Thursday, May 14, 2015

New Paper on Ashkenazi Jews: We should wait for ancient samples from the Levant

Seems as though we're in for a new paper on the ancestry of Ashkenazi Jews which seems to posit that they do indeed have European admixture but mostly of Southern European/ Italic origins.

It seems to be a rather valiant effort, mind you and even finds some Eastern European ancestry in Ashkenazi Jews but I must agree with David Wesolowski over at Eurogenes (the blog's author); this paper looks to be on to something but there's one key flaw; it's using modern populations and not ancient samples to make its inferences. This is relevant because if we're learning one thing through the constant sampling of ancient remains across Europe is that "Modern Populations Ancient Populations". 

This principal seems to even ring true for some ancient populations that existed as early as ~2,500 years ago. They've sampled three ancient Etruscans from about ~2,500 years in the past and surprisingly enough; they do not seem to be well-represented by modern day Tuscans in Italy despite modern Tuscany and surrounding parts of the Italian peninsula corresponding well with where the Etruscans once were. [1]

Modern populations in my humble opinion are simply not a viable proxy for the peoples who lived where they now toil away a few or several thousand years ago. They're surely descended from those people to some great extent but clearly not a frozen image of said ancient group's genome. 

And herein lies the problem; we lack ancient genomes from the Levant. And therefore we honestly lack a true proxy for what could be an ancient Levantine. David voices this concern on his blog; posting that he believes the ancient Near East wasn't genetically what it is now. And he's probably right. We can't be sure exactly how Southern European Ashkenazi Jews are because we lack an example of what a "pure" pre-Western Jew exodus and even pre-Arabization/ Arabian conquest Levantine looked like so we lack something concrete to compare them to and see just how much they've shifted away from what Yahudim were like before their exodus.

Modern Arabs in the Levant are mostly the Arabized descendants of former Aramaic speakers who do seem to clearly have some Peninsula Arabian genetic input as can be surmised from their
Haplogroups as you can see for example through the J1 Project. This effect seems to be greater for example in Muslim Levantines who prove somewhat distinct from their Christian neighbors though not at all by any note worthy amount. [2]

Cypriots may prove a good example of the ancient Levant perhaps because they're an island population given that Sardinians; a fellow island population come out to be a genetic isolate in Europe [3] [4], predominantly descended from Early European Farmers with very little Steppe derived ancestry. Islanders can at times prove a preservation of what close by mainland populations used to be like as they could have avoided whatever land expansion affected their mainland kin. 

However Cypriots who speak Greek for example could very well have Southern European admixture due to becoming Hellenized and shifting to Greek linguistically. Though any reader reading this must forgive me as I'm not too knowledgeable about Cypriot genetics other than that Cypriots seem to look like a Levantine population (similar to Western Jews and Arab Levantines more than anything else) especially in terms of their fundamental ancestral components and the proportions they have them at (Eurogenes K=8).

Other groups like Samaritans may prove to be reliable genetic isolates of the Levant but still; we're learning via Europe time and time again that assuming modern populations are a perfect example of their ancient predecessors is a slippery way of seeing things. 

Suppose Levantines from ~2,000 years ago or from right before the ancestors of Ashkenazi Jews departed prove to actually carry a notable amount of Western European Hunter-Gatherer and Early European Farmer-esque ancestry. Wouldn't that prove the results of this paper (the exact proportions of Italic-esque ancestry in Ashkenazis) to be incorrect? And Ashkenazim would suddenly look a lot more Near Eastern.

I'm doing a lot of blabbering here to say something quite simple in truth. We lack ancient samples from the Levant and neither Western Jews nor Arab Levantines are to be taken as a trustworthy example of the ancient Levant as both groups have seemingly experienced non-Levantine gene flow, one from Europe (mostly from Southern Europe) and the other from the Arabian Peninsula. Until we have ancient individuals from the Levant to compare these populations to; we should remain cautious about trusting how non-Levantine either group is.

