The Swat Protohistoric samples

In South Asian genetics, we suffer from a paucity of ancient DNA to study. We have about 100 samples from Pakistan, Gandhara to be precise. These samples range from the Late-Bronze Age to the Medieval Historic period. Then, we have about two dozen samples from Roopkund Lake that are generally from antiquity but going up to the middle ages. This is all we have to work with. So let's analyze the profile of the Swat Protohistoric samples first.

One thing I would like to discuss before we begin is the presence of BMAC/Oxus/Turanian Bronze Age DNA in these Swat samples. Many people take G25 models too seriously and believe there is upwards of 30-45% Oxus ancestry in the Gandhara samples. I think this is entirely wrong, as formal tools such as qpAdm reject BMAC decisively or give very little amounts of it (2-5%)

To illustrate my point, take a look at a G25 profile of the samples with BMAC + Sintashta.

30% BMAC in Loebanr_IA and 25% BMAC in Katelai_IA! Keep this ridiculously high number in mind. Now, let us see what qpAdm says. 

Katelai_IA (click for the file run)

1. weights
2. # A tibble: 3 × 5
3. target left weight se z
4. <chr> <chr> <dbl> <dbl> <dbl>
5. 1 Pakistan_Katelai_IA Russia_MLBA_Sintashta 0.163 0.0197 8.29
6. 2 Pakistan_Katelai_IA Indus_Gonur 0.816 0.0395 20.7
7. 3 Pakistan_Katelai_IA Uzbekistan_Dzharkutan_BA_1 0.0211 0.0459 0.459

2.1% BMAC/Oxus! down from the ridiculous 25% given before. 

Now, let's look at  Loebanr_IA

1. $weights
2. # A tibble: 3 × 5
3. target left weight se z
4. <chr> <chr> <dbl> <dbl> <dbl>
5. 1 Pakistan_Loebanr_IA Russia_MLBA_Sintashta 0.176 0.0194 9.03
6. 2 Pakistan_Loebanr_IA Indus_Gonur 0.832 0.0404 20.6
7. 3 Pakistan_Loebanr_IA Uzbekistan_Dzharkutan_BA_1 -0.00746 0.0463 -0.161

Pure BMAC is literally rejected as a source. Loebanr_IA gets modeled purely as Indus_Gonur + Sintashta.  This is doubt enough to make us deeply suspicious of G25 runs for South Asians that use pure BMAC as a source. What's likely happening here is an overfit + affinity to BMAC based on higher proportions of ANF/CHG ancestry that are missing from the Indus Valley samples we currently have. Increased sampling of the IVC might fix this. The only way Indians get any BMAC is indirectly, via Steppe sources mixed with BMAC like Dashti Kozy or later historic ones like Kangju or the Iron Age Yaz sample TKM_IA (Takhirbai_IA). This indirect BMAC ancestry peaks in North-Western populations at perhaps 15%, nothing more. G25 however is not able to differentiate IVC from BMAC at the moment, so all calculators using BMAC are not very useful at the moment.

This is indeed the conclusion that Narasimhan et al 2019 came to also. 

Therefore, here is a model of the Swat Protohistoric samples without BMAC/Oxus as a source.

Kumsay here serves as proxy of the kind of Central Asian ancestry the Andronovo Pastoralists might have picked up on there way to the subcontinent. Using the same model, here is what we get for modern North-West Indian and some Pakistani populations.

Modern samples have more Steppe than most of the ancient ones, but the devil lies in the detail and in population structure. The modern samples are fairly homogeneous (barring the Punjabi_Lahore set which is a mix of all kinds of Pakistani castes). Are the ancient sample sets also homogeneous? Let's see. 

Indeed, what we find is that the Iron Age samples are not homogeneous, which makes sense. The modern samples are from stratified and endogamous Indian caste groups that have avoided intermarrying each other for millenia, the ancient ones are a graveyard dump of all sorts of people. We see that some of the Loebanr_IA samples are as low as 5% Steppe (I12981, I12134) while some of the Katelai_IA are as low as 2% Steppe (I12446, I12470, I12460) while some are as high as 28% Steppe (I12141). The Udegram_IA, Saidu_Sharif_H and Butkara_IA ones are far more homogeneous. Saidu Sharif_H has one outlier that is like 33-35% Steppe and one outlier that is like <5% Steppe.

