Thursday, September 17, 2015

Ancient North Eurasian

Ancient North Eurasian is an ancestral component now somewhat common in population genetics... It was originally discovered through the genome of a Siberian boy who died over 20,000 years ago referred to as either Mal'ta boy or MA-1 and was backed up as being a real entity in pre-historic Eurasia through other ancient genomes like that of Afontova Gora-2. [1]

It's discovery really shook up a lot of things like our understanding of the origins of Europeans, Native Americans and even groups such as Central Asians, South Asians and various West Asians who seem to carry either Ancient North Eurasian or Ancient North Eurasian-related ancestry.

Lazaridis et al. 2013-2014 seemed to suggest that Europeans were basally a three-way mixture between Ancient North Eurasians / MA-1 related peoples, what they dubbed Western European Hunter-Gatherers based on the ancient genomes of various Mesolithic Hunter-Gatherers from Europe like Loschbour and then finally Early European Farmers who began entering Europe around the Neolithic from West Asia. 

Since then that model's become rather obsolete and has been replaced by one where all of the supposed Ancient North Eurasian ancestry in Europe is owed to the spread of the Indo-European languages by pastoralist peoples from the Pontic-Caspian Steppe. 

These pastoralists were carrying with them a foray of different ancestries from what looks to be Caucasian-like ancestry rich in what looks to be Ancient North Eurasian-related & West Asian ancestry and what is for now referred to by chaps like Wolfgang Haak of Haak et al. 2015 as "Eastern European Hunter-Gatherers (EHGs)". [2] 

EHGs almost fit as a mixture between Ancient North Eurasians & Western European Hunter-Gatherers but instead don't entirely look to be the result of such a mixture. Though as David Wesolowski who runs the Eurogenes genome blog and ancestry project once remarked in the quote below- :

"It depends how you define EHG, ANE and WHG, and the concept of pure components.
They can all be distinct pops, or EHG can be a mix of ANE and WHG, or even WHG can be a mix of EHG and something as yet unsampled."

-it's honestly rather iffy and tricky modeling these pre-historic groups with wildly different time stamps on them (Mesolithic for WHGs and EHGs and Paleolithic for ANEs) as mixtures of one another.

But David seems to assume groups like EHGs and WHGs are likely a mixture between groups that preceded them perhaps like Ancient North Eurasians and some other groups as yet unsampled. The cold hard truth of the matter is that we require more samples of pre-historic Hunter-Gatherer groups across West Eurasia to really understand what EHG and WHG are and how exactly they're connected to ANE because the current models seem inadequate.

 It could just be that Eastern European Hunter-Gatherers are somehow extra related to Ancient North Eurasians or somehow partially descended from them and something Western European Hunter-Gatherer related. We'd need more ancient genomes across time and space in Europe and other parts of Eurasia to truly grasp this with any kind of conclusive detail.

Early Neolithic = Early European Farmer

Although one thing is resolved for now... A group of "pure" Ancient North Eurasians didn't come and contribute Ancient North Eurasian ancestry to the ancestors of modern Europeans; this Ancient North Eurasian-related ancestry is ultimately owed to expansions from the Steppe. Whether EHGs are "WHG + ANE" or related to MA-1 in some other way or not.

Though it is worth-noting that the non-EHG and "Caucasian-like" ancestry in Pontic Caspian Steppe pastoralists like the Yamnaya did also carry Ancient North Eurasian-related ancestry and in this case; not seemingly owed to Eastern European Hunter-Gatherer ancestry. 

The redder a place or its "outline" is; the richer in ANE-related ancestry it is
In the end though what looks to be Ancient North Eurasian ancestry or Ancient North Eurasian-related like EHG ancestry is found all over Eurasia from Siberia to South Asia or Western Europe to Central Asia. In a modern context it tends to peak in Siberian groups like Kets [3] or various modern South Asians and in West Eurasia peaks in the Caucasus region.

It also really helped redefine our understanding of the origins of Native Americans who like many populations on this planet are now understood not to be some "pure" separate branch of the Homo Sapien Sapien family tree but a mixture of sorts like Europeans. In their case the mixture seems to be between Ancient North Eurasians and East Asian-related ancestry. [4]

If I had to quickly dive into where the component stands in Eurasia; it's essentially closest to Eastern & Western European Hunter-Gatherer and seems to share as geneticists suggest; a sort of earlier root with these components like it does with Western European Hunter-Gatherer in that Lazaridis et al. 2013 diagram I shared.