However I do not at all doubt the core of what this paper will be preaching (I did once though...) which is that Ashkenazim do seemingly have some substantial non-Levantine admixture mostly of a Mediterranean European nature and also a much much smaller amount of Eastern European admixture.

Reference List


Tuesday, May 12, 2015

I'd like to clear up some inaccuracies

In my very first blog post where I attacked the concept of racialism I made some statements about population genetics and well... I've learned more as I hope many who read this blog and the papers I cite have since. In this post I'd like to correct some inaccuracies in some of things I posted practically 6 months ago (it's surreal that it's been that long).

I've actually corrected these inaccuracies with my blog posts over the last several months (my second ever post in fact did make a point of adding new information to what I'd posted in my first one about Early European Farmers) but I'd like to touch upon them again but this time on their own rather quickly in this blog post.

I originally made the statement that Eastern Non-Africans/ East Eurasians like the Andamanese man to the right and his child were (alongside Australian Aborigines and Pacific Islanders) more distant from Africans like Niger-Congo speaking Africans and non-West Eurasian admixed East Africans than Europeans and West Asians were.

Well, some indeed are; at least in the case of Australian Aborigines and Papuans who have notable levels of Denisovan admixture which is presumed to be the cause for why they're more distinct from African populations like the ones I mentioned than populations like Europeans are. [1]

And I indeed was on the mark when I said that the man to the right and his son are full-blown Eurasians (of an 'Out of Africa' population) and don't have any post-Out of Africa African ancestry while many West Eurasians and North Africans such as Arab Levantines, Peninsula Arabians, Egyptians, Moroccans and so on do indeed have actual post Out of Africa African admixture so in this case; many West Asians and North Africans are closer to Africans than Eastern Non-Africans are. [2] [3] [4] However the claims I made that West Eurasians (Europeans + West Asians) as a whole thanks to Basal Eurasian are closer to Africans than Eastern Non-Africans are was not entirely correct as I was depending on Fst values to make these assumptions and I'll get into that more with the Basal Eurasian section below.

As that table above demonstrates; Papuans are more distinct/ varied from Yorubans than Frenchman and Han Chinese are, that is indeed true. [1] However as I mentioned in my East Eurasians focused post in the past; this is likely mostly due to them having their levels of Denisovan admixture. Not all non-East Asian East Eurasians (those who may lack the higher levels of Denisovan admixture found in Australian Aborigines and Papuans) are as distant as Papuans are from Niger-Congo speaking Africans, instead, I wager their variance from Yorubans would be comparable to what you see for the Frenchman and the Han above.

Basal Eurasian

My actual post on this component since I made my very first blog post was more or less spot on with
no real inaccuracies that swayed away from the peer-reviewed data I was depending on from what I recall. However in my first blog post I made the claim that Europeans for example for having Basal Eurasian admixture were closer to East Africans (those of a non-Eurasian admixed variety) and Niger-Congo speaking Africans than East Eurasians/ Eastern Non-Africans are. 

First off, Basal Eurasian isn't exactly what I said it was in my very first post but is what I said it was in my actual long post dedicated to it though even in my first post I mentioned fervently what  those in the field of academia more or less made of it for now (Out of Africa isolate). It's not a component (for the time being) with a real African affinity as I said with my first post but instead as I said in its own post; at best a Quasi-African component. It is closer to the East African origin point ("Non-African" in the diagram and sometimes dubbed "Proto-Eurasian") of all Out-of-Africa (OoA) populations (Eurasians, Pacific Islanders, Native Americans etc.) than other Eurasian/ OoA components are; it's highly divergent from all other Eurasian components and is seemingly more Basal to them than Ust-Ishim which Haak et al. finds to be basal to all so far discovered Eurasian ancestral components except for Basal Eurasian. [5] 

However it ultimately lacks any confirmed African affinity. It is clearly somehow still grounded in its Eurasian-ness, as it's clearly still a Eurasian component but again (as my post on it says); it's a statistical concept for now and we don't really have full knowledge of what it is. We may hopefully grasp it completely once we have ancient genomes from West Asia but for now; the academia are cautiously and understandably sticking to what their current data seems to be saying; that it's an Out-of-Africa isolate the way I explained it in my first post. [6] [7]

 Also; as I explained in my actual post about Basal Eurasian; Fst values aren't to be taken too seriously as a real measure of "genetic distance" / variance at least in some cases. And Fst values were what I was mainly depending on for my assumption that Europeans for example were closer to African populations than East Eurasians (Han, Papuans etc.) were.

