there has been selection on loci involved in susceptibility to type II diabetes. Finally, we search for local adaptation between geographically close populations, and highlight several examples.

Link

Dorothy King on Greek homosexuality

PhDiva Dorothy King has just deleted my comments (and one of her own) on her blog post, in which she states:

I love movies, but I sometimes worry that the general public gets a few odd ideas about the ancients from them.

For example in '300' the Spartans dismiss the Athenians for - and I may be paraphrasing - liking little boys. Actually ... whilst many Athenian men seem to have been bisexual, the Spartans institutionalized it as part of their military training and it played a more important role in their society. Greek 'naughty' vases with inscriptions almost all speak of the love of one man for another, and most of those great macho Greek warriors probably slept with more men than they did women given that access to women was limited.

In my response, I cited ancient sources only, yet PhDiva claims that:

I really can't be bothered to deal with 'all Greeks were heterosexual' propaganda by someone advocating using 300 as a source so have deleted a few comments.

This statement is false on two grounds: (i) I did not use "300" as a source; I contested King's criticism thereof on the basis of ancient sources, (ii) I certainly did not claim that "all Greeks were heterosexual", I contested her idea that the Spartans had institutionalized homosexuality, or that homosexuality was generally accepted by the ancient Greeks.

Here are the sources I cited, and which Ms. King has thought merited deletion. In the first one, I disputed King's presentation of homosexuality in Greek vases.

Martin F. Kilmer, Greek Erotica. London: Duckworth, 1993. Pp. xiv + 286; figs. 206. ISBN 0-7156-1519-X.

Reviewed by Keith DeVries, University Museum, University of Pennsylvania (kdevries@sas.upenn.edu).

[...]

Kilmer's deliberately narrow focus is an aspect of an overall carefulness of definition and rigor of study which produce solid results. A surprise to him was the relatively low number of male homosexual scenes of copulation: 13 to 15, as opposed to 82 heterosexual ones or, put another way, 18% of the total (using the higher figure). He had expected a stronger showing of the homosexual theme, "given the view scholarship has taken over the last century or so" (p. 173). While, as he says, "we must be cautious how we interpret this," his proportion is in line with that of a theme of red-figure vase painting he doesn't take up, the erotic pursuits by deities, which have been collected by Sophia Kaempf-Dimitriadou in her book Die Liebe der Götter in der attischen Kunst des 5. Jahrhunderts v. Chr. (1979). Of her 393 vase paintings, 14% have a male homosexual content, in the form of gods pursuing mortal adolescents. The finding also is in line with Attic comedies and the extant and known tragedies and satyr plays, where male-female sexuality is the norm, but male homoeroticism not unknown, occasionally being in fact at the dramatic center (as in Aeschylus' The Myrmidons, Euripides' Chrysippos, and presumably Sophokles' satyr play The Erastai of Achilles).

In the second, I disputed her claim of institutionalized Spartan homosexuality as part of the education system. Xenophon (5-4th c. BC writer) wrote:

This passage directly contradicts the idea of institutionalized Spartan homosexuality. So the idea about the Spartans abhorring "boy-love" is supported by the ancient sources and is not as "odd" as Ms. King apparently thinks.

King referred (in her own deleted comment) to Aelius [sic], and Plutarch, authors who postdate Xenophon by half a millennium or more. One has to wonder if Xenophon or these authors are more reliable sources about the state of Spartan society in the 5th c. BC, i.e., the setting of the "300". Would one rely on the attitudes of modern Manhattan residents towards homosexuality to infer the attitudes of early American colonists?

However, even these authors contradict her claim of a sexual nature to the mentoring relationship in Sparta. Aelian:
and Plutarch on the ancient Spartan customs:

Affectionate regard for boys of good character was permissible, but embracing them was held to be disgraceful, on the ground that the affection was for the body and not for the mind. Any man against whom complaint was made of any disgraceful embracing was deprived of all civic rights for life.

I further cited Aristotle who explicitly compared Spartans to Celts:

Again, the license of the Lacedaemonian women defeats the intention of the Spartan constitution, and is adverse to the happiness of the state. For, a husband and wife being each a part of every family, the state may be considered as about equally divided into men and women; and, therefore, in those states in which the condition of the women is bad, half the city may be regarded as having no laws. And this is what has actually happened at Sparta; the legislator wanted to make the whole state hardy and temperate, and he has carried out his intention in the case of the men, but he has neglected the women, who live in every sort of intemperance and luxury. The consequence is that in such a state wealth is too highly valued, especially if the citizen fall under the dominion of their wives, after the manner of most warlike races, except the Celts and a few others who openly approve of male loves.

