September 30, 2012

Armenians as Phrygian colonists, or, rolloff analysis of Armenians as a mixture of Sardinians+Balochi

I analyze the Yunusbayev et al. Armenians_Y sample in a similar manner as the South Indian Brahmins. The 30 lowest f3 statistics are:

Sardinian Velamas_M Armenians_15_Y -0.00349 0.000264 -13.23 239451
Sardinian Piramalai_Kallars_M Armenians_15_Y -0.003213 0.00028 -11.484 239389
Sardinian GIH30 Armenians_15_Y -0.002983 0.00023 -12.986 241310
Balochi Sardinian Armenians_15_Y -0.002837 0.000193 -14.681 241698
Sardinian Sindhi Armenians_15_Y -0.002794 0.000203 -13.757 241928
Sardinian Muslim_M Armenians_15_Y -0.002761 0.000295 -9.351 238639
Indian_D Sardinian Armenians_15_Y -0.002743 0.000224 -12.226 241916
Sardinian Kanjars_M Armenians_15_Y -0.002727 0.000281 -9.722 239240
Iyer_D Sardinian Armenians_15_Y -0.002718 0.000263 -10.322 238943
Brahui Sardinian Armenians_15_Y -0.002715 0.000196 -13.882 241885
Sardinian Dusadh_M Armenians_15_Y -0.002666 0.000281 -9.502 238994
Sardinian INS30 Armenians_15_Y -0.00265 0.000237 -11.162 240965
Iyengar_D Sardinian Armenians_15_Y -0.002624 0.000297 -8.847 238564
Sardinian Dharkars_M Armenians_15_Y -0.002501 0.000267 -9.359 239505
Sardinian North_Kannadi Armenians_15_Y -0.002463 0.000288 -8.545 239278
Sardinian Chamar_M Armenians_15_Y -0.002445 0.000275 -8.904 240102
Sardinian Kshatriya_M Armenians_15_Y -0.002372 0.000267 -8.897 239047
Pathan Sardinian Armenians_15_Y -0.00224 0.000199 -11.264 241759
Sardinian Brahmins_from_Uttar_Pradesh_M Armenians_15_Y -0.002189 0.00025 -8.774 239395
Jatt_D Sardinian Armenians_15_Y -0.001806 0.000273 -6.608 238465
Cypriots Kanjars_M Armenians_15_Y -0.001699 0.00026 -6.547 238237
Cypriots Velamas_M Armenians_15_Y -0.001642 0.000275 -5.965 238392
Cypriots Muslim_M Armenians_15_Y -0.001618 0.000279 -5.798 237762
Cypriots Dusadh_M Armenians_15_Y -0.001611 0.000279 -5.779 238096
GIH30 Cypriots Armenians_15_Y -0.001608 0.000223 -7.216 239819
Iyer_D Cypriots Armenians_15_Y -0.001562 0.000251 -6.217 238012
Sindhi Cypriots Armenians_15_Y -0.001544 0.000209 -7.383 240276
Cypriots North_Kannadi Armenians_15_Y -0.001464 0.000276 -5.298 238273
Cypriots Kshatriya_M Armenians_15_Y -0.001438 0.00026 -5.534 238076

I carried out rolloff analysis using the Balochi and Sardinians as references, for a total of 510,844 SNPs. Note that the Burusho were not used in this experiment, because they were culled due to more than 5% East Eurasian admixture, as per the followed procedure

The Balochi are very similar to the Burusho otherwise, and this also gives me the opportunity to see a Sardinian+Balochi population pair to complement a previous analysis of French as Sardinian+Burusho, which presented an f3 signal of quite similar intensity. The exponential fit is seen below.

The jackknife gives an age estimate of 113.194 +/- 14.674 generations, or 3,280 +/- 430 years, assuming a generation length of 29 years.

I had somewhat expected the Armenians to show a more recent signal of admixture than the French, as they lived much closer to the boundary of Europe and Asia, and may have had more opportunity to admix between Sardinian-like populations of Europe and "West Asian"-like populations of Asia.

But, the inferred date also raises another possibility. Herodotus says of the Armenians who were part of the army of King Xerxes:
the Armenians were equipped like Phrygians, being Phrygian colonists" (7.73)
Now, the Phrygians became masters of Central Anatolia during the tumultuous events near the end of the Bronze Age (12th century BC), following the collapse of the Hittite Empire. And, their ancestral homeland was in Thrace. And, there is fairly good evidence that Armenian is the closest language related to Greek within the Indo-European language family. And, we have some tantalising evidence that even during the Iron Age, the population of Thrace was Sardinian-like. And, the Armenians do contrast with their Caucasian neighbors in possessing ~10% of the Sardinian-like Atlantic_Med component that South and Northeast Caucasians lack.

All of the above combine to make a pretty compelling story. Could it be that Armenians preserve a legacy of admixture between a linguistically Indo-European speaking, genetically Sardinian-like population, which arrived in Asia Minor from the Balkans at the end of the Bronze Age, finally settling in the Armenian Highlands, and mixing with the local people they encountered?

The plot thickens. And, this is, certainly, a question that can be answered by ancient DNA research, e.g., by comparing the genomes of historical Phrygians and Armenians with those from Hittite-era, or earlier Anatolians.

The rise and wane of the cremation ritual

A thought occurred to me recently as I was reading about the Urnfield culture and the two components of the Andronovo horizon, the Alakul and Fedorovo cultures which contrasted in their practice of cremation vs. inhumation. It seems that the cremation ritual rose to prominence during the Bronze Age and then largely waned during the Iron Age.

Of course, this did not occur everywhere, not was it an entirely linear process. For example, most of the patrician Roman gentes practiced cremation into historical times. The Greeks, on the other hand, who mostly practiced inhumation during the Bronze Age, seem to have adopted cremation during the Dark Age, and this was the custom immortalized by Homer. Of the Indo-Iranians, one branch leading to the modern Hindus adopted a cremation ritual, while another, leading to the Zoroastrian Persians adopted the well-known exposure ritual.

But, nonetheless, it is a fact that the cremation burial first rose to prominence during the Bronze Age, and this requires an explanation.

I don't know whether this hypothesis has been advanced before, but it seems to me that the most practical reason for the cremation burial is to facilitate transportation of remains.

In modern times, the desire to be buried in familiar surroundings is often strong, and people are often buried in a different place than where they die. Of course, thanks to technological advanced related to preservation and transportation, this is often practical. But, this would not have been so in the past: cremation may have been devised as a way to dispose of the dead and carry their remains.

I have argued before that a sort of "globalization" took place during the Bronze Age, as extensive networks associated with metallurgy, combining prospecting, mining, metalworking, distribution, and security were formed. The non-local nature of these natures was driven by the need to co-ordinate a range of activities that took place in geographically distant areas: sources of ore needed to be identified and mined; metal needed to be worked on by talented experts who could fashion it into useful instruments of high added value; the end products had to be protected (because of their high value) and transported to areas where it would be in demand.

In the context of this theory, the rise of the cremation burial makes sense. In Paleolithic times, there was no concept of "home", as humans lived nomadic lives, endlessly driven away in search of resources. In Neolithic times, a strong concept of "home" emerged, as humans were tied to their crops and domesticated animals, and to the dwellings they had created. And, indeed, people were literally buried under their homes in the earliest Neoltihic.

The revolution of the Metal Age was the rise of mobility. This was facilitated by advanced in transportation technology associated with wheeled vehicles, and was driven by the trade in metal objects and other specialized, high-value items. The segment of the population involved in this business formed the elite, because of their access to weaponry and wealth, and these elites were intrinsically mobile for the reasons enumerated above. They, like other Neolithic peoples, had inherited a "love of home" and were territorial, but their way of life demanded that they live and fight away from "home".

Hence, the rise of the cremation ritual, which was then copied by others, due to its association with the elite, as well as its signalling effect, because a proper full cremation requires a large quantity of wood and is expensive to prepare and carry out. The intensification of warfare during the Bronze Age may have been an additional factor in the rise of the cremation ritual, because it is a convenient way to dispose of the dead at a battle site, or away from an established cemetery.

My hypothesis may not capture all the complexities of the phenomenon, but I think that a utilitarian origin of the ritual, which later assumed ideological, social, or religious connotations may make good sense of at least the origins of the practice at a wide level during the Bronze Age.

An obvious downside of the cremation ritual is its almost certain detrimental consequences for the preservation of ancient DNA. As more DNA evidence from the prehistoric past continues to accumulate, it is useful to remember that part of the puzzle may have been irretrievably lost, although I suspect that the transience of the practice in many parts of the world and its co-existence with inhumation in others may have left us with enough evidence to work out the larger picture.