Fst values like the ones represented in the diagram to the left of this text [8]; can be influenced by a whole foray of variables not truly indicative of a population's real variation level from another population. For example it can be skewed by a heightened level of genetic drift  and some such. And as an old friend put it:

"Fst looks at the variation between entire groups, which is why more isolated East Asians will have an increased distance to others, like e.g. Africans. This effect is the most pronounced in Native Americans, who tend to be the most divergent from Africans with respect to Fst distance."

A real measure of the variance between groups would be better and that is represented in the table I shared earlier showing you Papuans, Neanderthals, Han and the like... In that case Europeans don't truly show an African pull of sorts and Basal Eurasian's Out-of-Africa-ness seems rather solid for now. Though as I stated in the East African cluster's blog post; groups with ancient East African ancestry in Africa like Niger-Congo speakers (as per their mtDNA markers for example) do demonstrate a greater pull/ similarity toward Eurasians than groups that would mostly lack such ancestry like non-Bantu and East African admixed San. 

To be honest; I've encountered a lot of people who've been fooled by Fst values/ "Fst distance"; using as a real measure of the distance between populations; they're in truth not to be too relied upon for that though they can be quite useful in some cases. 

In essence; the only real mistake I'm trying to correct here is one that surfaced through me making too much of Fst distances and not seeing more reliable measures of the variance between populations and that lead me to make the still true statement that for example Papuans are more distant from Yorubans than Norwegians are but it's not because of Basal Eurasian being in Norwegians but most likely because Papuans are last I checked about ~5% Denisovan while Norwegians aren't (but not all East Eurasians are more distant from Africans than Europeans are. F.e. the Han's variation from them is comparable to that of a European population like the French) Basal Eurasian is a highly divergent ancestral component that we don't know everything about just yet but it doesn't make West Eurasians any closer to Africans than Eastern Non-Africans (East Eurasians) are and it's at best Quasi-African at least for its close-ness to the very base of Eurasians which is ultimately very ancient East African in origin as per the Haplogroup evidence (Y-DNA an mtDNA) and the very real affinity the East African component has for Eurasians.

Beyond that; I can't think of anything else that truly needs correcting especially if you've been keeping up with my other blog posts since that very first one. So... Take care and I hope you enjoy this blog.

Reference List:

6.  Ancient human genomes suggest three ancestral populations for present-day Europeans, Lazaridis et al.

7. Genome Sequence of 45,000-year-old modern human from western Siberia, Fu et al.

8. The Genetic Structure of Pacific Islanders, Friedlaender et al. 


1.  I made this post mostly because I noticed that my very first blog post gets a good amount of my traffic and well... It's much more important that you all actually read the other posts where I actually share information on various populations and so on rather than sifting through that old post where I was making a political statement more than anything (not really my forte at any rate) and well; I always advise you to consult the papers I link you to. 

You're not supposed to take my word for anything. My blog posts just like any book, Wikipedia article or even paper are not reliable on their own. Instead I advise you to always read the sources I or other sources share and the data we share as well and add that on top what we're saying to make your final judgments. Always think for yourself... 

But I assure you; as the making of this post demonstrates-> I take great pains to make sure I share the most objective and accurate information I possibly can on the subjects I touch upon and try to make sure you yourself are informed through your own research by sharing my various credible sources.

2. The Hodgson et al. paper I shared has flaws as I've touched upon in the past but it shows you how Egyptians and Arabians have African admixture so that was the point in sharing it as a source.

