Thursday, June 30, 2016

PCA & ADMIXTURE results for Natufians

That's a 3D interactive PCA (Principal Component Analysis) based on autosomal SNPs made by David Wesolowski who authors the Eurogenes genome blog and ancestry project. What's particularly interesting to me about it are the PCA positions of the Natufians and the Neolithic Levantines... With the former group pulling southwards toward African populations such as North, East & West-Central Africans. 

Eurogenes ANE K7

ENF: 77%
East African: 8%

Hunter_Gatherer vs. Farmer

Middle Eastern Herder: 64%
Mediterranean Farmer: 30%
East African Pastoralist: 7%

Eurogenes K12b

Southwest Asian: 54%
Mediterranean: 38%
East African: 8%

That pull along with the above ADMIXTURE results (via Gedmatch) of one Natufian seem to contradict what Lazaridis et al. was saying about the Natufians lacking African admixture but I would caution against using modern PCA positions (like those of Bedouins) and, of course, modern ADMIXTURE runs (with modern clusters based on modern genetic diversity) to gauge how "African" or "Eurasian/Out-of-Africa" an ~11,000-14,000 year old population was.

I.e. These Natufians are, of course, not "Southwest Asian" + "Mediterranean" but, instead, they're just showing the greatest affinity for these modern clusters. As in, populations probably quite like them to some degree; contributed to the formation of clusters like Southwest Asian & Mediterranean.  But, it's still strange that they'd show such an affinity for an African cluster like the East African one.

"However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day North Africans, who owe most of their ancestry to back-migration from Eurasia)."

If anything, it makes what Lazaridis et al. noticed with their analyses, as noted in the above quote, all the more interesting. It could, in my opinion, just be a quirk of their age. Mota, according to the academics who sampled him, didn't have any "Eurasian" admixture based on formal statistics (from what I recall) yet his PCA position (pulling toward Out-of-Africa populations more than the Southern Sudanese or Western Africans) on a global PCA implied otherwise:

Mota's ADMIXTURE results also implied some vague and broadly Out-of-Africa/Eurasian admixture:

Eurogenes ANE K7:

ANE: 3%
ASE: 2%    
East Eurasian: 2%
West African: 20.30
East African: 65.23
ENF: 7.65

Hunter_Gatherer vs. Farmer

Baltic Hunter Gatherer: 1%
South American Hunter Gatherer: 1%
South Asian Hunter Gatherer: 2%
East African Pastoralist: 56%
Oceanian Hunter Gatherer: 1%
Pygmy Hunter Gatherer: 25%
Bantu Farmer: 14%

Eurogenes K12b

East African: 54%
West African: 40%
South Asian: 2%
Siberian: 1%
Western European: 1%
East Asian: 1%

And Mota is only a ~4,500 year old Southwestern Ethiopian sample. So, I'd remain rather skeptical about what global PCA positions, where these pre-historics are thrown in alongside modern populations, have to say. And ADMIXTURE runs that were usually (not always) based on modern populations can also produce somewhat dubious results.

The fact that they lack African admixture (discounting whatever Basal Eurasian's cause will one day turn out to be) may still be quite the case if they truly do not share more alleles with African populations than other pre-historic Out-of-Africa samples do (such being Lazaridis et al. 2016's finding).

On another note, David's placement of them in his mostly Pan-West Eurasia PCA is rather intriguing as well. In this case, they do not cluster with any modern West Eurasian populations and; like NW Neolithic Anatolians, Early European Farmers and Sardinians; they break off from other West Eurasians as they seemingly lack the eastern (it's "northern" in this PCA, I suppose) pulling affinities (I.e. ANE-related admixture) which somewhat pull all the other populations away from them. 

