Saturday, June 18, 2016

Insights from New Pre-Historic Middle Eastern mtDNA

Lazardidis et al. 2016 collected genome-wide data, along with mtDNA, from 44 ancient Middle Easterners. 27 of 44 had enough mtDNA coverage to get haplogroup results. I added the new ancient mtDNA results to this spreadsheet Ancient Middle East which includes all of the ancient Middle Eastern mtDNA results I've collected that are at least 3,000 years old.

By the way I have upcoming posts on analysis of mito-genomes from specific haplogroups and regions, just like the one I did of JT recently. Analysis of mitogenomes of Southern Africa and haplogroups K1 and H1 are coming up next.

Preview: The new mtDNA results show that modern regional mtDNA diversity in West Eurasia had already began to form by the Neolithic and support the conclusions of Lazardidis et al. 2016 that Levant Neolithic and Anatolian Neolithic did not have a lot of recent common ancestry.

I broke up my post into two sections.

1. What "Middle Eastern mtDNA" is. 
2. The mtDNA relationship between Paleo/Neo/Chalcolithic Middle Easterners and modern West Eurasians.

Lazardidis et al. 2016 was an absolute masterpiece like all of the other ancient DNA papers created by the same team of researchers who appear to have dedicated their careers to unlocking the origins of humanity as a whole and the diversity within humanity by taking DNA from old bones.

Below listed regions and time periods  the new mtDNA results come from. .

Levant(Israel and Jordan).
Paleolithic 12,000-14,000 years old. N1b
Neolithic 9,000-10,000 years old. K1a4b, T1a, T1a2, R0a, R0a2
Bronze age 4,000-4,5000 years old H14a, X2m

SouthWestern Iran
Mesolithic 11,000 years old
Neolithic 10,000 years old X2, J1c10
Chalcolithic 6,000-8,000 years old K1a12a, K1a12a, U7a, U3a'c, I1c, H29, X2
Bronze age 3,500 years old U1a1

Chalcolithic 5,500-6,500 years old K1a8, K1a8, H, H2a1, U4a
Early Bronze age 4,500 years old H1u, X2f
Late Bronze age 3,500 years old T1a1'3

Western Turkey
Chalcolithic 6,000 years old K1a17

1. "Middle Eastern mtDNA"

I consider the below mtDNA hapologroups "Middle Eastern mtDNA".
R0(inlu. HV, H, V), U1, U3, U7, K(aka U8b2), U9, JT, N1, N2, X.

This is why I consider them Middle Eastern: We have over 100 mtDNA samples from European hunter gatherers ranging 38,000 to 8,000 years old. All but two belonged to haplogroup U(xK, U1, U3, U8, U9). Just about all of them belonged to European-specific forms of U. They contributed 10-25%(ranges by region) mtDNA to modern Europeans. The rest of European mtDNA falls under haplogroups that first appear in Europe when people from the Middle East migrated there starting 9,000 years ago. These newcomers to Europe also carried with them a new type of ancestry that didin't exist in Europe prior. It;s a Middle Eastern-specfic type of ancestry that all our new ancient Middle Eastern genomes share. Everywhere this Middle Eastern-specific ancestry is found today so are the above mtDNA haplogroups.

All of these Middle Eastern haplogroups are definitely over 30,000 years old. By 10,000-12,000 years ago they had gained many subclades and regional diversity. There was already a high amount of sharing between distant regions in the Middle East among distantly related populations and many "Expansion Point Lineages"(Definition of term is here). Most "Expansion Point Lineages" that exist today certainly already existed 10,000 years ago. This prediction of mine is supported by the new ancient Middle Eastern mtDNA results. By the time Middle Eastern mtDNA migrated into Europe, South Asia, and Africa there was a lot of mtDNA sharing within the Middle East and so today you'll find subclades of haplogroups(like T2a1a) that show no differentiation in Ireland and Yeman and Ethopia and India. You can't tell apart Ethopian T2a1a from Irish T2a1a.

