Wednesday, March 15, 2017

Farmer Moms, Pastoral Dads???

Image result for bronze age family

 Iosif Lazaridis, David Reich, Failure to Replicate a Genetic Signal for Sex Bias in the Steppe Migration into Central Europe, March 14, 2017
Goldberg et al., Familial migration of the Neolithic contrasts massive male migration during Bronze Age in Europe inferred from ancient X chromosomes, September 30, 2016

Were Bronze age Central Europeans the product of unions between Foreign Pastoral Men from the Eurasian Steppe and Native Farmer Women from Central/Eastern Europe? One study (Goldberg et al. 2016) says they were and the other says they weren't.

To determine if admixture between Steppe Pastrolites and European farmers was sex bias both studies estimated Steppe Pastrolite ancestry and European farmer ancestry in the X chromosome and autosomal chromosome of Bronze age Central Europeans.

But each used different methods to do so. Goldberg et al. 2016 used ADMIXTURE and the other used qpAdm. In my opinion qpAdm is a better method than ADMIXTURE. So although I'm undecided, if I had to guess I'd guess that Lazardis and Reich are correct.

Let's look at the mtDNA of Bronze age Central Europeans to see if there's any evidence of sex bias admixture.

Corded Ware. N=67.
mtDNA: Steppe 42% (28), Farmer 41% (27), Unknown 17% (12)
Y DNA: 100% Steppe.
Autosomal: ~75% Steppe, ~25% Farmer

Bell Beaker. N=42.
Steppe=38% (16), Farmer=36% (16), Unknown 26% (10)
Y DNA: 100% Steppe
Autosomal: ~50% Steppe, ~50% Farmer

Unetice. N=94
Steppe=36% (34), Farmer=28% (26), Unknown 36% (34)
Y DNA: 100% Farmer?(yHG I2, could be Steppe aswell)
Autosomal: ~60% Steppe, ~40% Farmer.

Keep in mind I counted originally hunter gatherer "WHG" mHG U5b as farmer. mtDNA data doesn't suggest admixture between Steppe Pastrolites and Native Central/East European farmers was sex bias except maybe in Corded Ware. At least 40% of Corded Ware mtDNA is of farmer origin but only 25% of their ancestry is.

mtDNA from modern Europeans in my opinion though does indicate sex bias admixture has occurred in European history. Specifically it indicates most of modern European mtDNA is "EEF" and "CHG", from the Neolithic Near East.

Is my mtDNA Farmer or Steppe?: If you want to know your mtDNA is of Eurasian Steppe Pastrolite or European Farmer origin email me your haplogroup to Most European mtDNA can be labelled as Steppe or Farmer. For example I know my mtDNA (U5b2a2) is from European hunter gatherers who were assimilated by farmers and my Y DNA (R1b) is of Steppe origin.

Sunday, March 12, 2017

Siberia, Past and Present

"West Siberia"=Green, "South Siberia"=Red

A decent amount of mtDNA from Siberia which dates between 6000 BC to 0 AD has been sequenced in the last 15 years or so. In this post I'll give a brief description of the similarities and differences between ancient and modern Siberians.

Below is a list of the ancient and modern Siberians which I'll compare to each other.

South Siberia
6800-5800 BPKitoi culture, N=40
5800-4000 BPSerovo-Isakovo-Glazkovo culture, N=16
2800-2000 BPAltai Scythians, N=34
ModernAltaians, N=110
ModernBuryats, N=386
ModernTuvinians, N=195
ModernKhakassians, N=110

West Siberia
6000-5000 BP, Ust Tartas and Odinivo Cultures, N=27
3800-3000 BPKrotovo, Andronovo, Barba cultures, N=44
ModernMansi, N=51
Modern, Tatars, N=220

Here's a link of mHG frequencies for the above populations; Siberia, Past and Present.

All of the primary East Asian mHGs; A, B, C, D, F, are represented in ancient Siberia except for B.

mHGs which link ancient Siberia to modern Siberia; C4a1, C5b1, D4b1, G2a, F1b, A8, U5a1d2b

mHGs unique to ancient Siberia; A10(West Siberia).
mHGs unique to modern Siberia; B, N9a, M7

South Siberia, Past and Present

mHG A is x2-x3 less popular in all the modern South Siberians than all the ancient South Siberians. mHG F was exceedingly more frequent in the ancient South Siberian Kitoi culture at 38% than in any other modern or ancient Siberians. All of their F belonged to F1b, a form of F which is more or less Siberian/North Asian specific today. F1b is frequent in modern South Siberians(~5%) but not a single Atali Sycthian belonged to F or F1b.

mHG G2a makes a significant mark on all the mtDNA in all of the ancient and modern South Siberians. In contrast modern and ancient West Siberians barely have any G2a. But G2a can be found at decent frequencies in parts of Eastern Asia.

