H13a1d [mtDNA]

It’s about my genetics research since “Eve” till through my mother, based on Mitochondrial DNA (mtDNA), which is passed from mother to children, but only female can pass it through ages via birth. So son and daughter have mtDNA but only daughter can pass it further by heritage.

In 2014/2015 I did mtDNA tests via FamilyTreeDNA (FTDNA) for myself and in 2015/2016 for my mother. Based on mtDNA phylotree Build 17 (as feb-2017) my maternal ancestry belongs to H13a1d subclade. So far I continue research mtDNA community to get all possible information about my female ancestry.

First Things First

What is mtDNA after all?

Here is quote from wikipedia:

Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also in plastids such as chloroplasts. In humans, the 16,569 base pairs of mitochondrial DNA encode for only 37 genes. Human mitochondrial DNA was the first significant part of the human genome to be sequenced. In most species, including humans, mtDNA is inherited solely from the mother.

From wiki:

The fact that mitochondrial DNA is maternally inherited enables genealogical researchers to trace maternal lineage far back in time. This is usually accomplished on human mitochondrial DNA by sequencing the hypervariable control regions (HVR1 or HVR2), and sometimes the complete molecule of the mitochondrial DNA, as a genealogical DNA test.

Unlike nuclear DNA, which is inherited from both parents and in which genes are rearranged in the process of recombination, there is usually no change in mtDNA from parent to offspring. Although mtDNA also recombines, it does so with copies of itself within the same mitochondrion. Because of this and because the mutation rate of animal mtDNA is higher than that of nuclear DNA, mtDNA is a powerful tool for tracking ancestry through females (matrilineage) and has been used in this role to track the ancestry of many species back hundreds of generations.

Note: Don’t be mislead, it’s not about X chromosome (which also “kinda” defines female side of genetics).

Mitochondrial Eve

Wiki (Mitochondrial DNA):

The concept of the Mitochondrial Eve is based on the same type of analysis, attempting to discover the origin of humanity by tracking the lineage back in time.

From “Mitochindrial DNA: The Eve Gene

Some molecular biologists say that, aeons ago, the mitochondrion was a free-living organism with its own DNA, and possessed the secret of generating lots of energy. It invaded single celled nucleated organisms and has stayed on ever since, dividing, like yeast, by binary fission.

Ultimately, every person alive today has inherited their mitochondrial DNA from one single great-great-great-…-grandmother, nearly 200,000 years ago.

When mtDNA is inherited from our mother, occasionally there is a change or mutation in one or more of the ‘letters’ of the mtDNA code – about one mutation every thousand generations. The new letter, called a point mutation, will then be transmitted through all subsequent daughters.

It turns out that the oldest changes in our mtDNA took place in Africa 150,000 – 190,000 years ago. Then new mutations start to appear in Asia, about 60,000 – 80,000 years ago. This tells us that modern humans evolved in Africa, and that some of us migrated out of Africa into Asia after 80,000 years ago.

 

Wiki (Mitochondrial Eve page):

The name “Mitochondrial Eve” alludes to biblical Eve. This has led to repeated misrepresentations or misconceptions in journalistic accounts on the topic. Unlike her biblical namesake, she was not the only living human female of her time. The title of “Mitochondrial Eve” is not permanently fixed to a single individual, but rather shifts forward in time over the course of human history as the Eve maternal mtDNA lineage becomes extinct.

Wikipedia: Through random drift or selection the female-lineage will trace back to a single female, such as Mitochondrial Eve. In this example over five generations colors represent extinct matrilineal lines and black the matrilineal line descended from mtDNA MRCA.

Wiki (Mitochondrial Eve page):

This leads to the construction of a DNA family tree where the branches are in biological terms clades, and the common ancestors such as Mitochondrial Eve sit at branching points in this tree. Major branches are said to define a haplogroup (e.g. CRS belongs to haplogroup H), and large branches containing several haplogroups are called “macro-haplogroups”.

 

mtDNA phylogenetic tree

Wikipedia version of tree:

mtDNA migration map [FTDNA]

 

The Seven Daughters of Eve

Wikipedia about book The Seven Daughters of Eve:

book by Bryan Sykes that presents the theory of human mitochondrial genetics to a general audience. Sykes explains the principles of genetics and human evolution, the particularities of mitochondrial DNA, and analyses of ancient DNA to genetically link modern humans to prehistoric ancestors.

Wikipedia: The seven “clan mothers” mentioned by Sykes each correspond to one (or more) human mitochondrial haplogroups.

Here is 2014 video with interview of Bryan Sykes, and I took a screenshot from it:

Here is another visualization by lynnsfamilytree.com

What he discovered is that nearly everyone with ancestral roots in Europe has only 7 unique types of mtDNA. That means that most people alive today can trace their mtDNA back through time to just 7 women, the so-called Seven Daughters of Eve.

mtDNA haplogroup H

ftdna

Haplogroup H2b, H6a1b, H13a1a1a and many other undetermined H subclades (including many probable H1 and H5) turned up among the mtDNA samples from the Yamna culture, which occupied the Pontic-Caspian Steppe during the Early Bronze Age. The Corded Ware culture, which is associated with the expansion of Y-haplogroup R1a from the steppes to Central Europe and Scandinavia, yielded samples belonging to H1ca1, H2a1, H4a1, H5a1, H6a1a and H10e. Ancient DNA from the Catacomb culture, strongly associated with Y-haplogroup R1a, yielded samples belonging to H1, H2a1 and H6. The Unetice culture, which is thought to mark the arrival of R1b in Central Europe (but overlapping with the previous R1a expansion), had individuals belonging to H2a1a3, H3, H4a1a1a2, H7h, H11a, H82a.

oxfordancestors.com

Here is text from Maternal Ancestry page.