Today a great majority of European mtDNA is "Middle Eastern". Don't let the term "Middle Eastern" confuse you. They were only in the Middle East 10,000 years ago but since then they have spread. Europeans, East Africans, and South Asians are to a large extent of Middle Eastern decent. Especially Europeans, most are over 50% and the impact is much greater on mtDNA than Y DNA.

2. The mtDNA relationship between Paleo/Neo/Chalcolithic Middle Easterners and modern West Eurasians.

Below is a comparison of the new ancient Middle Eastern mtDNA and already published mtDNA results from Neolithic Anatolia and Europe to modern mtDNA. In the end I give a concluding remark as to what this tells us about the origins of regional mtDNA diversity in West Eurasia today.

Natufian and Neolithic Levant mtDNA: N1b, K1a4b, T1a, T1a2, R0a, R0a2.

N1b  and R0a peaks in SouthWest Asia today are rarely found outside of the Middle East. T1a2 and K1a4b are Middle Eastern-specific haplogroups today(however T1a2 has a strong presence in Italy) and peaks in frequency in the Levant. Most of my SouthWest Asian K1a mito-genomes so far are K1a4b.

So in conclusion Natufian and Neolithic Levant mtDNA so far looks similar to mtDNA in the Levant today.

Neolithic Anatolia/Europe:

We have over 300 samples from them so there's no point in listing all those results. I will explain though how Neolithic Anatolian/European mtDNA was similar to modern European mtDNA.

>J1c, T2b, J2b1a: Today these are all European-specific clades of JT(see here). A similar ratio of Neolithic Anatolia/Europe's JT belonged to these subclades as modern Europeans, and in fact they had a higher frequency of them than any modern Europeans. Of the few high coverage J1c, T2b, and J2b1a genomes from Neolithic Anatolia/Europe we can see they had the same subclade combustion as modern Europeans. This includes popular subclades that are at >1% outside of Europe.

>K1a4a, K1a1b1, K1a2a, K1a3a: These are all K1a subclades that are rare or non-existent in my Middle Eastern mito-genomes and very popular in my European mito-genomes. They've all been found in the few K1a mito-genomes we have from Neolithic Europe. K1a4a is the most important one. It's the main K1a subclade in at least Denmark and White Americans, and was found in a 7,000 year old woman from Neolithic Spain. Her ancestors arrived in Spain only a few hundred years earlier from Anatolia.

>HV6-17, HV0(mostly V): These are the only popular forms of HV(xH) in Europe. They both are very rare outside of Europe. West Asia, especially SouthWest Asia, has a more diverse array of popular HV(xH). No HV(xH) sample has been found in Neolithic Anatolia/Europe except European-specific HV6-17 and HV0(mostly V) and both were fairly popular.

>H1, H3: H1 is very popular in all of Europe reaching 15% or higher outside of Italy and the Balkans. It is under 5% in all of the Middle East. H3 is at just over 5% in the British Isles, Scandinavia, France, and Iberia but is only at a few percent in the rest of Europe. H3 is at a >1% frequency in the Middle East.

Neolithic Central Europeans had a low frequency of H1(~5%) and even lower for H3(less than 1%). However Neolithic French and Spanish had high frequencies of both and most importantly H3. Most of their H was either H1 or H3. In some Neolithic grave sites in Spain H3 was more popular than H1. Notably typical Basque H3c was found in Neolithic Spain and typical Danish H1c was found in Neolithic Sweden.

Neolithic and Chalcolithic Iranian mtDNA: X2, J1c10, K1a12a, K1a12a, U7a, U3a'c, I1c, H29, X2

J1c10 is a very rare subclade of J1c. My J1c10s are from Bedouin, Italy, Sardinia, and Morocco. Nothing can be concluded about J1c10 from that. However I can say that J1c is the primary form of J in Europe and rare outside of Europe. It arrived in Europe 9,000 years ago from Neolithic Anatolia. It's very surprising to see J1c10, instead of J1b1b, in Iran 10,000 years ago. Very surprising.

