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

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.


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.

Spanish_Andalucia
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
U5b7812.5
U5a1750
U4325
U2312.5

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

Most U5b...

U5b
Sweden7.4
Andalusia Spain6.5
Galicia Spain6
BeloRussia6
North Poland5.4




Least U5b...


North Italy2
Denmark2
South Italy2.2
Ukraine2.5
Russia3

Most U5a...


Mari(Russia)12.5
East Baltic11.3
Ukraine10
Russia7.5
Sweden7.1

Least U5a...


Andalusia Spain2.5
South Italy2.6
Ireland3.3
Greece3.3
Galicia Spain3.5

Most U4...


NW Russia6
Bosnia5.7
East Germany5.6
East Baltic5.2
Poland5
Least U4...


North Italy0
SW France1.2
Andalusia Spain1.7
Ireland1.3
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. 

Wednesday, January 25, 2017

Finland

Related image

For the first time I have added Finland to my mtDNA database. My first collection of Finnish mtDNA is 287 mitogenomes. In this post I’ll give an intro to Finnish mtDNA.

Here are links to my analysis of Finnish mtDNA.
Finland: mHG frequencies, Founder Effects
mtDNA matches: A lists unique and rare haplogroups found in Finland and where in the world I’ve found those haplogroups also exist.

Summary: 50% of Finns belong to founder effect mHGs unique to the region Finland is in. Only 1% of Finns have Siberian mtDNA. Finland's mtDNA is super European. Finland's mHG frequencies are similar to their neighbors in NorthEastern Europe. Finnish H1/H3 is similar to Danish and White American H1/H3 but not similar to Basque H1/H3. A modern Finnish U5a1* shares a mutation with a Mesolithic Swedish U5a1*.

Dominated by Founder Effects

As you can see in the Finland spreadsheet about 50% of Finns belong to founder effect mHGs. I listed all of the founder effect haplogroups and the mutations which make them unique in the spreadsheet. All of these founder effect mHGs are unique to Finland and its neighbors. They are either nonexistent or very rare outside of Finland and its neighbors.

These are the most common Founder Effects in Finland.
U5b1b1a(5.20%), H3h1(3.1%), H1a[10](2.8%), H1f1(2.8%), K1c1c(2.2%), H1n4(2.1%), U5b1b2(2.1%).

Because of the high frequency of Finnish-specific mtDNA in Finland I can confirm you have a Finnish maternal lineage if you email me your mtDNA at sammyisaac107@gmail.com.


Close Affinity to Karelia

When comparing Finnish mtDNA to other populations I discovered Finland shares several unique mHGs with its neighbor Karelia. Many of the founder effect mHGs in Finland I just discussed are also found in Karelia. Here’s a list of mHGs unique to Finland and Karelia and probably nearby peoples.

H1a(10), H1a(11), H1f1, H2a1(o), H3h1, V7a, U5a2a1a, U5b1b1a, U1b, D5a3a1a.

The H1 mHGs above and H3h1 take up 10% or more of Finnish and Karelian mtDNA. That’s a sizable fraction.

Archetypal European mtDNA

Only 1% of Finnish mtDNA is Siberian. The rest is West Eurasian. 99%(or whatever the actual percentage is) of it belongs to archetypal European mHGs. Finland’s mHG frequencies are pretty similar to its neighbors in NorthEastern Europe; see European mHG frequencies here.

European-specific mHGs found in Finland. They take up 65% of Finnish mtDNA. The number is certainly higher because not all European mHGs have been discovered.
H1 H3 H11a V HV0(xV) HV6-17 T1a1 T2b T2a1b1a J1c J2a1a J2b1a K1a4a, K1a1b K1c1 U5 U4 U2e U8a1a I

Some of the above European-specific mHGs are too vague; J1c, H1, H3, U5, and so on. I thoroughly compared Finland's J1c, H1, etc. subclades to other Europeans. In most of those mHGs Finland belongs to subclades either typical for all Europeans or only to ones geographically close to Finland.