The Early European Farmers and Neolithic Anatolians pull much more west toward WHG/Villabruna-type peoples while the Natufians cluster just south of Negevite Bedouins which implies that they have the least "WHG" related affinities when compared to the Neolithic Levantine, Anatolian and European samples. Which is, roughly, what Lazaridis et al.'s ADMIXTURE run implied:

It really does, as I pointed out earlier, look like these Natufians (and their Neolithic Levantine counterparts) might, for the most part, be the modern Southwest Asian cluster or David's old ENF/ Near Eastern cluster (or Lazaridis et al. 2013-2014's Near Eastern component) in the flesh. The Neolithic Levantines, in the Pan-West Eurasia PCA, just look like somewhat WHG-shifted versions of the Natufians. Perhaps this shift is why they are supposedly about ~15% less Basal Eurasian than their Natufian predecessors:

At any rate, I'll leave it at that for now... I'll be interested in seeing what analyses from third parties like David such as d-stats turn up on these Natufians (haven't really sifted through those yet).

Reference List:


1. Gedmatch kit number for the Natufian: M041601 AND the Gedmatch kit number for Mota: M261275

2. I'm open to these Natufians having African ancestry. Just pointing out that PCA positions and the current ADMIXTURE runs we have might not be the way to go. Nevertheless, it is interesting that these Natufians and not the later (~7,500 year old) Neolithic European samples like Stuttgart (F999916) show such African affinities in ADMIXTURE runs. Might just be because of the very heightened WHG-shift in a Neolithic European Farmer like Stuttgart and perhaps the sample's younger age by ~4,000-7,000 years.

3. Mota's Eurasian admixture in those calculators also, unlike the Natufians' African admixture, looks more broad (I.e. ANE + East Eurasian + ENF etc.) and looks more like an affinity. The Natufians, on the other hand, seem to mostly lean toward the East African cluster which looks less like a broadly African affinity and more like actual admixture, quite frankly.

4. Most of the Natufians do clearly have a bit of a western-shift though. They don't cluster exactly where David's "ENF" cluster theoretically would (only one of them does).

Saturday, June 18, 2016

Natufians and Neolithic Levantines lack African admixture?

Whilst Neolithic Levantines and Natufians seem to have a good amount of what looks to be Y-DNA E-M35 (specifically 2 E-Z830 samples among the Natufians) and seemingly no Y-DNA J so far- :

Natufians (Epipaleolithic Levant):

I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT


I0867: H2 (PPNB)
I1414: E(xE2, E1a, E1b1a1a1c2c3b1, E1b1b1b1a1, E1b1b1b2b) (PPNB)
I1415: E1b1b1 (PPNB)
I1416: CT (PPNB)
I1707: T(xT1a1, T1a2a) (PPNB)
I1710: E1b1b1(x E1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c) (PPNB)
I1727: CT(xE, G, J, LT, R, Q1a, Q1b) (PPNB)
I1700: CT (PPNC)

-they don't seem to show any affinities for African populations (ones who lack West Eurasian admixture or have negligible amounts of such admixture) on an autosomal level according to this Pre-print:

"However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians (Extended Data Table 1). (We could not test for a link to present-day North Africans, who owe most of their ancestry to back-migration from Eurasia)."

This is quite interesting, truth be told. It implies that, despite seeming clearly old, the African admixture in the Levant is perhaps, at least, Post-Neolithic? Some of it (particularly non-East African cluster-related admixture), as I've noted in the past, is definitely owed to the Arab Slave Trade but some of it does also seem rather ancient.  

As for PCA (Principal Component Analysis) positions; Natufians in particular look to cluster essentially to the direct east of Anatolian Neolithic and Early European Farmers (and somewhat southwards of some of them) whilst Levantine Neolithic Farmers seem less Basal Eurasian and more northern shifted than their Epipaleolithic predecessors. I'll be more interested in seeing David over at Eurogenes throw these samples into his own Pan-West Eurasia PCA and a global PCA once the genomes are made publicly available when this paper is published in a peer-reviewed journal (a month or less, not sure). The PCAs in these studies can be a bit wonky due to issues like projection-bias.

I'll be interested in seeing if David and other 3rd parties will either confirm or deny that Natufians lack African admixture (whatever Basal Eurasian turns out to be aside).