K1a12 is almost completely absent in close to 1,000 K1 mitogenomes from Denmark, Finland, and White Americans. That covers small parts of Europe. My only K1a12(all but two are K1a12a) samples are from Armenia, Kuwait, Iran, Turkey, Druze(Levant), and Italy. It isn't particularly popular but my data so far supports the idea it's mostly West Asian and even Northern West Asia(where Iran is).

U7 doesn't reach 1% in frequency in any region of Europe. It's nonexistent in close to 500 mtDNA samples from pre-historic Europe. U7 is at 1.3% in the Levant, 3-5% in Turkey and Iraq, and a whopping 10% in Iran. U7 is also one of the most popular West Eurasian haplogroups in India. The U7a result from Chalcolithic Iran directly connects them maternally to modern Iranians and South Asians.

U3 varies from 1-3% in Europe, is at 3% in Iran, and 5% in the Levant. It peaks in SouthWest Asia but has a decent presence in all of West Eurasia. I do have a large collection of U3 mito-genomes but haven't looked at them in detail yet. Most are U3b not U3a'c in every region, including Iran.

Chalcolithic, Bronze age Armenia and Anatolia mtDNA: K1a8, K1a8, K1a17, H, H2a1, U4a, H1u, X2f, T1a1'3

K1a8 and K1a17: Both are rare. My only examples of K1a8 are from the Levant(several countries. My only examples of K1a17 are from Levant, Arabia, Italy, Egypt, and Kuwait.

U4a: U4a is of "EHG"(Mesolithic East Europe) origin no doubt about it. It's consistent with the EHG ancestry that Lazardidis et al. 2016 modeled Chalcolithic Armenia as having. Looking at the evidence presented by  Lazardidis et al. 2016 I'm very confident Chalcolithic Armenians had EHG ancestry.

H2a1: It found at least 1% in all of my West Eurasian regional sample sets except Iran, Spain, Balkans. It peaks in my samples from the NorthEastern corner of Europe(Baltic, BeloRussia, Karelia and Russia) stats at about 3%. Frequencies of H2a1 can't tell you anything about its history. Only a large amount of H2a1 mito genomes can.

Something significant I can say though looking at ancient mtDNA that H2a1 is absent in over 300 samples from Neolithic Europe but existed in Eneolithic and Bronze age Russia and then later in Bronze age Central Europe after people from Russia migrated there. It's existence in Chalcolithic Armenia, suggests it originated in the Caucasus region and then migrated to Russia and from there Central Europe.

H1u: Very rare subclade of H1. I have over 1,000 H1 mito genomes from Basque, Danish, Finnish, Italy, and White Americans. Two are H1u, one from Denmark and one from a White American. I have a much smaller amount of H1s(maybe 20) from the Middle East and have found two examples of H1u and both are from Druze.

X2f: It is absent in my European samples. It exists in just about every Northern West Asian population I have examples from; Georgia, Armenia, Iran. I also have an example from Druze.

T1a1'3: T1a1'3 is the common ancestor of T1a1 and T1a3. Chances are this sample had T1a1 or T1a3, but because of low coverage it couldn't be discerned which one he had. T1a3 is unheard of today, my only examples are from three White Americans and one Isreali. T1a1 on the other hand is the most popular form of T1a in Europe and Iran. In Northern Europe <90% of T1a is T1a1, while in Iran and Italy T1a1 is most popular but you'll commonly find other forms of T1a. Many examples of T1a1 have been found in Bronze age Europe and Central Asia(immigrants from Europe). It was popular in Bronze age Steppe populations and likely brought to Europe from the Steppe, and ultimately from ancient Northern West Asia.

Nothing can be deciphered from a X2 results(instead of X2b, X2f, etc). I don't have any I1c mito-genomes as of far. I1 is the most popular I subclade in most of West Eurasia and first appears in Europe with Steppe admixture(ultimately from populations similar to Chalcolithic Iran?).

Concluding Remark: These new results and already published result suggest that by the Early Neolithic much of the mtDNA diversity in West Eurasia had formed. We see Levant-specific mtDNA in Neolithic Levant, Northern West Asian-specific mtDNA in Neolithic/Chalcolithic Iran, and European-specific mtDNA in Neolithic Anatolia.

