Clusters Galore analysis of East Africans

I have included the new data from Pagani et al. (2012) together with various other East African datasets available to me, including various East African Dodecad Project participants.

The first four PCA dimensions can be seen below:

Project participants can find their co-ordinates in the first four dimensions below:

I have also run MCLUST over the first 4 dimensions, which resulted in 12 clusters inferred:

All Project participants fall in the expected clusters, so there is no need to report any individual clustering results.

Assessing East Africans of Pagani et al. (2012) using 'weac2'

Thanks to the publication of new data from Pagani et al. (2012), we now have 235 more individuals from East Africa, mainly Ethiopians, but also Somalis and South Sudanese with dense genotype data.

Naturally, I wanted to make sure that everything was in order, so I applied the 'weac2' calculator on the new data. Here are the normalized median admixture proportions:

I have also created population portraits for the 12 different populations, which appear to show rather homogeneous samples.

Here are the descriptions of the data from the original paper:

The populations sampled (numbers) were the Semitic-speaking Amhara (26) and Tigray (21); the Cushitic-speaking Oromo (21), Ethiopian Somali (17), and Afar (12); the Omotic-speaking Ari Cultivators (24), Ari Blacksmiths (17), and Wolayta (8); and the Nilotic-speaking Gumuz (19) and Anuak (23). In addition to these groups, we also generated South Sudanese data from mixed populations (24) and Somali data from Somali populations (23).

Newer versions of the Dodecad tools will of course take into account the new samples, which ought to  help better define the "East_African" component that often arises at higher levels of detail.

And, of course kudos to all researchers who make their data publicly available and hence provide genome bloggers such as myself with much appreciated "fuel" for their inquiries.

Ethiopian origins (Pagani et al. 2012)

The study attempts to answer four questions:

Our current study is motivated by four questions. First, where do the Ethiopians stand in the African genetic landscape? Second, what is the extent of recent gene flow from outside Africa into Ethiopia, when did it occur, and is there evidence of selection effects? Third, do genomic data support a route for out-of-Africa migration of modern humans across the mouth of the Red Sea? Fourth, assuming temporal stability of current populations, what are the estimated ages of Ethiopian populations relative to other African groups?

Link to press release. Link the supplemental data.

The authors reiterate that modern humans left Africa 50-70kya, a hypothesis that seems to me pretty much dead in the light of recent archaeological evidence.

The lack of antiquity in the Ethiopian population, even in only the African component thereof argues against that population being ancestral to modern humans. Note that if the Out-of-East Africa hypothesis is correct, then skulls like Omo I represent ancestral modern humans and they are followed much later by modern humans anywhere else. So, while anatomical modernity may have emerged in East Africa --or maybe not; let's not forget that we have early modern skulls from the region in part because of the excellent preservation conditions and excess of scholarly interest-- there is no evidence that they spread from there.

I have little doubt that my own theory about substantial back-migration of Eurasians into Africa will eventually win the day. Of course, I am not referring to the recent (in the last 3,000 years) admixture with West Eurasians that the Ethiopian population has undergone, but rather to the more ancient migration that was probably associated with Y-haplogroup DE-YAP.

The fact that the African component of diverse African populations is more closely related to West than to East Eurasians is one piece of evidence among many for that scenario. Hopefully, it can be tested soon using whole genome data which may have enough density to detect much older admixture events.

UPDATE I: Since the dates in the paper are based on ROLLOFF, a piece of software that is not publicly available more than a year after its announcement, and which contradicts other software released by the same authors, I will take the Queen of Sheba stories circulated in the media with a huge grain of salt.

The American Journal of Human Genetics, 21 June 2012 doi:10.1016/j.ajhg.2012.05.015

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

Luca Pagani et al.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified “African” and “non-African” haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

Link

Ancient mtDNA from Poland

Polish Genes points me towards a doctoral thesis by a Polish researcher, which includes ancient DNA results from Poland including Roman and Medieval period samples. The thesis is in Polish, but you can probably fairly easily work through the text with the aid of Google Translate, and the data speaks for itself. Here is an unedited dump of the conclusions:

• Populations from the Roman and medieval remains in a relatively homogeneous group of European populations (with the exception of Finland and Latvia). The relatively large genetic distance between them and the population of Polish contemporary may reflect real differences at the genetic level, or may be the result of very small population of the Roman period and Middle Ages.
• The largest number of informative haplotypes from the Roman period was jointly shared with the population of contemporary Polish and Lithuania / Latvia, Sweden and Finland / Estonia. This may indicate that, in what is now Polish there is continuity of certain genetic lines, at least from the Roman period to the present, as well as close contacts of the population of the Roman period of Bałtami, Germans and Finnougryjskimi populations.
• The population of the Middle Ages shared the largest number of informative haplotypes shared with the population of modern Belarus, Ukraine and Bulgaria.
• Among the surveyed population identified haplogroup fuels such as X2, R0a or N1a, which in modern populations occur in low frequencies. Their presence in small fossil populations may be due to selection bias or a higher frequency of these haplogroups in Roman and medieval times.
• The populations of the Roman period and Middle Ages was the presence of four unique haplotypes, including one of the Przeworsk culture, belonging probably to podhaplogrupy N1a1a2. This means that Przeworsk culture of the Roman period, considered by some archaeologists as the cradle of the Slavs, could presumably be derived from the Corded Ware culture, which is associated haplotype tested.