One somewhat off-topic matter to note is that it seems as though we've more or less discovered a close equivalent to David's "ENF"/Near Eastern cluster from his old Fateful Triangle~K=8 model, a cluster also noted by Lazaridis and company prior to the release of this pre-print. 

The Natufians and Neolithic Levantines are essentially dominated by the blue ADMIXTURE cluster that seems to make up most of the ancestry in the Neolithic Anatolians and Early European Farmers. This seems, to me, like we're seeing Southwest Asian/ENF/Near Eastern in the flesh. The way it's differentiated from Neolithic Iranians is intriguing though given that Natufians (Epipaleolithic Levantines) and Neolithic Iranians are comparable in terms of Basal Eurasian ancestry; it must be the non-Basal Eurasian ancestry that's causing the differentiation or there's just really significant genetic drift at play here or both.

In this model above, where Natufians and the Hotu cave Iranian were not included, the Caucasus Hunter-Gatherer (CHG) samples seem to carry notable EHG/ANE-related ancestry as prior analyses like David's K=8 ADMIXTURE run might've implied. Initially, I figured what was differentiating the Neolithic Iranians from Natufians was perhaps ANE-related admixture in the former but that might not really be the case.

As I said in a prior post; things will become more clear when third-parties like David over at Eurogenes get their hands on these genomes once the paper's published at a peer-reviewed journal and also once we have even more ancient genomes someday.

Reference List:


1. I also must add that we should be cautious given that these are just 6 Natufian samples from one area. There might be some variation with future samples from other areas in regards to Y-DNA although I doubt there will be very much variation in terms of autosomal DNA given their similarity to Levantines from later periods.

New Information on Basal Eurasian

Well, this new study does have some new information/data on the whole idea of "Basal Eurasian" posed in Lazaridis et al. 2013-2014. 

For one, we have this helpful figure and what they seem to be posing with it is that more Basal Eurasian ancestry correlates with a depletion in Neanderthal ancestry:

"We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers."
Though, it does seem like the Basal Eurasian Vs. Neanderthal allele sharing relationship doesn't entirely perfectly correlate. I.e. CHGs and Chalcolithic Iranians are more or less equally Basal Eurasian but one shares alleles with Altai Neanderthals much more.

"West Eurasians harbour significantly less Neanderthal ancestry than East Asians, which could be explained if West Eurasians (but not East Asians) have partial ancestry from a source diluting their Neandertal inheritance. Supporting this theory, we observe a negative correlation between Basal Eurasian ancestry and the rate of shared alleles with Neanderthals (Supplementary Information, section 5; Fig. 2). By extrapolation, we infer that the Basal Eurasian population had lower Neanderthal ancestry than non-Basal Eurasian populations and possibly none (ninety-five percent confidence interval truncated at zero of 0-60%; Fig. 2; Methods). The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans 50,000-60,000 years ago largely occurred after the splitting of the Basal Eurasians from other non-Africans."

But if they're right about Basal Eurasian having a negative effect on Neanderthal ancestry; I did initially think this could led some credence to those, including myself, who used to argue that Basal Eurasian may in fact be some pre-historic crypto-North/East African admixture into pre-historic West Asians but the location of the supposedly single most Basal Eurasian individual does make that possibility rather puzzling:

Hotu cave is apparently 5 km from there

We'll need more samples and data in the future but, for now, it seems like Basal Eurasian has more of a pull toward Iran than the Levant (the latter area being adjacent to Africa) and it doesn't, so far, seem like it's any sort of "African" admixture. Perhaps some at Anthrogenica might be right about the Gulf Oasis or perhaps they might be wrong.

Time will tell...

Reference List:

Friday, June 17, 2016

The genetic structure of the world's first farmers

Abstract for pre-print:

"We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia."

I haven't read through the pre-print yet (just looked at the abstract so far) and will do a post concerning it sometime soon, I'm sure. Enjoy...

