New Ancient mtDNA Reveal Hunter Gatherer Origins of "ENF" mtDNA

There's a type of ancestry that arrived Europe from West Asia with farming in 7000 BC and takes up the majority of ancestry in modern West Asians. It was coined "ENF" by Eurogenes author Davidski.

"ENF" is short for "Early Neolithic Farmer". The reason it was named this is it was believed this type of ancestry expanded out of West Asia with farming

"ENF" arrived in Europe with a package of new mtDNA haplogroups: R0(inclu. H), JT, K, W, X, and N1. Posters at blogs and forums theorized these mtDNA haplogroups must have originated with Early Neolithic West Asian farmers along with "ENF" ancestry. It was a nice and simple story for the origins of Middle Eastern and to a large extent European mtDNA.

I was against this idea. I argued there's just too much mtDNA diversity in West Asia for them to be descended from the same small population only 10,000 years ago. I argued "ENF" and "ENF mtDNA" existed in hunter gatherer populations all over West Asia for 10,000s of years.

In the last few weeks two papers(Hofmanová 2015, Jones 2015) have proven my argument correct. They document "ENF" ancestry in pre-Neolithic Georgia alongside "ENF mtDNA" in pre-Neolithic Georgia and Greece.

7605–7529 BC Thessaly, Greece: K1c
7288–6771 BC Thessaly, Greece: K1c
11000 BC West Georgia: H13c
7700 BC West Georgia: K3

H13c, K3, and K1c are very rare. As far as I know K3 and H13c have basically only been found in the Caucasus region today. And K1c has only been found in Europe, but is very rare.

In Conclusion
These new DNA results reveal the very complicated  and old Paleolithic origins of "ENF" mtDNA. It did not expand with farming. It had been running around in hunter gatherer populations of West Asia(and Europe?) for 10,000s of years. "ENF" itself is a mixture of at least two distinct ancient Eurasian populations, so "ENF" mtDNA is likely also a composite of mtDNA from earlier populations. We need 1000s of mtDNAs from West Asia ranging 45,000 to 3,000 years to understand its origins and history.

Lots of new ancient mtDNA from Anatolia, Spain, and Samara Russia

The new Mathieson 2015(Eight thousand years of natural selection in Europe) included dozens of new mtDNA results from Neolithic Anatolia, Copper age Spain, and Eneolithic-Bronze age Samara Russia. I added the results to my mtDNA DataBase. The results confirm trends revealed earlier by ancient mtDNA. Below are two mtDNA-related highlights from Mathieson 2015.

The mtDNA of (some of)Europe's First farmers came from Anatolia

26 mtDNA samples were taken from people who lived in farming communities at the western edge of Anatolia in circa 6300 BC. The results don't differ at all from mtDNA results of Europe's first farmers in Central Europe and Spain from 5500-5000 BC. Y DNA and autosomal DNA confirm these Neolithic Anatolians were the ancestors of Early Neolithic Central Europeans and Iberians.

It's important to note T2b, J1c, K1a, N1a1a take up the majority of Neolithic Anatolian and Early Neolithic European mtDNA. T2b and J1c today are considered European-specific and modern Europeans certainly inherited them from Neolithic Anatolia(or near by regions). The form of K1a the Neolithic Anatolians carried was all K1a4 and K1a2, except for one K1a3. All these forms of K1a have been found in Neolithic Europe and are popular in Europe today.

U3, U8b, H5, W1c'i, and X2a-o are minor lineages shared between Neolithic Anatolians and Central Europeans. None of the Neolithic Anatolians had U5 or U4 which exists at around 5% in Early Neolithic Europeans, possibly reflecting their 7% "WHG" admixture reported based on autosomal DNA by Mathieson 2015.

Not all Neolithic mtDNA from Europe is very similar to Neolithic Anatolians. mtDNA data from Neolithic Romanians is slightly differnt. They have a much high frequency of H and lack T2 and N1a1a and all their T was T1 like most T in the Balkans today.

Although Neolithic Anatolian and Central Europeans belonged to many European-specific lineages their mtDNA differed in many ways to modern European mtDNA. Whatever happened to N1a1a? Why is K1a and T2b not so popular today? Why is H so popular today? Autosomal DNA tells us Neolithic Anatolians are direct ancestors of modern Europeans, however there's lots of mystery as to why stark differences exist in mtDNA between the two.

T1a1, I, H6a, H2a1 are Steppe-lineages?

I,  H6, and H2a1 don't appear in ancient European mtDNA till Steppe peoples from Ukraine and Russia migrated into Central Europe in the 3rd millennium BC. T1a existed in Neolithic Europe but was at a higher frequency in Steppe populations and first appears in Germany with Corded Ware after being absent for 2,000 years.