Though as I said; we really need more samples from across Eurasia (West Eurasia, Siberia, Central Asia, South Asia etc.) from various time periods to really understand the true nature of groups like Ancient North Eurasians, Western European Hunter-Gatherers and Eastern European Hunter-Gatherers because as it stands; things stand on somewhat unsure and confused ground.

For all we know; what looks to be non-Steppe derived "ANE" ancestry in groups like South Asians, Central Asians and West Asians may not be owed to some sort of "pure" Ancient North Eurasian group like we once thought was the case for Europeans...

It could instead mean that these groups owe their Ancient North Eurasian-related ancestry to Eurasian Hunter-Gatherer groups somehow related to Ancient North Eurasians or who carry ANE ancestry themselves in some way or other; more ancient DNA analysis is needed... I say this a lot and before this blog post is over will say it again because it can't be emphasized enough.

This uncertainty I highlighted above is essentially why I insist on sometimes writing "Ancient North Eurasian-related ancestry" rather than undoubtedly assuming some of these non-European populations have direct ANE ancestry.


Nevertheless, for the time being what we dub "Ancient North Eurasian" is highly divergent from Western European Hunter-Gatherers despite the seemingly closer relations between ANEs and European Hunter-Gatherers when compared to Eastern Non-African groups, to a point where Native Americans will often seem more similar or closer to Mal'ta boy than Europeans are like in analyses such as IBS:


This being the case despite the fact that the East Asian-related ancestry that makes up the rest of Native Americans' ancestry is less related to Ancient North Eurasians like Mal'ta boy / MA-1 than the European Hunter-Gatherer ancestry in Europeans is, though Europeans might be shifted away a bit by the highly divergent Basal Eurasian component in their West Asian / Near Eastern-related ancestry.

Eurogenes K=8 is a good representation of the levels of Ancient North Eurasian-related ancestry found across various global populations

Nevertheless, ANE is a pretty distinct ancestral cluster of its own with what seems to be a very large spread across Eurasia of either ANE or ANE-related ancestry showing up in small amounts even in some East Asian populations as well as somewhat in Egyptians, a Northeast African population.

Reference List:


1. What shows up as Ancient North Eurasian in East African groups like the Gumuz or Anuaks in the K=8 admixture analysis isn't actually ANE ancestry. From what David once told me; it's essentially some sort of archaic Eurasian element these groups demonstrate that just won't fit into the runs other clusters/components. 

These East African cluster rich groups in my experience do tend to show an odd as of yet unexplained very small Eurasian / Out-of-Africa (related to Non-African populations) element in various runs especially at K=2; just don't make much of it for the time being. 

2. I've put a little time into formally explaining components like Ancient North Eurasian or the Near Eastern / West Asian ancestry (Early Neolithic Farmer) in Early European Farmers because many I've encountered who've just gotten recently interested in population genetics sometimes might need a more straightforward explanation for what these components are / what we for now understand of them without having more ancient samples to paint a better picture so here are your explanations.

3. The world map that shows various ANE levels across the globe via the colors green and red is owed to a chap David/the author Eurogenes refers to as Sergey as mentioned here. And the MA-1 IBS spreadsheet if you're wondering is owed to David.

4. This is a direct note quoted from David/ the author Eurogenes I'm sharing because it's rather interesting: [-]

ASI = Ancestral South Indian, you can learn a little about it here. It's essentially a "South Indian" centered Andamanese & perhaps also Australo-Melanesian related component though we'll need ancient DNA from South Asia to really grasp it as for now it's not even "purely" made up of such ancestry and as David notes; is "mixed" in that it carries ancestry like Ancient North Eurasian-related ancestry. That's because all the models of it we have for now are based on modern South Asians who are all mostly a mixture between West Asian-related, ANE-related, Pontic Caspian Steppe-derived & "ASI" ancestry.  The only way to get a good and unmixed edition of it would be sufficient ancient DNA from South Asia where it can be found in such a state. 