List of Y-Chromosome Haplogroups for the new samples:


I1407: L1a
I1632: L1a
I1634: L1a

Iran_Mesolithic (Hotu Cave):

I1293: J(xJ2a1b3, J2b2a1a1)


I1945: P1(xQ, R1b1a2, R1a1a1b1a1b, R1a1a1b1a3a, R1a1a1b2a2a)

I1949: CT

Iran_Late Neolithic:

I1671: G2a1(xG2a1a)


I1662: J(xJ1a, J2a1, J2b)
I1674: G1a(xG1a1)

Natufians (Epipaleolithic Levant):

I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT


I0867: H2 (PPNB)
I1414: E(xE2, E1a, E1b1a1a1c2c3b1, E1b1b1b1a1, E1b1b1b2b) (PPNB)
I1415: E1b1b1 (PPNB)
I1416: CT (PPNB)
I1707: T(xT1a1, T1a2a) (PPNB)
I1710: E1b1b1(x E1b1b1b1a1, E1b1b1a1b1, E1b1b1a1b2, E1b1b1b2a1c) (PPNB)
I1727: CT(xE, G, J, LT, R, Q1a, Q1b) (PPNB)
I1700: CT (PPNC)

Levant_Bronze Age:

I1705: J1(xJ1a)
I1730: J(xJ1, J2a, J2b2a)


Wednesday, June 15, 2016

The African & West Eurasian elements in Aris

Aris, similar to other Horn Africans, have both African and West Eurasian ancestry. They have notably less than Somalis, Oromos, Amharas, Agaws, Wolaytas and the like but the ancestry is most certainly present:

Their West Eurasian admixture, from an autosomal perspective, also seems quite old, much like most of the West Eurasian elements in Somalis. In fact, it seems even "older" than some of what is found in Somalis in that their West Eurasian admixture, at least in the case of Ari Blacksmiths who mostly lack Somali-like/Cushitic speaker related admixture unlike Ari Cultivators, lacks more northerly West Asian affinities:

At K=5 above; you can see Somalis, Oromos and co. show "Arabian" & "European" like ancestry but Ari Blacksmiths show only Arabian-like ancestry. They seem to be bereft of the more Mediterranean and/or Caucasus-Gedrosia related elements in the Cushitic and Ethiopian Semitic speaking populations and are chiefly made up of Southwest Asian related elements. As in, very basal West Asian type ancestry much like David Wesolowski's old ENF cluster from his K=8 run or Lazaridis et al. 2013-2014's Near Eastern component.

Now, we don't have any actual time-stamps for their West Eurasian admixture (reliable ones, anyway) but the fact that it seems to be such basal looking stuff which lacks affinities that would signify later (perhaps even Post-Neolithic) West Asian-related admixture into the Horn region, such as Anatolian Neolithic-like (Mediterranean) or Caucasian Hunter-Gatherer-like (Caucasian or Caucasus-Gedrosia) ancestry, definitely implies that this is likely quite pre-historic admixture perhaps from a time when certain areas of West Asia such as the Levant lacked Caucasus Hunter-Gatherer-like and more overt Villabruna/WHG-like elements, the latter of which causes a similarity to Neolithic Western Anatolians and Early European Farmers.

It's interesting, in that case, to note that the dominant West Eurasian Y-DNA Haplogroup among Omotic speaking populations such as the Ari is actually J (J*, J1 & J2) rather than T which seems much more dominant among Cushitic speaking Horn Africans with very little to practically none of the later West Eurasian elements in their kin further inland in the Horn (I.e. Somalis). 

Is a lot of their Y-DNA J inherited from Cushitic and Ethiopian Semitic speakers? What about the interesting case of J* though? Could it be that a lot or most of their Y-DNA J lineages date back to when their ancestors first acquired the West Eurasian ancestry in the f-statistics based table from Pickrell et al. 2013 above? That most of their J lineages will turn out to be wildly divergent from some of what's found in Cushitic and Ethiopian Semitic speakers? It'll be interesting to know someday when we have more high-resolution data and can pinpoint their exact subclades.

But, there's little point in meticulously mulling over the rather low-resolution data we have for the time being.

