Saturday, October 14, 2017

3,000ybp Pastoralist proves an old point

Well, a while ago now I pointed out that, simply using modern DNA, various Southeast Africans clearly looked partly descended from peoples closely related to modern Somalis and other Horn-Africans of Erythraeic and Ethiosemitic speaking origins (see here and here) and it seems ancient DNA is now backing this up:

[1] "distance%=0.3802 / distance=0.003802"


Tanzania_Luxmanda_3000BP 50.7
Dinka 49.3

That's an nMonte model above utilizing a new 3,000 year old pastoralist sample from Tanzania belonging to the Savanna Pastoral Neolithic culture strongly tied to South-Erythraeic speaking people who began leaving the Horn of Africa for Southeast Africa some 3,000-4,000 years ago. You can see the fit is decent, showing significant Savanna Pastoral Neolithic related ancestry in this average for the Maasai Kinyawa samples in the Global-10 PCA.

We owe this new sample to a study headed up by Pontus Skoglund and it comes with a lot more details I'll be poring over to some extent quite soon but for now; I'm just putting this paper out there and sharing that we finally have some aDNA backing for what modern DNA, archaeology and linguistics have been positing for quite a while now regarding South-Erythraeic speakers and their influencing of Southern and Southeastern Africa.

Do read the study in the meantime, though.


Reconstructing Prehistoric African Population Structure, Skoglund et al.

Kostenki-14's Craniofacial Morphology

Saw this post over at Eurogenes and felt I had to read the study being shared. The study Eurogenes' author shared makes two main claims:

  • That Kostenki-14, a 36,200-38,700 year old European, does not look like Papuans and Melanesians (Australo-Melanesians) as previously claimed by authors such as M.M Gerasimov and G.F. Gebets.

  • That Kostenki-14 supposedly fits with what they call the "Caucasian complex".

The first statement would make some sense and, as far as I recall, craniometric data on other Upper-Paleolithic Europeans didn't tend to imply a strong similarity to Papuans or Melanesians or the like.  So, it would be rather odd if Kostenki-14 looked a lot like those populations. He'd be something of a strange outlier, I believe. Gerasimov and company seem to have just exaggerated the affinities based on certain traits Kostenki-14 has like marked alveolar prognathy which this new paper, for the record, finds he does actually have going.

M.M. Gerasimov (left) and A.N. Rogachev during work at Kostenki 14 site (Markina Gora), 1954.

The second statement, however, is what's suspect. Firstly, if we're talking about a so-called "Caucasian complex" where Kostenki-14 seems overall more similar to various pre-historic Europeans than to Southeast Asians, Ryukuans, Papuans and Melanesians then it seems clear that he would fit within such a complex and prove to, overall, share more craniofacial similarities with fellow pre-historic (and probably even modern) Europeans but it's otherwise clear that he does not actually fit into the more modern definition of what constitutes being "Caucasoid" in cranioform:

The position of the Kostenki 14 man in the CV I–II space is illustrated by a graph (see Fig. 1a): this individual, by the sum of craniometric indicators, is unambiguously characterized by the European complex of characters and shows no noticeable deviation toward tropical groups. Note that we are not speaking about its full similarity to any individual ancient European series. On the contrary, the results of our analysis show a sufficiently noticeable anthropological distinctness, which CV IV demonstrates (see Table 1). It separates the Kostenki 14 individual from all the series included in the analysis (see Fig. 1b). The size of differences is very great, amounting to 43% of the total variability range according to CV IV. This vector practically fully depends on one character, namely, the nose height, which is extremely small in the Kostenki 14 individual. Interestingly, the face height in this case is of little significance.

As someone who was once quite interested in craniometrics (and still somewhat am); I'd seen Kostenki-14's skull years ago and how low his nose height in particular seemed even at face-value was never lost on me:

Simply compare that to this archetypal example of a modern male "Caucasoid" skull of European origin from Bone Clones Inc., Osteological Reproductions:

Just so some are following, having just this much of an outlier nose height would would disqualify him from being an actual "Caucasoid" in the more traditional and modern craniofacial sense of the term, and this without even going into other ways in which he looks distinct such as his marked alveolar prognathism and likely rather paleolithic robusticity.

Kostenki-14 reconstruction by M.M. Gersasimov

Now, finally, there's one other statement that really stuck-out to me in the Eurogenes post and that's that Mikhail Mikhaylovich Gerasimov's reconstruction of Kostenki-14 is wrong. This is not true, as far as I know. The Russian paper doesn't even touch upon the reconstruction's validity (they actually display it without any sort of refutation against it in their study); all they seem to refute about Gerasimov's previous work on Kostenki-14 is the morphological affinity Gerasimov and company noted toward groups such as Australo-Melanesians.

The types of reconstructive techniques Gerasimov employed have been reportedly rather accurate. And reconstruction itself, when done right, can definitely be more of a science than an art.