The new mtDNA data from Mathieson 2015 adds to the list of Ancient Steppe people who belong to T1a, I, H6a, and H2a1. Various branches of U5a, U4, and U2e are also quite obviously mostly of Steppe-decent in Europe today. Today the highest frequency of Steppe-related mtDNA is found in Volga Russia, Scandinavia, NorthEast Europe, and the Balkans. Steppe-specific subclades are also found in West Asia, Iberia, and Italy. In the Hindu Kush there's a decently high frequency of U4, U2e, and U5a which might have mostly Steppe origins.

The reason the title says T1a1 not T1a, is high coverage Steppe T1a from Mathieson 2015 is specifically T1a1. There are also several examples of T1a1 in Late Neolithic Europeans who had a lot of Steppe-ancestry. Today T1a1 takes up almost 100% of T1a in Europe and a very small percentage of West Asian T1a. It's an obvious Steppe mtDNA haplogroup.

Part 2: Looking for mtDNA diversity in West Eurasia

Previously I showed that within haplogroups JT, R0(xHV), HV(xH), U(xK), N1 diversity follows a West Asia vs Europe pattern. 75%+ of European/West Asian JT, R0(xHV), HV(xH), U(xK), and N1 falls under European/West Asian-specific clades which separated from each other in the Neolithic or earlier.

In today's post I'll show diversity within haplogroup H, shared haplotypes and deep subclades among West Eurasians in JT and UK, and how Pre-Historic European mtDNA is ancestral to modern European mtDNA. Later I'll edit this post and make it more attractive with some PCAs and graphs.

Sorry, I can't give all the details the data reveals. There isn't enough room. I let the data speak for itself. If you don't understand feel free to post any question. 

H diversity is also West Asia vs Europe

In my first post haplogroup H, the most popular haplogroup in West Eurasia, remained undiversified. So I searched on Google for studies that tested H-subclade SNPs. I found several studies with a lot of useful data on H-subclade frequencies in West Asia and Europe. I'm not assuming H diversity follows a West Asia vs Europe trend before I look at the data the data speaks for itself. Here are the results....

H Frequencies, West Eurasia

The most significant differences are that H1 is usually 15% or more in all of Europe and less than 5% in all of West Asia, H3 also has a noticeable high frequency in all of Europe except in the East Baltic, Sweden, and Karelia. H13 has a slightly high frequency in all of West Asia.

The majority of West Asian H is not  H1 through H7 while 75% of European H is. This means more research is needed on West Asian H to learn what sub-lineages the 50%+ other part of West Asian H falls under. In most H sub clades there aren't any significant trends. I'm not going to split hairs and pretend there are trends where there aren't. 

JT, UK haplotype sharing in West Eurasia

The majority of my data is only of HVR1 coverage. This means most of my data can only be put under old haplogroups and diversity is hard to find. The best one can do to find diversity when his data is only of HVR1 coverage is to look for HVR1-haplotype sharing. 

I went through every single  JT/UK HVR1 haplotype and searched for matches. If a haplotype existed in two more populations I found the frequencies of that haplotype in all  populations. 

Here are the results....

JT haplotypes

UK haplotypes

I'm excited about the results for JT and UK. There lots of sharing and regional trends. I broke up the JT and UK haplotypes according to what region it appears they're most popular. I added Pre-Historic matches to the spreadsheet. There are some interesting ancient/modern matches.

How Pre-Historic European mtDNA is ancestral to modern European mtDNA

Here you can see I updated my haplotype sheet with Pre-Historic data. 

I added the following Pre-Historic European meta-populations to the same analysis I did for modern West Eurasians in my first post. 

Pre-Historic European meta-populations:

Early Neolithic Central Europe, Early Neolithic SouthWest Europe, Middle Neolithic North Europe, Middle Neolithic SouthWest Europe, Neolithic Romania, Bronze age Steppe, and Bronze age Central Europe.

Haplogroup Frequencies(Modern and Pre-Historic)

JT+N1: Pre-Historic      Modern.

U: Pre-Historic      Modern 

No Europeans have majority or very significant West Asian mtDNA. All have majority pre-3000 BC European mtDNA. Neolithic Anatolians(ancestors of Europe's first farmers), Mesolithic Europeans, and an unknown Near Eastern ancestor of Yamnaya are the primary mtDNA ancestors of Europeans.

Almost all Pre-Historic European mtDNA fall under European-specific haplogroups. But none have every European-specfic haplogroup. Looking at Pre Historic European mtDNA you can  see which pre-Historic Europeans are the source for each European-specific haplogroup. J1c, T2b, HV0, HV6-17, H1, H3 look like they decend from Europe's first farmers. U5b looks like it descends from Mesolithic Central and West Europeans. U5a, U4, T1a, J1b1a1 T2a1b look like they descend from the Bronze age Steppe.