At any rate, the non-Eurasian ("African") elements in them are much more intriguing, in my humble opinion. For one, a large segment of it seems very much like the majority of the African elements in Somalis & Habeshas or, essentially, very much like most of the ancestry in populations such as Anuaks and Dinkas:

Notice how at the K=6 results above; most of the ancestry in the two Ari groups belongs to the Nilo-Saharan cluster (essentially what I took to calling the East African cluster over a year ago) which shows among the Sudanese (Southern) and Anuak samples at a level comparable to that of the Ari Blacksmiths and Cultivators.

The rest seems to be some odd African Hunter-Gatherer like elements (as in, ancestry seemingly quite similar to but not the same as what dominates the San & African Pygmies like Mbutis). In fact, even the ancient Mota man, who shares a lot of alleles with Aris, shows an affinity for these groups who remained Hunter-Gatherers/Foragers all the way into the Modern era:

Notice how Mota breaks the line between the Somali-Beta Israel cluster & Western African cluster; he breaks off and pulls toward the "San" samples alongside Hadzas who also seem like an intriguing mixture of what looks to be very old East African-like ancestry and something similar to groups like the San and Mbutis.

The rest of the non-Eurasian ancestry in Aris (which seems to make up much more of their ancestry than this San-Mbuti-like stuff) seems to be very similar to most of the African ancestry in Somalis & populations such as Dinkas as mentioned before. In fact, despite its West Eurasian & Mbuti-San-like elements, the Ethiopic/Omotic cluster which turns up in some ADMIXTURE runs is rather close in regards to Fst divergence to the "Nilo-Saharan" / East African cluster of which it often seems to be made up of at the lower Ks:

However, I would consult an old post of mine where I basically delved into how things such as Fst can be misleading when dealing with various African populations. You see, the African elements in Somalis aren't very "divergent" from the African elements that make up about +95% of Yorubas' ancestry if we're consulting parameters such as Fst which can be good at picking up on the genetic drift between populations.

This is partly because pre-historic African populations seemingly had much larger population sizes than Eurasian ones [5] and thus didn't seemingly diverge from one another as much as Eurasians did via genetic drift with population dips such as the "Eurasian bottle-neck" (the shared ancestral population between all Out-of-Africa populations from Native Americans, Eastern Non-Africans and West Eurasians) can be quite conducive to. And Humans mostly diverge via these two mechanisms:

Genetic Drift

For genetic drift what happens is; Population A & Population B are more or less "identical" and each have 1,000 people in them but they are geographically separated for 10,000 years... Population A doesn't experience any odd population losses and just continues to prosper from the original 1,000 roster but Population B loses 800 people due to an Earthquake very early on and the descendants of Population B find themselves being descended, 10,000 years into the future, from only those 200 folks who survived the Earthquake; losing a lot of their population's prior genetic diversity and diverging from Population A as a result of this alongside later mutations and selection and so on.

"Admixture" on the other hand would mean Population B's 1,000 remained intact in terms of numbers but they discovered a far away Population C with ancestry distinct from Population A & B and then intermixed with them to form a new mixed population that is now divergent from Population A due to being a mixture between Population B & C.

Between various African populations; genetic drift is not something that was as relevant during their pre-histories given their generally larger population sizes so they largely maintained and built upon their prior genetic diversity rather than experiencing the constant founder effects and bottlenecks, on an autosomal level, found outside of Africa. Though some notable drift definitely occurred.

So, when consulting something like Fst which focuses on differences in allele frequencies; things may not prove as useful when comparing various African populations as they might when comparing Africans to Out-of-Africa populations or OoA populations to each other. What might in fact prove more useful would be Haplotypic divergence datings or the general differences implied by Haplogroups (Y-DNA and mtDNA). 