I also reproduce the MDS plot based on haplogroup frequencies. Note that of the two ancient populations, the "left" one is the Roman-era one, and the "right" one is from medieval times.



The first dimension contrasts modern populations with LBK Neolithic inhabitants of Germany, while in the second one, there appears to be a contrast between Northeastern Europe and the rest, represented here by Germans and Balkan Slavic populations.



Ethnogenesis ot the Slavs in the light of ancient DNA analyses

Juras, Anna

For many years the origin of the Slavs has been the subject-matter in archaeology, anthropology, history, linguistics and recently also genetics. By now there is no unambiguous answer to a question where, when and in what way the Slavs originated. For the purposes of this dissertation, the analysis of ancient human mitochondrial DNA was applied. The ancient DNA was isolated from 72 specimens which came from graveyards from the area of current Poland. Mitochondrial DNA haplogroups have been assigned for 20 medieval and 23 Iron-Age specimens. The analysis of shared haplotypes and population genetic distances illustrated by multidimentional scaling has been done. The differences on genetic level and quite high genetic distances (FST) between medieval and Iron-Age populations as well as significant number of shared informative medieval haplotypes with Belarus, Ukraine and Bulgaria may evidence genetic discontinuity between medieval and Iron-Ages. From the other side, the highest number of shared informative haplotypes between Iron-Age and extant Polish population as well as the presence of subhaplogroup N1a1a2, can confirm that some genetic lines show continuatinuity at least from Iron Age or even Neolith in the areas of modern Poland. The results obtained in this work are considered to be the first ancient contribution to building the genetic history of the Slavs.

Link

Saharan dairying 7,000 years ago

Pottery shards put a date on Africa’s dairying

Yoghurt may have made it on to the menu for North Africans around 7,000 years ago, according to an analysis of pottery shards published today in Nature1.

The fermented dairy product left tell-tale traces of fat on the ceramic fragments, suggesting a way that the region’s inhabitants may have evolved to tolerate milk as adults.

The same team had previously identified the earliest evidence for dairying in potsherds nearly 9,000 years old from Anatolia2. But the findings from 7,000 years ago still predate the emergence and spread of the gene variants needed for the adult population to digest the lactose found in milk, says biomolecular archaeologist Richard Evershed of the University of Bristol, UK, who led the study with archaeological scientist Julie Dunne. He suggests that making yoghurt may have made dairy products more digestible.

Related: Earliest evidence for milk in the Near East and Southeastern Europe

Nature 486, 390–394 (21 June 2012) doi:10.1038/nature11186

First dairying in green Saharan Africa in the fifth millennium bc

Julie Dunne et al.

In the prehistoric green Sahara of Holocene North Africa—in contrast to the Neolithic of Europe and Eurasia—a reliance on cattle, sheep and goats emerged as a stable and widespread way of life, long before the first evidence for domesticated plants or settled village farming communities1, 2, 3. The remarkable rock art found widely across the region depicts cattle herding among early Saharan pastoral groups, and includes rare scenes of milking; however, these images can rarely be reliably dated4. Although the faunal evidence provides further confirmation of the importance of cattle and other domesticates5, the scarcity of cattle bones makes it impossible to ascertain herd structures via kill-off patterns, thereby precluding interpretations of whether dairying was practiced. Because pottery production begins early in northern Africa6 the potential exists to investigate diet and subsistence practices using molecular and isotopic analyses of absorbed food residues7. This approach has been successful in determining the chronology of dairying beginning in the ‘Fertile Crescent’ of the Near East and its spread across Europe8, 9, 10, 11. Here we report the first unequivocal chemical evidence, based on the δ13C and Δ13C values of the major alkanoic acids of milk fat, for the adoption of dairying practices by prehistoric Saharan African people in the fifth millennium BC. Interpretations are supported by a new database of modern ruminant animal fats collected from Africa. These findings confirm the importance of ‘lifetime products’, such as milk, in early Saharan pastoralism, and provide an evolutionary context for the emergence of lactase persistence in Africa.

Link

Evolving music

I would say that this is a good indirect argument for democracy; by pooling raters' opinions, a compromise that wasn't too horrible was arrived at. Of course, democracy won't produce Bach, but it will also not produce something as horrible as Schoenberg.

The coverage of this paper in Science NOW has sample audio.

PNAS doi: 10.1073/pnas.1203182109


Evolution of music by public choice

Robert M. MacCallum et al.

Abstract

Music evolves as composers, performers, and consumers favor some musical variants over others. To investigate the role of consumer selection, we constructed a Darwinian music engine consisting of a population of short audio loops that sexually reproduce and mutate. This population evolved for 2,513 generations under the selective influence of 6,931 consumers who rated the loops’ aesthetic qualities. We found that the loops quickly evolved into music attributable, in part, to the evolution of aesthetically pleasing chords and rhythms. Later, however, evolution slowed. Applying the Price equation, a general description of evolutionary processes, we found that this stasis was mostly attributable to a decrease in the fidelity of transmission. Our experiment shows how cultural dynamics can be explained in terms of competing evolutionary forces.