September 29, 2012

More on the surprising link between Africans and Denisovans

In a previous post, I showed that there is an unexpected link between Africans and Denisovans. Papuans appeared more "Denisovan" than other populations irrespective of SNP subset used, but Africans appeared more "Denisovan" than Eurasians for both a subset of SNPs polymorphic in Eurasians and monomorphic in Africans, as well as a subset of SNPs polymorphic in all 5 major populations.

In the current post, I explore this issue further by using the SNP ascertainment panels released by Patterson et al. (2012). In particular, I use panel #3, which involves 48,531 SNPs ascertained in a Papuan individual.

 MbutiPygmy French ; Denisova Chimp 0.0234 2.597

 Yoruba French ; Denisova Chimp 0.0303 3.970
 San French ; Denisova Chimp 0.0334 3.475
 BantuKenya French ; Denisova Chimp 0.0206 2.625
 MbutiPygmy Sardinian ; Denisova Chimp 0.0224 2.413
 Yoruba Sardinian ; Denisova Chimp 0.0293 3.683
 San Sardinian ; Denisova Chimp 0.0324 3.319
 BantuKenya Sardinian ; Denisova Chimp 0.0196 2.399
 MbutiPygmy Dai ; Denisova Chimp 0.0331 3.347
 Yoruba Dai ; Denisova Chimp 0.0401 4.694
 San Dai ; Denisova Chimp 0.0428 4.265
 BantuKenya Dai ; Denisova Chimp 0.0307 3.524
 MbutiPygmy Japanese ; Denisova Chimp 0.0366 3.833
 Yoruba Japanese ; Denisova Chimp 0.0436 5.256
 San Japanese ; Denisova Chimp 0.0463 4.724
 BantuKenya Japanese ; Denisova Chimp 0.0342 4.070
 MbutiPygmy Karitiana ; Denisova Chimp 0.0187 1.611
 Yoruba Karitiana ; Denisova Chimp 0.0252 2.320
 San Karitiana ; Denisova Chimp 0.0287 2.457
 BantuKenya Karitiana ; Denisova Chimp 0.0158 1.461
 MbutiPygmy Surui ; Denisova Chimp 0.0303 2.486
 Yoruba Surui ; Denisova Chimp 0.0368 3.260
 San Surui ; Denisova Chimp 0.0398 3.265
 BantuKenya Surui ; Denisova Chimp 0.0275 2.429

All of these are positive, and many of them are significant with a Z-score greater than 3. Africans appear more "Denisovan" than West/East Eurasians and Amerindians using this panel. So, perhaps, this is another indication of the "surprising link" I discovered in my previous post.

This link may have been overlooked in previous analyses which found that Africans are less Denisovan than all Eurasian groups. But, as I argue in my previous post, this is potentially due to introgression of archaic African alleles into living Sub-Saharan Africans which shifted them away from Denisovans. So, the African story may involve admixture between a population somehow related to Denisovans (whether due to an early Out-of-Africa that affected them, or due to an Into-Africa event), and divergent native Palaeoafrican populations.

It would be worthwhile to follow up on these observations using the high-quality Denisovan genome recently published, to see how they might hold up.

rolloff analysis of South Indian Brahmins

Populations with 5+ individuals and which belonged no more than 5% in African or East Eurasian components at K=7 were retained. South Indian Brahmins were combined from the Iyer_D and Iyengar_D datasets of the Dodecad Project. Other populations were from the current version of the Old World dataset used for the K7b/K12b calculators.

The lowest f3 statistics were the following:

English_D North_Kannadi South_Indian_Brahmin -0.006119 0.000339 -18.06 236533
North_Kannadi Orkney_1KG South_Indian_Brahmin -0.005987 0.000311 -19.223 237162
Irish_D North_Kannadi South_Indian_Brahmin -0.005958 0.000317 -18.817 237023
British_Isles_D Chamar_M South_Indian_Brahmin -0.005931 0.000334 -17.757 237112
Dutch_D North_Kannadi South_Indian_Brahmin -0.005914 0.00034 -17.416 236008
British_Isles_D North_Kannadi South_Indian_Brahmin -0.005914 0.000342 -17.273 236064
North_Kannadi Baleares_1KG South_Indian_Brahmin -0.005878 0.000367 -16.012 235743
German_D North_Kannadi South_Indian_Brahmin -0.005838 0.000306 -19.048 237156
Georgian_D North_Kannadi South_Indian_Brahmin -0.005827 0.000366 -15.924 235091
CEU30 North_Kannadi South_Indian_Brahmin -0.005818 0.000315 -18.461 237266
Greek_D North_Kannadi South_Indian_Brahmin -0.005812 0.000314 -18.527 237028
Orcadian North_Kannadi South_Indian_Brahmin -0.005807 0.000329 -17.649 236669
Austrian_D North_Kannadi South_Indian_Brahmin -0.005803 0.000371 -15.659 235187
North_Kannadi Pais_Vasco_1KG South_Indian_Brahmin -0.005796 0.000337 -17.193 235754
British_D North_Kannadi South_Indian_Brahmin -0.005794 0.000336 -17.243 236613
Mixed_Germanic_D North_Kannadi South_Indian_Brahmin -0.005778 0.000344 -16.794 236047
French North_Kannadi South_Indian_Brahmin -0.005773 0.000312 -18.493 237461
North_Kannadi Cornwall_1KG South_Indian_Brahmin -0.00577 0.000306 -18.846 237375
Armenians Chamar_M South_Indian_Brahmin -0.005759 0.000279 -20.674 238398
Orkney_1KG Chamar_M South_Indian_Brahmin -0.005757 0.000287 -20.042 238463
Hungarians North_Kannadi South_Indian_Brahmin -0.005756 0.000311 -18.482 237196
Serb_D North_Kannadi South_Indian_Brahmin -0.005751 0.000371 -15.499 235625
Iraq_Jews Chamar_M South_Indian_Brahmin -0.005742 0.000303 -18.968 237341
Greek_D Chamar_M South_Indian_Brahmin -0.005736 0.000293 -19.57 238374
North_Kannadi Aragon_1KG South_Indian_Brahmin -0.005733 0.000347 -16.526 235610
Armenians_15_Y Chamar_M South_Indian_Brahmin -0.005723 0.000293 -19.5 237884
German_D Chamar_M South_Indian_Brahmin -0.005719 0.000294 -19.483 238514
Orcadian Chamar_M South_Indian_Brahmin -0.005701 0.000305 -18.707 237880
French_Basque North_Kannadi South_Indian_Brahmin -0.005698 0.000333 -17.104 237119

Links between Western Europe and South Asia have turned up in many of the Project's analyses (e.g., the West European in Dodecad v3, or the Gedrosia component in K12b, or even earlier the "Dagestan" component in both West Europe and South Asia). 

Of course, we don't have to imagine a migration all the way from the the British Isles to South Asia, anymore than we may imagine a migration from South America to Europe to explain the strong negative f3(European; Karitiana, Sardinian) signals previously detected. I don't know what to make of this tendency to minimize f3 for the "longest possible clines". 

In any case, I carried out rolloff analysis using Orcadians and North_Kannadi. This is not the strongest signal, but it is very close to it, and also has the twin advantages of involving public data (so the analysis can be repeated) and a large number of SNPs, which were 466,644 in total. The fit can be seen below:

This appears to be excellent visually. The inferred date from the jackknife is 110.155 +/- 11.345 generations, or 3,190 +/- 330 years, assuming as always a generation length of 29 years.

The obvious candidate for this admixture signal is of course the arrival of the Indo-Aryans into South Asia. 

September 28, 2012

La Bastida, Bronze Age Iberian fortified site

From a website dedicated to it:

La Bastida (Totana, Murcia) is one of the most important archaeological sites of Prehistory in Europe. It was inhabited about 4000 years ago in the Bronze Age, and it has a great potential to understand our past and the heritage and cultural projection of Murcia Region. 
The archaeological site is located in the Sierra Tercia, on a steep hill at  confluence of the Rambla de Lebor and Salado Cliff around 6 km west of Totana town. The four hectares of surface make it one of the most extensive sites and it can only be compared to the one that occupied the present town of Lorca.

