Tuesday, June 20, 2017

LBK-like mtDNA in Lengyel Poland (Cylenski 2017)

In March, Cylenski 2017 published one mito genome from Mesolithic Poland, one from LBK Poland, and three from Lengyel Poland. This study went unnoticed by DNA forums. I discovered it while searching for studies on modern mtDNA.

Here are the results from the paper....

Mesolithic, 5644-5374 cal BC, Jan1, U5b1b1
LBK culture, ----, Sam1, N1a1a1a
Lengyel culture, ----, Kz6, N1a1a1a3
Lengyel culture, ----, NHp1, H5*
Lengyel culture, 4255–4145 cal BC, R18_1, K2a-16398A
Lengyel culture, ----, KM1, U5b1b*

N1a1a1a3, K2a-16398A distinctive Neolithic Hungary/Germany Lineages

The N1a1a1a3 and K2a-16398A samples directly link Lengyel Poland to Neolithic Hungary and the LBK culture in general.

My database holds over 1,000 mtDNA samples from ancient Europe and about 12,000 mtDNA samples from modern Europe. And amazingly, besides a few exceptions, N1a1a1a3 and K2a-16398A reside exclusively in Neolithic Germany/Hungary.

None of my modern samples belong to K2a-16398A and only three belong to N1a1a1a3(Austria, Saudi Arabia, Yeman). Interestingly Austria also provides one of my only modern examples of N1a1a1a2, which could mean there's significant LBK-like mtDNA there. Most modern European N1a1a1 belongs to different subclades than what is found in Neolithic Germany/Hungary.

K2a-16398A and N1a1a1a3 were actually quite popular in Neolithic Germany/Hungary but apparently barely exist or don't exist at all in modern Europe.

U5b1b1, a clue to the origin of Eastern European U5b1b1a and U5b1b1[c]?

The only Mesolithic sample from this study belonged to U5b1b1. The meaning of this result goes beyond U5=European HG, the subclade this Polish HG belonged gives more in-depth insight than that.

In the past year dozens of Mesolithic mitogenomes have been sequenced but U5b1b1 has popped up in only one sample: Kretuonas4, an individual from the Narva culture who belonged to U5b1b1a.

U5b1 frequencies varied in Mesolithic Europe. It looks like it peaked in the Narva culture and in Germany/France.....
     
Ukraine(39) U5b1=0
Serbia/Romania(39) U5b1=2
Germany/France(23) U5b1=7
Narva Lithuania(17) U5b1=5
Mesolithic Latvia(19) U5b1=1
Comb Ceramic(12) U5b1=1

There are at least five U5b1 clades unique to Eastern Europe today; U5b1b1a, U5b1b1[c], U5b1b2, U5b1b[3], and U5b1e1[b],

10% of Finns belong to those subclades and basically all Finnish U5b falls under those U5b1 subclades. 41% of all my U5b samples from NorthEastern Europe belong to those U5b1 clades, that's 66 out of 160 samples.

So I'm thinking that Mesolithic Eastern Europe harbored U5b1 and especially U5b1b rich WHG populations which were later absorbed by farmers and herders.

Friday, June 16, 2017

Three new U5b subclades in Eastern Europe

Recently I've focused my work on trying to find widespread shared haplotypes aka unclassified subclades under West Eurasian haplogroups which can help better understand the mtDNA gene pool in West Eurasia. I've had lots of success.

Last month I discovered a new very basal form of U2, which I named U2[f], see here. Back then I knew of four samples belonging that subclade: two from Neolithic Hungary and two from modern Bulgaria. Since then I've found an additional example from Neolithic Britain and another from modern Picardy France.  

Unlike U2[f], these newly discovered basal U5b subclades might actually be kind of popular. Also they might be geographic specific because all the representatives for each are from Eastern Europe. 

mHG name: defining mutations.
U5b2a2[d]16192! 16217 16234 1117 3834 8941: Poland, Belarus, Volga Tatar.
U5b1b[3]: 16192! 16147 3708 3849 6302: Slovakia, Livi Ukraine, Ryazan Oblast Russia, Smolensk Oblast Russia, Volga Mordovian.
U5b1a[1]10373 204 207 235: Slovakia, Romania, Serbia, Russia.