Link

Is Burushaski Indo-European?

I try to shy away from linguistic controversies, and I doubt that the idea of the Indo-European origin of Burushaski will go down without a fight. The JIES is a little behind the times when it comes to online access, so I can't quite comment on the substantive part of Prof. Casule's theory.

We'll have to wait to see how much of this is press release hype and how much is new evidence. This idea has been in circulation for a while, but if there is indeed an issue of JIES dedicated to it, it probably deserves our attention.

Here is a paper critical of the thesis. Here is a seminar abstract by Prof. Casule with some more citations.

Cracking the code on the origins of a new European language

There is strong evidence to support the discovery of a new European language.

Macquarie University historical linguistics researcher, Associate Professor Ilija Casule, discovered that the language, known as Burushaski, which is spoken by about 90,000 people who reside in a remote area of North West Pakistan, is Indo-European in origin, not Indo-Iranian.

Professor Casule’s discovery, which has now been verified by a number of the world’s top linguists, has excited linguistics experts around the world. An entire issue of the eminent international linguistics journal The Journal of Indo-European Studies is devoted to a discussion of his findings later this month.

More than 50 eminent linguists have tried over many years to determine the genetic relationship of Burushaski. But it was Casule’s painstaking research, based on a comprehensive grammatical, phonological, lexical and semantic analysis, which established that the Burushaski language is in fact an Indo-European language most likely descended from one of the ancient Balkan languages. Professor Casule believes that language is most probably ancient Phrygian.

The Phrygians migrated from Macedonia to Anatolia (today part of Turkey) and were famous for their legendary kings who figure prominently in Greek mythology such as King Midas who turned whatever he touched into gold. They later migrated further east, reaching India. Indeed, according to ancient legends of the Burushashki people, they are descendants of Alexander the Great.

Tracing the historical path of a language is no easy task. Professor Casule said he became interested in the origins of Burushaski more than 20 years ago.

“People knew of its existence but its Indo-European affiliation was overlooked and it was not analysed correctly. It is considered a language isolate – not related to any other language in the world in much the same way that the Basque language is classified as a language isolate,” he said.

The remoteness of the area that was independent until the early 1970s when it became part of Pakistan, ensured Burushaski retained certain grammatical and lexical features that led Professor Casule to conclude it is a North-Western Indo-European language, specifically of the Paleobalkanic language group and that it corresponds most closely with Phrygian.

Dr Casule’s work is groundbreaking, not only because it has implications for all the Indo-European language groups, but also provides a new model for figuring out the origins of isolate languages – where they reside in the linguistic family tree and how they developed and blended with other languages to form a new language.

Image: Map of Burushashki speaking areas

Greece stays in the Euro

Εκλογές 17ης Ιουνίου 2012

Κείμενο της ομιλίας.

Το μέλλον της Ελλάδας

Το Μέλλον της Ελλάδας

Η οικονομία μπορεί να ανακάμψει εντός της Ευρωζώνης. Επιστροφή στη δραχμή θα ήταν δημοσιονομική αυτοκτονία.

των Ν. ΟΙΚΟΝΟΜΙΔΗ, Γ. ΙΩΑΝΝΙΔΗ, Ε. ΠΕΤΡΑΚΗ, Χ. ΠΙΣΣΑΡΙΔΗ ΚΑΙ Θ. ΣΤΕΓΚΟΥ

Αυτή την Κυριακή οι Έλληνες θα προσέλθουν στις κάλπες με σύγχυση, φόβο και βιώνοντας μια τρομακτική επιδείνωση του βιοτικού τους επιπέδου. Κατά τα τελευταία δύο χρόνια, το μέγεθος της κρίσης στην Ελλάδα και την Ευρωζώνη έχει πιάσει επανειλημμένα τις χρηματοπιστωτικές αγορές απροετοίμαστες. Οι ψηφοφόροι της χώρας βρίσκονται τώρα αντιμέτωποι με ένα κρίσιμο δίλημμα που θα καθορίσει το μέλλον της Ελλάδας για πολλές γεννιές: Να μείνουν στο ευρώ ή να διαπράξουν δημοσιονομική αυτοκτονία με μια επιστροφή στην δραχμή. Η επιλογή των Ελλήνων ψηφοφόρων θα επηρεάσει σημαντικά τη μελλοντική σύνθεση της ζώνης του ευρώ και τους κανόνες που οι χώρες-μέλη της ακολουθούν.


Με μια πρώτη ματιά, υπάρχει μια εύκολη απάντηση στο δίλημμα: Παραμονή στο ευρώ- προτίμηση του 80% περίπου των Ελλήνων, σύμφωνα με τις δημοσκοπήσεις. Από δική της πρωτοβουλία και σύμφωνα με τις δεσμεύσεις της δανειακής συμφωνίας με τη ΕΕ-ΔΝΤ, η Ελλάδα έχει υποστεί σοβαρή λιτότητα για περισσότερο από δύο έτη. Ήταν σε ύφεση για πέντε έτη, ενώ κατάφερε να μειώσει δραματικά το πρωτογενές έλλειμμα του 5% το 2010 από 10,4% το 2009. Πρωτογενές πλεόνασμα βρίσκεται στον ορίζοντα.