Here’s the primary subclade of some of those European mHGs in Finland.
H1: H1a, H1b, H1c, H1f, H1n
H3: H3h, H3b.
V: V7a, V1a, V(29)
J1c: J1c2, J1c3
U5: U5b1b, U5a1b1.
U4: U4a2a, U4d1
I: I5a, I1a1

My collection posses an abundance of mitogenomes from only a few West Eurasian population whom I can compare to Finland; Iran, Denmark, Druze, Caucasus, Basque, White Americans.

Finland’s H1 and H3 is closely related to White American and Danish H1/H3. However it is pretty unrelated to Basque H1/H3. Also you can see in the mtDNA Matches document that Finland matches most often with Danish and White Americans. *****I must warn you to not misinterpret the matching because almost half of my mitogenomes are from White Americans and Danish.

Siberian mtDNA: D5a3a1a, G3a1

Three of the Finnish mito genomes belonged East Asian mHGs; two Ds and one G. More specifically the Ds were D5a3a1a and the G was G3a1. In my database these mHGs only exist in non Slavic Russians, Karelians, and Siberians. Therefore it’s safe to assume they travelled from Siberia to Finland at some point.

U5b1b1a, U5b1b2, U5b1e1, U5a1*

I think it's pretty likely that these U5 lineages unique to Finland and its neighbors; U5b1b1a, U5b1b2, U5b1e1, and U5a1* are descended from ancient NorthEastern Europea Hunter Gatherers. Finns have extra European hunter gatherer ancestry which can't be explained by Corded Ware or Funnel Beaker, see here.

The single U5a1* Finnish sample I'm referring to has already found a match with a NorthEastern European Hunter Gatherer.

Modern Finn:
U5a1*. Extra mutations: 195C 5237A 5460A 6267A 13651G
Mesolithic Swede(Motala3).
U5a1*. Extra mutations: G5460A, G8860A, A9389G, C16519T


Saturday, January 14, 2017

North Africa's West Eurasian mtDNA




North Africans are a mixture of people related to Sub Saharan Africans and West Eurasians. In this post I’ll examine mostly North African mtDNA, but also Y DNA and autosomal DNA, to gain insight into who their West Eurasian ancestors were.

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Summary

In my opinion NorthWest African mtDNA is mostly descended from Neolithic Near Easterners closely related to Neolithic Europeans. Whether it visited Europe before arriving in NorthWest Africa or not is impossible to detect at this point. Egyptian mtDNA is mostly Ancient Near Easterners aswell but from Near Easterners related to Natufians and Neolithic Levanties not Europeans.

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The spreadsheet below displays the frequency of Eurasian mHGs, mHG H subclades, mHG JT subclades, and European vs Middle Eastern vs Eurasian African mHG frequencies in North Africa.

West Eurasian HG frequencies

NorthWest Africans’ Eurasian mtDNA, especially in Berbers, mostly belong to European-specific and Northern African-specific lineages. Egyptian mtDNA though belongs mostly to Middle Eastern-specific lineages.

The frequency of European-specific mHGs is on average 40% in NorthWest Africa but at only 4% in Egypt. The frequency of Middle Eastern-specific mHGs in Egypt is 51.2% but at only about 10% in NorthWest Africa.

The region of the Middle East Egyptian mtDNA is most similar to Arabia. R0a, T1a(xEuropean and Iranian T1a1), and H2a peak in Egypt and Arabia.

Here’s some graphs visually displaying the links between NorthWest Africa to Europe and Egypt to the Middle East.

NorthWest Africa=Algeria, Tunisia, Tunisia, Morocoo.
Egypt=Egypt.
Europe=Spain, Ukraine.
Middle East=Syria, Arabia, Turkey.



U6, M1: Eurasian mHGs most popular in Africa

U6 and M1 are mHGs which branch from the Eurasian mHGs U and M that are most popular in Africa. U6 peaks in NorthWest Africa at about 8%. U6 exists in SouthWest Asia and Egypt at about 1-3%. It exists in Iberia and Southern Italy at about 0.5-1%. M1 is at about 7-10% in NorthWest Africa and Egypt. M1 exists in SouthWest Asia at about 1-3%. I don't have a lot of Eastern or Western African mtDNA data yet but I do know U6 and M1 exist in both of those regions aswell.


Neolithic European-related Ancestry in NorthWest Africa?

