Sunday, October 11, 2015

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.

Sunday, October 4, 2015

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....

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....

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.

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.