Παρά το γεγονός ότι η Ελλάδα έχει χάσει την ανταγωνιστικότητά της σε όρους μοναδιαίου κόστους εργασίας από το πρώτο τρίμηνο του 1999, όπως και όλες οι χώρες της ευρωζώνης εκτός από τη Γερμανία και την Αυστρία, η Ελλάδα έχει υιοθετήσει σημαντική μείωση μισθών και απολαβών, και τώρα βρίσκεται στο άνω ήμισυ των χωρών της ευρωζώνης όσον αφορά την εξέλιξη της ανταγωνιστικότητας της. Κατά τα τελευταία δύο χρόνια η χώρα έχει διαγράψει σχεδόν το ένα τρίτο του χρέους της και τώρα έχει πολύ χαμηλά επιτόκια στο υπόλοιπο του χρέους της. Η μελλοντική επιτυχία της εξαρτάται από την εφαρμογή δραστικών μειώσεων των δημοσίων δαπανών, πιο αποτελεσματική συλλογή φόρων, καθώς και βελτιώσεις στην παραγωγικότητα.

Υπάρχουν τεράστιες αρνητικές επιπτώσεις από την έξοδο από το ευρώ και την εκτύπωση νέων δραχμών. Αν μια Ελληνική έξοδος από την ευρωζώνη μοιάζει σχεδόν βέβαιη μετά από τις εκλογές της Κυριακής, θα δούμε ένα πλήρη τραπεζικό πανικό. Οι ελληνικές τράπεζες θα κατέρρεαν αν η Ευρωπαϊκή Κεντρική Τράπεζα δεν λάμβανε έκτακτα μέτρα, ενδεχομένως, κατά παράβαση του καταστατικού της. Η νομισματική ισοτιμία είναι πιθανό να είναι δύο ή τρεις δραχμές για ένα ευρώ, η οποία θα διπλασιάσει ή θα τριπλασιάσει την ελληνική τιμή των εισαγόμενων προϊόντων μέσα σε λίγες ημέρες. Οι τιμές των περιουσιακών στοιχείων, συμπεριλαμβανομένης της ακίνητης περιουσίας, θα κατέρρεαν. Όσοι μετακίνησαν καταθέσεις τους στο εξωτερικό θα είναι σε θέση να αγοράσουν αυτά τα περιουσιακά στοιχεία φθηνά, γεγονός που οδηγεί σε σημαντική, οπισθοδρομική αναδιανομή του πλούτου της Ελλάδας.


Εκτός από τον πληθωρισμό την πλευρά της προσφοράς, θα υπάρξει πρόσθετος πληθωρισμός αφού η Ελλάδα θα εκτυπώσει δραχμές για να χρηματοδότησει το έλλειμά της. Τέλος, οι επιχειρήσεις δεν θα είναι σε θέση να εισαγάγουν χωρίς να πληρώσουν εκ των προτέρων με σπάνια ευρώ. Τα απαραίτητα αγαθά θα τελειώσουν σύντομα και το εμπόριο θα είναι σε στασιμότητα. Η Ελλάδα θα αναγκαστεί σε μια κρίση πολλαπλάσιας έντασης από τη σημερινή, τροφοδοτώντας περαιτέρω την κοινωνική αναταραχή.

Όμως τρεις βασικές δυνάμεις εργάζονται ενάντια στην παραμονή της Ελλάδας στη ζώνη του ευρώ. Πρώτον, οι Έλληνες ψηφοφόροι δεν είναι καλά πληροφορημένοι. Ενώ αισθάνονται την σημερινή τους ταλαιπωρία πολύ έντονα, δεν ξέρουν ή δεν κατανοούν πλήρως τις συνέπειες για τους ίδιους από την έξοδο από την ευρωζώνη. Λαϊκιστές πολιτικοί υποβαθμίζουν αυτές τις τρομερές συνέπειες.

Δεύτερον, ορισμένα ελληνικά πολιτικά κόμματα υποστηρίζουν ότι οι συνέπειες της εξόδου της Ελλάδας από την ευρωζώνη θα είναι πιο σοβαρές για την ΕΕ από ό, τι για την Ελλάδα. Προτείνουν ένα παιχνίδι της "κότας" με τη Γερμανίδα Καγκελάριο Άνγκελα Μέρκελ και απειλούν να καταργήσουν τη συμφωνία της προηγούμενης κυβέρνησης με τους δανειστές της. Αν αυτά τα κόμματα πάνε καλά την Κυριακή και οι απειλές τους γίνουν πραγματικότητα, είναι δύσκολο να δούμε τι θα μπορούσε να σταματήσει μια σχεδόν άμεση έξοδο της Ελλάδας από την ευρωζώνη.