Kostenki 14's location on map
But also, reconstruction is a different matter entirely from the sorts of craniometric measurements conducted in this new paper or that were once put together by Gerasimov and others. Their measurements or findings in that respect being off and overstating an affinity toward Australo-Melanesians does not actually play into how accurately they reconstructed Kostenki-14's looks. Though I would be interested to see other anthropologists take a crack at reconstructing Kostenki 14 in the future.

But all in all, he wasn't "Caucasoid" in the traditional sense and yes; that reconstruction, as far as we know, was roughly what he looked like in terms of facial features.


1. The Upper Paleolithic Man from Markina Gora: Morphology vs. Genetics?, Khartanovich and Zubova 2017

2. Facial reconstruction – anatomical art or artistic anatomy?, Wilkson 2010

3. Facial Reconstruction, Jenny Omstead 2011

Thursday, October 5, 2017

Lowdown on the recent Minoan and Mycenaean samples

I've had some ask me questions on how things seem regarding the new Minoan and Mycenaean samples and since I've slowly been getting back in the game lately, I figured I'd wade into things simply and swiftly.

I often tend to think PCAs (principal component analyses based on autosomal SNPs) are more straight-forwardly telling and useful for getting a point across and the one above really helps summarize how these new samples generally look.

The Minoan samples

In the PCA, the Minoans nearly join what I'd dub the EEF/ANF/LNF/LHG continuum. A continuum formed by populations seemingly rich in VHG-related ancestry and Basal Eurasian ancestry with Natufians (LHGs/Levantine Hunter-Gatherers) so far proving the most Basal Eurasian and Early-European-Farmers (EEFs), descended from a mixture between Anatolian Neolithic Farmers (ANF) and European Hunter-Gatherers of the so-called Villabruna-cluster, proving the most VHG-related.

This continuum's source is ultimately West-Asia with its most VHG-related end (various EEFs) acquiring more VHG-related ancestry in Europe after their ancestors migrated to the region from Anatolia, bringing agriculture along with them to the formerly Hunter-Gatherer dominated region.

The Minoan samples from Lasithi and Odigritia practically do fall within this continuum and would seemingly sit right in-between Anatolian-Neolithic-Farmers and Levantine-Neolithic-Farmers (LNF) if not for a clear eastern-pull being present within them which implies ancestry outside of this continuum giving them an elevated Ancient North Eurasian-related affinity and the study does address that in its abstract alone:

"Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean and most of the remainder from ancient populations related to those of the Caucasus and Iran."

Basically, they've found that the Minoans have ancestry from what I'd call the aforementioned continuum's opposite continuum: a continuum of sorts between Caucasian Hunter-Gatherers, Iranian Neolithic Farmers (INF) and a Hunter-Gatherer sample from the Hotu cave in Iran. These particular pre-historics seem to be largely composed of Ancient North Eurasian-related ancestry and Basal Eurasian ancestry as well as perhaps some Villabruna-related ancestry as in the case of CHGs.

And the paper shares some formal-stat based models in its supplementary information to back what its abstract says up:

The models above basically show that the Minoans can be modeled as part something related to Neolithic Anatolians and part something related to Neolithic Iranians and Caucasian Hunter-Gatherers with those models, as you can see with the second set, showing the lowest standard errors/fitting the best. The paper basically summarizes the nature of the Minoan samples in the researchers' opinions with this bit in the supplementary information pdf:

"The Minoans themselves could be modelled as a mixture of Neolithic Anatolians and Caucasus hunter-gatherers, but they could not be successfully modelled as mixtures of later populations."

The emboldened bit is somewhat interesting as I doubt, for obvious reasons, that these Minoans are really a direct intermixture between Neolithic Anatolians and Caucasian Hunter-Gatherers or Neolithic Anatolians and Iranian Neolithic Farmers. It's obviously much more likely that they got such ancestries and affinities by way of proxy from later populations. I.e. from neighboring populations in Anatolia carrying something like Chalcolithic Iranian-related ancestry:

[1] "distance%=0.5658 / distance=0.005658"

Greece_N:Klei10   68.8
Anatolia_BA:I2683 31.1

In the above nMonte model using Global-10 PCA positions, a population akin to Bronze Age Anatolians that intermixed with the earlier ANF/GNF type inhabitants of Crete would have been responsible for the more eastern-pull carrying CHG/INF/IHG related ancestry. And I'd say it's more sensible to assume this sort of way is how the admixture made its way to the area (by way of proxy) but I'm of course not at all detracting from the authors' findings which is that these Minoans look to carry ancestry related to the CHG/INF/IHG continuum. [Important Note]

That being said, I'd also say the lowdown is that these Minoans are visibly distinct from modern Cretans and neighboring mainland Greeks. They're notably more ANF/GNF-related and seem to lack the steppe-related influences in later inhabitants which makes good sense given that they are generally accepted by scholars to not have been Greek/Indo-European speakers and, as a result, seem to trace the majority of their ancestry back to pre-historic West Asia.