I wrote “Neolithic European-related” not “Neolithic European” because the similarity in mtDNA between NorthWest Africa and Neolithic Europe could have been caused by common ancestry from the Near East not direct descent.

H1, H3, and HV0 are more frequent in NorthWest Africa than Europe itself(if you don’t count Sub Saharan mtDNA). Ancient mtDNA indicates HV0, H1, and H3 in modern Europe descend from Neolithic European farmers. They were especially frequent in Neolithic Iberians and French(See here).

NorthWest African mtDNA isn’t completely consistent with having lots of Neolithic European ancestry. T2b, K1a, and J1c took near 40% of Neolithic European mtDNA but aren’t frequent in modern NorthWest Africans(5-10%). Though NorthWest African JT is more similar to Neolithic and modern European than to Middle Eastern JT.

Neolithic Middle Eastern-related Ancestry in Egypt?

There’s a decent amount of Middle Eastern-specific mHGs in all of North Africa, not just Egypt, which are unheard of in Europe. R0a, HV(xHV0), U1, U3, and J2a2 exist in both NorthWest Africa and Egypt. J1b(xJ1b1a1), J1d1, T1a7, and U7 are Middle Eastern-specific lineages only found in Egypt. So in no way can NorthWest African mtDNA be a simple European+Sub Saharan mix.

There’s much less published ancient Middle Eastern mtDNA than European but important matches already exist between ancient Middle Eastern mtDNA and NorthWest Africa.

7722-7541 BC. Jordan. R0a(20.3% in Egypt).
11840-9760 BC. Israel. J2a2.
7446-7058 BC. Jordan. T1a.
3956-3796 BC. Iran. U7(Only exists in Egypt).
11000 BC. Israel. N1b.

Autosomal DNA Reflection

Here are results modelling North Africans as a mixture of ancient West Eurasians and Sub Saharan Africa. I used D-stats provided by David Wesoloski at Eurogenes blog to produce these results.

Morocco
Levant Neolithic: 60.05%
Anatolia Neolithic: 0%
Caucasus Paleolithic: 5.4%
Iran Neolithic: 7.95%
Europe Mesolithic: 9.45
Sub Saharan African: 17.15%

Egypt
Levant Neolithic: 60%
Anatolia Neolithic: 0%
Caucasus Paleolithic: 0%
Iran Neolithic: 23%
Europe Mesolithic: 10%
Sub Saharan African: 7.05%

So basically autosomal DNA indicates NorthWest Africans are mostly Neolithic Near Eastern and Sub Saharan African with a little Neolithic Iranian. Egyptians are the same mixture with more Neolithic Iranian and less Sub Saharan African.

Keep in mind Neolithic Near Easterners were closely related to Neolithic Europeans. Therefore the above results are consistent with the high amount of Neolithic European-like mtDNA in NorthWest Africa.

Y DNA Reflection

Like mtDNA and autosomal DNA, Y DNA connects Northern Africans mostly with ancient Near Easterners. Both Egyptian and NorthWest African Y DNA are mostly E1b1b and J1. NorthWest African Eb1b is specifically M81, with few exceptions. Ancient DNA indicates J1 is from the Mesolithic Caucasus and Iran and documents the presence of E1b1b in Mesolithic Israel(Natufians). 

Sunday, January 8, 2017

The First mtDNA from Mesolithic Greece is K1*

Image result for theopetra cave
Theopetra Cave. The Cave in Greece which Theo5 and 1 were found in.

Last June Hofmanova et al. 2016 published the first mtDNA results from Mesolithic Greece for two samples named Theo5 and Theo1. They labelled the two Mesolithic Greeks as K1c. Ian Logan has posted the rCRS mutations of these two samples on his site. So with that information I checked if the K1c label given by Hofmanova et al. 2016 is accurate and discovered it isn't. Instead these samples are best labelled as K1*.

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What K1 in Mesolithic Greece says about their affinity to modern and ancient populations
K1 is a West Eurasian haplogroup. About 5% of people in West Eurasia belong to K1. About 20%  of Neolithic Europeans and Anatolians belonged to K1. Essentially 100% of modern K1 and all ancient K1 tested so far belong to K1a, K1b, or K1c. K1*s like the ones found in Mesolithic Greece are rare. Until we get autsomal DNA from Mesolithic Greece we can't be confident about their affinities to other ancient populations but their K1s do suggest they were closely related to Neolithic Anatolians and Near Easterners.