Οι Έλληνες έχουν επίσης ταυτίσει την ευρωπαϊκή συμφωνία για το χρέος με τη λιτότητα, τις απολύσεις, και τις περικοπές στους μισθούς και τις συντάξεις, λόγω του γεγονότος ότι η ΕΕ, η ΕΚΤ και το Διεθνές Νομισματικό Ταμείο έχουν τοποθετήσει την προώθηση των αναπτυξιακών μεταρρυθμίσεων σε δεύτερη θέση, πίσω από τη δημοσιονομική εξυγίανση, όταν θέσπισαν τους όρους για την υποστήριξή τους προς την Ελλάδα.

Υποθέτοντας ότι η λογική θα επικρατήσει την Κυριακή, μια νέα ελληνική κυβέρνηση-κατά πάσα πιθανότητα ένα κυβερνητικός συνασπισμός-θα βεβαιώσει εκ νέου την προσήλωση στο ευρώ και στις υφιστάμενες δανειακές συμφωνίες για την Ελλάδα έως το τέλος του μήνα. Η Ελλάδα θα ζητήσει από την ΕΕ για να απαλύνει τα μέτρα λιτότητας της και να δεσμευτεί σε σημαντικές επενδύσεις σε υποδομές. Η ΕΕ σε αυτό το σημείο θα πρέπει ανασάνει με ανακούφιση και να συμφωνήσει και για τις δύο αιτήσεις, διότι είναι σαφές ότι η σκληρή λιτότητα από μόνη της δεν θα φέρει σταθερότητα στην Ελλάδα.

Η ΕΕ πρέπει επίσης να βοηθήσει την Ελλάδα να επιτύχει άμεσα διαρθρωτικές μεταρρυθμίσεις για να βελτιώσει ριζικά την ευκολία με την οποία οι επιχειρήσεις μπορούν να λειτουργήσουν, καθώς και για τη μείωση της φοροδιαφυγής, την εξάλειψη της διαφθοράς στις δημόσιες συμβάσεις και την φιλελευθεροποίηση των αγορών εργασίας και προϊόντων. Πρέπει να τα κάνει όλα αυτά, διασφαλίζοντας παράλληλα την εποπτεία σε όλη την Ελλάδα από τις αρχές ανταγωνισμού, τη βελτίωση της αποτελεσματικότητας του δικαστικού συστήματος και του τομέα της υγείας, και το άνοιγμα της πρόσβασης σε τεχνητά κλειστές αγορές της στον τομέα των μεταφορών, των φαρμακευτικών προϊόντων και της μηχανικής, μεταξύ άλλων.


Οι μεταρρυθμίσεις αυτές είναι απολύτως απαραίτητες για την ανάπτυξη ενός δυναμικού παραγωγικού τομέα στην Ελλάδα προσανατολισμένου στην ποιότητα και τις εξαγωγές. Η Ελλάδα θα πρέπει επίσης να επιστρέψει άμεσα στην πολιτική σταθερότητα για να μπορέσει να προσελκύσει επενδύσεις. Με τη υλοποίηση αυτών των μεταρρυθμίσεων και ένα πρωτογενές πλεόνασμα πολύ κοντά, η ελληνική οικονομία μπορεί να ανακάμψει.

Αυτές οι μεταρρυθμίσεις θα βελτιώσουν επίσης την ποιότητα της ζωής των Ελλήνων και θα είναι επωφελείς για την υπόλοιπη ζώνη του ευρώ. Αλλά όσο η Ελλάδα αφήνει την πόρτα ανοιχτή στις καταστροφικές συνέπειες της εξόδου από ευρώ, το υπόλοιπο της νομισματικής ζώνης θα πρέπει να ασχοληθεί με τη μετάδοση στην ισπανική, ιταλική και σε άλλες αγορές ομολόγων και τις τράπεζες, μέσω της άμεσης παρέμβασης από την ΕΚΤ. Όπως και στην κατάρρευση της Lehman, μπορεί να υπάρχει ένας αριθμός αγορών που θα πληγούν σοβαρά από μια έξοδο της Ελλάδας και που δεν είναι άμεσα προφανείς. Καθυστέρηση στην αντιμετώπιση αυτών των προβλημάτων, ή άρνηση ότι υπάρχουν, θα κάνει τις επιπτώσεις πιο ακριβές.

Ο κ. Οικονομίδης είναι στο New York University Stern School of Business, ο κ. Ιωαννίδης στο Tufts University, ο κ. Πετράκης στο Πανεπιστήμιο της Κρήτης, ο κ. Στέγκος στο University of Guelph, ο κ. Πισσαρίδης στο London School of Economics και κάτοχος του βραβείου Νόμπελ 2010. Οι συγγραφείς είναι όλοι καθηγητές οικονομικών.

(το παρόν δημοσιεύτηκε στην WSJ στις 14 Ιουνίου 2012 στα Αγγλικά υπό τον πρωτότυπο τίτλο The Future of Greece και μεταφράστηκε εδώ από τον Διηνέκη Ποντικό)

Bones of John the Baptist (?)

Mysterious bones may belong to John the Baptist

A small handful of bones found in an ancient church in Bulgaria may belong to John the Baptist, the biblical figure said to have baptized Jesus.

There's no way to be sure, of course, as there are no confirmed pieces of John the Baptist to compare to the fragments of bone. But the sarcophagus holding the bones was found near a second box bearing the name of St. John and his feast date (also called a holy day) of June 24. Now, new radiocarbon dating of the collagen in one of the bones pegs its age to the early first century, consistent with the New Testament and Jewish histories of John the Baptist's life.