Sunday, May 10, 2015

The Khazar Theory: Give it a Rest

This theory comes up quite often, as a matter of fact; it did just recently at a forum I frequent where a chap was essentially spewing the usual "Western Jews are not 'Middle Eastern'/ 'West Asian' " rhetoric and in his case; he evoked the whole frankly retarded "Theory of the Khazars".

Cyprus is often counted as part of the region as well

To get what the Khazar idea is out of the way: it's predicated on the notion that for example Ashkenazim derive a large portion of their ancestry from the region ruled over by the Khazar Empire/ Khaganate, basically claiming that they're not really native Levantines but substantially Caucasian, the Khazars themselves being a semi-nomadic Turkic speaking people who experienced a Jewish presence within their realm. One Dr. Eran Elhaik wrote a paper basically supporting this. [1]

Khazar Khaganate

He got the following reply from over 20 geneticists:

"The origin and history of the Ashkenazi Jewish population have long been of great interest, and advances in high-throughput genetic analysis have recently provided a new approach for investigating these topics. We and others have argued on the basis of genome-wide data that the Ashkenazi Jewish population derives its ancestry from a combination of sources tracing to both Europe and the Middle East. It has been claimed, however, through a reanalysis of some of our data, that a large part of the ancestry of the Ashkenazi population originates with the Khazars, a Turkic-speaking group that lived to the north of the Caucasus region ~1,000 years ago. Because the Khazar population has left no obvious modern descendants that could enable a clear test for a contribution to Ashkenazi Jewish ancestry, the Khazar hypothesis has been difficult to examine using genetics. Furthermore, because only limited genetic data have been available from the Caucasus region, and because these data have been concentrated in populations that are genetically close to populations from the Middle East, the attribution of any signal of Ashkenazi-Caucasus genetic similarity to Khazar ancestry rather than shared ancestral Middle Eastern ancestry has been problematic. Here, through integration of genotypes on newly collected samples with data from several of our past studies, we have assembled the largest data set available to date for assessment of Ashkenazi Jewish genetic origins. This data set contains genome-wide single-nucleotide polymorphisms in 1,774 samples from 106 Jewish and non- Jewish populations that span the possible regions of potential Ashkenazi ancestry: Europe, the Middle East, and the region historically associated with the Khazar Khaganate. The data set includes 261 samples from 15 populations from the Caucasus region and the region directly to its north, samples that have not previously been included alongside Ashkenazi Jewish samples in genomic studies. Employing a variety of standard techniques for the analysis of populationgenetic structure, we find that Ashkenazi Jews share the greatest genetic ancestry with other Jewish populations, and among non-Jewish populations, with groups from Europe and the Middle East. No particular similarity of Ashkenazi Jews with populations from the Caucasus is evident, particularly with the populations that most closely represent the Khazar region. Thus, analysis of Ashkenazi Jews together with a large sample from the region of the Khazar Khaganate corroborates the earlier results that Ashkenazi Jews derive their ancestry primarily from populations of the Middle East and Europe, that they possess considerable shared ancestry with other Jewish populations, and that there is no indication of a significant genetic contribution either from within or from north of the Caucasus region." [2]

I reckon no further delving into how fallacious the notion that Ashkenazim are basically a Caucasian population is needed but in case you need simple examples of how fallacious the notion always was-> here's an example of the fundamental pre-historic ancestral components in Caucasian, Turkish, Iranian & Levantine populations from the work of a genome blogger I often cite here (Eurogenes/ David Wesolowski):


EE = East Eurasian


 WHG = Western European Hunter-Gatherer

As you can see, Ashkenazim & Sephardim (both "The Jews of Germany" & "The Jews of Spain" as their names mean respectively) are more or less identical while clearly not fitting amongst Caucasians, Turks/ Anatolians & West Asian Iranian speakers like Kurds. Lacking the heightened Ancient North Eurasian input found in these populations that I noted a while back. Instead they fit much more decently amongst "Arab" Levantines like Syrians & the Lebanese whether Christian or Muslim.