The Argaric society was a milestone of  sedentary life, urbanism, metallurgy and political and economic inequalities. La Bastida offers a unique and exceptional opportunity to understand this key stage of our past.
From a recent press release:

La Bastida unearths 4,200-year-old fortification, unique in continental Europe 
Similar characteristics have not been observed in other constructions of the Bronze Age, with three-metre thick walls, square towers originally measuring up to seven metres, a monumental entrance and an ogival arched postern gate; a fully conserved architectural element unique in Europe in that period. 
The wall protected a city measuring 4 hectares located on top of a hill. With architectural elements reminiscent of people with Eastern styled military skills, its model is typical of ancient civilisations of the Mediterranean, such as the second city of Troy. 
One of the most relevant architectural elements discovered is the ogival arched postern gate, or secondary door, located near the main entrance. The arch is in very good conditions and is the first one to be found in Prehistoric Europe. Precedents can be found in the second city of Troy (Turkey) and in the urban world of the Middle East (Palestine, Israel and Jordan), influenced by the civilisations of Mesopotamia and Egypt. This indicates that people from the East participated in the construction of the fortification. These people would have reached La Bastida after the crisis which devastated their region 4,300 years ago. It was not until some 400 to 800 years later that civilisations like the Hittites and Mycenaeans, or city-states such as Ugarit, incorporated these innovative methods into their military architecture.

Related: 4.2 kiloyear event, and El Argar.

September 27, 2012

A surprising link between Africans and Denisovans

I took the following populations from the version of the HGDP released by Patterson et al. (2012). I use the _AHOA suffix (Affymetrix Human Origins Array) to distinguish them from other versions of the same populations:
  • MbutiPygmy_AHOA 11
  • Italian_AHOA    11
  • Miao_AHOA       10
  • Papuan_AHOA     12
  • Karitiana_AHOA  8
I identified the following SNP subsets:
  • AFRICA: 67022 SNPs that were polymorphic in MbutiPygmy and monomorphic in the other populations
  • EURASIA: 94858 SNPs that were polymorphic in at least one non-African population and monomorphic in MbutiPygmy
  • AFRICA_EURASIA: 367051 SNPs that were polymorphic in both MbutiPygmy and at least one non-African population
  • ALL: 528931 SNPs that were polymorphic in at least one population
  • GLOBAL: 168640 SNPs that were polymorphic in all 5 populations
Note that the union of AFRICA, EURASIA, and AFRICA_EURASIA is the ALL set.

Here is a Venn diagram of SNP sharing:

I then calculated all D-statistics of the following form:

D(Pop1, Pop2; Archaic, Chimp)

where Archaic is either Neandertal or Denisova, and Pop1, Pop2 is any possible pair of the modern populations. These D-statistics were calculated for all 5 SNP subsets.

Below, you can find all D-statistics, followed by their Z-scores

Italian_AHOA MbutiPygmy_AHOA Neander_AHOA Chimp_AHOA 0.3357 0.1231 0.0038 0.0297 -0.0041 19.575 6.041 1.099 8.052 -0.882
Italian_AHOA Miao_AHOA Neander_AHOA Chimp_AHOA 0 -0.0393 -9e-04 -0.0044 8e-04 0 -3.271 -0.251 -1.161 0.184
Italian_AHOA Karitiana_AHOA Neander_AHOA Chimp_AHOA 0 -0.0243 3e-04 -0.0019 0.0067 0 -1.765 0.063 -0.43 1.406
Italian_AHOA Papuan_AHOA Neander_AHOA Chimp_AHOA 0 -0.0348 -0.0088 -0.0113 -0.0017 0 -2.212 -2.027 -2.335 -0.341
MbutiPygmy_AHOA Miao_AHOA Neander_AHOA Chimp_AHOA -0.3357 -0.1646 -0.0046 -0.0331 0.0048 -19.575 -7.399 -1.208 -7.949 0.998
MbutiPygmy_AHOA Karitiana_AHOA Neander_AHOA Chimp_AHOA -0.3357 -0.147 -0.0036 -0.0311 0.0104 -19.575 -6.089 -0.821 -6.852 2.013
MbutiPygmy_AHOA Papuan_AHOA Neander_AHOA Chimp_AHOA -0.3357 -0.1467 -0.0114 -0.0387 0.0024 -19.575 -6.381 -2.661 -7.947 0.45
Miao_AHOA Karitiana_AHOA Neander_AHOA Chimp_AHOA 0 0.0165 0.0013 0.0027 0.0061 0 1.263 0.296 0.63 1.291
Miao_AHOA Papuan_AHOA Neander_AHOA Chimp_AHOA 0 8e-04 -0.0083 -0.0074 -0.0025 0 0.05 -1.987 -1.631 -0.532
Karitiana_AHOA Papuan_AHOA Neander_AHOA Chimp_AHOA 0 -0.0136 -0.0094 -0.0099 -0.0083 0 -0.804 -1.861 -1.853 -1.568
Italian_AHOA MbutiPygmy_AHOA Denisova_AHOA Chimp_AHOA 0.2354 -0.1057 -0.0102 -0.0014 -0.0147 13.01 -5.396 -2.806 -0.378 -3.156
Italian_AHOA Miao_AHOA Denisova_AHOA Chimp_AHOA 0 -0.0131 0.0023 0.0012 0.0058 0 -1.193 0.713 0.369 1.452
Italian_AHOA Karitiana_AHOA Denisova_AHOA Chimp_AHOA 0 -0.0046 -0.0024 -0.0025 -0.0012 0 -0.364 -0.563 -0.623 -0.255
Italian_AHOA Papuan_AHOA Denisova_AHOA Chimp_AHOA 0 -0.1248 -0.0349 -0.0421 -0.0193 0 -8.966 -7.553 -9.218 -3.71
MbutiPygmy_AHOA Miao_AHOA Denisova_AHOA Chimp_AHOA -0.2354 0.0808 0.0121 0.0023 0.0199 -13.01 3.832 3.24 0.617 4.251
MbutiPygmy_AHOA Karitiana_AHOA Denisova_AHOA Chimp_AHOA -0.2354 0.0939 0.0082 -7e-04 0.013 -13.01 4.085 1.853 -0.16 2.596
MbutiPygmy_AHOA Papuan_AHOA Denisova_AHOA Chimp_AHOA -0.2354 -0.0781 -0.0201 -0.0343 -0.0042 -13.01 -3.458 -4.554 -7.527 -0.795
Miao_AHOA Karitiana_AHOA Denisova_AHOA Chimp_AHOA 0 0.0092 -0.0051 -0.004 -0.0069 0 0.718 -1.221 -0.996 -1.503
Miao_AHOA Papuan_AHOA Denisova_AHOA Chimp_AHOA 0 -0.1158 -0.0391 -0.0455 -0.0253 0 -8.253 -8.608 -10.045 -5.24
Karitiana_AHOA Papuan_AHOA Denisova_AHOA Chimp_AHOA 0 -0.1242 -0.034 -0.0414 -0.0176 0 -7.973 -6.447 -7.892 -3.195

Some brief observations, before we get to the "main course" of this post:
  • Eurasians appear substantially Neandertal/Denisovan-admixed when SNPs polymorphic in Africans and monomorphic in Eurasians are used. I can think of no other explanation than archaic African admixture for this finding.
  • Papuans appear Denisovan-admixed across the board. 
  • For the GLOBAL set, population differences in Neandertal admixture are all non-signficant. Given that the GLOBAL set includes SNPs likely to have existed in the ancestral modern humans, this indicates a fairly symmetrical relationship of to Neandertals.
The most unexpected and surprising finding, is doubtlessly, the evidence that Africans have more Denisovan ancestry than all Eurasians (except Papuans) when SNPs polymorphic in non-Africans and monomorphic in Africans are used (EURASIA panel). I highlight some comparisons:

First of all, clearly Papuans have a special relationship with Denisovans compared to all the remaining 4 populations:

Italian_AHOA Papuan_AHOA ; Denisova_AHOA Chimp_AHOA -0.1248 -8.966
MbutiPygmy_AHOA Papuan_AHOA ; Denisova_AHOA Chimp_AHOA -0.0781 -3.458
Miao_AHOA Papuan_AHOA ; Denisova_AHOA Chimp_AHOA -0.1158 -8.253
Karitiana_AHOA Papuan_AHOA ; Denisova_AHOA Chimp_AHOA -0.1242 -7.973

But, look at this:

Italian_AHOA MbutiPygmy_AHOA ; Denisova_AHOA Chimp_AHOA -0.1057 -5.396
MbutiPygmy_AHOA Miao_AHOA ; Denisova_AHOA Chimp_AHOA 0.0808 3.832
MbutiPygmy_AHOA Karitiana_AHOA ; Denisova_AHOA Chimp_AHOA 0.0939 4.085

That's right: Mbuti Pygmies are actually closer to Denisovans than Eurasians over the subset of SNPs that are polymorphic in Eurasians and monomorphic in the Mbuti.

