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.

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

U3-16166 16311=3
T2-16172 16274=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.