Here are all the runs posted. 

For Katelai_IA, will split it in 2 screenshots.

Similarly for Loebanr_IA due to large number of samples.

Even after accounting for most of the outliers, we can see that in general, the Iron/Bronze Age and Historic samples are about 5-8% lower Steppe_MLBA than modern North Westerners. Perhaps this points to different waves of migration and a different wave of Indo-Aryans giving rise to modern North Westerners (with differences amongst themselves too). This can be confirmed by Y-DNA to a regard, where tribes such as Khatris get 65% R1a-Z93 with most of it being the Indian L-657 while the Swat Protohistoric samples are maxxed out in J2, E1b, L-M20 with barely any R-Z93s. Hence, clearly different paternal lineages gave rise to lot of these tribes. Those lineages must've different in their exact autosomal profile too, even if it was very similar. For more on the Swat haplogroups, see this post of mine

Haplogroups of the Swat Indians..

Andronovo "camp-sites" in Oxus?

Remote Sensing and Survey of the Murghab Alluvial Fan, Southern Turkmenistan: The Coexistence of Nomadic Herders and Sedentary Farmers in the Late Bronze Age and Early Iron Age

Together with other peculiarities, the presence of seven large kilns testifies to the political-administrative importance of the tepe . Surrounding artefact concentrations represent rural villages, individual housing units and manured fields. In addition, traces of Andronovo camp-sites, characterized by the presence of Incised Coarse Ware (ICW), were recorded close to the main tepe . During the Achaemenid period, site 1529 together with its satellite settlements was an important and strategic political-administrative centre whose main function was the supervision of the desert border. The site also has the potential to shed light onto the relationship of nomadic and sedentary groups during the Bronze and Iron Ages.

In the same transect, specialised camp-sites were recorded interspersed betweensedentary agricultural communities, which indicate the beginning of interaction between nomads and farmers and an incipient process of sedentism (Cattani 2008a,2008b; Cattani et al  . 2008). An impressive ICW site (1468), c . 0.64 ha in size, with the evidence of three sunken dwellings, stone pestles and millstones was recorded approximately 7 km to the east of Takhirbai 3. The complexity and remarkable extent of the site suggests it may have been of an important new scale for the Andronovo community, possibly even a ‘center’ for their interaction with the settled communityof Takhirbai. Elaborate incised pottery characterises this site (Cerasetti 1998: 67-70;Tosi and Cerasetti 2010: 94-95). Farther to the east, numerous sites with wheel-made Bronze Age wares were found surrounded by scatters of ICW pottery on the sands. 

In one ofthe survey transects we found an impressive 3 ha Andronovo compound (Fig. 8). Thesite, located mainly on sands, is characterized by a pottery spread and eight distinctconcentrations. The central mound is separated from the other areas by sand dunes, which in some cases obscure continuous artefact distributions. The area with the highest concentration of sands yielded large quantities of hand-made pottery, mainly very large ICW fragments. 15  The presence of a small number of Late Bronze Age wheel-made sherds testifies to interaction with sedentary communities. Numerous cooking-ware fragments suggest the presence of a living area to the north-west of themain mound. A craft production area with evidence for kiln, kiln-slags, metal prills and numerous stone tools is located c . 40 m to the south-west. Numerous fragments ofwattle-and-daub building materials, typical for Andronovo camp-sites in the Murghab alluvial fan, were found scattered across the site. This site is the first example of a sedentary community with an Andronovo cultural identity.