I do not quite know what to make of this surprising signal. I can think of two explanations:
  1. An early Out-of-Africa movement that affected "Denisovans" and Papuans but not other Eurasians. Living Africans are pulled away from Denisovans because of their archaic African ancestry and towards them because of contributions from their ancestors to the Denisovan population. Hence, they appear less Denisovan-like in African-polymorphic sites (where there is an excess of archaic admixture in Africans) and more Denisovan-like in African-monomorphic sites.
  2. An Into-Africa movement of a population related to Denisovans, a kind of "reverse bottleneck" where a subset of Denisova-like variation entered Africa, hence leaving Eurasians polymorphic and Africans monomorphic.
I would like to stress that these results do not really depend on the choice of the MbutiPygmy population. I have also seen them when I carried out similar experiments using Yoruba and Mandenka.

I often get the feeling that the problem of human origins as it stands is one of too little data for too many variables. But, I am more or less convinced that admixture between very divergent populations of Homo heidelbergensis played a major role in shaping modern humans. 

UPDATE (29 Sep): I continue the investigation of this link in a new post.

September 24, 2012

rolloff analysis of French as a mixture of Sardinian+Burusho

I obtain f3(French; Sardinian, Burusho) = -0.002652 (Z=-13.541) on the basis of 446,917 SNPs. This is the strongest signal of admixture in the French that involves a population that is high on the "West_Asian" component whose influence I have been investigating.

I thus carried out rolloff analysis using the French as a target population and the Sardinians and Burusho as reference populations. The exponential fit can be seen below:

The jackknife gives 239.556 +/- 50.553 generations for this admixture, which corresponds (assuming a generation length of 29 years) to 6,950 +/- 1,470 years.

Analysis of autosomal DNA from the Tyrolean Iceman and a Neolithic TRB farmer from Sweden have revealed an absence of the West Asian ancestral component and a Sardinian-like Neolithic population c. 5ka in Europe. This population may have extended to at least to the Balkans in space and down to the Iron Age in time.

In my opinion, the simplest explanaton for the evidence is that the admixture picked up by rolloff took place in West Asia itself c. 7ka, and then this population begun its movement into Europe at some post-5ka time period.

Importantly, the K=12 Caucasus component appears as a mixture of the K=7 West_Asian and Southern components. The former (West_Asian) is the most important one in the Burusho, and the latter (Southern) is the most important one in Sardinians.

European Neolithic farmers, of presumably West Asian origin only possessed Y-haplogroup G2a out of the wide variety of haplogroups found in West Asia today. They also lacked the West_Asian component which is modal in West Asia today. There is also physical anthropological evidence from Greece and Anatolia, for an introduction of new population elements during the Bronze Age.

These facts combine to make me believe that there were population movements across West Asia which preceded the Indo-European invasion of Europe during late pre-history. That event is then best seen as an extension of a broader Eurasian phenomenon that affected substantially both the western parts of Asia and Europe.

Taking all the evidence into account, I hypothesize that:
  • a "Southern"/"Atlantic_Med"/Sardinian-like population substratum existed in West Asia, and this spawned the early European Neolithic.
  • a new "West_Asian"/Burusho-like population arrived from the east, perhaps associated with the Halaf/Hassuna cultures, or from some other unknown center of dispersal in the Transcaucasus or Iran. Mobility may have been encouraged post-8.2 kiloyear event.
  • these two elements began mixing ~7 thousand years ago in West Asia
  • the admixed population expanded at some post-5ka period into Western Europe.
This scenario is also compatible with the lack of "Southern"/"Atlantic_Med" influences in the Indian subcontinent and Central Asia: if the West_Asian component originated to the east of the Sardinian-like population then it would not have the opportunity to incorporate "Southern" elements in its eastern expansion.

(Obviously, more rolloff analyses are needed to study these ideas; the current one took about ~3 days, which was a little faster than I expected.)

Related (?): Is Burushaski Indo-European?

Image credit: Don Perrault (source)

September 22, 2012

ESHE 2012 abstracts

Some abstracts of interest from the European Society for the study of Human Evolution 2012 meeting (pdf). To avoid making this too long, I will just post the titles and the most relevant quotes. You can read the abstracts in the linked pdf for authors names and more information.

Neandertal and Denisovan Genomes from the Altai 
Susanna Sawyer  et al.
In 2010 a draft genome sequence was determined from a small finger bone found in Denisova Cave in southern Siberia. Its analysis revealed that it derives from an individual who belonged to a population related to, but distinct from, Neandertals. A molar has also been described from Denisova Cave and has shown to carry an mtDNA genome closely related to that of the finger bone.  We have recently determined the DNA sequence of the Denisova genome to a quality similar to present-day human genomes. We have also retrieved a complete mitochondrial genome and nuclear DNA sequences from an additional molar found in Denisova Cave. Furthermore, we have determined a high-quality nuclear genome from a pedal phalanx found in Denisova Cave in 2010. We show that the pedal phalanx derived from a Neandertal and thus that Neandertals as well as Denisovans have been present in the cave. We will discuss the genetic history of Denisovans as well as Neandertals in light of these new genome sequences. 

The discovery of a Neandertal genome from Denisova cave is certainly interesting. I have previously commented that:
If Vindija and Denisova, two caves less than 5,000km apart were home to people more divergent from each other than any two humans are today, it's strange to think that only "modern humans" inhabited Africa at the same time.
Now, it appears that Neandertals and Denisovans were present (when?) not only 5Mm apart, but literally on the same spot. Much later, during the Neolithic we see very differentiated humans co-existing in Europe. And, we get archaic hominins in Africa long after the appearance of anatomically modern humans there. I think the evidence is looking good for my hypothesis that regional human populations have recently gotten more similar over time through extensive admixture between divergent hominin groups, rather than that they became more dissimilar over time  through tree-like divergence.

On the same topic, here is more evidence for Neandertal presence in the Altai:

A Neanderthal mandible fragment from Chagyrskaya Cave (Altai Mountains, Russian Federation)
Both the mandible and the dentition preserve numerous derived Neanderthal traits: among else a posteriorly placed mandibular foramen, an oblique mylohyoid line, an asymmetrical P4 and continuous mid-trigonid crests on the M1 and M2. ... Ongoing ancient DNA analyses of the hominin remains from Chagyrskaya cave and absolute dates for the site will hopefully help to clarify the origin of the Altai Neanderthals, and their relationship with the Denisovans.

An hypothesis for the phylogenetic position of Homo floresiensis
Our cladistic analysis places H. floresiensis unequivocally as part of a clade with H. habilis
Who are you calling ”modern”? An assessment of the dental morphology and metrics of Homo sapiens

Although dental reduction has long been cited as a derived feature of H. sapiens, our data indicate this claim may be no longer tenable ... the single metrical assessment that groups all H. sapiens (early, Upper Paleolithic and recent) apart from other taxa is the ratio between mandibular:maxillary crown areas.  the results of our study are important for assessing recent claims of great antiquity for H. sapiens outside of Africa
Neanderthal in Malthusian demographic trap

It can be hypothesized that the demography of the Neanderthal metapopulation, living under conditions where extreme environmental instability with short periods was the norm, was primarily stagnant,
with frequent bottlenecks and episodes of decline.
 A New Framework for the Upper Paleolithic of Eastern Europe

The results of field and laboratory research during the past decade require a new classificatory framework for the Upper Paleolithic in Eastern Europe. It is now apparent that people making artifacts assigned to the Ahmarian industry occupied both the southern and northern slopes of the Caucasus Mountains (i.e., Ortvale Klde, Layer 4d; Mezmaiskaya Cave, Layer 1C). Their sites probably indicate a separate movement of anatomically modern humans (AMH) from the Near East directly into Eastern Europe, establishing an independent line of development during the earlier Upper Paleolithic that parallels the Proto-Aurignacian and Aurignacian sequence in Western and Central Europe. this East European industry is most fully represented at the Kostenki-Borshchevo sites on the Don River before 40,000 cal BP (e.g., Kostenki 14, Layer IVb). It is followed by a closely related industry, also characterized by bladelet production, that is dated to the interval between 40,000 and 30,000 cal BP in Crimea and the East European Plain. The proposed new framework reflects recognition of these distinctive East European entities and of two environmental events that had significant impacts on human settlement in Eastern Europe: (1) the Campanian Ignimbrite (CI) volcanic eruption (40,000 cal BP); and (2) the Last Glacial Maximum (LGM) ( 25,000 cal BP). It has been suggested that the early Upper Paleolithic (EUP) industry present in Eastern Europe before 40,000 cal BP should be labeled an eastern variant of the contemporaneous Proto-Aurignacian of Mediterranean Europe. However, given the separate movement of people from the Near East via the Caucasus Mountains, and independent development of the East European EUP, this industry is more appropriately termed “Proto-Gravettian.” The younger bladelet industry, which includes assemblages at Buran-Kaya III (Layer 6-1), Mira (Layer II/2), Kostenki 8 (Layer II), and probably Shlyakh (Layers 4C, 6), may be termed “Early Gravettian” to distinguish it from the classic Gravettian industry that dates to less than 30,000 cal BP (e.g., Avdeevo, Zaraisk).The upper temporal boundary of the Proto-Gravettian corresponds to the CI eruption (40,000 cal BP), while the classic Gravettian of the East European Plain appears to have been effectively terminated by the LGM ( 25,000 cal BP). Several sites that date to the 40,000–30,000 cal BP interval (e.g., Kostenki 1, Layer III) contain elements that suggest a connection with the Aurignacian technocomplex of Western-Central Europe. These assemblages may be placed into the category of “Eastern Aurignacian,” which reflects differences in content with the West and Central European sites. The apparent spread of this industry into Eastern Europe from Central Europe may be related to the impact of the CI eruption on portions of the East European Plain. 
 Conflicting dates for the Late Aterian
First at the huge Ifri n’Ammar sites, TL dates have indicated 80,000 years for the Late Middle Palaeolithic/Aterian levels. Our new C14 dates yield 35,000 BP for exactly the same levels. At the “grotte des Contrebandiers”, formerly dated at 28,000 BP by Debenath and his team, is now dated at 100,000 years by new TL dates. As starting points, this kind of methodological contradiction should be confronted, understood and resolved.
 The Rio Secco Cave in the North Adriatic Region, Italy. A new context for investigating the Neanderthal demise and the settllement of Anatomically Modern Humans
A sequence of several thin layers dated to 46.0–42.1ky Cal BP represents the final Mousterian.
The Dhofar Nubian Tradition: an enduring Middle Stone Age technocomplex in southern Arabia

