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


  1. Thanks for your elaborate analysis, Krefter. My Anatolian Turkish paternal grandmother is from the interior Anatolian part (Cappadocia to be more specific) of Turkey. She belongs to mtDNA haplogroup T2b (she did mtDNA full sequence test at FTDNA and she is not assigned to any of the known subclades of T2b, sadly I have not added her mtDNA raw data to GenBank yet, but I will do it in the near future). So can we say that her mtDNA haplogroup is European (you define T2b as a generic European mtDNA haplogroup)? If you want, I can share with you her mtDNA raw data, I have your email.

  2. I call T2b "generic European' because it is most popular in Europe. European T2b however is ultimately from Neolithic Anatolia. So your grandma's. T2b could very well have never lived in Europe. I think I already have your grandma's mtdna saved somewhere and I can check if she has any matches amount my other T2bs.

  3. @Onur,

    Your paternal grandmother has a match with a T2b from Georgia. T2b has a lot of rare basal subclades and your paternal grandmother belongs to one which hasn't been officially named.

  4. Thanks for your assessment, Samuel (aka Krefter). Yes, I sent you the FASTA files of myself and my tested relatives (all fully sequenced by FTDNA) some months ago. By the way, did you include my paternal grandmother in your JT analysis?

    In your email reply to me you term the T2b subclade of my paternal grandmother and of a Georgian mtDNA match of my paternal grandmother that you define based on sharing of the 11929C mutation as T2b54. Is T2b54 specific to West Asia and the Caucasus?

    In case you are wondering, my paternal grandmother is from Niğde province in Cappadocia.

  5. "By the way, did you include my paternal grandmother in your JT analysis?"

    Yes I just added her to my spreadsheet of JT mito genomes.

    "Is T2b54 specific to West Asia and the Caucasus?"

    There's no way to know because I only have found two examples. It would make sense T2b54 is specific to that part of West Asia but we would literally need 1,000s of T2b mitogenomes to know for sure. T2b probably originated in that area and it's possible T2b54 has always been living around Turkey.

    "In case you are wondering, my paternal grandmother is from Niğde province in Cappadocia.'

    Yep thanks for the precise location. I wrote that down in my spreadsheet of JT mitogenomes.

  6. Thank you for including my paternal grandmother in your JT analysis.

    Another thing I would like to know is whether the Anatolian and Greek Neolithic Y-DNA (G and other) and mtDNA (H, JT and other) haplogroups cluster with modern European or modern West Asian (the Caucasus included) Y-DNA and mtDNA haplogroups.

    Note: The Armenian ancient genomes are from the Bronze and Iron ages, so they do not represent the Neolithic of Armenia.

  7. I was surprised to see a j1c17 in Sardinia since I am from Trabzon, Turkey. And that is the only mention about a j1c17 that I could find on the web. The other occasion is an ancient DNA from Oberwiederstedt-Unterwiederstedt, UWS4, Germany which is 5209-5070 cal BCE old. Therefore that makes us three from the same subgroup.