Simply put; the Khazar theory is nonsensical. Genetically speaking, Jews like Ashkenazim and Sephardim are more or less a Mediterranean population more genetically similar on a fundamental level to populations like Sicilians, Lebanese, Tuscans, Syrians, Cypriots and so on than anything else.

Pan West Eurasia PCA (Principal Component Analysis) / Cluster

I repeat (with the backing of virtually every respectable geneticist out there familiar with West Asian and Jewish population genetics); the Khazar theory is bullshit... We live in an age where wild speculation about Human or population origins based on hearsay, myths and "cranio-metric data" is obsolete. Mostly thanks to population genetics. And the genetic data of Ashkenazi Jews for example is pretty clear; not Khazars (not even from the Caucasus).

Reference List:

2. No Evidence from Genome-wide Data of a Khazar origin for Ashkenazi Jews, Behar et al.


1. Despite their linguistic standing; Greek Cypriots are genetically a Levantine population-> more similar to the populations of the Levant than anything else as you can see from that ADMIXTURE analysis showing you the ancient ancestral components that make those populations up. Though Greeks as a Mediterranean population like them, especially one of a more easterly geographic position, are quite similar to them anyway (on a fundamental level).

2. "Early Neolithic Farmer" is essentially what you get when you remove/ account for the Western European Hunter-Gatherer (native European component) admixture in an Early European Farmer (EEF) or EEF-like component. It's what carries Basal Eurasian and seems to be the main native West Asian component; it for now peaks in Peninsula Arabians and can be found to be the dominant ancestral component across West Asia and most of the Mediterranean.

3. Cranio-metric data can have its uses and there are somewhat respectable peer-reviewed papers on the subject (I can't seem to find one right now but I'll update this post with a link when I do) but ultimately; the conclusive evidence lies in sampling a population's genome. Cranio-metric/ facial data can be quite misleading (as with the obsolete painting of the old "Caucasian Race").

Sunday, May 3, 2015

South Cushitic Admixture in Southeast Africa

South Cushitic is a subbranch of the Cushitic branch of the Afro-Asiatic language family, historically spoken by peoples living south of the Horn of Africa (where most Cushitic speakers are situated), these Cushites seemingly made it as far as Southern Africa as early as 2,000 years ago or more [1], having reached areas like Kenya and Tazania much earlier. 

Mainland Southeast Africa

Some sources claim they were in some areas South of the horn as early as the 1st to 3rd millennium BCE. [2] At any rate, they ended up having a profound effect on several groups across Southeast and even Southern and Central Africa and the effect they had on several Southeast African groups is ultimately the focus of this post.

Above you can see an STRUCTURE analysis (quite similar to an ADMIXTURE analysis) from Tishkoff et al. 2009 [3]. In it we have an actual South Cushitic speaking group. The Iraqw who in this case are the peak of Tishkoff's "Cushitic" or at least "pseudo-Cushitic" cluster/ component (coloured purple) and as you can see; this component which peaks in a Southern Cushitic group that currently inhabits Tanzania- 

- is profuse all over Southeast Africa. Among the Maasai, among the Datog, among the Sandawe, the Mbugu etc. This is essentially because all of these groups (many of whom also display West Eurasian/ West Asian admixture) have Cushitic admixture/ West Asian admixed East African pastoralist admixture.

The Maasai, for example, tend to be about ~50% Cushitic, the Datog even exceed that percentage while various other populations such as the Kikuyu in Kenya and countless other Bantu speaking groups in Southeast Africa also have Cushitic admixture all owed to a South Cushitic source/ something ancestral and similar to the Iraqw who are among the last few remnants of what was arguably a much bigger subbranch of the Cushitic branch.

Many of them such as the Maasai have even taken on Cushitic customs such as the one outlined above. That same practice of drinking cattle blood with milk is one that was utilized by Bejas (North Cushites) in Northern Sudan as early as 100 BCE as noted by the geographer Artemidorus. It was also utilized by Somalis (East Cushites) as early as 800-900 CE during the Middle Ages as noted by a Chinese source of the time. [4] It's also apparently, a generally known Cushitic custom. [5]

But of course, many of these groups such as the Bantu speaking groups inherited much more than shared ancestry with populations such as Somalis, Agaws, Ḥabeshas, Afars and Oromos; they also inherited things such as lactase persistence through this Cushitic admixture from South Cushites.