Between 2010 and 2012, the Dhofar Archaeological Project has located and mapped 260 Nubian Complex occurrences across the Nejd Plateau of southern Oman. Diagnostic Nubian artifacts werefound cemented in fluvial sediments at the site of Aybut Al Auwal in Dhofar, with two OSL dates around 106 ka BP; hence, roughly contemporaneous with the African Nubian Complex (Rose et al. 2011). Many of these lithic assemblages, such as that from Aybut al Auwal, are technologically homologous to the Late Nubian Industry found in northeast Africa, sensu stricto, while others may represent local facies of the greater “Afro-Arabian Nubian Technocomplex.” This presentation describes the various reduction strategies encountered at a sample of Nubian Complex sites from Oman, explores inter-assemblage variability, and begins to articulate technological units within the “Dhofar Nubian Tradition.” To achieve this aim, we have developed an analytical scheme with which to describe technological variability among Nubian Levallois reduction strategies in both Africa and Arabia. Our analysis indicates at least two distinct Nubian industries. The first, which we refer to as the “Classic Dhofar Nubian,” is virtually identical to Late Nubian Industry from the Lower Nile Valley and Red Sea Hills in Egypt. Thee subsequent group of assemblages in Dhofar, called the “Mudayyan,” exhibits a technological shift toward diminutive Nubian Levallois cores and that, recurrent bidirectional cores with opposed, faceted striking platforms. We interpret this evidence to indicate an enduring, local Nubian tradition in Dhofar that is ultimately rooted in the African Nubian Complex. 
From Late Mousterian to Evolved Aurignacian: New evidence for the Middle-to-Upper Paleolithic transition in Mediterranean Spain
Combined, the evidence from CA and FDM indicates that, in chronostratigraphic terms, the Middle-to-Upper Paleolithic transition in Murcia consists of the replacement of a Late Mousterian by an Evolved Aurignacian and occurred some time during the 38th millennium cal BP

Structural stability and ancient connections between languages

From the press release:

Using a large database and many alternative methods Dediu and Levinson show that both positions are right: there are universal tendencies for some features to be more stable than others, but individual language families have their own distinctive profile. These distinctive profiles can then be used to probe ancient relations between what are today independent language families.  
"Using this technique we find for instance probable connections between the languages of the Americas and those of NE Eurasia, presumably dating back to the peopling of the Americas 12,000 years or more ago," Levinson explains. "We also find likely connections between most of the Eurasian language families, presumably pre-dating the split off of Indo-European around 9000 years ago."

From the paper:
Quite convincing is the evidence that Core Eurasian families (comprising Altaic – or Mongolic + Turkic –, Dravidian, Indo-European, Uralic and the Caucasian families) might form a group (p=0.0013, 5 methods, and , p=0.094, 4 methods, when controlling for geography).
The authors were also able to reject the "broad" Afroasiatic group "comprising Afro-Asiatic, Indo-European, Dravidian and Uralic". I think this makes some sense, since Afroasiatic is basically an African language family with a Near Eastern offshoot, so I did not expect it to group with the Eurasian language families.

The Core Eurasian group seems very interesting in light of accumulating evidence about contacts between human groups across Eurasia. Such a group is pushing the limits of what can be inferred using linguistic data, and, perhaps, archaeogenetics might provide some evidence that might be used to plausibly argue for such a relatively broad group.

PLoS ONE 7(9): e45198. doi:10.1371/journal.pone.0045198

Abstract Profiles of Structural Stability Point to Universal Tendencies, Family-Specific Factors, and Ancient Connections between Languages

Dan Dediu, Stephen C. Levinson

Language is the best example of a cultural evolutionary system, able to retain a phylogenetic signal over many thousands of years. The temporal stability (conservatism) of basic vocabulary is relatively well understood, but the stability of the structural properties of language (phonology, morphology, syntax) is still unclear. Here we report an extensive Bayesian phylogenetic investigation of the structural stability of numerous features across many language families and we introduce a novel method for analyzing the relationships between the “stability profiles” of language families. We found that there is a strong universal component across language families, suggesting the existence of universal linguistic, cognitive and genetic constraints. Against this background, however, each language family has a distinct stability profile, and these profiles cluster by geographic area and likely deep genealogical relationships. These stability profiles seem to show, for example, the ancient historical relationships between the Siberian and American language families, presumed to be separated by at least 12,000 years, and possible connections between the Eurasian families. We also found preliminary support for the punctuated evolution of structural features of language across families, types of features and geographic areas. Thus, such higher-level properties of language seen as an evolutionary system might allow the investigation of ancient connections between languages and shed light on the peopling of the world.


ADMIXTURE analysis of Schlebusch et al. (2012) data

The ADMIXTURE analysis of Schlebusch et al. (2012) did not include Eurasian references, but thanks to the fact that the authors have made their data publicly available, anyone can carry out additional analyses on it. I am sure that this data will be very useful in the future. The list of included populations, with sample sizes are:

  • ColouredColesberg_Sch 20
  • ColouredWellington_Sch 20
  • Khomani_Sch 39
  • Karretjie_Sch 20
  • Khwe_Sch 17
  • GuiGhanaKgal_Sch 15
  • Juhoansi_Sch 18
  • Nama_Sch 20
  • Xun_Sch 19
  • SEBantu_Sch 20
  • SWBantu_Sch 12

As is my convention, the _Sch ending denotes that these populations are from the Schlebusch et al. paper

As always with a new dataset, after processing it, I ran a quick test to make sure everything seemed to be alright. This time, I included the 220 individuals in the released datasets together with 28 HGDP Sardinians and 10 HGDP Dai, and ran a quick K=4 ADMIXTURE analysis:

These appear to make sense. The "green" Dai-like element in the Coloured samples is probably a stand-in for Indian ancestry in that population. The plot of individuals shows considerable variation within several populations:

September 21, 2012

Complex origins and natural selection of the Khoe-San

The Khoe-San were recently made the object of a study by Pickrell et al. in a paper that was posted on arXiv and ought to appear in journal form in the near future. Good things come in pairs, so on the heels of that study, a new paper in Science by Schlebusch et al. deals with a similar set of populations. The former paper used the Affymetrix Human Origins Array which contains sets of SNPs ascertained in different individuals from around the world, and the dataset will be comparable to the HGDP set genotyped on the same chip. The current study uses the Illumina Omni 2.5, which would make its data to comparable to the 1000 Genomes data, as well as to a variety of other data genotyped on Illumina platforms. So, from the data perspective, I would say that the two nicely complement each other.

There is an abundance of good stuff in the 176 pages of supplementary material which are freely available in the Science website.

One important technical proposition in the paper is the use of a concordance ratio. As I understand it, this is based on the idea that when populations split, initially the signal that they did so is very weak, and becomes stronger with more time (and drift). So, by taking the ratio of concordant minus discordant alleles over concordant plus discordant ones, they can show support for a topology and estimate population split times.