For example, observe the "Khoesan" cluster (makes up pretty much all of the ancestry in the San samples) & the "Niger-Congo" cluster (makes up pretty much all of the ancestry in Yoruba samples) and notice that the Niger-Congo cluster is closer to the Khoesan cluster than it is to the East Asian one. However, when observing divergence dating between various populations such as Yorubas and the San:

The Yoruba are actually closer to all Out-of-Africa populations than they are to the San. As in, they seemingly share an ancestral population with Out-of-Africa populations that they do not share with the San which is why you very often see diagrams like this one being thrown around by various studies when trying to simplify the Homo Sapien Sapien family-tree:

The Yoruba and the San are not as drifted from one another as East Asians (i.e. The Han) and the Yoruba are but it seems obvious that when grouping these populations together; the Yoruba look to belong under the same branch as West Eurasians and Eastern Non-Africans which then shares an ancestor with the San. [important note]

What was my point in explaining this? Well, the point is simply that given people like the Aris' distinct Y-DNA profile; despite the majority of their ancestry not seeming particularly "divergent" from most of the similar African ancestry in Somalis and Nilo-Saharan speakers such as the Dinka; it may very well have diverged from the predominant African elements in these populations a very long time ago. Just as Haplogroups imply to us that the African element in Yorubas, as I mentioned here, whilst seemingly very close to the African element in Somalis, likely diverged from it well-over 20,000 years ago. 

So when observing various African populations (the ones that mostly lack Eurasian admixture); I would not allow myself to be fooled by the sometimes low, or simply not as high as you would expect, divergence between them when utilizing analyses such as IBS, Fst and so on which, in a way, have a bit of a Eurasian bias about them in that they're used so much because they make sense for Eurasian/Out-of-Africa populations but not as much for numerous African populations.

In fact, Wolaytas, despite being substantially Ari Blacksmith-related in ancestry, will have Somalis seem closer to them in terms of IBS (Identity-by-State) than Tigrinyas who have more Ari Blacksmith-related admixture than Somalis:

That's because Wolaytas are only a little bit less West Eurasian, on average, than Somalis whilst most of the African elements in them, however long-ago some of it cut-off from the African elements in Somalis, is still not very drifted/diverged from what's in Somalis so the two populations ultimately seem quite genetically close even though, in terms of actual shared ancestry within the last 3,000-10,000 years; Somalis are much closer to Tigrinyas.

I for one will be interested in seeing what we learn via ancient DNA across Africa period by period when the time comes. We do have some samples on the way such as 10,000 year old samples from Kenya from what I recall... For all I know; a lot of what I've touched upon here will be very redefined by ancient DNA data.

Reference List:

1. Early Back-to-Africa Migration into the Horn of Africa, Hodgson et al.

2. Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia, Plaster et al.

3. mtDNA variation in East Africa unravels the history of afro-asiatic groups, Boattini et al.

4. Ancient west Eurasian ancestry in southern and eastern Africa, Pickrell et al.

5. Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history, Kim et al.

6. Admixture into and within sub-Saharan Africa, Busby et al.

7. Genetic history of an archaic hominin group from Denisova Cave in Siberia, Reich et al.

8. Ancient gene flow from early modern humans into Eastern Neanderthals, Kuhlwilm et al.

Tuesday, June 14, 2016

Genetic History of Ice Age Europe


"Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000–7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3–6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory."

I never dug into this study soon after it came out as I usually do with studies of its sort but part of that is that it honestly felt as though there was too much to talk about and all I should've done was guided people interested in this field toward giving it a good read if they, by any means, managed to get their hands on the full paper or the supplemental, the latter of which is freely available.

So, consider this me strongly recommending that it be read as it's very important in keeping with the ancient DNA game. I am, in the future, going to reference concepts and terms owed to the study and I just might make some future posts focused on certain aspects of this study.

Link to study

Friday, June 10, 2016

Omotic speakers: Y-DNA & mtDNA data

As I've stated in the past; I don't tend to dig into Y-DNA & mtDNA data very much but I thought it'd be a good idea to have Omotic speakers' Haplogroup data in one place dedicated just to that very purpose. So, here goes:

Above is a low-resolution example of their Y-DNA copied from Ethio-Helix. But, to be fair, the sample size (~2,385 samples) is quite massive and thus grants us representative images for each ethnic group (100-130 samples per group) in regards to their frequencies for certain Haplogroups.