Recommended reads:

Wednesday, September 16, 2015

Is the Eastern Non-African situation more complex?

A recent study based on cranio-metric data essentially proposed something quite preposterous once genetics is taken into account and that's the following:

"Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity."

It's preposterous because it's quite obvious at this point that Eastern Non-African (ENA) populations (I formerly referred to them collectively as "East Eurasians") at large share a lot of drift with West Eurasians or at least with the non-African & non-Basal Eurasian ancestry in West Eurasians like the African ancestry in Arabians or the Basal Eurasian in all West Eurasians. [1] [6]

This shared drift and closeness between Eastern Non-Africans and West Eurasians whether ancient or modern is seemingly owed to the fact that all Out-of-Africa populations are essentially descended from an extremely ancient pre-historic bottle-necked population like the following diagram from Lazaridis et al. 2013 [2] displays:

There seems to be little doubt in terms of autosomal DNA about this fact and their Haplogroups somewhat support this as well. Then there's the fact that Haak et al. [3] from what I recall proved Ust-Ishim [4] occupies a basal position to Eastern Non-African groups like the Andamanese Onge and East Asians alongside European Hunter-Gatherers groups such as Western European Hunter-Gatherers as the quote below stipulates:

"Ust’-Ishim was inferred to occupy a basal position to eastern non-African and European hunter-gatherer populations but not to modern Europeans, which was interpreted as due to admixture from a population occupying an even more basal position to Europeans"

This in a vague sense means that Ust-Ishim was in a state that Western European Hunter-Gatherers, East Asians and groups like the Onge are ultimately only "downstream" from as in they diverged from a shared state quite like Ust-Ishim regardless of whether or not he was alive around the time when the ancestors of Eastern Non-Africans, Ancient North Eurasians & Western Hunter-Gatherer-related groups diverged.

The Out-of-Africa model in terms of how it exactly happened and whether or not there were various slow dispersals rather than one is not entirely known from what I recall but one thing's for sure:

All of the ancestry in Europeans including their Basal Eurasian ancestry and all of the Homo Sapien Sapien ancestry in Eastern Non-Africans; ultimately diverged from seemingly one bottle-necked population (the original "Non-African" group in Lazaridis et al.'s diagram) and all of the Homo Sapien Sapien ancestry in Eastern Non-African groups like the Onge or even Papuans is seemingly a downstream development from the state Ust-Ishim was in.

So some idea where a distinct group of ancient Africans left the continent for Eurasia and then made it to areas like Melanesia and Australia with a second migration carrying the distinct ancestors of Europeans and East Asians is just not in line with the genetic data and that's what's ultimately most relevant in making such inferences about populations and their relations to each other; genetics.

Another big issue for this model is simple, in truth. Australo-Melanesians, Andamanese and East Asians are seemingly closer to each other than they either is to Europeans often prompting various population geneticists to lump them into a sort of "clade" with one another like "Eastern Non-African" in Lazaridis et al. 2013 or similarly in Kay Prüfer et al. 2014 [5] as I touch upon here.

Australian Aborigine man

The argument perhaps being that they share extra ancestry with each other that they don't share with Ancient North Eurasians or Western European Hunter-Gatherers, suggesting that there's another extra node in the Out-of-Africa family tree that they ultimately diverged from like you see in that Lazaridis et al. table where the East Asian-related ancestry in Native Americans like Karitianas seemingly comes from the same "ENA" node as Onges.

The question I'm merely posing here is simple; will things grow more complicated for this supposed node or part of  the Out-of-Africa family tree?

This is a possible outcome in my humble opinion especially once we get ancient DNA data from across Oceania, Southeast Asia & East Asia.

This grouping may even collapse to some extent and make it seem more like Eastern Non-Africans are partially descended from separate Out-of-Africa nodes downstream of Ust-Ishim that merely intermixed to some great extent in pre-history hence their closer affinity to each other over pre-historic West Eurasians like Western European Hunter-Gatherers; a model I've come to suspect but that could be entirely wrong. [note]


For now I'd say one thing is for sure... Papuans, Australian Aborigines, the Andamanese; these groups are closest to East Asians and Polynesians when it comes to the Human family tree but how this will make sense someday within the Out-of-Africa family tree in general like whether or not this Eastern Non-African clade will remain for the most part is what could be shifty but the greater closeness between these groups is not going to change.