If the Spartans, or indeed any substantial subset of Greeks "openly approved of male loves", then it is strange indeed that Aristotle would use the Celts as an example.

Furthermore, I cited Diodorus Siculus who makes the comparison more explicit:

The men are much keener on their own sex; they lie around on animal skins and enjoy themselves, with a lover on each side. The extraordinary thing is they haven’t the smallest regard for their personal dignity or self-respect; they offer themselves to other men without the least compunction. Furthermore, this isn’t looked down on, or regarded in any way disgraceful…

Diodorus is surprised at this proclivity. Whether or not his account is true, the passage shows that he apparently did not think that male homosexuality was neutral or even positive.

Perhaps Ms. King is better suited to writing fruit cake recipes, than to serious evidence-based discussion of ancient Greece, for which she obviously has no stomach.

PS: Or, perhaps she can write another book on Greek homosexuality, since her last one on the Elgin Marbles wasn't exactly well-received.

Variability of anatomically modern humans and Out of Africa

This paper touches on a theme I have blogged about before, namely the fact that early Africans did not form a single mating population, a subset of which filtered into Eurasia, but were rather subdivided themselves. This is evidenced by the substantial variability of the first anatomically modern humans:

Our results thus revealed that shape variability of early AMH was highest among all tested groups, i.e., within a sample of the genus Homo embracing the last 1.8 million years. The shortest connections between early AMH are either with other specimens of this group or recent modern humans, for instance, Omo 2 [recently dated to ~195 ka (1)] and LH 18, two of the earliest east African candidates for the emergence of modern human morphology (18), and the Levantine Qafzeh 6 connect with recent Australian aboriginals (cf. ref. 19). We also find a connection between 3,500-km-distant sites in the Levant and northwest Africa, i.e., between the more archaic looking Jebel Irhoud 1 and Skhul 5, whereas Jebel Irhoud 2 connects to recent Europeans. Qafzeh 9 (Levant) is linked to a European UP specimen. We find, however, no single link between Neanderthals and AMH, including Upper Paleolithic specimens.

[...]

Our data on neighbors and variability is unsupportive of the strict forms of a single-origin model but does not conflict with another approach, the model of ‘‘isolation by distance,’’ which predicts that genetic and phenotypic dissimilarity increases with geographic distance (24, 29–31). The metapopulation framework would predict the same because frequency and magnitude of genetic exchange would follow the likelihood of 2 populations to meet, which declines with geographical distance from the early AMH epicenter in Africa. Our fossil AMH data, however, suggest that before there was isolation by distance from Africa, there already existed (at least temporally) isolation by distance within Africa during the Pleistocene.

But what about the observed low genetic diversity found in humans?

Genetic diversity among living modern humans is known to be very low when compared with extant apes (32, 33). To reconcile this observation with our proposed metapopulation model within Africa, it is necessary to assume that genetic diversity of early AMH(and maybe even earlier fossil groups of Homo) must have been relatively low as well. The only fossil human group for which such genetic data are available, the Neanderthals, support this contention; their level of genetic variability also is low when compared with living apes (34, 35).

UPDATE: John Hawks discusses the paper.

PNAS doi:10.1073/pnas.0808160106

Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario

Philipp Gunz et al.

Abstract

The interpretation of genetic evidence regarding modern human origins depends, among other things, on assessments of the structure and the variation of ancient populations. Because we lack genetic data from the time when the first anatomically modern humans appeared, between 200,000 and 60,000 years ago, instead we exploit the phenotype of neurocranial geometry to compare the variation in early modern human fossils with that in other groups of fossil Homo and recent modern humans. Variation is assessed as the mean-squared Procrustes distance from the group average shape in a representation based on several hundred neurocranial landmarks and semilandmarks. We find that the early modern group has more shape variation than any other group in our sample, which covers 1.8 million years, and that they are morphologically similar to recent modern humans of diverse geographically dispersed populations but not to archaic groups. Of the currently competing models of modern human origins, some are inconsistent with these findings. Rather than a single out-of-Africa dispersal scenario, we suggest that early modern humans were already divided into different populations in Pleistocene Africa, after which there followed a complex migration pattern. Our conclusions bear implications for the inference of ancient human demography from genetic models and emphasize the importance of focusing research on those early modern humans, in particular, in Africa.