In my database U5b2a2, which is the haplogroup I belong to, peaks in Poland, Belarus, and Austria. A large majority, maybe something like 70%, of U5b2a2 belongs to U5b2a2a or U5b2a2b. So the discovery of a new U5b2a2 subclade which extends from Poland to Russia is a pretty big deal. Based on the low diversity in U5b2a2 I suspect that it "expanded" in Central-East Europe during the Mesolithic or Neolithic. But that's really just pure speculation. 

U5b1b[3] might be a fairly important U5b subclade in Russia considering most examples of it are from Russia. There are two other popular U5b1b subclades near Russia; U5b1b2 in Finland and U5b1b1a in the Saami country. 

Maybe U5b1b[3], U5b1b2, and U5b1b1a all descend from WHG heavy Neolithic foragers who were absorbed by new groups from the south like Corded Ware who first began to arrive in 2600 BC. An example of U5b1b1a has already been found in a Neolithic forager from Lithuania, see here

Thursday, June 1, 2017

First look at ancient Egyptian mtDNA


Thanks to Schuenemann 2017 we finally have DNA from the ancient Egyptians. It sequenced three ancient Egyptian genomes and 90 ancient Egyptian mtDNA genomes. All of the samples come from Middle Egypt and range in age from about 1300 BC to 300 AD.

The genetic affinity of the ancient Egyptians doesn’t carry any surprises. They were native to the Middle East. With published ancient DNA we can trace their roots back 12,000 years to that region. But unlike other ancient Middle Eastern DNA, the ancient Egyptians also harbored a little bit of some sort of Sub Saharan African ancestry(5-10%).

I’ve taken a close look at the ancient Egyptian mtDNA results. So here’s a first glimpse into the mtDNA affinity of the ancient Egyptians…..

Like their genome-wide affinity the ancient Egyptian’s mtDNA is distinctively Near Eastern. Not just Middle Eastern but Near Eastern. Recall earlier this year I pointed out that modern Egyptian mtDNA shows affinity to the Near East not NorthWest Africa. They share most mtDNA first with modern Egyptians but then also Arabians and peoples in the Levant(Syria, Lebanon, etc). A mere 1%(1 sample) belonged to Sub Saharan African mHG L(xM, N). Modern Egypt though has a frequency of 20% frequency!

A handful of mHGs characterized ancient Egyptian mtDNA. 44% belonged to the following mHGs: R0a 7.8%, HV1 6.7%, J2a2 6.7%, T1a 14.4%, M1a 5.6%, I 4.4%. 

Every single one of those mHGs is specific to the Near East-North Africa except for U6a and M1a which make a significant presence Iberia and many parts of Africa.

Today R0a, HV1, and J2a2 interesting all peak in Egypt. And the ancient Egyptians had as high of a frequency in those mHGs as you’ll find in any modern population. Their high frequency of J2a2(6.7%) is even more interesting considering it has been found in the Natufians. J2a2 seldom appears outside of the SouthWest Asia-North Africa. Last year I classified it Near Easter(See here). J in Europe is dominated by J1c while J1b-J1d dominates J in much of the Middle East.

R0a has a more international distribution than J2a2 and HV1. Like J2a2 it peaks in the Near East but it also surprisingly has a strong presence as far east as India. Several examples R0a have been found in Neolithic and Bronze age Jordan.

Saying the ancient Egyptians had a lot of T1a doesn’t say much considering T1a is equally popular in most of West Eurasia(from Ireland to Iran). The T1a clades the ancient Egyptians belonged to: T1a7, T1a2, T1a5, T1a8, all are Near Eastern-specific. None of them belonged to European-SC Asian T1a1. Most of my modern T1a7 samples are from Egypt.  All of my Egyptian T1a7 samples belong to an unclassified T1a7 clade, it’ll be interesting to see if these ancient Egyptians belonged to that clade.