As mentioned above, the progressive decrease in land suitable for agriculture presenteda simultaneous increase of grazing areas during the Bronze Age. One can imagine thatas a result, farmers leased their territories to cattle breeders in exchange for productssuch as milk and meat as well as textiles or pelts. Technology, including agriculturaltechniques, metalworking and possibly even architectural traditions seems to have been exchanged (Shishlina and Hiebert 1998: 222, 231 

Climate Change and the Rise and Fall of the Oxus Civilization in Southern Central Asia

 https://link.springer.com/chapter/10.1007/978-3-030-00728-7_14

Abstract

During the Final Bronze Age (around 3750/3700 BP), the proto-urban sedentary cultural entity in southern Central Asia—known as the Oxus civilization or Bactria-Margiana Archaeological Complex—underwent major social transformations in different field aspects leading to a deep cultural change in the middle of the 4th millennium BP. Among the different reasons suggested to explain these sociocultural changes, the hypothesis of global climate change in Central Asia at the beginning of the 4th millennium BP has been emphasized by different scholars. In this paper, I will examine current paleo-environmental data in relation with the climate evolution during the Mid- and Late Holocene. A critical assessment of the hypothesis of climatic change in Central Asia at the beginning of the 4th millennium BP allows to stimulate the discussion anew. I argue that the present data do not support a drastic climate change during the first half of the 4th millennium BP as a responsible factor for the fall of the Oxus civilization, although local environmental modifications should also not be underestimated and further investigated in a more integrated perspective of co-evolution of the ecological environment and the human societies.

Sanauli Chariots?

•  No precedence exists for the copper antennae tilt swords from mature harappan sites
•  No precedence exists for the cart burials
• Sanauli finds are efinitely a bullock-cart, round wheels too heavy to be pulled by horses. Word for bullock cart in Sanskrit is from Dravidian and replaced IE anas. 
• Daimabad late harappan finds definitely show it was a bullock cart.
• Sanauli burials are 100% a part of the OCP culture, OCP vases found there
• Also confirms Copper Hoards are part of OCP culture?
• Iconography of bulls found in the burials but no horses or horse bones, confirms they are bullock carts
• Parpola suggests BMAC influence/origin for the swords
• Corrects a lot of his grossly incorrect takes from The Roots of Hinduism. No longer believes that Catacomb is Proto Iranian. Does not believe Abashevo is Proto Indo Aryan, but that PIA was Fedorovo/Eastern Andronovo while Srubnaya was Proto Iranian.
• He points out that post-urban BMAC settlements are surrounded by Andronovo pastoralist campsites but south of this region, neither Andronovo pottery, nor its barrows are found. So logical assumption is Aryans adopted BMAC culture and continued their southward spread in the garb of this BMAC culture.
• Thinks a wave of Proto Indo Iranians came to India from the Petrovka culture, a Sintashta successor, and that these PII are responsible for the Sanauli finds (extremley implausible). Then these Indo Aryans introduced a magic/tantra based pre-Atharvavedic cult. 

https://journal.fi/store/article/view/98032

Uralic loans, BMAC substratum and agricultural terms of Indo-Iranian

Some important papers that discuss the three different possible loaning events of Indo-Iranian. It's well known that Indo-Iranian (henceforth, Aryan) had a limited agricultural vocabulary, and skipped many of the agriculture-related semantic shifts that characterize PIE > Proto-European as the livestock breeding Yamnaya shifted to a more farming culture after contact with the European Neolithic. Fatyanovo-Balanovo, the pre-Proto-Aryan culture, mostly survived of foraging and livestock breeding, with very little to no macrofossil evidence for any kind of agriculture, though some slash and burn has been suggested based on circumstantial evidence. This means it's important to pay close attention to the agricultural vocabulary of Aryan, since this would mostly have picked up from one of the many farming oriented Turan Neolithic societies in Central Asia, or later from the Harappans or Elamites. We also know that it's pretty likely that the Proto-Aryans (Abashevo? Sintashta-Petrovka?) were in direct contact with the Proto-Uralics (Sejma-Turbino Metallurgists?) and there is clear evidence of borrowings from Proto-Aryan into Uralic, though the reverse is less studied, and even lesser studied are possible Proto-Iranic and Proto-Indic borrowings in Uralic, as well as parallel borrowings by different branches of Uralic. Regardless, the Uralic borrowings are certain, and merit a review paper of their own.