For example, Tutsis who clearly have a profuse amount of West Asian/ Cushitic admixture (the ones in the PCA above look to be by majority Cushitic/ "Horner") given how close they plot to Somalis and Ḥabeshas in the above 23andme PCA (Principal Component Analysis) cluster (with other lines of evidence which show that Hutus also have some Cushitic admixture [3]) are lactase persistent while their various Bantu neighbors who at times may lack Cushitic admixture from South Cushites; are simply not lactase persistent. [6] 

This South Cushitic admixture is also likely why many groups in Southeast Africa such as the Tutsi, Maasai and so on; sometimes display rather "Horner-esque" facial features (facially similar to various Cushitic and Ethiopic speaking populations in the Horn, for example). 

The Maasai woman above, for example, could quite easily pass in the Horn of Africa among populations like Oromos, Afars, Somalis etc. Though her ethnic group is essentially a mixture between South Cushites (who were from the Horn and closely related to groups such as Somalis, Afars, Oromos and so on) and "Nilotes" with some "Pygmy", "Khoisan" and Niger-Congo (Bantu) peppered in.

Modern South Cushites themselves have somewhat clearly mixed with their surrounding Nilotic, "Khoisan" and Bantu neighbors which is likely rather demonstrable in their haplogroups (Y-DNA for example [7] [8]):

E1b1a/ E-V38 is ultimately a marker most common among/ characteristic of Niger-Congo speakers/ people such as the Bantu while Haplogroup B can seemingly be rather common among the Nilotic of Southeast Africa.

Nevertheless they've maintained a E1b1b/ E3b majority (very common all over the Horn and Northeast Africa) whilst also having Haplogroup T/ T-M184 carriers among them, a marker found all over the Horn (mostly peaking in Somalis; especially those of Dir and Isaaq origins). Now, keep in mind that Haplgroups merely mark migrations for the most part; being 22% E1b1a does not mean they are about 22% Bantu admixed.

 A population could carry a marker at a rate of 60% and be, in terms of autosomal DNA/admixture (a real representation of their ancestry), completely distinct from the other populations this Haplogroup occurs amongst, like I demonstrated with Finns with my last blog post. All things considered, it's clear that the Iraqw and South Cushites like them weren't the only ones spreading ancestry; their Nilotic and Bantu neighbors ultimately had an affect on South Cushites as well.

Observe the West Eurasian (West Asian) admixture in populations such as the Luhya, Maasai and so on; mostly or entirely owed to South Cushites

In the end, various groups from Rwanda to Kenya to Tanzania to Mozambique have clearly been touched by ancient (and also perhaps not necessarily ancient) South Cushitic speaker expansions across their region; which had not only a cultural impact on some of them but also a genetic one; making some populations such as the Datog by majority "Cushitic" and others such as the Maasai essentially half.

So next time you're in Tanzania or Kenya and you meet a non-Somali or Oromo who looks strikingly like they're from the Horn even though they claim no Somali or Oromo ancestry; you know where that ancestry mostly came from now.

Reference List:


 1. The Pie Chart honestly just simplifies the percentages (f.e. the Iraqws tested in Hirbo et al. [8] were about 13% T-M184 rather than 11%; I made it that way to better fit the diagram); it's just supposed to put the point across that their main markers are E3b subclades followed by E1b1a, T-M184 and Haplogroup B. Also, keep in mind that in Hirbo et al.; Haplogroup T is listed as "K2" (it used to be called this but isn't anymore). It's also a bit of a shifty representation as it adds together the results of two different papers; Hirbo et al. [8] and Wood et al. [7] but it serves its purpose in putting the point across about the haplogroup frequencies I mentioned.