C4a1 was quite common in Atali Sycthians(12%) as it is in modern Tuvinians(12%) and Tofalar(34%). The only modern South Siberians who don't have at least 5% C4a1 are the Altaians(0%).

Several  mHGs exist in modern but not ancient South Siberia. Here they are...
B(primary B4), N9a, M7, M8, Y.

Both B and M7 are frequent in Eastern Asia(Japan, China, Burma, Tawian, etc).

West Siberia, Past and Present

Like in South Siberia, in West Siberia mHG A frequencies are considerable lower in moderns than in ancients. The Ust Tartas and Odinivo Cultures' high frequency of Z(19%) differentiates it from all other ancient and modern Siberians. 0% of modern West Siberians have Z.

mHG F, mostly F1b, is present in modern West Siberians but is absent in ancient ones. M7 and B are present in modern but not in ancient West Siberians. Besides that all the major mHGs in modern West Siberians are present in ancient ones.

West Eurasian mtDNA

West Eurasian mtDNA is present in every ancient and modern Siberian population. Ancient Siberians' WE mtDNA belonged exclusively to mHG U(U5a, U4, U2e) until the appearance of the Afanasievo(3000 BC)  and Andronovo cultures(1800 BC) from Eastern Europe. They brought with them large amounts of H, U5a, U4, T2, T1a, and smaller amounts of other West Eurasian mHGs.

Up until 1000 BC all of the WE mtDNA found in Siberia looks like it's from Eastern Europe. In 1000 BC mHGs never found in Europe but frequent in Western and SC Asia appear; U1a, U7, J1b, and others. Possibly after migrations from Eastern Europe(eg, Afanasievo) peoples from SC Asia or the Caucasus migrated into Siberia. 

Sunday, March 5, 2017

First mtDNA from Mesolithic Sardinia; J2b1 and I3

Modi, A. et al. 2017 just published mito genomes of two 10,000 year old Mesolithic individuals from Sardinia. One belongs to J2b1 and one to I3. Neither belongs to hg U, the lineage which 97% of 100+ other Mesolithic European mtDNA samples belong to.

A J2 and a hg I dating around 10,000 years old have been found in the Near East. Their presence in Mesolithic Sardinia indicate Mesolithic Europe, maybe specifically Mediterranean Europe, exchanged genes with the Near East before Near Eastern farmers migrated en masse into Europe in the Neolithic.

Saturday, March 4, 2017

More ancient Eastern European mtDNA

Two new papers with ancient Baltic mtDNA: Saag et al. 2017 and Mittnik et al. 2017, were posted at bioRxiv yesterday. Together the two produced 29 new mtDNA samples from ancient Baltic hunter gatherers, 9 from Baltic Corded Ware, and 17 from the Baltic Bronze age. The new data has been added to my European Hunter Gatherers and Bronze age North Europe mtDNA spreadsheets.

The news results contain only a few pieces of interesting information.

  • Two Baltic HGs don’t belong to mHG U; H11a and K1b2
  • One Baltic HG belongs to “Saami” U5b1b1a
  • 47% of Bronze age individuals belong to mHG H
  • No Siberian mtDNA.

Regarding the Baltic hunter gatherer H11a and K1b2, both mHGs today are more or less European specific today. H11a peaks in Poles, not in a particular large region, which is interesting. Also K1b2 is well documented in Europe but to my knowledge only one non European(Armenia) is known to carry it.

In a post I made about Finnish mtDNA a few months ago I speculated that mHG U5b1b1a descends from ancient NorthEast European hunter gatherers. Well now there’s good evidence that is the case: Kretuonas4 an ancient NorthEast European hunter gatherer of the Narva culture belonged to U5b1b1a. Today U5b1b1a is NorthEast European specific but has also been found in locations such as England, Spain, and Turkey.

The new data suggests Baltic mHG frequencies changed in a big way after the Late Neolithic. Can you guess how? If you read my blog you should know. This will help you; Natural Selection Did It!. mHG H frequencies skyrocketed. I’ve been speculating for a while that for some reason in Bronze age Europe natural selection drove mHG H frequencies upand the frequencies of other mHGs like T2 and K down. mtDNA data from Iron age Poland, Scandinavia, and Spain also display high frequencies of H unlike earlier people from the same locations. My natural selection hypothesis is looking stronger and stronger.