The three kinds of loaning events in Aryan likely are

1) Into/from Uralic?
2) From BMAC/Turanian Neolithic?
3) From Dravidian/Language X into Indo-Aryan & Elamite > West Iranian?

The first one offers the best overview on the Uralic situation.

Indo-Iranian borrowings in Uralic : Critical overview of sound substitutions and distribution criterion

This dissertation discusses the Indo-Iranian loanwords in the Uralic languages. The loanwords that have been suggested in earlier research are critically analyzed and commented based on modern views of Uralic and Indo-Iranian historical phonology and etymology. The etymologies are analyzed on the basis of the general methods of loanword research: arguments of phonology, distribution and semantics are taken into account. In addition to the analyzis of older etymological proposals, also some new etymologies are presented. Also the research history of the topic is discussed. The aim of this study is to establish rules for the sound substitutions and bring new light to the relative chronology of the loanwords. Because the phoneme systems of Proto-Indo-Iranian, Proto-Iranian and later Iranian languages were very different from those of Proto-Uralic and its daughter languages, the phonemes of the Indo-Iranian donor languages have been substituted in various ways in the Uralic languages. Differences reflect both conditional developments (different substitutions in different environments) and chronological differences, and it is often difficult to distinguish between the two.

 The second paper by Alexander Lubtosky reviews the substratum (collection of possible non-Indo-European origin words) in Aryan and lists out likely/unlikely inherited vocab, as well as the basic laws for establishing non-IE words in Aryan, and possible Wanderworts.

The Indo-Iranian substratum

In my paper, I shall apply this methodology to the Indo-Iranian lexicon in search of loan words which have entered Proto-Indo-Iranian before its split into two branches. As a basis for my study I use the list, gleaned from Mayrhofer's EWAia, of all Sanskrit etyma which have Iranian correspondences, but lack clear cognates outside Indo-Iranian. The complete list of some 120 Indo-Iranian isolates is presented in the Appendix. The words of this list are by default characterized by the first of the above-mentioned criteria, viz. limited geographical distribution, but this in itself is not very significant because thelack of an Indo-European etymology can be accidental: either all other branches have lost the etymon preserved in Indo-Iranian, or we have not yet found the correct etymology. Only if aword has other features of a borrowing, must we seriously consider its being of foreign origin.The analysis of phonological, morphological and semantic peculiarities of our corpus will be presented in the following sections, but first I would like to make two remarks.

I use the term substratum for any donor language, without implying sociological differences in its status, so that substratum may refer to an adstratum or even superstratum. It's possible that Proto-Indo-Iranian borrowed words from more than one language and had thusmore than one substratum.Another point concerns dialect differentiation. In general, we can speak of language unity as long as the language is capable of carrying out common innovations, but this does not pre-clude profound differences among the dialects. In the case of Indo-Iranian, there may have been early differentiation between the Indo-Aryan and Iranian branches, especially if we assume that the Iranian loss of aspiration in voiced aspirated stops was a dialectal feature which Iranianshared with Balto-Slavic and Germanic (cf. Kortlandt 1978: 115). Nevertheless, Proto-Indo-Iranian for a long time remained a dialectal unity, possibly even up to the moment when the Indo-Aryans crossed the Hindukush mountain range and lost contact with the Iranians

The last paper is really a chapter by Martin Kümmel for the book 'Language Dispersals Beyond Farming' and so specifically takes a look at the agriculture related vocabulary of Aryan.

