Saturday, July 15, 2017

The age of ULTIMATEness!

Image result for nuclear explosion

A new age for mtDNA Atlas has begun; The age ULTIMATEness!! This new age is named after ‘ULTIMATE’ which is a spreadsheet of mine that currently contains 33,185 mtDNA samples. I won’t share ULTIMATE with anyone.

ULTIMATE allows me to look at mtDNA data at angles I could never do before. Thanks to ULTIMATE my knowledge of West Eurasian mtDNA has quadrupled over the past month. Stay tuned for some interesting posts in the second half of 2017.

ULTIMATE can show me the distribution of any mtDNA haplogroup or mtDNA haplotype in the blink of an eye.

I used ULTIMATE to do a haplotype analysis of about 20,000 samples from Europe and the Middle East. What I found is pretty interesting. Most of the stuff I've learned I'm going to keep top secret for a while. I have lots of new theories on the ancient origin of mHGs that I will post about soon. I think many of you will find them interesting.

Haplotype sharing correlates with geography pretty well. Because of my haplotype analysis of West Eurasia I can classify about 10% of the mtDNA in every population in West Eurasia to a specific sub region such as Iberia or Balkans or Eastern Europe.

Here’s an introduction to what will be the new norm on this blog.

Haplotype sharing results.

Poland.

Macedonia.

Lebanon.

Tuesday, July 4, 2017

16 unique Balkan haplotypes

I’ve discovered 16 haplotypes unique to the Balkans. Combined they make up about 5% of total Balkan mtDNA and a whopping 10% of the mtDNA in Eastern Herzegovinian speakers (Bosnia, Serbia, Kosovar, Croatia). Most of these haplotypes have a representative in four or more Balkan populations. That confirms all of these haplotypes are widespread in the Balkans but pretty much never found anywhere else in the world and can therefore be called ‘Balkan haplotypes.’

This map gives an idea where the haplotypes are found….


They are not as frequent in all Balkan populations. Greece and Slovenia only have 1%. The haplotypes seem to specifically be centered around the relatively small range of former Yugoslavia.

It’s tempting to then argue that they are 'Yugoslavian haplotypes'. But that wouldn’t be able to explain why Albanians and Bulgarians have almost as much as former Yugoslavia.

The haplotypes did pop up in some non Balkan populations; Estonia, Ukraine, Iraq, and Southern Italy. Southern Italy has the most. Though Southern Italy is separated by ocean, it almost kisses the Balkan peninsula, so it would make sense that Southern Italy has a lot of Balkan ancestry.

The presence of four of these haplotypes in Southern Italy indicates they are pre-Slavic because Southern Italy doesn't seem to have any Slavic ancestry.

Balkan haplotypes.

H1c 16042 16288
H1a 16258c
H13a2c1
H 16189! 153 204
HV2(a) 16243 16261
R0a2c 16168 16265
U5b1 16293 16186 16189! 16192!
U5b1a 204 207 235
U4c1a 16362 16051G
U2e(1) 16209
U1a(2) 16179t 16129!
W1c'i 16193t 152!
W 16172 16231 [199]
N1b1 16244A
N1b1 16241g 245c

Tuesday, June 27, 2017

U5a1d2b, an Eastern U5a1 branch.

Haplogroup U5a1d2 has two branches; U5a1d2a and U5a1d2b. U5a1d2a is more or less exclusively European but U5a1d2b has a much more eastern distribution. U5a1d2b is more or less exclusively found in non Indo Europeans from far eastern Europe and Siberia. It peaks in the Mari of Russia and the Tubular of the Atlai region in Siberia.

Ancient DNA supports the idea U5a1d2b is sometype of far eastern/north Eurasian U5a1 branch. It was relatively common in Siberian Afanasievo, Andronovo, and later in Siberian Sycthians who lived in the same land as modern Tubular. U5a1d2b has also popped up in Comb Ceramic twice, Yamnaya once, and Sarmatians once.

U5a1d2b's strong presence in both Siberian Afanasievo and Siberian Scythian indicates that Scythians had some Afanasievo ancestry.

U5a1d2b's presence in Saami might be able to be explained by Comb Ceramic, considering Sycthians never lived near Scandinavia. And its strong presence in both Volga Russia and Siberia definitely looks like a legacy of the Sycthians.

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