Here’s the most important differences between ancient Egyptian mtDNA and modern Egyptian+Near Eastern mtDNA: moderns have a lot more J1b, H, U3, and African L(xM, N).

Thursday, May 25, 2017

Haplotype Analysis of Bulgaria and Romania

For the first time a sizable number of samples from Romania and Bulgaria are in my database. I did extensive haplotype analysis on the data which unveiled many unclassified lineages. Romania and Bulgaria share more haplotypes with each other than with any other population and both share a decent number of unique haplotypes with other Eastern Europeans.
Here are some unique haplotypes which make a presence in both Bulgarian and Romanian mtDNA.

T1a(xT1a1’3)-16390: Bulgaria=3, Romania=6
T2f2: Bulgaria=2, Romania=1
T2b-16111T 16311C 16327T: Bulgaria=2, Romania=1
K1c1e: Bulgaria=2, Romania=7
U4-152 185 189: Bulgaria=1, Romania=2
HV0-16311: Bulgaria=6, Romania=7
N1b1-16244A 146C: Bulgaria=2, Romania=8
M-16129 16291 16298: Bulgaria=1, Romania=8
W-16172C 16231C 210: Bulgaria=6, Romania=4

Although the mtDNA composition of Bulgaria and Romania are of course not identical. Here are some significantly frequent haplotypes the two countries don’t share.

Bulgaria
H1a3-16075 16172=6
U5b-16192! 16189! 16465=7
U2(f)-16092 16111 16179=2
T2-16287=6
J1c2e(xJ1c2e2, J1c2e1)=10
J1c2e1=4

Romania
H5-189=7
H5-16209=5
U3-16166 16311=3
T2-16172 16274=3
X2e1b-152!!=8
I5a4-16374=3

I also searched for haplotypes Romania and Bulgaria share with other populations. I organized what I found into this spreadsheet; Romania, Bulgaria Haplotypes. As you can see in the spreadsheet both countries share many haplotypes with other Eastern Europeans. But haplotypes centered in Western Europe and the Middle East also pop up.

Below is a list of what I think are the most interesting haplotypes in that spreadsheet…

Eastern Europe
M-16129 16298 16291: Bulgaria=1, Romania=8, Greece=3, Poland=1, Volga=1, Burusho=1
U5b1a-204 207 235: Romania=2, Slovak=1, Bosnia=1, Serbia=1, Russia=1
U4a2a: Romania=1, Poland=7, Russia=6, Ukraine=4, Belo=2, Slovak=2, Austria=2, Volga=1, Algeria=1, South Italy=1
J1c7: Bulgaria=2, Russia=1, Poland=1, Ukraine=1, Czech=1, Austria=1, BeloRussia=2, Balt=1, Andalusia=1, Valencia=1
H11a2a2: Bulgaria=2, Romania=2, Poland=13, Russia=1, Ukraine=1, Belo=1, Volga=1, Balkan=4, Greece=1, Slovenia=1, SW Turkey=1

Middle East
U4a2b: Bulgaria=5, Romania=3, Poland=4, Greece=1, SW Turkey=3, Syria=1, Egypt=1, Morocoo=1
T1a(xT1a1’3)-16390: Bulgaria=3, Romania=6, Sweden=1, Lebanon=3, Egypt=1.
HV2-16243: Romania=2, Bosnia=1, South IndiaTamil=1, Persian=1, Makrani=1, Uzbeck=1.

Western Europe
U4a1-16240: Romania=1, NW France=2, Andalusia=3, Y Leon=1, South Italy=1, Balt=3
U5b2b3: Romania=1, Andalusia=3, Y Leon=2, Madrid=1, Portugal=2, Ireland=1, Britain=2, Algeria=1, Neo France=2, Neo Spain=4, Unetice=1

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.