However, given that you can model even modern mainland Greeks as being close to a 60% Minoan population - :

[1] "distance%=0.0682 / distance=0.000682"

Minoan_Lasithi   48.25
Ukrainian_West   20.05
Yamnaya_Kalmykia 16.25
Minoan_Odigitria 13.90
Polish            1.55

[1] "distance%=0.0499 / distance=0.000499"

Minoan_Lasithi   59.40
Srubnaya         30.75
Ukrainian_East    4.25
Minoan_Odigitria  3.65
Srubnaya_outlier  1.95

- we're not remotely talking population replacement here. We're just looking at a shift over-time toward Europe caused by various migrations (like that of early Greek speakers and medieval Slavic speakers) bringing in elements such as ancestry from the Pontic-Caspian Steppe.

The Mycenaean Samples

As both the PCA and the study impart, there's not a huge difference at all between the Minoan and Mycenaean samples but there is a difference.

The Mycenaeans come quite close to entering yet another continuum of sorts. This continuum, however, is much more modern. It's been dubbed by some, including myself, as the Eastern Mediterranean continuum and is essentially a cluster inhabited by Sicilians, the Maltese, Western Jews, various Greek islander populations such as modern Cretans, and, finally, Cypriots. 

This is essentially a continuum for populations that serve as a sort of bridge between mainland Southern Europe and the Levant with Cypriots being the most Levantine shifted population:

[1] "distance%=0.4026 / distance=0.004026"

Lebanese_Christian 71.2
Greek              28.8

And Sicilians being the most mainland Southern Europe shifted population:

[1] "distance%=0.5027 / distance=0.005027"

Italian_Tuscan     65.7
Lebanese_Christian 34.4
These Mycenaeans look to lie somewhere in-between the two and have, as the PCA implies, something of a lower eastern-pull than usual, bringing them just a smidgen closer to the EEF/ANF/LNF/LHG continuum. The study itself imparts the following:

"We have successfully modelled Mycenaeans as a mix of (i) Neolithic populations of Anatolia, Neolithic Iran or Caucasus hunter-gatherers, and eastern European huntergatherers or Upper Paleolithic Siberians, (ii) Neolithic Anatolians and Chalcolithic-to-Bronze Age people from Armenia, or (iii) Minoans and Bronze Age people from the Eurasian steppe (or from mainland Europe after the arrival of steppe ancestry there)..."

This is indeed quite easily noticeable via means such as nMonte when a non-academic like myself takes a look:

[1] "distance%=0.2597 / distance=0.002597"

Minoan_Lasithi   85.0
Sintashta         8.4
Yamnaya_Kalmykia  6.6

[1] "distance%=0.2985 / distance=0.002985"

Minoan_Lasithi      84.1
Srubnaya            15.9

The general picture just seems like they're basically close to a majority Minoan-like population that just had some steppe admixture (~10-15%) tacked onto it. This makes sense given that the Mycenaeans were Greek speakers, they were in fact the first known culture to have written Greek down, and the Indo-European language they were speaking would have most likely been brought to Greece by people substantively descended from Bronze Age Steppe pastoralists very similar in ancestry to the pre-historic peoples of the Yamnaya, Srubnaya and Sintashta cultures.

Although, I wouldn't simply interpret this as "The Mycenaeans are descended from the Minoans and are just them + some steppe ancestry." I'd say it's more sound to assume there were Minoan-like peoples in the areas of mainland Greece that these Mycenaean samples are from and it was these people who acquired early Greek alongside steppe admixture intermixed with a complex cultural framework that was already present via being influenced by the likes of the Minoans to herald the first true pre-modern Greek civilization.

Now, there's more information to be had like the uniparental (Y-DNA and mtDNA) results of some of these new samples or some phenotypic data acquired via genomic analysis but this post was ultimately just concerned with summarizing the autosomal affinities shown by these Minoan and Mycenaean samples so I'll leave it at that for now. I also advise reading the full study + its supplementary materials if you wish to know more, of course.


1. Genetic origins of the Minoans and Mycenaeans, Lazaridis et al. 2017


1. You can understand how nMonte works by going here. And my thanks go to the author of the Eurogenes genome blog for the PCAs used for nMonte and the one shared visually in this post.

2. I've noticed that some people are making a big deal about the lack of either R1a or R1b subclades found among the Mycenaeans given that they, unlike the Minoans, would have been Indo-European speakers, and I'd just like to point out that the Y-DNA sample-size here is literally n=1. 1 sample that's J2a1, that's it. I'm sure once we have more samples some R1b and the like will pop-up given the obvious steppe ancestry these Mycenaeans carry.

3. This is a somewhat decent discussion on the study to check out, though it slightly goes off the rails at times later into the thread.

4. For those wondering why I haven't made a post on the recent African papers; this post was mostly done several weeks ago, I just made some minor edits today and posted it. I'm a little busy lately but will try to make posts on those African studies soon.