I.e. The above chart doesn't tell us exactly which subclades of J are most common among the Shekecho or what have you but it's probably pretty representative of their frequencies for  J, E (xE-V95) and A-M13 in general.

 But, Ethio-helix did ultimately, from what I understand, get his hands on more higher-resolution results for at least one of the 20 Omotic speaking ethnic groups in the former chart and that'd be the Maale, as you can see above. The Maale live in the SNNP region of Ethiopia where most Omotic speakers can be found and where the Omo river, which the Omotic branch is named for, can also be found.

If they're at all "representative" then we can assume other Omotic speaking groups in the SNNP region and elsewhere probably have a good amount of Y-DNA E-M329, a subclade of E-V38 which is lightly found in populations such as Amharas and Oromos who seem to show Ari Blacksmith-like admixture on an autosomal level.

E-M329 is also the Y-DNA Haplogroup of the Mota-man... The first ancient genome from Africa to be published who was named for the Mota cave in the SNNP region, where he was found. He also shares a lot of drift with Aris (Blacksmiths & Cultivators) so this seems like what might be a hallmark Y-DNA Haplogroup among Omotic speakers who are currently concentrated within the region (SNNP) where Mota was discovered.

The other markers are interesting as well such as the Maales' E-M34, a subclade of E-M35, which is also found in populations such as Oromos and Amharas (see here) who have notable admixture from peoples very similar to Ari Blacksmiths in terms of autosomal DNA so I can't help but wonder if Omotic speakers in the Horn were key in spreading this marker, and if most of these Omotic speaking populations are, in terms of autosomal DNA, quite similar to Aris.

At any rate, I won't go into much more detail beyond that because this post, like this older post on Somali mtDNA, is more about sharing the data rather than explaining or pruning through it.

 Now, we unfortunately don't have mtDNA data, even at a low-resolution, for several ethnic groups as we do for Y-DNA data but we do have 137 Dawro-Konta samples and 11 Hamer samples. Both Omotic speaking populations from the Horn whose data Ethio-Helix had shared long before I did but I decided to compound their results together to create the pie chart above.

There would be too much to drone on about if I decided to sincerely pry into the mtDNA data so I'll leave it at that but one thing worth noting is that Mota's mtDNA Haplogroup was L3x2a and, as can be seen above, L3x (and though no further subclade is divulged, at least from what I recall... I'm betting there's some L3x2a in there given that this marker already exists in modern Ethiopia, to my knowledge) is quite common among Omotic speaking groups such as the two groups I compounded together.

This, the overlap in Y-DNA E-M329 and the notable levels of shared drift between Mota and the Ari lends some clear credence to the notion that various Omotic speaking populations may in large part be descended from people related & very similar to the ~4,500 year old Mota-man.

I'll be quite interested in seeing more Haplogroup data, particularly more high-resolution results, on Omotic speakers in the future.

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1. As much I've somewhat done this myself in the past and even with this post (somewhat, anyway)... I'll stand by what I wrote in a recent post in that "Linguistics is linguistics & genetics is genetics". I.e. I would not advise people to take a 1:1 stance when looking at how much a group's genetic profile will correlate with the language they speak (and also what language family or branch that language is of). One of the populations present in this post (Wolaytas), is seemingly, on a rather basal level, more similar to Oromos and Somalis than to Ari Blacksmiths. Wolaytas also look to have a lot of admixture from Habesha~Agaw-like people as noted here.

So, don't expect "Omotics" to be some sort of homogeneous genetic block simply because they're Omotic speakers or even be extremely similar once we have autosomal DNA data (as well as more high-resolution Haplogroup data) on all these ethnic groups. Though some clearly notable related-ness already seems apparent. Languages and genetic profiles can definitely correlate and one can compliment our understanding of the other quite a bit but it's important to refrain from an over-the-top 1:1-ing of the two.