The mtDNA differentiation between Anatolia Neolithic and Levant Neolithic are consistent with conclusions by Lazardidis et al. 2016, that farming spread to Anatolia without much gene flow from the Levant.

Friday, June 10, 2016

Indepth Look at Haplogroup JT

mtDNA haplogroup JT is the daughter of Pan-Eurasian haplogroup R and one of the primary haplogroups in West Eurasia but can also found in many parts of Africa and Asia. It's a very old lineage and covers a lot of land, and therefore has a lot of phylogenetic diversity and regional diversity. In a previous post(LINK) I used HVR1 data from JT samples to display JT regional diversity. To learn more about JT diversity I collected and analysed over 1,000 JT mito-genomes from Ian Logan's site.

I broke this post into four sections to give a good understanding of what I've learned about JT.
1: My Strategy for Analyzing mito-genomes
2: Description of Samples and Spreadsheets used for Analyse
3: Results
4: Comparison to JT mito-genomes from Ancient DNA

My Strategy for Analyzing mito-genomes: My strategy when analyzing mito-genomes is to look for what I call "Expansion Point" haplogroups. An "Expansion Point" haplogroup is a haplogroup which is popular but doesn't have any popular subclades. The reason I this is my strategy is"Expansion Points" are the youngest haplogroups and can tell us the most about the origins of mtDNA in modern populations. They tell us the most about the origins of human mtDNA because most humans belong to "Expansion Point" haplogroups and very rarely do two humans from the same population have maternal lineages that are related beyond being apart of a popular "Expansion Point" Lineage. There are dozens or hundreds of "Expansion Point" haplogroups which take up some 90% of the mtDNA in human populations. Most are fairly young, less than 20,000 years old. For those of you who are familiar with European Y DNA an example of a Y DNA "Expansion Point" haplogroup is R1b-L151.

Description of Samples and Spreadsheets used for Analyse: Most of the samples were used by Maria Pala et al. 2012. They came from various locations in West Eurasia, Siberia, and South Asia. I also added about 500 JT mito-genomes provided by Ian Logan from Denmark, Italy, Arabia, and Iran.

I fully analysed the relationship between all about 1,000 mito-genomes used by Maria Pala et al. 2012. I found over 60 new haplogroups but none of them are popular(aka "Expansion Point" haplogroups) outside of single populations and so not very helpful to know about.

Here's a spreadsheet of that Analysis: Analysis of 1000 JTs.

With the about 500 JT mito-genomes I added to the ones used by Maria Pala et al. 2012, I was able to gather enough samples to create five regional populations to compare their frequencies in JT subclades. The five populations are: Denmark, Italy, USA, Near East, and Northern West Asia. The USA population consists of Americans who's maternal line is from Europe and probably specifically from Britain or Germany.

Here's the spreadsheet of a comparison of those five regions: Regional Frequencies of JT

Results: As I said before my strategy when analyzing mito-genomes is to find "Expansion Point" haplogroups, so here are the "Expansion Point" JT haplogroups I found. I color them according to which of these regions they are most popular in: Generic West EurasianGeneric Europe, NorthWest Europe, ItalyGeneric West Asia, Iran, Near East.

T2a1a, T2a1b1a(T2a1b1a1b), T2b(T2b4, T2b23, T2b31), T2c1(T2c1c, T2c1d1, T2c1d1a, T2c1e, T2c1a), T2e, T2f1a1T2g1aT2iT1a1, T1a2T1a7T1a11, T1b(T1b2, T1b3).

J1c1(J1c1b, J1c1b1a, J1c1d), J1c2(J1c2b, J1c2o), J1c3, J1c15, J1b1a1, J1b1b(J1b1b1), J1b2, J1b3, J1d(J1d1a)J2a1a1a(J2a1a1a2), J2a2a, J2b1a, J2b1(xJ2b1a)

And that's it. Those are all the "Expansion Point" haplogroups of JT. Most JT falls under these clades. There isn't anymore I can do. All subclades of these haplogroups are so rare and exist in most of West Eurasia that they tell nothing about regional diversity. It's amazing there are still pretty basal JT subclades which show no regional variation. T2c1 and T2a1a in Italy and Yeman aren't distinguishable from each other.