Agricultural terms in Indo-Iranian

The article investigates the agricultural lexicon of Indo-Iranian, especially its earlier records, and what it may tell us about the spread of farming. After some general remarks on “Neolithic” vocabulary, a short overview of the animal husbandry terminology shows that this field of vocabulary was evidently well established in Proto-Indo-Iranian, with many cognate terms. Words for cattle, horses, sheep and goats are well developed and mostly inherited, while evidence for pigs is more limited, ad the words for donkey and camel look like common loans. A more extensive discussion of plant terminology reveals that while some generic terms for grain are inherited, more specific words for different kinds of cereals show few inherited terms and/or irregular variation, and the same is even clearer for pulses and some other vegetables. The terminology for agricultural terminology is largely different from that of most European branches of Indo- European. The conclusion is that the cultural background behind these linguistic data points to spreading of a mainly pastoralist culture in the case of Indo-Iranian.

An Iranian from 1800 BCE

While scourging through the Narasimhan supple, I found a sample that caught my eye. It clustered on a PCA with modern Iranians and on G25 distances, it had the lowest distances to modern Iranians; however, it was from the post-BMAC site of Sappali Tepe in Uzbekistan and dated to ~1800 BCE cal. 

The supplementary describes it as such.

BMAC_o2 (n=1): This individual has a significantly elevated proportion of ancestry related to

Central_Steppe_MLBA. We call this individual by the BMAC_o2 analysis label and the

Sappali_Tepe_BA_o split label.

• UZ-ST-010, Sappali Tepe (ST) 1975, 6, Grave 02-05 (I7493): Context date of 2000-1600

BCE. Genetically male.

Distance to: UZB_Sappali_Tepe_BA_o

0.03315719 Iranian_Zoroastrian
0.03528786 Iranian_Fars
0.04027134 Iranian_Persian_Shiraz
0.04254455 Azerbaijani_Dagestan
0.04405072 Ezid
0.04435116 Iranian_Mazandarani
0.04586352 Iranian_Lor

On a PCA, Sappali Tepe clusters with other Iranians as well, shifted a bit to the extreme end of the West Iranian Steppe % The rest of the Sappali Tepe site is regular post-BMAC and accordingly clusters with other BMAC (Gonur1) and post BMAC (Bustan BA) sites. So it's obvious this outlier has BMAC + Steppe ancestry. Not that out of the ordinary, right? Even TKM_IA has this mixture.

Target: UZB_Sappali_Tepe_BA_o:I7493
Distance: 4.9056% / 0.04905551
65.2 UZB_Sappali_Tepe_BA
34.8 RUS_Sintashta_MLBA

Poor distance, but where it gets interesting is when you add West Iranian farmer ancestry.  

Target: UZB_Sappali_Tepe_BA_o:I7493
Distance: 3.0157% / 0.03015733
48.2 IRN_Seh_Gabi_C
33.2 RUS_Sintashta_MLBA
18.6 UZB_Sappali_Tepe_BA

This is great, the distance improves a lot. This must mean this individual is a mix of West Iranian type farmers + early East Iranian (TKM_IA) type ancestry. Now, interestingly enough, this must mirror the actual process by which modern West Iranians came to be. Steppe pastoralists mix with Turan_BA (BMAC) type people and form a hybrid 50:50 ish population in the region surrounding modern Tajikistan. This population eventually comes down to the Iranian plateau and mixes with the native Elamite farmers to form modern West Iranians. 

So, let's model it with TKM_IA too, but first add in Indus Valley. 

Target: UZB_Sappali_Tepe_BA_o:I7493
Distance: 2.3048% / 0.02304809
57.2 IRN_Seh_Gabi_C
32.8 RUS_Sintashta_MLBA
10.0 IRN_Shahr_I_Sokhta_BA2

Modern Iranians likely received an additional wave of Levant_C or Anatolia_C that mixed with their Sehi_Gabi type pop, so might as well as try it with that too.

Target: UZB_Sappali_Tepe_BA_o
Distance: 2.1811% / 0.02181055
52.2 TKM_IA
26.6 IRN_Seh_Gabi_C
12.4 Levant_ISR_C
8.8 Indus(Sis2+Gonur)

Yep, way better fits. TKM_IA likely also absorbs nearby WSHG/ANE type ancestry.

Can we replicate this on qpAdm? Let's try. 