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Here's a list of the haplogroups leading to K1, the subclades of K1, and their rCRS mutations. Mutations the two Mesolithic Greeks possessed are highlighted in green and mutations they didn't possess are highlighted in red.

U: A11467G  A12308G  G12372A
U2'3'4'7'8'9: A1811G 
U8: T9698C 
U8b'c:  A3480G
U8b: G9055A  C14167T
K: A10550G  T11299C  T14798C  T16224C  T16311C!
K1: T1189C  A10398G!

K1 subclades.
K1a: C497T  (T16093C)
K1b: G5913A
K1c: T146C!  T152C!  C498d
K1d'e'f: T16362C

Extra Mutations.
KU171094: T146C A215G C3107T T6351Y G6446A C13967T T16249C
KU171095: T146C A215G C3107T T6351Y G6446A C13967T T8462C A10113G

These Mesolithic Greeks possessed 1 of 3 of K1c's mutations but not all three. Therefore they can't confidently be labeled as K1c. They're best labelled as K1*.

Both Mesolithic Greeks shared many unique mutations. They form a unique K1 subclade. I checked my collection of 1,000s of ancient and modern Ks, including over 1,000 K mitogenomes, for matches with this Mesolithic Greek K1 lineage.

I could only find HVR1 matches for KU171094. I found the 16249C mutation KU171094 had in two Romanian Ks, a Punjab Northern Indian K, and three Neolithic LBK Ks from Germany. 16249C is a rare mutation. These individuals probably do/did infact belong to the same K1 lineage as these Mesolithic Greeks did.

It wouldn't be surprising if Mesolithic Greek mtDNA or mtDNA from close relatives of Mesolithic Greeks existed in modern Romania. It would be a surprise however if the same was true for modern India. As I discussed in my previous post modern Indian's West Eurasian ancestry is primary from ancient Iran and Russia. Their ancient Russian ancestry though may have included some ancestry from Neolithic Europeans who may have had ancestry from Mesolithic  Greeks which could explain a K in modern India being related to a K from Mesolithic Greece.

Monday, January 2, 2017

South Asia's West Eurasian mtDNA

South Asians are a two way mixture of West Eurasians and a people(s) distantly related to East Asians known as ASI. ASI is more likely to be the native population of South Asia and West Eurasians probably arrived in multiple waves from the NorthWest. A decisive majority of India's mtDNA is ASI but a big chunk is West Eurasian. In this post I’ll look at West Eurasian mtDNA in South Asia to gain insight into who their maternal West Eurasian ancestors were.


Bronze age European Steppe+Neolithic Iran


Lazaridis 2016 successfully modeled South/Central Asians as a mixture of Neolithic Iran, Bronze age Steppe, and East Asians(as a proxy for ASI). The results they got are below.

Y DNA so far is consistent with this idea. The most common West Eurasian yHGs in South Asia are R2, R1a-Z93, J2, and G. R2, J2, and G have been found in ancient Iran. R1a-Z93 has been found in the Bronze age European Steppe.


mtDNA is also consistent with this model. A large percentage, almost 50%, of South Asia’s West Eurasian mtDNA belongs to mHGs found in remains from Neolithic Iran and the Bronze age Steppe. I still think we should be open to more complex origins of South Asians’ West Eurasian ancestry though.




Mostly Middle Eastern with a dose of European?


mHG Frequencies: Haplogroup Frequencies of West Eurasian mtDNA in India and a few other South Asians. Clade Origins: Deep subclades of West Eurasian haplogroups found in India and where in West Eurasia they’re most common.
Clade Origins: Deep subclades of West Eurasian haplogroups found in India and where in West Eurasia they’re most common.


The region of West Eurasia India shares the most mtDNA with is first Iran and second the rest of the Middle East. U7, U1, HV2, HV14, R0a, R2, J1b1b, J1b3, J1d are Middle Eastern-specific lineages found in India. Most of them peak around Iran. U7 is by far the most common. It’s more common, when not counting ASI, than anywhere in the Middle East.


A string of European-like mtDNA exists in South Asia aswell especially in Afghanistan and Pakistan. U5a, U4, U2e, J1b1a1, T1a1, J2b1a, J1c, T2b all have a consistent presence throughout South Asia. U5a1a1, U5a1b are the main U5a1 clades in Europe aswell as South Asia. U5a and U4, which are two of the three most common European-like mtDNAs in South Asia, today peak in NorthEast Europe, Siberia, Scandinavia, and YugoSlavia.


On average about 18% of India’s West Eurasian mtDNA belongs to those European-specific subclades and about 44% belongs to the Middle Eastern-specific subclades I listed earlier. SC Asia(Afghanistan, Pakistan) has significantly less Middle Eastern-specific mtDNA and slightly more European-specific mtDNA.


South Asian mtDNA also has trends and haplogroups which aren’t comparable to anything in West Eurasia. There are subclades of West Eurasian haplogroups specific to South Asia; H2b, U7a3b, U7a7, U7a6, U7c, U5a1g, and several W subclades. mHG X, which has a presence in all of West Eurasia and parts of North America, is non existent in South Asia. In contrast mHG W is extraordinarily more popular than anywhere in West Eurasia.


Matches with Ancient West Eurasians


There are many interesting examples of modern South Asian mtDNA belonging to the same subclades as ancient West Eurasian. Examples are listed at at the bottom.


Kalash mtDNA in particular has lots matches with the Bronze age European Steppe. It’s mostly madeup of a four founder effects. 3 of 4 are typical of the Bronze age European Steppe. The only two Kalash mtDNAs I found that weren’t apart of these founder effects belonged to U4b1a4 and T2a1a, both of which have been found in the Bronze age European Steppe.


Two other interesting matches were found between the Bronze age European Steppe and modern SC Asia. I possess over 1,000 H mito-genomes and the only H2bs in my collection are from an ancient Yamnaya individual and several modern SC Asian individuals.  U5a1g today is mostly in Iran and SC Asia but an ancient Corded Ware individual from Germany belonged to it as well.


R2: 1.5% in India, 6% in SC Asia.
 Neolithic Iran, 8000-7700 BC.


HV2: 2.4% in India, 1% in SC Asia.
 Neolithic Iran, 9100-8600 BC.


R0a: 1% in India, 2% in SC Asia.
 Neolithic Levant, 7722-7541 BC


U7a: 20% in India, 9% in SC Asia
 Chalcolithic Iran 3956-3796 BC


I1c: Existent in all of SC Asia
 Chalcolithic Iran, 3972-3800 BC


U5a1a1: India existent but unknown %, 1% in SC Asia.
 Yamnaya Russia 3000 BC,
 Afanasievo Siberia 3322-2923 BC
 Bell Beaker Germany 2300 BC


U5a1b1: Existent in India.
 Corded Ware Germany 2400 BC
 Bell Beaker Germany 2500–2050 BC
 Bell Beaker Spain 2492-2334 BC
 Xijing China(Tarim Mummy) 2000 BC
 Unetice Poland 1885-1693 BC
 
T1a1: India existent but unknown %, 3% in SC Asia.
 Potapovka Russia 2125-2044 BC
 Srubnaya Russia 1850-1200 BC
 Germany 2570-2471 BC
 Hungary 2000 BC
 Sweden 1200 BC
 
T2a1a: India existent but unknown %, 1% in SC Asia.
 Yamnaya Russia 2887-2634 BC
 Sweden 1300 BC


U2e1h: Found in Kalash and Hazara
 Potapovka Russia 2200-1900 BC
 Sintashta Russia 1960-1756 BC


U4b1a2: Found in Kalash.
 Catacomb Russia 2700-2500 BC


U4a1: Found in all South Asian populations.
 Neolithic Hungary 5500 BC
 Yamnaya Russia 3000 BC
 Catacomb Russia 2500-2000 BC
 Andronovo Siberia 1746-1626 BC
 Corded Ware Germany 2400 BC


H2b: Existent in India and SC Asia
 Yamanya Russia 3000 BC