Of course, Khoe-San populations cannot really be seen as having split from the rest of mankind at some particular time. Pickrell et al. argue for this on the basis of admixture LD in even the most "unadmixed" populations (such as HGDP San), but the most obvious reason why the simple split scenario cannot be true comes from the fact that the Khoe-San possess a substantial percentage of Y-haplogroup E, which links them to other Sub-Saharan Africans, and even Eurasians within a ~50ka framework at most, and probably much lower, since they carry derived sublineages within E that were founded much more recently.

Nonetheless, this admixture was probably not so great to destroy the evidence of isolation, and the authors give an estimate of ~100ka for the split:

This division forms the deepest divergence among extant humans (Fig. 2A, S32) and, assuming an effective population size (Ne) of 21,000 individuals (11, 12), the maximum likelihood divergence time is Ts = 0:083 × 2Ne generations (95% ML CI: 0.075-0.091) corresponding to ∼100,000 years ago (14), in agreement with previous estimates of 110,000-160,000 years ago (11, 12).

But, this estimate disagrees with the idea that Khoe-San split off 250-300 thousand years ago, which has been advanced on the basis of the slower autosomal mutation rate. Many of the news headlines on the paper talk about the paper showing that Khoe-San diverged before Out-of-Africa, but, actually, using the new slow mutation rate, a date of 100ka is actually around the time, or even after Out-of-Africa, which now appears to have taken place twice as early as previously thought.

Thankfully, Schlebusch et al. do not only give absolute age estimates, but also express their age estimates in terms of the effective population size. But, the effective population size is indirectly linked to the autosomal mutation rate, as I noted in my review of Gronau et al. and Veeramah et al., i.e. the two papers cited for the effective population size of 21,000 individuals. In order to generate the same amount of genetic divergence, a slower mutation rate requires a higher population size. Ergo, I don't think the estimates of Schlebusch et al. are discordant with those of Scally and Durbin, and, the two may harmonize once effective population sizes are re-calculated on the basis of the slow human autosomal mutation rate.

The authors do acknowledge the possibility of archaic admixture in Africa. In my opinion, the presence of this admixture can harmonize the evidence of shallow common ancestry with Eurasians and African farmers (e.g., in the form of Y-haplogroup E) with the deep autosomal divergence times.

I am also looking forward to getting the new data when it appears at the Jakobsson lab data page. Together with the HGDP San (on both Affymetrix and Illumina platforms), and the Henn et al. data, there will shortly be no shortage of data on the Khoe-San. And, together with the data from Pagani et al. on Ethiopia it may be a good idea to update my africa9 calculator when I find the time for it.

Science DOI: 10.1126/science.1227721

Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

Carina M. Schlebusch et al.

The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ~2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations >=100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.


September 20, 2012

rolloff analysis of North European admixture in Greeks.

One of the signals of admixture in my recent post on the Greeks on the crossroads of Eurasia was between north European and Near Eastern populations, with several pairs of such populations showing a significant negative f3(Greek_D; North European, Near Eastern) statistic. I used rolloff to estimate the date of this admixture.

Note that rolloff assumes a pulse model of admixture, whereby the two populations mix at a point in time, rather than experience gene flow over a protracted period. This may not be applicable in the case of Greeks, since gene flow may have occurred repeatedly throughout history. Also, rolloff estimates admixture times in the absence of very accurate ancestral populations, by exploiting allele frequency differences between them. So, for the first example below, with Finnish_D and Yemen_Jews as reference populations, which showed the most negative f3 statistic, this does not mean that Greeks are the product of admixture between Finns and Yemen Jews, but rather that allele frequency differences between these two populations reflect a contrast between North Europeans and Near Eastern populations, which may, presumably map, to the west Eurasian cline of diminishing Near Eastern "Neolithic" ancestry.

This experiment was performed on a set of 292,223 SNPs, and using the Rutgers map for Illumina chips. The first plot is using Finnish_D and Yemen_Jews as references. The fit does not visually appear extremely convincing, perhaps due to a smaller number of SNPs, or to the aforementioned deviation from the pulse admixture model.
(NB: I used the script with default parameters to do the exponential fit/plotting; note that negative weighted correlation points are not visible in the produced output)

The jackknife estimate of this admixture is 87.849 +/- 20.254 generations, or, assuming a generation length of 29 years, into 2,550 +/- 590 years.

The second plot uses Polish_D and Saudis as references:
The jackknife gives 67.235 +/- 22.148 generations, or 1950 +/- 640 years. The fit seems to capture the rise of the exponential for smaller cM genetic distances reasonably well.

Recently, Graham and Coop used fastIBD to identify a signal of possible Slavic admixture in the Balkans dating to the medieval period, using a similar generation time of 30 years. That method uses shared IBD segments between populations, so it may be limited to uncovering the most recent signal of admixture. Another piece of evidence comes from an abstract in ASHG 2012, according to which an Iron Age individual from Bulgaria was Sardinian-like. Since the Iron Age starts at the conclusion of the 2nd millennium BC, it might seem that a northern European element -whether present or not- had not admixed yet with the people who lived in the Balkans at the time. This seems to parallel the situation in two other earlier locations (c. 5ka in the Tyrolean Iceman and Gok4 Swedish TRB farmer), in which the North_European component was absent, although we cannot yet exclude its absence from the Iron Age Bulgarian, since a little such admixture might still leave an individual mostly Sardinian-like. Finally, levels of the North_European component in Greek individuals seem fairly variable, and this might indicate that levels of this element of ancestry had not had sufficient time to even out in the population.

(A different possibility is that the admixture signal reflects admixture of a Near Eastern kind. I consider this less likely, since there is evidence of "Southern" and "Southwest Asian" ancestry (in the K7b/K12b sense) already in Neolithic Europe.)

More research on the issue is certainly needed, but a first reading of the evidence suggests that this type of admixture may reflect events that took place during the historical period of Greek history.

Each of these experiments took about 1.5 days to complete. I am currently running another set of experiments with ~2-fold more SNPs, and assuming that finishes in good time, I may re-visit the question addressed in this post, to see if standard errors decrease and/or time estimates change with denser coverage.

Selection at FADS gene cluster in Africa

A couple of quick comments. First, from the paper:
Given 207 fixed differences between chimpanzee and human in this region, we estimate a TMRCA of 1.49 (SEM = 0.23) million years for the human haplotypes. Similarly, only considering the number of mutations within the haplotype group D1, the TMRCA was 85,000±84,000 years, thus suggesting that selection in Africa occurred approximately 85 kya. 
Jointly, these two sets of data support the hypothesis that advantageous mutations within the FADS gene cluster occurred prior to human migration out of Africa (~85 kya), and swept to fixation within African but not European or Asian populations.
I don't know how 85+/-84 can be used to infer that this selection occurred prior to the human migration Out-of-Africa. It seems to me that 85+/-84 is compatible with a wide variety of events. On top of this, this date depends on human-chimp split (=6.5Ma), for which a recent estimate of 7-13Ma has been advanced recently, but also 3.7-6.6Ma. So, I would say that uncertainty about when this selection took place leaves little room for pronouncements that it took place either before, or after Out-of-Africa.

Look at the following frequency map:

I sometimes think that intellectual commitment to recent Out-of-Africa-and-never-back is so strong, that the obvious explanation is overlooked. When Africans are polymorphic and Eurasians are not, this is explained as the result of the OoA bottleneck. When Africans are monomorphic and Eurasians are not -as in this paper- this is explained as the result of selection-to-fixation in Africans.

Now, I don't doubt that there was selection in Africans at the FADS gene cluster. But, rather than imagine that African humans were "tethered to marine sources for LC-PUFAs in isolated geographic regions" throughout the ecologically diverse and geographically huge continent of Africa, I can simply imagine that there was a spread of the adaptive haplotype into Africa, followed by selection, as modern humans, who originated, perhaps, in North Africa, had to drastically shift their diet as they entered Sub-Saharan Africa. I am not convinced that this is what happened, but it is certainly worthy of consideration.

PLoS ONE 7(9): e44926. doi:10.1371/journal.pone.0044926

Adaptive Evolution of the FADS Gene Cluster within Africa

Rasika A. Mathias et al.

Long chain polyunsaturated fatty acids (LC-PUFAs) are essential for brain structure, development, and function, and adequate dietary quantities of LC-PUFAs are thought to have been necessary for both brain expansion and the increase in brain complexity observed during modern human evolution. Previous studies conducted in largely European populations suggest that humans have limited capacity to synthesize brain LC-PUFAs such as docosahexaenoic acid (DHA) from plant-based medium chain (MC) PUFAs due to limited desaturase activity. Population-based differences in LC-PUFA levels and their product-to-substrate ratios can, in part, be explained by polymorphisms in the fatty acid desaturase (FADS) gene cluster, which have been associated with increased conversion of MC-PUFAs to LC-PUFAs. Here, we show evidence that these high efficiency converter alleles in the FADS gene cluster were likely driven to near fixation in African populations by positive selection ~85 kya. We hypothesize that selection at FADS variants, which increase LC-PUFA synthesis from plant-based MC-PUFAs, played an important role in allowing African populations obligatorily tethered to marine sources for LC-PUFAs in isolated geographic regions, to rapidly expand throughout the African continent 60–80 kya.


September 18, 2012

Out-of-Asia and Into-Africa (?)

The publication of version 2 of the Pickrell et al. paper on South Africa is as good an opportunity as any to discuss something anew something that I've been hinting at for some time now.

First things first: Pickrell et al. find West Eurasian admixture in the Hadza and Sandawe:
Both of these are consistent with west Eurasian (either European or, more likely, Arabian), gene  ow into these populations. To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly speci ed reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations ( 2500 years) ago for the Hadza and 66 generations ( 2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al. [65] in Ethiopian populations.
The presence of West Eurasian ancestry in the Hadza and Sandawe was anticipated in my world9 calculator, where both these populations were shown to possess Caucasoid admixture entirely of the "Southern" component. This component peaks in Arabia, and is unaccompanied by any other type of Caucasoid element really only there. So, it is very likely that there was indeed such a migration into East Africa. What Pickrell et al. have added to our knowledge is that this migration is fairly recent.

Razib repeats one of his favorite analogies about events taking place in Africa after the pyramids were rising in Egypt. I will use a Greek epic analogy, by pointing out that at the time that Memnon the Ethiopian led his contingent to the aid of Troy, these events had not yet taken place.

Depictions of Memnon changed during classical antiquity, from a Caucasoid norm, as in the red-figure kylix on the left, to a more stereotypically African form by Roman times. This is sometimes taken as simply a consequence of the fact that the ancient Greeks were unfamiliar with African phenotypes, and changed their portraiture of Ethiopians as they became more familiar with them during Hellenistic and Roman times.

But, the very name of Aithiopes first attested in Homer (8th c. BC) attests to the fact that the Greeks were aware of what Ethiopians looked like, at least in terms of their dark pigmentation. And, there are depictions of Africans in classical art, as well as a famous quote in Herodotus which makes abundantly clear that he was aware of the physical characteristics of what we would call "Sub-Saharan Africans".

We don't only need to look at Ethiopia for evidence of the strange events that were taking place in Africa during classical antiquity. A great punch-in-the-face reminder of these events comes from the much later Greek author Pausanias who records that a statue of Athena he observed in Attica had blue eyes which he ascribed to the Libyan origin of her myth. How strange it seems to us that one would look to Africa for an explanation for the blue-eyed goddess.

Libya was of course, the ancient name for Africa, and especially Africa west of Egypt, what we might call Berber-land. Egypt was often reckoned by the ancient as part of Asia. In any case, Pausanias' strange assertion finds support in the Egyptian monuments that really do depict the ancient Libyans (=Berbers) as Caucasoid, and often lighter than Middle Eastern people. This would also accord with Coon's famous discovery of "Irish-like" Berbers among the Riffians; I often dismissed such assertions, but in a landscape of human prehistory that is getting stranger by the month, it is worth digging for gold nuggets in old texts.

A recent study claimed that there was back-to-Africa gene flow into Eurasia more than 12,000 years ago. On the other hand, both HAPMIX and StepPCO estimate the admixture in Mozabite Berbers as taking place ~120 generations ago, or, about 3.5kya assuming a generation length of 29 years as Patterson et al. (2012) do. I have observed that rolloff produces generally lower dates than these two methods, so I would not be surprised if that is the case here as well.

It seems that as recently as a few thousand years ago, West Eurasian populations were moving into Africa from both north and east. As Pickrell et al. have discovered, their eastern branch also contributed to South Africans, tagging along the dispersal of pastoralists from East-to-South Africa.

The big question is: did West and Central Africa escape this population movement?

I seriously suspect that it did not. I base that assertion on several arguments, of varying strength:

  1. Why would they? If they inundated East and North Africa, why would they not venture further?
  2. Living Sub-Saharan African farmers are not symmetrically related to West and East Eurasians: they are closer to the former. West Eurasian back-migration would explain this phenomenon.
  3. The Great Event in Sub-Saharan Africa was doubtlessly the Bantu explosion, and it is a curious coincidence that this took place precisely close to the time of these events
  4. The Iwo Eleru crania from Nigeria are of late Pleistocene age, archaic in character, and unlike modern West Africans. Something did happen in West Africa over the course of, say, the last 10,000 years
And, I always try to remind myself of the Kiffians and Tenerians. I have not seen any follow-up work on them, but if anyone has an ancient DNA lab, I'd think they would be prime candidates for a study.

Speaking of ancient DNA, this unexpected archaeogenetic study from the University of Khartoum, hints at important changes in Africa:

The area known today as Sudan may have been the scene of pivotal human evolutionary events, both as a corridor for ancient and modern migrations, as well as the venue of crucial past cultural evolution. Several questions pertaining to the pattern of succession of the different groups in early Sudan have been raised. To shed light on these aspects, ancient DNA (aDNA) and present DNA collection were made and studied using Y-chromosome markers for aDNA, and Y-chromosome and mtDNA markers for present DNA. Bone samples from different skeletal elements of burial sites from Neolithic, Meroitic, Post-Meroitic and Christian periods in Sudan were collected from Sudan National Museum. aDNA extraction was successful in 35 out of 76 samples, PCR was performed for sex determination using Amelogenin marker. Fourteen samples were females and 19 were males. To generate Y-chromosome specific haplogroups A-M13, B-M60, F-M89 and Y Alu Polymorphism (YAP) markers, which define the deep ancestral haplotypes in the phylogenetic tree of Y-chromosome were used. Haplogroups A-M13 was found at high frequencies among Neolithic samples. Haplogroup F-M89 and YAP appeared to be more frequent among Meroitic, Post-Meroitic and Christian periods. Haplogroup B-M60 was not observed in the sample analyzed.
I was reminded of it recently when this curious abstract came up, which I still believe is missing a zero somewhere, but these days you never know.

Evidence that Sub-Saharan Africans too have experienced gene flow from West Eurasians occasionally comes up, but formal tests of admixture, e.g., f3(Yoruba; San, French) usually do not achieve significance. But, we must be cautious: South Africans do appear admixed between San and East Africans, but this is a consequence of the fact that admixture is recent, leaving a trail of populations of varying East African ancestry, and the San still exist and can serve as one pole in a comparison of admixture.

David Reich has hinted at dual origins for West Africans. I am looking forward to learning what he means by it, but I would not be surprised if it involves admixture between a Eurasian-like population with a Palaeoafrican population of indigenous West African hunter-gatherers.

In any case, ex Africa semper aliquid novi even today. But, interdum, aliquid novum in Africam.

UPDATE: Pickrell and co-authors discuss their paper here.

In favor of recent Out-of-Africa (Eriksson et al. 2012)

A new paper in PNAS argues for a recent (~60kya) expansion of modern humans Out-of-Africa. After reading the title, I was not sure what date the authors were arguing for, and I went straight for the movie in the supplemental material, which is a pretty cool depiction of the authors' scenario.

However, I disagree with the conclusions of this paper, for a variety of reasons. First, the climate history of Africa is consistent with older dispersal scenarios. The authors of the current paper follow other researchers into attributing the Skhul/Qafzeh hominins to an Out-of-Africa-that-failed, but that proposition is increasingly untenable.

The halving of the human autosomal mutation rate implies that Eurasians and Africans split before 100 thousand years ago, and African hunter-gatherers may have split as much as 300 thousand years ago. These dates are not set in stone, but can be downsized if one allows for substantial archaic African admixture. But, doing so weakens the case for a sub-Saharan origin of Homo sapiens.

Second, the Nubian Complex is a direct archaeological link between NE Africa and S Arabia pre-100ka. It becomes increasingly difficult to argue that the pre-100ka expansion fizzled when you have the triple evidence of Mt. Carmel, the Nubian Complex, and Jebel Faya, providing a combination of anthropological and archaeological evidence for African-Asian interaction prior to 100ka.

Some of the conclusions of this paper may be influenced by their choice of the dinucleotide mutation rate:

The dinucleotide stepwise mutation model mutation rate for these markers was estimated in the work by Dib et al. (46) to μdi = 1.52 × 10−3 mutations per generation.
But, Sun  et al. seem to report a much slower dinucleotide mutation rate, as well as a deviation from the stepwise symmetrical model that would bias age estimates downwards if that model is used. So, I am not very confident in the age estimates provided in this paper.