Lastly not a single individual in these two studies belonged to an Siberian mtDNA haplogroup. As far as I know  the autosomal DNA from these ancient individuals don't suggest they had any Siberian-like ancestry either. So it looks like Siberian ancestry, possibly along with yHG N1c and Uralic languages, arrived in the Baltic during the Bronze age or later. Siberian mtDNA(C5b1, Z, D) dating 3,500 years old was found in Karelia. So maybe Siberian ancestry existed in some parts of NorthEastern Europe during the Bronze age and then it gradually expanded. 

Friday, February 24, 2017

European Farmer mtDNA in the Cucuteni-Trypillia Culture

                             Image result for Cucuteni-Trypillia CultureImage result for Cucuteni-Trypillia Culture

Nikitin et al. 2016 just published mtDNA results for nine members of the East European Neolithic Cucuteni-Trypillia Culture. They died around 3500 BC and were buried in the Verteba cave in SouthWestern Ukraine. The results are below...

H5*, H5b*, H1b1*, H
U8b1a2b, U8b1b

This dose of mtDNA from Cucunteni-Trypillia is made up entirely of typical Neolithic European farmer lineages. This confirms, like farmers in other parts of Europe, that they weren't simply local forgers who learned how to farm but were instead to a large extent descended of Neolithic farmers from Southeast Europe and the Near East.

As Steppe pastoralists, like Yamnaya, moved westward to Europe around 3000 BC they ran into and (probably)intermarried with the farmers of Eastern Europe, like the Cucunteni-Trypillia farmers. The genes of Eastern European farmers could have therefore been carried alongside Steppe genes to many parts of Europe during the Chalcolithic and Bronze ages.

Interestingly ancient farmers from Romania had an impressively high frequency of mHG H(about 60%). The new data from Ukraine is consistent with that high frequency of H. Four of the Nine of these Cucunteni-Trypillia farmers belonged to mHG H. Maybe farmers from Eastern Europe can help explain high frequencies of mHG H in modern Europeans. Maybe. The data doesn't strongly support this idea or storngly not support. I'm just throwing out the possibility that farmers from Eastern European contributed lots of ancestry to modern Europeans.

Not only does it appear Eastern European farmers had a lot of H but one of the Cucunteni-Trypillia farmers belonged to typical modern (Eastern)European mHG H1b. Not a single H1b exists in the about 600 mtDNA samples from Neolithic Germany, Hungary, and Spain. But today every part of Europe has at least 1% H1b. Eastern Europeans; Poles, Lithuanians, Slovaks, Bosnians, etc., have the most H1b(3-4%). Though H1b is mostly European it has also been found in the Near East, Iran, and Western Siberia

Below are the only other instances of H1b in ancient DNA...

4700-4500 YBP, Poland/Ukraine border.
1358 BC, Mongolia.

The Bronze age H1b individual from Mongolia was of mixed Eastern European and North Asian ancestry, his H1b was from Eastern Europe.

Saturday, February 18, 2017

Spain, Past and Present

A lot of changes arose in Spanish mtDNA after the Neolithic. mtDNA sequenced from Iron age Spain indicates those changes had occurred by circa 300 BC.

Modern and Spanish mHG frequencies are included in the following spreadsheets along with mHG frequencies of other ancient and modern Europeans…Spain
mHG Frequencies
JT, N1, U5

For convenience here is a picture comparing modern and ancient Spanish mHG frequencies. mHGs with significantly different frequencies in modern and ancient Spain are highlighted....Notice Iron age Spain is similar to Modern

The two mHG which differ in frequency the most are H and K.

Neolithic Spain had a whopping 27-30% K and an unimpressive 20-25% H. Modern and Iron age Spain has/had a whopping 40-45% H and an unimpressive 7% K.

mHG frequencies in modern Spain are basically indistinguishable to mHG frequencies in most of modern Europe. mHG frequencies in Neolithic Spain were basically indistinguishable to mHG frequencies in Neolithic Germany and Hungary.

The same mtDNA changes which occurred in Spain after the Neolithic occurred in much of Europe. I think a mixture of migration from “Asia”(inclu. mostly “Eastern Europe”) and natural selection caused(I gave my reasons in this post) those changes to occur.