...

The human bones in the box included a knucklebone, a tooth, part of a cranium, a rib and an ulna, or arm bone. The researchers could only date the knucklebone, because radiocarbon dating relies on organic material, and only that bone had enough collagen for a good analysis. The researchers were able to reconstruct DNA sequences from three of the bones, however, showing them to be from the same person, likely a Middle Eastern man.

There is a documentary on this to air in National Geographic UK:

He was loved by the public and feared by those in power, this revolutionary popularised a practice that ultimately became central to Christianity.

But he was not Jesus; he was John the Baptist, whose story shows how he threatened the Roman Empire to such an extent that King Herod Antipas claimed his life, supposedly before parading his head in front of his guests during a party.

There, the story ends abruptly. Or does it? Where was this famous saint buried, and what happened to his body?

Find out in the UK premiere of Head Of John The Baptist on Sunday 17 June at 8pm, as experts reveal how a rumour emerged that John the Baptist’s body was retrieved.

Any UK-based readers feel free to comment after the program has aired with any details regarding the DNA testing done on the remains.

Dating of Paleolithic art from Spain

I see absolutely no reason to hypothesize that Neandertals had anything to do with this art, given the clear evidence for an earlier presence of AMH in Europe before this time. Indeed, the latest evidence may suggest that not even all modern humans who entered Europe had highly developed art, and indeed such art is lacking in many contexts associated with modern humans outside Europe. In short, rather than hypothesize that art was a pastime of not only modern humans, but also Neandertals, we must rather accept the most plausible idea that art was a cultural innovation that began with a subset of anatomically modern humans.

Science 15 June 2012: Vol. 336 no. 6087 pp. 1409-1413 DOI: 10.1126/science.1219957

U-Series Dating of Paleolithic Art in 11 Caves in Spain

A. W. G. Pike et al.

Paleolithic cave art is an exceptional archive of early human symbolic behavior, but because obtaining reliable dates has been difficult, its chronology is still poorly understood after more than a century of study. We present uranium-series disequilibrium dates of calcite deposits overlying or underlying art found in 11 caves, including the United Nations Educational, Scientific, and Cultural Organization (UNESCO) World Heritage sites of Altamira, El Castillo, and Tito Bustillo, Spain. The results demonstrate that the tradition of decorating caves extends back at least to the Early Aurignacian period, with minimum ages of 40.8 thousand years for a red disk, 37.3 thousand years for a hand stencil, and 35.6 thousand years for a claviform-like symbol. These minimum ages reveal either that cave art was a part of the cultural repertoire of the first anatomically modern humans in Europe or that perhaps Neandertals also engaged in painting caves.

Link

Chris Stringer on the status of Homo heidelbergensis

The Natural History Museum has an overview of the status of Homo heidelbergensis, the widely accepted common ancestor of modern humans and Neandertals. This accompanies Chris Stringer's article that will soon appear in Evolutionary Anthropology. The piece from the NHM is quite instructive as it highlights the dubious attribution of the Sima de los Huesos remains to heidelbergensis; Stringer expresses doubts on both their 600ky antiquity and their taxonomic classification, preferring to assign them to early Neandertals.

There was an earlier story in the Guardian with a rather misleading title which quotes some other opinions on the controversy.

(I'll add the abstract to this paper and any further comments on it when it appears on the journal website).

UPDATE (Aug 3): Abstract added; paper is open access.

Evolutionary Anthropology Volume 21, Issue 3, pages 101–107, May/June 2012

The status of Homo heidelbergensis (Schoetensack 1908)

Chris Stringer

The species Homo heidelbergensis is central to many discussions about recent human evolution. For some workers, it was the last common ancestor for the subsequent species Homo sapiens and Homo neanderthalensis; others regard it as only a European form, giving rise to the Neanderthals. Following the impact of recent genomic studies indicating hybridization between modern humans and both Neanderthals and “Denisovans”, the status of these as separate taxa is now under discussion. Accordingly, clarifying the status of Homo heidelbergensis is fundamental to the debate about modern human origins.

Link

ESHG 2012 abstracts

I had posted some interesting titles in April, and it is finally time for us, mere mortals, to have access to the abstracts. A few of the abstracts:


Title: P10.39 - Analysis of mitochondrial DNA haplotypes of old human populations from the Bronze and Iron Age from Romania

Keywords: mitochondrial DNA; haplotypes; Bronze and Age populations

Authors: A. Rodewald1, G. Cardos2, C. Tesio3;