Here are a two very important lessons I learned about West Eurasian JT.
Recent contact across all of West Eurasia
>Rare and young non-"Expansion Point" subclades are found in every part of West Eurasia.
>Regional specific and young "Expansion Point" subclades are found in every part of West Eurasia, it's just they're more popular in some parts.
West Asia vs Europe, with Italy and Turkey/Cyprus as intermediates
>NorthWest Asia/Near East and Italy/NorthWest Europe aren't perfect subpopulations, but each member in these subgroups are by far most similar JT to each other. Italy however has a significant amount of typical West Asian JT haplorgoups; e.g. T1a2, T1b, J1b2, J1d1a and Turkey/Cyprus have a significant amount of typical European JT haplogroups; e.g. J1c, J1b1a1, T1a1.
>The majority of West Asian and European JT split well over 8,000 years ago.

Comparison to JT mito-genomes from Ancient DNA

Below is a list of all of the ancient JT mitogenomes I know of. All of the results are from Europe or European ancestors/immigrants who lived in Asia, except for the single Armenian sample. All of them have typical JT clades for modern Europeans, except the Armenian who had T1a2 which is more typical of Western Asia included Northern West Asia(Where Armenia is) today.

6500-6200 BC, Barcın Turkey J1c11
6500-6200 BC, Barcın Turkey J1c
5311-5218 BC Spain J1c3
5000 BC, LBK culture Germany J1c17
2500-2050 BC Corded Ware Germany J1c2e
2880-2630 BC Spain J1c1
3000 BC Spain J1c1b1
2625-2291 BC Corded Ware Germany J1c1b1a
2298-2045 BC Sintashta Russia J1c1b1a
2000 BC? Germany J1c1b
2500-2050 BC Corded Ware Germany J1c5
2290-2130 BC Bell Beaker Germany J1c5
2851-2492 BC Denmark J1c4
2128-1909 BC Hungary J1c9
2863-2498 BC Corded Ware Germany J1b1a1

2880-2630 BC Spain J2b1a3
2126-1896 BC Sintashta Russia J2b1a2a
1850-1200 BC Timber Grave Russia J2b1a2a
1000 BC Siberia J2b1a
3900-3600 BC Spain J2a1a1
2880-2630 BC Spain J2a1a1
2500-2050 BC Germany J2a2a

6500-6200 BC, Barcın Turkey T2b
6500-6200 BC, Barcın Turkey T2b
5000 BC? LBK culture Germany T2b
5000 BC? LBK culture Germany T2b
5000 BC? LBK culture Germany T2b
5000 BC? LBK culture Germany T2b
5000 BC? LBK culture Germany T2b
3360-3086 BC Germany T2b
2500 BC? Czech Republic T2b
2034-1784 BC Hungary T2b3
2000 BC? Hungary T2b
1866-1619 BC Hungary T2b
1800-1600 BC Timber Grave Russia T2b4
794-547 BC Denmark T2b
5178-5066 BC Spain pre-T2c1d2
5000 BC? LBK culture Germany T2c1d'e'f
5100-4800 BC LBK culture Germany T2c1d1
4000 BC? Germany T2c1d1
3000 BC? Yamnaya T2c1a2
5500-4800 BC LBK culture Germany T2e
5000 BC? LBK culture Germany T2e
3640-3510 BC Germany T2e1
2887-2634 BC Yamnaya T2a1a
1432-1292 BC Sweden T2a1a
2454-2291 BC Corded Ware Germany T2a1b1
2464-2210 BC Germany T2a1b1
1800-1400 BC Andronovo Siberia T2a1b

2570-2471 BC Germany T1a1
1395-1132 BC Sweden T1a1
2000 BC? Hungary T1a1
1850-1200 BC Timber Grave Russia T1a1
1048-855 BC Armenia T1a2