Reference List:


1. The non Non-Homo-Sapien-Sapien ancestry in Eastern Non-Africans I'm referring to would be both Neanderthal & Denisovan admixture.

2. From what I can tell; Haak et al. didn't include groups like Papuans in its analysis when it made that statement about Ust-Ishim being basal European Hunter-Gatherers and Eastern Non-Africans so I contacted Iosif Lazaridis who was involved in the study and he essentially confirmed that Ust-Ishim would indeed be basal to Eastern Non-Africans like Papuans or Australian Aborigines as well though he noted that the Denisovan admixture in these groups can complicate such models.

3. Hodgson et al. (the sixth reference) is not relevant in anyway here except in showing those parties interested; direct proof that groups such as Arabians have African admixture. You can basically consult any of its admixture analyses to see that proven for you or even observe Lazaridis et al.'s K=20 admixture analysis to see the same kind of data where ancestry related to the ancestry in groups like Dinkas and Yorubas surfaces in various "Arab" populations including Peninsular Arabians.

4. There's also the fact that Eastern Non-African groups haven't been as focused on in population genetics as West Eurasians so a good amount of their lack of strong differentiation might be due to this...

Sunday, September 13, 2015

Early Neolithic Farmer: The West Asian ancestry in Early European Farmers

 I've often shared results from the Eurogenes K=8 admixture run where the "Early Neolithic Farmer / Near Eastern"component turns up or perhaps referred to pre-historic "West Asian" ancestry and I'd like to take this opportunity to quickly explain what this component is.

It's simply as Iosif Lazaridis of Harvard Med ultimately says in that email reply to me above. It's what you would get if you account for the Western European Hunter-Gatherer-related ancestry in Early European Farmers or what looks to be the non-African ancestry in the Bedouin B samples often tossed around between various studies who are Bedouins from Negev.

Israel's South District, roughly coterminous with the Negev

Long story short; Farmers from West Asia migrated to Europe during the Neolithic and intermixed with the Hunter-Gatherer groups present there like what Lazaridis et al. 2013-2014 [1] dubs "Western European Hunter-Gatherers". 

These farmers as we've recently learned through observing some low coverage data on a Neolithic Anatolian Farmer; might have been carrying some Western European Hunter-Gatherer-related ancestry before entering Europe and then acquired more of such ancestry within Europe itself.

The rest of their ancestry was what Iosif Lazaridis refers to as "Near Eastern" or David Wesolowski who runs the Eurogenes genome blog and ancestry project refers to as either "Near Eastern" or "Early Neolithic Farmer". 

(Above are groups this component tends to peak in)

For the time being it's a shaky model for what certain parts of West Asia among other neighboring regions might have predominantly looked like in terms of Non-African ancestry

It's shaky because it's ultimately based around the non-African ancestry in Bedouin Bs who seem to lack Ancient North Eurasian / Mal'ta boy-related ancestry or the kind of Western European Hunter-Gatherer-related ancestry that appears in Early European Farmers. [note]

The component seems to carry an excess of the illusive Basal Eurasian component along with what in my humble opinion is probably ancestry related to groups like Western European Hunter-Gatherers but honestly; we'll need ancient DNA data from West Asia, North Africa & perhaps even East Africa to fully grasp "Early Neolithic Farmer" or "Near Eastern" as well as Basal Eurasian.

West Eurasia
For now any parties curious about this component should just understand it for being what is described above and as being a "West Eurasian" component seemingly native to West Asia that's been found in pre-historic groups like Early European Farmers and Pontic-Caspian Steppe pastoralists such as the Yamnaya. [2]

Its current modern spread is far and wide where it can be found in various distinct populations all over the world from Fulanis in the African Sahel to Tamils in the Indian subcontinent; signifying shared pre-historic ancestry presumably from West Asia or the general "Middle East" region between these numerous distinct Homo Sapien Sapien populations.

We'll know more someday and have a much keener understanding of pre-historic West Asia and neighboring regions once we have adequate ancient DNA samples from the region and other regions adjacent to it but for now; that's mostly all that needs grasping in respect to this component and what it is.

Reference List: