Wednesday, May 10, 2017

Heaps of new ancient European DNA



Today three new papers were posted on bioRxiv. Combined they add something like 300 new genomes from ancient Europe.

Olalde et al. 2017 confirmed that Britain experienced a near complete population replacement when Bell Beaker folk from the continent arrived in around 2400 BC. And it looks like the British Isles, besides England(English have Anglo Saxon ancestry), hasn't received any significant foreign immigration since then. Which means modern British and Irish, including their mtDNA, are basically Central European Bell Beaker folk 4,000 years later.

Olalde et al. 2017: Neolithic to Bronze age(4600 to 1000 BC) Western Europe but focuses on the Bell Beaker culture(~2200 BC).
Mathieson et al. 2017: Mesolithic to Bronze age (10,000 BC-500 BC) SouthEastern Europe.
Martiniano et al. 2017: Neolithic, Copper Age, and Bronze age Portugal.

In the last year I have focused on European mtDNA in preparation for these papers. In this post I'll tell the mtDNA affinity of every ancient population analysed in these new studies for the first time.

Ukraine Hunter Gatherers ~10,000-7,000yo. N=38
All individuals posses mHG U5 or U4 or U2. Most of their U5a1 is U5a1b, most of their U5a2 is U5a2a, and most of their U4 is U4b1.

The high frequency of U5a1b is interesting because a high ratio of modern U5a1 is U5a1b and UkraineHGs are the only European HGs found with U5a1b. Furthermore, U5a1b has been found in many Steppe-influenced ancient Eurasians(eg; Bell Beaker, Corded Ware, Scythian, Tarim Mummies). About 5% of British Bell Beaker and Bronze age individuals have U5a1b.

UkraineHG had a very high frequency of U4; 38%. UkraineHG ancestry could explain the high frequency of U4 found in later Catacomb culture and Andronovo and modern Eastern Europeans. Combined U4b1a and U4b1b make a strong presence in Ukraine HG. These two subclades consume a large percentage of modern U4 and they can be found from Pakistan to Ireland.

Iron Gate(Serbia, Romania border) Hunter Gatherers ~9,000-8,000yo. N=37.

76% have U5 or U4. 19% have K1. 3% have U8b1b. 3% have H.

U5b1d1, U5b2a1a, U5a1c, U5a2d, U5a2a, U4b1b1, K1c swallow 50% of Iron gate HG's mtDNA.

Coincidentally today both U5b2a1a and U5a1c  peak in Spain. By peak I mean Spain has like 1% of each while other Europeans have 0.(something). U5a1c was also quite popular among East Baltic hunter gatherers but hasn't been found in hunter gatherers outside of Iron Gate and the East Baltic.

K1's persistent presence in Iron Gate renders it unique from other European hunter gatherers. K1c is its most popular K1. Recall a pair of K1* possibly K1c was found in Mesolithic Greece a few years ago.

Bulgaria, Romania, Ukraine Neolithic Farmers. ~8,000-6,000yo. N=24. 

Typical Neolithic European farmers.

All belonged to one of the following mHGs; H, K1a, T2(T2e, T2b), T1a, J1c, U5a. And their frequencies of those haplogroups are similar to other Neolithic Europeans.

H1b popped up in Trypillia in a second straight study. H1b peaks in Eastern Europe today and can be found all over Eurasia.

Only 8%(2 of 24) had hunter gatherer mtDNA; U5a2* and U5a1c.

Globular_Amphora Ukraine and Poland. ~5,000yo. N=11.

Typical Neolithic European farmers.

H28=3, H1b=1, U5b=2, J1c=2, T2b=1, K1b1a1=1, W5=1.

British Neolithic. ~5500-4500yo. N=36. 

H 25%
  H1 14%
  H3 3%
  H5: 6%
K 19%
  K1a4 6%
  K1b1a1 6%
U5 16%
  U5b 8%
  U5a 5%
J1c 11%
T2 8%
X 3%
W 3%

Yep, typical Neolithic European farmers. Interestingly I see a lot of similarities to Iberia Neolithic. Also two had H1c which has been found in Funnel Beaker Sweden and is quite popular in Europe today.

British Bell Beaker, Bronze age. ~4500-3500yo. N=55.

H 13%
  H1 5%
  H3 2%
  H5 0%
  H6 2%
K 5%
U5 27%
  U5b 15%
  U5a 12%
U4 2%
J1c 5%
T2 13%
X 2%
W 2%
I 9%

Mostly Neolithic European farmer but shows significant Steppe influences.

Interestingly U5 frequencies are much higher than in modern British. All of British BBC/BA's U5a falls under distinctively Steppe subclades; U5a1a and U5a1b.

mHG I reaches strangely high frequencies in British BBC/BA like it does in Unetice. mHG I isn't a Steppe lineage but at least in Europe it first appears alongside Steppe ancestry.  

Monday, May 8, 2017

New U2 clade found in Europe

New U2 subclade
U2(f): 16092C, 16179A, 152C

mHG U2 has weak presence in Europe (Frequency of 1-2%) European U2 is quite homogeneous, basically all of it is U2e. And U2d covers 99% of other U2 in Europe. So it is worth noting I just discovered a new type of U2 in Europe which is a cousin of U2e and U2d. 

This newly discovered U2 clade has been found in only two populations who live(ed) roughly in the Eastern half of Europe. Below are all the examples of this U2 clade I have found.

Year, Country, Culture
5200 BC, Hungary
5000 BC, Hungary
2013 AD, Bulgaria
2013 AD, Bulgaria

Haplogroup U2 breaks up into three branches.
U2-Kostinki: Only example exists; a man who died in Russia 38,000 years ago.
U2a'b: Basically exclusive to South Asia.
U2'c'd'e: U2c peaks in South Asia. U2d and U2e are found everywhere in Eurasia except Eastern Asia.

All three branches probably date more than 40,000 years. An early form of U2e is documented in Paleolithic Western Europe(~30kya). In addition U2e had a presence in Mesolithic Europe. U2(f) most likely belongs to U2'c'd'e. It could have been involved in early European or Western Eurasian human settlements like U2e and U2d.  

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 sammyisaac107@gmail.com. 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...

H=4 
H5*, H5b*, H1b1*, H
U8b1=2
U8b1a2b, U8b1b
T2b*=1
HV6-24=1
HV0=1

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.