Link

Admixture analysis in Central Europeans

Polish Genetics points me to a new paper in Nature which includes an admixture analysis of Central Europeans. The supplementary data is freely available (pdf).

The IARC study of lung cancer in central Europe was conducted with cancer institutes in 6 countries including Czech Republic (Prague, Olomouc, Brno), Hungary (Borsod, Heves, Szabolcs, Szolnok, Budapest), Poland (Warsaw, Lodz), Romania (Bucharest), Russia (Moscow) and Slovakia (Banska Bystrica, Bratislava, Nitra) between 1998 and 2002.

A little random deviation from the (1,0,0) (Europe, Africa, Asia) point in the triangle plot is expected, and this is visible along the Europe->Africa axis where the presence of any level of Sub-Saharan African ancestry seems improbable. A stronger degree of deviation along the Europe->Asia axis is consistent with a small degree of East Eurasian admixture in these mainly Eastern European populations.

Nature doi:10.1038/nature06885

A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25

Rayjean J. Hung et al.

Abstract

Lung cancer is the most common cause of cancer death worldwide, with over one million cases annually1. To identify genetic factors that modify disease risk, we conducted a genome-wide association study by analysing 317,139 single-nucleotide polymorphisms in 1,989 lung cancer cases and 2,625 controls from six central European countries. We identified a locus in chromosome region 15q25 that was strongly associated with lung cancer (P = 9 times 10-10). This locus was replicated in five separate lung cancer studies comprising an additional 2,513 lung cancer cases and 4,752 controls (P = 5 times 10-20 overall), and it was found to account for 14% (attributable risk) of lung cancer cases. Statistically similar risks were observed irrespective of smoking status or propensity to smoke tobacco. The association region contains several genes, including three that encode nicotinic acetylcholine receptor subunits (CHRNA5, CHRNA3 and CHRNB4). Such subunits are expressed in neurons and other tissues, in particular alveolar epithelial cells, pulmonary neuroendocrine cells and lung cancer cell lines2, 3, and they bind to N'-nitrosonornicotine and potential lung carcinogens4. A non-synonymous variant of CHRNA5 that induces an amino acid substitution (D398N) at a highly conserved site in the second intracellular loop of the protein is among the markers with the strongest disease associations. Our results provide compelling evidence of a locus at 15q25 predisposing to lung cancer, and reinforce interest in nicotinic acetylcholine receptors as potential disease candidates and chemopreventative targets5.

Link

Ancient mtDNA of Wari and post-Wari populations from the Andes

Wikipedia on the Wari culture.

American Journal of Physical Anthropology doi:10.1002/ajpa.21037

Genetic continuity after the collapse of the Wari empire: Mitochondrial DNA profiles from Wari and post-Wari populations in the ancient Andes

Brian M. Kemp et al.

Abstract

The Wari empire flourished in the central, highland Peruvian Andes from AD 600-1000, and although the events that led to its demise are unknown, archaeological evidence indicates that Wari control waned at the end of the first millennium. Here, we test the hypothesis that, despite the major shift in social and political organization at the fall of the Wari empire, the mitochondrial DNA (mtDNA) composition of populations from the Ayacucho Basin, the former imperial heartland of the empire, remained essentially unchanged. Results show that mtDNA haplogroup frequencies among the Wari and post-Wari groups differ, but the difference is not statistically significant (2 = 5.886, df = 3, P = 0.1172). This is the first study in the Andes to use haplotypic data to evaluate the observed genetic distance between two temporally distinct prehispanic populations (FST = 0.029) against modeled expectations of four possible evolutionary scenarios. None of these simulations allowed the rejection of continuity. In total, at both the haplogroup and haplotype levels these data do not allow us to reject the hypothesis that post-Wari individuals sampled in this study are the maternal descendants of those sampled from the Wari era site of Conchopata. However, genetic homogeneity in the mitochondrial gene pool, as seen in the late prehispanic southern Andes, may also characterize our study region. But, prior to this research, this was unknown. If our new data show mtDNA homogeneity, then this could limit the detection of female migration if, in fact, it occurred. Nonetheless, the novel mtDNA data presented here currently do not support the hypothesis that there was an influx of genetically distinct females into the former Wari heartland after the Wari collapse. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc.