Basque vs Danish

•  VS 

In my last post I discovered large differences between West Asian and European mtDNA with low coverage mtDNA data. Within Europe  and most of West Asia it is impossible to find such large differences between differnt regions/ethnic groups with low coverage mtDNA data.

Now, I have been able to find a great amount of mtDNA differences between two European ethnic groups: Danish and Basque, because I have high coverage mtDNA data from both of them.

Here's my comparison analysis of Danish and Basque mtDNA.
Basque, Danish mtDNA H
Basque, Danish Other mtDNA
Basque vs Danish mtDNA Frequencies

All of the Danish data was fully-sequenced but for Basque only their H was fully-sequenced.  So, I wasn't able to find a lot of differences between most non-H in Basque and Danish.

H takes up nearly half of European mtDNA and 90%+ of H remains undefined with low coverage testing. Fully-sequenced Danish and Basque H  reveals European H is far from uniform. Nearly 50% of the H from each appears to have separated from each other 8,000+ years ago.

Most noteworthy is that about 60% of H1/H3 in Basque and Danish probably separated from each other 8,000+ years ago. This is noteworthy because H1/H3 take up 40-50% of pan-European H and are very rare in West Asia. They're probably the most important part of the history of H in Europe.

Outside of H Danish differentiation with Basque reflects their higher amount of "Steppe" ancestry(U5a, U4, T1a, J1b1a, J2a1a1, and I).  Outside of H Basque differentiation with Danish mostly reflects Basque-specific founder effects(U5b1f1a, J1b1a-16368, J1c5c1) and a higher amount of "EEF/WHG" ancestry(K1a, HV0(xV), T2(xT2b, T2c1, T2a1b, T2f, T2e)).

Part 1: Looking For mtDNA Diversity in West Eurasia

All useful Links can be found here: Analysis of West Eurasian mtDNA

Below is a tree showing the relationship between the 6 maternal lineages that combined reach a frequency of 80%+ in most of West Eurasia and are very rare elsewhere. The 6 lineages are: R0, R2'JT, U, N1, N2, X. I also added subclades of those lineages which are able to be identified with low coverage mtDNA testing. Click on the image to enlarge.

It can be confusing how in a region as big as West Eurasia everyone could be so related maternally. Each one of those 6 haplogroups are over 40,000 years old, therefore one would propose there must be differences within those haplogroups between differnt West Eurasians.

So, what I've done is analysed 1,000s of mtDNA samples from West Eurasia to find diversity.

Locations of my samples: Map of mtDNA samples
To look at the raw mtDNA data yourself: Haplotypes
Studies where I got my data: References 
Frequencies of Haplogroups: Haplogroup Frequencies.

Almost all my samples were tested at such low coverage that I could only dissever the subclade of 5 haplogroups U, R2'JT, R0(xH), HV(xH), and N1. For the majority of West Eurasian mtDNAs it was impossible to find diversity.

In each one of those 5 haplogroups stark differences between Europe and West Asia appeared. To display these differences I made spreadsheets of the frequencies of U, JT, and N1 subclades in West Asian and European populations.

Europe/West Asia JT+N1

Europe/West Asia U

I also made a spreadsheet showing the frequency of typical West Asian and typical European subclades of R2'JT, R0, U, and N1.

West Asian vs European mtDNA Frequencies

70%+ of West Asian/European mtDNA in the 5 haplogroups that can find a deep subclade with low coverage belong to subclades exclusive to their region(West Asia, Europe). It's very consistent.

Frequency of "Steppe" mtDNA

For fun I wanted  see what the maternal-relationship between Bronze age "Steppe" people(Yamnaya, Catacomb) is with modern/ancient West Eurasians. In my next post I'll discuss more about the possible ancestors of West Eurasian mtDNA.

There are 10 subclades that can be identified with low coverage mtDNA testing that were popular in Bronze age "Steppe" people. I made a spreadsheet showing the combined-frequency of those subclades in modern and ancient West Eurasians.

Frequency of Steppe mtDNA

Something that stood out to me is that 4/8 of Bronze age Armenian mtDNA falls under typical "Steppe" subclades. Autosomal DNA and Y DNA(R1b-Z2103) also confirm some-type of relationship between Bronze age Armenia and Steppe.

Among modern people "Steppe mtDNA" peaks in the Volga/Ural region of Russia and next in North Europe. "Steppe mtDNA" is  least popular in Iberia and West Asia. This is consistent with autosomal DNA.