Abstract: Our genetic study was focused on old human populations from the Bronze and Iron Ages from Romania in order to analysed their genetic variation and their genetic kinship al mitochondrial DNA(mtDNA)level with today´s Romanian populations and other modern European populations. The ancient DNA(aDNA)was extracted from skeletal remains of 50 individuals from the Bronze and Iron Age by a phenol-chloroform DNA extraction method.MtDNA HVR I and HVR II regions were amplified by PCR and sequenced by the dideoxy chain terminator method.The aDNA data were analysed in comparison with corresponding mtDNA data of modern Romanian people and other 11 European populations.The ancient mtDNA haplotypes were framed into 12 haplogroups. The most frequent mtDNA haplotype identified in the old individual sample from Romania was the CRS-like, and the most frequent haplogroup was H. Significant differences in haplogroup frequencies between the old people and modern Romanians were found. Low values of internal standard genetic diversity indices suggested reduced genetic variability within old human populations from the Bronze and Iron Age from Romania, in contrast to all modern European populations and also modern Romanians, which showed higher mitochondrial haplogroup diversity values. This fact might be the result of social and cultural local organization in small tribes, partially reproductively isolated. Concerning the genetic relationships at mitochondrial level, old human populations from Romania have shown closer genetic relationship to Turks of Thracian origin,while modern Romanians were closer to modern Bulgarian, Italian, Greek and Spanish populations.

The relationship between prehistoric Romanian mtDNA and modern Thracian Turkish one is not very surprising, given that the latter are basically descended from populations of indigenous origin that converted to Islam during the Ottoman era. It will be worthwhile to see exactly which locations/communities were used to sample from. It is awesome that we are beginning to get ancient DNA data from southeastern Europe.



Title: P10.40 - Complete mitochondrial DNA diversity in Iranians
Keywords: Mitochondrial DNA; population; Iran
Authors: A. Bahmanimehr1, M. Derenko2, B. Malyarchuk2, G. Denisova2, M. Perkova2, S. Farjadian3, L. Yepiskoposyan1;

Abstract: The complete sequencing of mitochondrial DNA has contributed a great deal to the understanding of the timing and direction of human dispersals around the world. To elucidate the early stages of human colonization process outside of Africa and to investigate the demographic history of human populations from the Middle East we have completely sequenced the mtDNAs of 275 Iranians represented by Persians (N=105), Mazandaranians (N=4), Azerbaijanians (N=22), Kurds (N=5), Lurs (N=5), Armenians (N=10), Bakhtiarians (N=2), Gilakis (N=2), Indians (N=1), Turkmens (N=10), and Qashqais (N=109). Overall diversity is very high, with 252 different sequences falling into 75 major haplogroups within macrohaplogroups L, N and M. The majority of Iranian mtDNAs (90.9%) belongs to Western Eurasian component composed of haplogroups N1, N2, X, R2’JT, U, and R0, though the impact of African (L2a, L3d, L3f), Southern Asian (R8, M4, M5, M18, M42), and Eastern Eurasian (A4, B4, C4, C5, D4, F1, G2a) lineages is also perceptible being found at frequencies of 1.5%, 2.5%, and 5.1%, respectively. Results of molecular dating of Iranian mtDNA lineages show that macrohaplogroup N and its haplogroups N1, R, U, R2’JT coalesce to the time of 45-60 kya, marking the first stages of modern humans movement out of Africa. The ancient ancestry of Iranian gene pool is also confirmed by revealing of the unique N23 lineage survived both in Persians and Qashqais, albeit at low frequencies. This study was supported by Russian Foundation for Basic Research (11-04-00620) and by Far-East Branch of the Russian Academy of Sciences (12-III-A-06-101).

Title: P10.58 - A Y -chromosome portrait of modern Bulgarians as viewed from different spatiotemporal aspects
Keywords: Y chromosome; Bulgarians; haplogroup
Authors: S. Karachanak1,2, V. Grugni2, D. Nesheva1, N. Al-Zahery2, V. Battaglia2, C. Nici2, V. Carossa2, Y. Yordanov3, A. Torroni2, A. S. Galabov4, O. Semino2,5, D. Toncheva1,5;

Abstract: To address the structure and evolution of the Bulgarian paternal gene pool, we have examined the Y chromosome variation in 809 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within certain haplogroups. The biallelic markers were analyzed by PCR/RFLP and PCR/DHPLC assay. Seventeen fast-evolving Y-STRs were amplified using the multiplex AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems) and were read on ABI 310 genetic analyzer with GeneMapper software.We found that the Bulgarian Y chromosome gene pool is primarily contained within haplogroups common in Europe and surrounding areas. Furthermore, when patrilineal relationships are visualized in a broader context by principal component analysis, Bulgarians are located among European populations. The analysis of molecular variance shows that the genetic variation within the country is structured among Western, Central and Eastern Bulgaria, rather than among the Black Sea coast, the Danubian Plane, Thrace and the Southwest mountainous region; which indicates that the Balkan Mountains have been permeable to human movements.
Y-STR variation ages and median joining networks of haplogroups E-V13, J-M241, R-M458, R-L23 and I-M423 were calculated together with data from other populations. For this purpose, the analyses of STR variation within haplogroups were based on 8 STR loci, with the exception of haplogroup R-M458, for which the STR profiles were further reduced to 7 loci. In general, the Y-STR data reveal that different prehistoric and historic events have left detectable traces in the Bulgarian Y chromosome gene pool.

This is quite welcome, as Bulgaria has been a bit of a "black hole" in population genetics. Finally having an authoritative sample on its Y-chromosome composition is extremely important.


Title: P10.45 - Population isolates from Greece offer potential for powerful disease gene mapping: the HELIC-Pomak and MANOLIS studies
Keywords: population isolate; genetic association; rare variants
Authors: I. Tachmazidou1, A. Farmaki2, L. Southam1, K. Palin1, N. W. Rayner1,3, E. Daoutidou2, I. Ntalla2, K. Panoutsopoulou1, G. Dedousis2, E. Zeggini1;

Abstract: The study of low-frequency and rare variants can be empowered by focusing on isolated populations, in which rare variants may have increased in frequency and linkage disequilibrium tends to be extended. Sequencing is efficient in isolates, because variants are shared in extended haplotype contexts, supporting accurate imputation. Here we assess sample sets collected from two Greek populations: the Pomak villages are a set of religiously-isolated mountainous villages in the North (population size 11,000); Anogia is a mountainous village on Crete, with high levels of longevity (population size 4,000). 747 and 1118 individuals respectively were typed on the Illumina OmniExpress platform. We calculated genome-wide IBS statistics to assess the degree of relatedness and compared it with the general Greek population (707 samples with OmniExpress data, TEENAGE study). We additionally calculated the proportion of individuals with at least one “surrogate parent” as a means for accurate long-range haplotype phasing and imputation, as proposed by Kong et al, Nature Genetics 2008. We find 1-1.4% of individual pairs with pi-hat>0.05, and ~0.4% with pi-hat>0.1 in the isolates compared to 0% in the general Greek population. We also find that ~80%-82% of subjects have at least one surrogate parent in the isolates, compared to ~1% in the outbred Greek population. We have established the HELIC-Pomak and MANOLIS cohorts as genetic isolates and are currently whole-genome sequencing 250 individuals to enable imputation and subsequent association testing. This approach has the potential to identify novel robust associations with disease-related complex traits.

It will be wonderful if some of these population samples become publicly available.

Geographic orientation and cultural homogeneity

Excellent coverage of this article at Nature News:

The researchers found that if a country had a greater east–west axis than a north–south one, the less likely it was for its indigenous languages to persist. The relationship isn't straightforward, but the model suggests that Mongolia, which is about twice as wide as it is tall, would have 5% fewer indigenous languages than Angola, which is roughly square. Meanwhile, Peru — about twice as tall as it is wide — would be predicted to have 5% more persistent languages than Angola. The result, say the authors, supports Diamond's theory because it indicates that east–west countries have more homogeneous cultures.

PNAS doi: 10.1073/pnas.1205338109

Geographic axes and the persistence of cultural diversity

David D. Laitin et al.

Jared Diamond’s Guns, Germs, and Steel [Diamond J, (1997) Guns, Germs, and Steel (WW Norton, NY)] has provided a scientific foundation for answering basic questions, such as why Eurasians colonized the global South and not the other way around, and why there is so much variance in economic development across the globe. Diamond’s explanatory variables are: (i) the susceptibility of local wild plants to be developed for self-sufficient agriculture; (ii) the domesticability of large wild animals for food, transport, and agricultural production; and (iii) the relative lengths of the axes of continents with implications for the spread of human populations and technologies. This third “continental axis” thesis is the most difficult of Diamond’s several explanatory factors to test, given that the number of continents are too few for statistical analysis. This article provides a test of one observable implication of this thesis, namely that linguistic diversity should be more persistent to the degree that a geographic area is oriented more north-south than east-west. Using both modern states and artificial geographic entities as the units of analysis, the results provide significant confirmation of the relationship between geographic orientation and cultural homogenization. Beyond providing empirical support for one observable implication of the continental axis theory, these results have important implications for understanding the roots of cultural diversity, which is an important determinant of economic growth, public goods provision, local violence, and social trust.

Link

Assessing Neolithic Europeans with 'weac2'

I have used the West Eurasian cline calculator 'weac2' to assess the Tyrolean Iceman and Neolithic Swedes. The admixture proportions can be seen below, and appear largely consistent with all previous analyses of the same individuals:

It is interesting that Gok4, the Swedish Megalithic TRB female belongs to the Atlantic_Baltic and Near_East components, while the two major Y-chromosome haplogroups associated with West European Neolithic sites so far are I2a1 and G2a (Treilles and Dolmen of La Pierre Fritte) whose distribution very well parallels these two components: Atlantic_Baltic/I2a1 in Europe, and Near_East/G2a in the Near East.

The simplest explanation, based on the available evidence, is that the Neolithic populations of Europe were descended from G2a-bearing pioneers entering Europe from the southeast, and encountering an I2a1-bearing population of pre-farmers in Europe itself. The high frequency of I2a1 in Sardinia, as well as the presence of G2a in that population serves to underscore the substantial genetic continuity between ancient Neolithic Europeans and modern Sardinians.

The absence of the South_Asian component in 'weac2' in all of these individuals is also important. This component captures ancestry (both Caucasoid and Ancestral South Indian) from further east and south, where both G2a/I2a1 are quite rare. As I have noted before, both Europe and South Asia have been affected in late/post-Neolithic times by migrations from West Asia.

It is tempting to associate this population movement with the spread of Indo-European languages, and we can only eagerly await more autosomal ancient DNA samples that will reveal the arrival of the "missing components" over the Neolithic substratum.