Link

mtDNA and mental illness

PLoS ONE doi:10.1371/journal.pone.0004913

Mitochondrial Variants in Schizophrenia, Bipolar Disorder, and Major Depressive Disorder

Brandi Rollins et al.

Abstract

Background

Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA) sequence have been reported in SZ and BD patients.

Methodology/Principal Findings

Dorsolateral prefrontal cortex (DLPFC) from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C) was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017) in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK) was significant (p = 0.004) and independent of postmortem interval time.

Conclusions

Focusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.

Link

Decline of inbreeding over time?

Genetic Future points me to a new paper which aims to show that there has been a decrease in consanguinity over the large century or so.

Such an effect may indeed be real, as higher mobility has increased opportunities for mating between individuals from distant locations. However, the paper is completely ignoring an alternative explanation which may contribute, at least in part, to the observed data.

The authors studied the genomes of individuals of different ages for runs of homozygosity (ROH), i.e., continuous regions of DNA where the two strands are identical to each other. Such regions are typical of inbred individuals, who inherit identical big chunks of genetic material from both parents -- these chunks can be traced to recent common ancestors shared by these parents.

They were able to discover that older individuals had more significant ROHs than younger ones. Ergo -according to them- older generations had more inbred individuals than more recent ones: inbreeding has decreased over time.

There is, however, one catch to this whole argument: older individuals (and they tested individuals up to 99 years of age) are not a random sample of their generations: they are the survivors, the people whose genetic makeup allowed them to reach old age.

Is there any reason to think that surviving older people are similar in terms of their ROHs to the now-dead members of their generation? Here are some relevant data:

Increase of homozygosity in centenarians revealed by a new inter-Alu PCR technique

a significant increase in homozygote genotypes frequency was observed in centenarians. These counterintuitive results suggest that increased homozygosity contributes to human longevity.

The Unusual Genetics of Human Longevity

In no species other than humans do cultural, social, and biological factors interact with each other in modulating complex phenotypes. Thus, the identification of genetic factors that affect human longevity is a true challenge. The model of centenarians provides us a unique opportunity to tackle this challenge. In this Perspective, we discuss some recent findings (the impact of geography and demography on the longevity phenotype, the relationship between longevity and homozygosity, the role of the nuclear-mitochondrial genome cross-talk) by which new ideas are suggested, such as the concept of a complex allele timing as a pivotal process in modulating the probability of achieving longevity.

Homozygosity - not always a bad thing

“Longevity seems to be linked to homozygosity,” Passarino says. This may be because certain copies of some genes boost lifespan, and carrying two of them doubles the effect. A number of DNA analyses have located regions of the genome where centenarians show an unusually high level of homozygosity, he says.

The conclusion: inbreeding may have decreased over time, but testing the homozygosity of people who are alive today is no way to demonstrate it. Direct genomic testing of people from 100 years ago seems plausible, and may disclose whether increase of autozygosity with age is due to reduced inbreeding over time, or to increased lifespan of homozygous individuals.

PLoS Genetics doi:10.1371/journal.pgen.1000415

Measures of Autozygosity in Decline: Globalization, Urbanization, and Its Implications for Medical Genetics

Michael A. Nalls et al.

Abstract

This research investigates the influence of demographic factors on human genetic sub-structure. In our discovery cohort, we show significant demographic trends for decreasing autozygosity associated with population variation in chronological age. Autozygosity, the genomic signature of consanguinity, is identifiable on a genome-wide level as extended tracts of homozygosity. We identified an average of 28.6 tracts of extended homozygosity greater than 1 Mb in length in a representative population of 809 unrelated North Americans of European descent ranging in chronological age from 19–99 years old. These homozygous tracts made up a population average of 42 Mb of the genome corresponding to 1.6% of the entire genome, with each homozygous tract an average of 1.5 Mb in length. Runs of homozygosity are steadily decreasing in size and frequency as time progresses (linear regression, p less than 0.05). We also calculated inbreeding coefficients and showed a significant trend for population-wide increasing heterozygosity outside of linkage disequilibrium. We successfully replicated these associations in a demographically similar cohort comprised of a subgroup of 477 Baltimore Longitudinal Study of Aging participants. We also constructed statistical models showing predicted declining rates of autozygosity spanning the 20th century. These predictive models suggest a 14.0% decrease in the frequency of these runs of homozygosity and a 24.3% decrease in the percent of the genome in runs of homozygosity, as well as a 30.5% decrease in excess homozygosity based on the linkage pruned inbreeding coefficients. The trend for decreasing autozygosity due to panmixia and larger effective population sizes will likely affect the frequency of rare recessive genetic diseases in the future. Autozygosity has declined, and it seems it will continue doing so.