Uzbekistan_SappaliTepe_BA_o

Turkmenistan_IA.SG 49.2% ± 9.4

Iran_C_SehGabi 19.8% ± 9.5

Israel_C 20.1% ± 5.6

Indus 10.9% ± 7.3

p-value:  0.300

(Outgroups: Mbuti, EEHG, WEHG (Iron Gates), WSHG, ESHG, Han, Tianyuan, TurkeyN, IranN, Levant PPN, Iberomaurusian/Natufian (optional), CHG, MA1 (optional), Kostenki14 (optional))

This is pretty close to our G25 results. This would mean Sappali Tepe has around ~25% Sintashta ancestry, thus being a perfect fit to model modern Iranians with (who have quite a bit lower Sintashta).

By the way, I tried Anatolia_C and Rus_Maykop_Nosovko as sources too. Former gives quite decent fits on qpAdm and works equally well as a source, but drops TKM_IA to 40% ish. Latter is a poor source, but I decided to try it anyways as some outliers in Bronze Age Turan carry Caucasus ancestry (like the Dzharkutan outliers from Uzbekistan which are Caucasus + Steppe). 

I also tried out other IranN rich profiles such as Sarazm, Geokysur, Parkhai, Namazga as well. They give much poorer fits on G25 and qpAdm. Anyway, let's just do a Dstats run to see if there is indeed allele sharing b/w the two, and to what extent.

result:  Chimp.REF Uzbekistan_SappaliTepe_BA_o Anatolia_C   Israel_C     -0.0235    -4.133     -    7424   7781 153314 

Significant negative Z score, so it looks like Anatolia_C is actually preferred as the Chalcolithic source over Israel_C.  G25 shows the same, the fit improves when we use Anatolia_C. 

Regardless of the exact Chalco source, let's try and model Modern Iranians with the Sappali outlier.

Target	Distance		IRN_Seh_Gabi_C	IRN_Shahr_I_Sokhta_BA2	Levant_ISR_C	MNG_Slab_Grave_EIA_1	UZB_Sappali_Tepe_BA_o	Yoruba
Iranian_Bandari	0.02025044	•	26.6	20.8	0.8	0.0	48.8	3.0
Iranian_Fars	0.01639102	•	27.2	0.8	7.0	2.2	62.8	0.0
Parsi_India	0.01486118	•	10.8	29.2	13.4	0.8	45.8	0.0
Parsi_Pakistan	0.01436086	•	9.6	27.4	12.8	0.8	49.4	0.0
Iranian_Lor	0.01120472	•	35.8	0.0	10.8	1.2	52.2	0.0
Iranian_Mazandarani	0.01877939	•	44.8	3.4	0.0	0.0	51.8	0.0
Iranian_Persian_Shiraz	0.01724956	•	29.0	3.6	9.4	2.6	55.0	0.4
Iranian_Zoroastrian	0.01704363	•	22.4	0.0	6.6	0.0	71.0	0.0
Average	0.01626760	•	25.8	10.7	7.6	0.9	54.6	0.4

Very good fits. If Sappali is around 24-27% ish Steppe, then this gives Iranian Zoroastrians around 18-19% Steppe, which sounds just about right. So this individual from 1800 BCE Uzbekistan is indeed quite close to a modern West Iranian. 

His haplogroup is Q1b2, which is an India specific branch of Q1 (found in the Swat Valley Loebanr samples) and this kinda gives more evidence for the 10-11% Indus Valley ancestry in him. 

This individual is remarkably similar to another outlier from 1500 BCE Uzbekistan, who I discussed in my substack here. However, this outlier clusters with modern Indo-Aryans and contains the 3 way Steppe + Indus + Onge admix that characterizes modern Indians. The Sappali Tepe outlier contains the 3 way mix that characterizes modern Iranians: Steppe + BMAC + Iranian chalcolithic farmer. 

Now, we cannot be possibly sure what language this outlier spoke, but my bet is it was likely some form of early Iranian, thereby meaning the genepool that characterizes modern Indians and Iranians had already formed in Central Asia by 1600-1800 BCE.