There is a good reason to favor a recent human expansion: if Out-of-Africa happened pre-100ka, as I have argued, then what did modern humans wait for to conquer the rest of the planet (a greater than 50ka hiatus until they begin appearing all over Eurasia). However, that problem can be solved if we acknowledge the fact that modern humans prior to 100ka may have been anatomically "like us", but behaviorally they were not much different from other hominins living on the planet at the time. These pre-100ka H. sapiens were just another set of hunter-gatherers: they may have had a chin, a smaller face, and a more globular braincase, but they did not appear to behave in any drastically different way than other humans who lacked these features.

There are three factors that drive migration: curiosity, need, and ability. One may wonder "what's on the land beyond the sea", but one needs the ability to build a lasting boat to find out. One may have the ability to build a boat, but has no need to do so, if there is game-a-plenty around camp and a beautiful woman with a few beautiful babies in the shelter.

I think that 2-3 reasons contributed to the hiatus:

  1. The going was good in Arabia prior to the climate crisis of ~70kya
  2. The way north was blocked by Neandertals
  3. Whether or not modern humans had the genetic capacity to outcompete the Neandertals, they did not yet have the behavioral expression needed to achieve this

I don't know to what extent changes in the modern human lineage made the mental hardware of early Homo sapiens something like a transistor-based computer that had to compete against the older triode-based models that filled the planet. As we sample more ancient hominins, we may eventually find out whether our wiring was really much improved.

But, one does not really need the best of wiring to conquer a planet. Few would argue today, I suspect, that English mental hardware was superior to e.g., Bavarian mental hardware, but the English brought half the planet under their domination, partly because of their fortunate geographical position which gave them (and other West Europeans) access to the lands beyond the sea. Similarly, few would argue that the Mongols had an innate ability to conquer half of Eurasia, but they happened to have a combination of drive, leadership, organization, and military hardware that allowed them to do so.

This is what I suspect was the real cause for the success of modern humans: they may have had some genetic advantage over others, but their success was partly unintended (the consequence of the drying up of the Sahara-Arabia region that forced them out c. 70kya), and partly the result of them having some vital technological "edge" over other Homo populations.

There may have been interplay between the "need" and "ability" causes of the great human diaspora: as modern humans were pushed out by the advancing desert, they had to adapt to dwindling resources, the challenge of new environments, and the challenge of contact and competition with archaic hominins in both Eurasia and Africa. Adversity does not always breed success: it most often results in failure. But, while many long-forgotten peoples may have faced formidable challenges during the long aeons of geological time, at least one of them had the combination of luck and the "right stuff" to rise to the occasion, and we are their descendants.

PNAS doi: 10.1073/pnas.1209494109

Late Pleistocene climate change and the global expansion of anatomically modern humans

Anders Eriksson et al.

The extent to which past climate change has dictated the pattern and timing of the out-of-Africa expansion by anatomically modern humans is currently unclear [Stewart JR, Stringer CB (2012) Science 335:1317–1321]. In particular, the incompleteness of the fossil record makes it difficult to quantify the effect of climate. Here, we take a different approach to this problem; rather than relying on the appearance of fossils or archaeological evidence to determine arrival times in different parts of the world, we use patterns of genetic variation in modern human populations to determine the plausibility of past demographic parameters. We develop a spatially explicit model of the expansion of anatomically modern humans and use climate reconstructions over the past 120 ky based on the Hadley Centre global climate model HadCM3 to quantify the possible effects of climate on human demography. The combinations of demographic parameters compatible with the current genetic makeup of worldwide populations indicate a clear effect of climate on past population densities. Our estimates of this effect, based on population genetics, capture the observed relationship between current climate and population density in modern hunter–gatherers worldwide, providing supporting evidence for the realism of our approach. Furthermore, although we did not use any archaeological and anthropological data to inform the model, the arrival times in different continents predicted by our model are also broadly consistent with the fossil and archaeological records. Our framework provides the most accurate spatiotemporal reconstruction of human demographic history available at present and will allow for a greater integration of genetic and archaeological evidence.


September 17, 2012

Quantifying Karitiana-like admixture in Eurasia

Using the same dataset as in a previous experiment, I decided to calculate the extent of East Eurasian-like admixture in Eurasia.

First, I identified, using qp3Pop a set of population with significantly negative f3(Sardinian, Karitiana, Target) statistics:

This is actually a very helpful figure, as it shows how the f3 signal of admixture becomes weaker for more drifted populations (e.g., Finns) even if they have more of the investigated admixture than others (e.g., French).

It also shows that most West Eurasian populations appear admixed between Sardinians and Karitiana, whereas most East Eurasian ones (see spreadsheet) do not appear to be so, at least on the basis of the f3 test.

I next used qpF4Ratio to estimate the extent of this admixture. This depends on the following topology (Fig. 4 of Patterson et al. 2012):

I used: A=Papuan, B=Karitiana, C=Sardinian, and O=San, with X= any of the different investigated populations.

Note that this topology does not really hold for all X target populations whose admixture we are investigating. In particular, some populations have African admixture, hence O=San is not really an outgroup for them.

In the following, you can see the admixture proportion estimates using the F4 ratio test:

It should be obvious now how admixture estimates using the f4 ratio method depend on an appropriate outgroup. The f3-statistics indicate that all the above-listed populations are admixed between a Sardinian-like and a Karitiana-like population. But, the estimate of admixture based on the f4 ratio becomes negative, because f4(Papuan, San; X, Sardinian) is negative in populations where X has African admixture.

So, the Karitiana-like admixture of populations such as Spanish_D (est. 1.2%) is lower than their actual such admixture, because Spanish_D includes African admixture. For the Portuguese_D (est. -3.3%) where African admixture is even more significant, the effect is even stronger, and a nonsensical negative admixture score appears.

The converse took place when the f4 ratio method was applied by Moorjani et al. (2011). In that case, negative f4 scores with CEU as a parental population were taken as evidence of African admixture. But, since CEU has Amerindian-like admixture, the estimates of African admixture in that paper were higher than the actual values.

It will be interesting to derive corrected African admixture estimates after taking into account that CEU have Amerindian-like admixture, and, covnersely, corrected Karitiana-like admixture estimates after taking into account African admixture in some populations.

In any case, the data used for the above plots can be found in the spreadsheet, together with the list of all considered populations.

September 16, 2012

Greeks on the crossroads of Eurasia

I used the qp3Pop program of ADMIXTOOLS which implements a 3-population test of admixture (Patterson et al. 2012), using Greek_D as a target population and any pair of other populations as possible parental populations. My dataset is similar to that used for the K7b/K12b, but includes all the new data that has accumulated since those tools were released. The number of SNPs is 186,241, and I have also limited the analysis to 115 populations with 10+ individuals.

For more details on the f3 statistic, you should really read the linked paper. Briefly, you should remember the following:

  1. Significant negative f3 statistics indicate that the target population and the two parentals do not form a simple tree, but are related in a complex way
  2. Positive f3 statistics are consistent with either a simple tree or a history of admixture followed by genetic drift
  3. It is not necessary for the parental populations to be themselves unadmixed
The full set of results can be seen in the spreadsheet.

Below you can see the 30 most negative f3 statistics.

The first thing that immediately jumps out is that Sardinians participate in most of these comparisons. And, given the mounting evidence for a Sardinian-like population in prehistoric Europe, including the Balkans, it does appear likely that a Sardinian-like element in the ancestry of Greeks is quite possible.

A different element that is paired up with Sardinians in the most negative f3 statistics consists of a variety of South Asian populations; these comparisons appear stronger than the Sardinian+East Asian ones. This dataset does not include Amerindian populations, for which the effect was strongest in the Patterson et al. paper. I suspect that South Asian populations give out stronger f3 statistics than East Asian ones, because South Asians are composed of a West Asian-like element and an Ancestral South Indian element which is related to East Eurasians. So, South Asians appear as a parental population on account of both the East Eurasian-shift effect observed by Patterson et al., as well as the West Asian-shift effect I've described in a few posts such as this.

A third set of significant comparisons involve Northern Europeans vs. Near Eastern populations, with extrema in the Baltic area and Arabia, which seems to correspond quite well with what I've called the "West Eurasian cline", with populations of northeastern Europe likely possessing a higher degree of continuity with the Mesolithic hunter-gatherers.

Overall, this exercise has convinced me that 2-way admixture models do not capture the complexity of Eurasian prehistory. The Greek population appears intermediate on a number of different clines, the two most important ones being between Sardinia and far Asia and between the Baltic and the Near East.

I will probably repeat this experiment with other populations from this set. I will also probably try to get some admixture dates using as many SNPs as possible, although rolloff appears to have fairly long running times, so I am not sure how practical that will be.