Link

Body proportions in Neolithic Germany

Homo doi:10.1016/j.jchb.2008.05.006

Population continuity, demic diffusion and Neolithic origins in central-southern Germany: The evidence from body proportions.

Gallagher A, Gunther MM, Bruchhaus H.

Abstract

The transition to agro-pastoralism in central Europe has been framed within a dichotomy of "regional continuity" versus exogenous "demic diffusion". While substantial genetic support exists for a model of demographic diffusion from an ancestral source in the Near East, archaeological data furnish weak support for the "wave of advance" model. Nevertheless, archaeological evidence attests the widespread introduction of an exogenous "package" comprising ceramics, cereals, pulses and domesticated animals to central Europe at 5600calBCE. Body proportions are under strong climatic selection and evince remarkable stability within regional lineages. As such, they offer a viable and robust alternative to cranio-facial data in assessing hypothesised continuity and replacement with the transition to agro-pastoralism in central Europe. Humero-clavicular, brachial and crural indices in a large sample (n=75) of Linienbandkeramik (LBK), Late Neolithic and Early Bronze Age specimens from the middle Elbe-Saale-Werra valley (MESV) were compared with Eurasian and African terminal Pleistocene, European Mesolithic and geographically disparate recent human specimens. Mesolithic Europeans display considerable variation in humero-clavicular and brachial indices yet none approach the extreme "hyper-polar" morphology of LBK humans from the MESV. In contrast, Late Neolithic and Early Bronze Age peoples display elongated brachial and crural indices reminiscent of terminal Pleistocene and "tropically adapted" recent humans. These marked morphological changes likely reflect exogenous immigration during the terminal Fourth millennium cal BC. Population expansion and diffusion is a function of increased mobility and settlement dispersal concomitant with significant technological and subsistence changes in later Neolithic societies during the late fourth millennium cal BCE.

Link

Identification of two missing Romanov children

This is a different paper from the earlier one by Rogaev et al. on a similar topic.

PLoS ONE doi:10.1371/journal.pone.0004838

Mystery Solved: The Identification of the Two Missing Romanov Children Using DNA Analysis

Michael D. Coble et al.

Abstract

One of the greatest mysteries for most of the twentieth century was the fate of the Romanov family, the last Russian monarchy. Following the abdication of Tsar Nicholas II, he and his wife, Alexandra, and their five children were eventually exiled to the city of Yekaterinburg. The family, along with four loyal members of their staff, was held captive by members of the Ural Soviet. According to historical reports, in the early morning hours of July 17, 1918 the entire family along with four loyal members of their staff was executed by a firing squad. After a failed attempt to dispose of the remains in an abandoned mine shaft, the bodies were transported to an open field only a few kilometers from the mine shaft. Nine members of the group were buried in one mass grave while two of the children were buried in a separate grave. With the official discovery of the larger mass grave in 1991, and subsequent DNA testing to confirm the identities of the Tsar, the Tsarina, and three of their daughters – doubt persisted that these remains were in fact those of the Romanov family. In the summer of 2007, a group of amateur archeologists discovered a collection of remains from the second grave approximately 70 meters from the larger grave. We report forensic DNA testing on the remains discovered in 2007 using mitochondrial DNA (mtDNA), autosomal STR, and Y- STR testing. Combined with additional DNA testing of material from the 1991 grave, we have virtually irrefutable evidence that the two individuals recovered from the 2007 grave are the two missing children of the Romanov family: the Tsarevich Alexei and one of his sisters.