Furthermore there are many mHGs which exist in modern Spain at over 1% or just under 1% but haven’t been found in Neolithic Spain yet…..
L(xM, N): Modern Spain(2%), Neolithic Spain(0.5%)
M1: Modern Spain(0.7%), Neolithic Spain(0%)
N1b1: Modern Spain(0.5%), Neolithic Spain(0%)
R1: Modern Spain(0.3-0.5%), Neolithic Spain(0%)
U6: Modern Spain(2%), Neolithic Spain(0%)
U5a: Modern Spain(2-3%), Iron age Spain(4%)Neolithic Spain(0.5%)
U8b1, U8a1a: Modern Spain(0.5-1%), Neolithic Spain(0%)
U9a: Modern Spain(0.5%), Neolithic Spain(0%)
T1a: Modern Spain(1.5-2%), Iron age Spain(2%)Neolithic Spain(0%)
T2c1: Modern Spain(1-1.5%), Neolithic Spain(0.5%)
I: Modern Spain(2-3%), Neolithic Spain(0%)
H6: Modern Spain(1-2%), Neolithic Spain(0%)
HV6-24: Modern Spain(1.5-2%), Neolithic Spain(0%)
W: Modern Spain(1%), Iron age Spain(6%)Neolithic Spain(0%)

U6, L(xM, N), and M1 indicate modern Spanish have maternal ancestry from Africa which Neolithic Spanish did not have. The L(xM, N) mHGs modern Spanish belong to are mostly the same L(xM, N) mHGs NorthWest Africans belong. The two most common L(xM, N) mHGs in both locations are L1b and L2a1. The single L(xM, N) from Neolithic Spain belonged to L1b.

The other mHGs don’t conclusively indicate maternal ancestry from any particular region. U5a, T1a, T2c1, I, R1, W, HV6-24, and H6 are all present in ancient mtDNA from Central and Eastern Europe at high frequencies. It’s possible that region lent Spain those mHGs. But I and T1a are also frequent in the Middle East.

Along with differences there are also noticeable similarities between Neolithic and Modern Spanish mtDNA. Both have a higher frequency of J2b1a, J2a1a, T2a1b, U5b, U5b3, and U5b1i than ancient and modern Europeans from other regions.

Nuclear DNA confirms considerable genetic changes took place in Spain after the Neolithic age. Here’s how modern Spanish come out when they’re modeled as a mixture of Neolithic Spanish and other ancient and modern humans.

Middle Neolithic Spain: 48%
Eastern Europe(Yamnaya): 24%
Near East(Cypriot): 22%
Africa(Mozabite): 6%

So nuclear DNA Spain probably received migration from Eastern Europe(Yamnaya), the Near East(Cypriot), and Africa(Mozabite) after the Neolithic. mtDNA is pretty consistent with this.

Friday, February 3, 2017

New mtDNA from Stone age Eastern Europe(Latvia, Ukraine)

Yesterday Jones at al. 2017 published genome-wide, including mtDNA, data of 8 ancient individuals from Latvia and Ukraine. Three are Mesolithic Latvians, one is a Mesolithic Ukrainian, one is a Early Neolithic Ukrainian, two are Middle Neolithic Latvians, one is a Late Neolithic Corded Ware Latvian.

Here's a link to Jones at al. 2017's Figure 1 which displays the mtDNA results of these 8 Stone age Eastern Europeans. I added the new ancient mtDNA to my European Hunter Gatherer and Bronze age Northern European spreadsheets.

These Stone age Eastern Europeans can potentially give detailed insight into the origins of modern Europeans. Because of other ancient DNA we know all modern Europeans are mostly a mixture of the "Steppe", "EEF", and "WHG" populations but we don't know which "Steppe", etc. populations contributed to which modern Europeans.

Maybe people similar to these Stone age Eastern Europeans specifically gave modern Eastern Europeans a lot of their "WHG" ancestry. Maybe other Europeans got a lot of their "WHG" from WHGs who lived in other parts of Europe.

Mesolithic Baltic(Sweden, Latvia, Lithuania) HGs can be labeled as WHG or at least very similar. Their mtDNA makeup though is different from Western European WHGs.

Western Europe HGsBaltic HGs

Now let's look at who in Europe today has the most and least U5b, U5a, and U4.

Most U5b...

Andalusia Spain6.5
Galicia Spain6
North Poland5.4

Least U5b...

North Italy2
South Italy2.2

Most U5a...

East Baltic11.3

Least U5a...

Andalusia Spain2.5
South Italy2.6
Galicia Spain3.5

Most U4...

NW Russia6
East Germany5.6
East Baltic5.2
Least U4...

North Italy0
SW France1.2
Andalusia Spain1.7
South Italy1.8

U5b, U5a, and U4 frequencies in modern Europe have geographic trends. U5a and especially U4 peak in Eastern Europe. Is this because Eastern European hunter gatherers had a lot of U4 and U5a? Does U5b peak in Iberia because Western European hunter gatherers had a lot of U5b? That's all just hypothesis, we'll have to wait for more data to confirm it.

I've recently gathered a lot of new European data and will make a post about haplogroup frequencies in Europe soon so stay tuned.