Link

Genetic structure in northern Europe revisited

The results of the STRUCTURE analysis are quite interesting. When Finland is included (B), it is the first one to be separated from other Northern Europeans, confirming previous results. Sweden, and to a lesser degree Denmark seems to possess some admixture with the Finnish-related (red) element. The next split (blue vs. green) differentiates continental Germnics (esp. Scandinavians, and somewhat less Dutch) from Irish-British and Australians of largely British ancestry.

When Finland is not included (C) and for K=4, it becomes obvious that the UK population includes three components ("Dutch" green, "Scandinavian" red, and "British Isles" blue).
See also a previous study on the topic.

Genome Research doi:10.1101/gr.083394.108

Geographical structure and differential natural selection amongst North European populations

Brian P McEvoy et al.

Abstract

Population structure can provide novel insight into the human past and recognizing and correcting for such stratification is a practical concern in gene mapping by many association methodologies. We investigate these patterns, primarily through principal component (PC) analysis of whole genome SNP polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, UK, Netherlands, Denmark, Sweden, Finland, Australia and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like the British Isles, and this information can then be applied to finely dissect the ancestry of the European-Australian and -American samples. They simultaneously point to the importance of considering population stratification in what might be considered a small homogenous region. There is evidence from FST based analysis of genic and non-genic SNPs that differential positive selection has operated across these populations despite their short divergence time and relatively similar geographic and environmental range. The pressure appears to have been focused on genes involved in immunity, perhaps reflecting response to infectious disease epidemic. Such an event may explain a striking selective sweep centered on the rs2508049-G allele, close to HLA-G gene on chromosome 6. Evidence of the sweep extends over 8Mb/3.5cM region. Overall the results illustrate the power of dense genotype and sample data to explore regional population variation, the events that have crafted it and their implications in both explaining disease prevalence and mapping these genes by association

Link

Y chromosome distribution in northwestern Russia

As usual, the use of the "effective mutation rate" renders the age estimates in this paper useless (they need to be divided roughly by 3).

Indeed, in this paper they attempt to use Batwing to estimate ages using the effective rate. Batwing employs a Bayesian method with coalescent simulations, and thus takes into account "population history", the effects of which are supposedly encapsulated in the effective mutation rate. Thus, they are "correcting" (inappropriately of course) for population history twice.

This is clearly evident in the Table, where the Batwing age estimates exceed significantly those based on Y-STR variance, prompting the authors to reject the Batwing results as not "credible". Not credible indeed, if one blindly picks a "mutation rate" and a piece of software from the literature and combines them to arrive at an "estimate".

The R1a1 age estimates are properly all within a Neolithic time frame. Of course, the network topologies and associated Y-STR variance argue strongly against a simple Out-of-Eastern Europe scenario of the dispersal of R1a1, as non-star topologies with very high variance are found in India and Pakistan. This parallels another recent study in which a substantial subset of Indian R1a1 Y-chromosomes appeared to be distinctive from those of Europe.

Together, with the recent work on horse domestication, these results point to the fact that there is something wrong in the equation of R1a1 "PIE-speaking Bronze Age horse riders from the Pontic-Caspian steppe". Clearly, the picture is more complex, and will only be resolved when new SNPs resolve the phylogeny of this widespread haplogroup.

Also of interest:

As older ages are observed when grouping All Asians versus All Europeans (Table 5) for N1c, the available data suggest that the mutation may have originated in northern China as previously reported,14,15 but may have traversed through a different migratory route than has been postulated elsewhere,15 reaching northeastern European populations before the Urals

European Journal of Human Genetics doi:10.1038/ejhg.2009.6

Y-Chromosome distribution within the geo-linguistic landscape of northwestern Russia

Sheyla Mirabal et al.

Abstract

Populations of northeastern Europe and the Uralic mountain range are found in close geographic proximity, but they have been subject to different demographic histories. The current study attempts to better understand the genetic paternal relationships of ethnic groups residing in these regions. We have performed high-resolution haplotyping of 236 Y-chromosomes from populations in northwestern Russia and the Uralic mountains, and compared them to relevant previously published data. Haplotype variation and age estimation analyses using 15 Y-STR loci were conducted for samples within the N1b, N1c1 and R1a1 single-nucleotide polymorphism backgrounds. Our results suggest that although most genetic relationships throughout Eurasia are dependent on geographic proximity, members of the Uralic and Slavic linguistic families and subfamilies, yield significant correlations at both levels of comparison making it difficult to denote either linguistics or geographic proximity as the basis for their genetic substrata. Expansion times for haplogroup R1a1 date approximately to 18 000 YBP, and age estimates along with Network topology of populations found at opposite poles of its range (Eastern Europe and South Asia) indicate that two separate haplotypic foci exist within this haplogroup. Data based on haplogroup N1b challenge earlier findings and suggest that the mutation may have occurred in the Uralic range rather than in Siberia and much earlier than has been proposed (12.9plusminus4.1 instead of 5.2plusminus2.7 kya). In addition, age and variance estimates for haplogroup N1c1 suggest that populations from the western Urals may have been genetically influenced by a dispersal from northeastern Europe (eg, eastern Slavs) rather than the converse.

Link

Earliest horse domestication in Kazakhstan

I had previously blogged about the Botai culture. From the news release:

The researchers have traced the origins of horse domestication back to the Botai Culture of Kazakhstan circa 5,500 years ago. This is about 1,000 years earlier than thought and about 2,000 years earlier than domestic horses are known to have been in Europe. Their findings strongly suggest that horses were originally domesticated, not just for riding, but also to provide food, including milk.

Science doi:10.1126/science.1168594

The Earliest Horse Harnessing and Milking

Alan K. Outram et al.

Abstract

Horse domestication revolutionized transport, communications, and warfare in prehistory, yet the identification of early domestication processes has been problematic. Here, we present three independent lines of evidence demonstrating domestication in the Eneolithic Botai Culture of Kazakhstan, dating to about 3500 B.C.E. Metrical analysis of horse metacarpals shows that Botai horses resemble Bronze Age domestic horses rather than Paleolithic wild horses from the same region. Pathological characteristics indicate that some Botai horses were bridled, perhaps ridden. Organic residue analysis, using ¹³C and D values of fatty acids, reveals processing of mare's milk and carcass products in ceramics, indicating a developed domestic economy encompassing secondary products.

Link

Genetic differentiation at the village level in Sardinia

The take-home lesson is that wherever gene flow is impeded, no matter how geographically close, population differentiation can be recovered with dense autosomal genotype data.

Really fine-scale ancestry analysis is now possible; I suspect that a combination of geography, religion, social class, language, and ethnic identification will be found to be predictive of a person's broad genetic makeup and vice versa. But, to discover these correlations, a large-scale collection of genotypic data is required.

PLoS ONE doi:10.1371/journal.pone.0004654

High Differentiation among Eight Villages in a Secluded Area of Sardinia Revealed by Genome-Wide High Density SNPs Analysis

Giorgio Pistis et al.

Abstract

To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates.

Link

Geographical affinities of HapMap samples

PLoS ONE doi:10.1371/journal.pone.0004684

Geographical Affinities of the HapMap Samples

Miao He et al.

Abstract

Background

The HapMap samples were collected for medical-genetic studies, but are also widely used in population-genetic and evolutionary investigations. Yet the ascertainment of the samples differs from most population-genetic studies which collect individuals who live in the same local region as their ancestors. What effects could this non-standard ascertainment have on the interpretation of HapMap results?

Methodology/Principal Findings

We compared the HapMap samples with more conventionally-ascertained samples used in population- and forensic-genetic studies, including the HGDP-CEPH panel, making use of published genome-wide autosomal SNP data and Y-STR haplotypes, as well as producing new Y-STR data. We found that the HapMap samples were representative of their broad geographical regions of ancestry according to all tests applied. The YRI and JPT were indistinguishable from independent samples of Yoruba and Japanese in all ways investigated. However, both the CHB and the CEU were distinguishable from all other HGDP-CEPH populations with autosomal markers, and both showed Y-STR similarities to unusually large numbers of populations, perhaps reflecting their admixed origins.

Conclusions/Significance

The CHB and JPT are readily distinguished from one another with both autosomal and Y-chromosomal markers, and results obtained after combining them into a single sample should be interpreted with caution. The CEU are better described as being of Western European ancestry than of Northern European ancestry as often reported. Both the CHB and CEU show subtle but detectable signs of admixture. Thus the YRI and JPT samples are well-suited to standard population-genetic studies, but the CHB and CEU less so.

Link