The clan of Helena (Greek for light) is by far the largest and most successful of the seven native clans with 41% of Europeans belonging to one of its many branches. It began 20,000 years ago with the birth of Helena somewhere in the valleys of the Dordogne and the Vezere, in south-central France. The clan is widespread throughout all parts of Europe, but reaches its highest frequency among the Basque people of northern Spain and southern France.

The Oxford Ancestors offers “MatriLine Classic DNA Service” for 199£ and “MatriLine Classic: Additional Certificates” for 30£. No need for me to order, but rather maybe for the nice picture of results for me.

To show how results looks like, I took  results visualization from the Internet – example for Eugene Allen Field from liciefield.net.

45% of all present day western Europeans have descended. Hélèna lived 20,000 years ago somewhere in the Dordogne River Valley in south central France.

This example is very close to data results for me and my mother, because of H haplogroup.

My main point here is that my maternal mtDNA ancestry to H haplogroup, in terms of book belongs to “Helena” clan.

 

mtDNA haplogroup H13 => H13a1d

ftdna

Mitochondrial haplogroup H is a predominantly European haplogroup that originated outside of Europe before the last glacial maximum (LGM). It first expanded in the northern Near East and southern Caucasus between 33,000 and 26,000 years ago, and later migrations from Iberia suggest it reached Europe before the LGM. Its branch H13 is found at low frequencies in Europe, the Near East, and the Caucasus. Among the oldest branches of H, H13 dates to before the LGM.

NCBI

Complete Mitochondrial DNA Diversity in Iranians

As shown, H13 has a likely LGM time depth characterized by an overall coalescence time estimate of 20–24 kya. Three of its major sub-clades, H13a, H13b, and H13c, have roughly similar ages of 17–23 kya, 16–19 kya and 17–24 kya, respectively. Haplogroup H13a, the most represented of H13 clades, is further subdivided into two principal sub-clades, H13a1 and H13a2, each containing several independent branches.

I’m not yet sure, how old H13a1d is, but I found Polish language article “Przydatność DNA mitochondrialnego w genealogii” by Stanisław Plewako, where he mentioned, that H2a1c “born” somewhere close to 1800 years ago, which is somehow defined by the moment when G3834A mutation appeared. My point is, that H13a1d should also have definitive mutation and it’s age.

Open Question #1 – Age of H13a1d ???

UPD, Jul-04-2017: After personal email to Ian Logan, he replied me:

 Usually say, allow 400 years for a non-coding mutation –  HVR1, HVR2 and the other little areas,
and 1,600 years for a coding region mutation. So ‘H13a1d’ is defined by a HVR1 mutation, and the sequences on GenBank have the odd HVR1/HVR2 mutation, and now there is your heteroplasmy as well (and, significantly there are no extra coding region mutations). Perhaps, therefore, 1,800-2,000, is a bit on the large side; and I think I would consider 1,000 years +/- might be better.

Eupedia.com

Quote from Information about H haplogroup

Haplogroup H2b, H6a1b, H13a1a1a and many other undetermined H subclades (including many probable H1 and H5) turned up among the mtDNA samples from the Yamna culture, which occupied the Pontic-Caspian Steppe during the Early Bronze Age. The Corded Ware culture, which is associated with the expansion of Y-haplogroup R1a from the steppes to Central Europe and Scandinavia, yielded samples belonging to H1ca1, H2a1, H4a1, H5a1, H6a1a and H10e. Ancient DNA from the Catacomb culture, strongly associated with Y-haplogroup R1a, yielded samples belonging to H1, H2a1 and H6. The Unetice culture, which is thought to mark the arrival of R1b in Central Europe (but overlapping with the previous R1a expansion), had individuals belonging to H2a1a3, H3, H4a1a1a2, H7h, H11a, H82a.

Note: More about what is Y-haplogroup R1a, you can read in my old article “R1a vs. I2a [Y-DNA]“.

Here is cut from eupedia.com about H13 tree:

  • H12: found in Italy (Sicily)
  • H13: found mostly around the Caucasus, Iran, Anatolia, and Sardinia, but also across along the Mediterranean coasts of Europe
  • H13a
    • H13a1
    • H13a2
  • H13b
  • H13c
  • H14: found mostly in the Near East and Caucasus

 

Wikipedia

Full H haplogroup is huge, and contains sub branches H1 – H25. Full picture based on Build 16 (February 2014) is here. And here is cut from Wikipeida about only H13 tree:

Note: Jul-02-2017, and Wikipedia version of tree doesn’t contain H13a1d yet.

 

mtdnacommunity.org

According to Human mtDNA Phylogeny tree doesn’t have H13a1d:

ianlogan.co.uk

There is H13 chart, but it’s out of date. Looks like last update was in 2009 year. Here is small snapshot/cut near to H13a1:

SNPedia.com

Nice resource, when I analyze rs-genes but regarding mtDNA it’s out of date. I have captured screenshots in Mar-2016, and information is still the same – no H13a1d on page about H haplogroup.

There is also section Associated Genosets, where Haplogroup H and Subclades listed alphabetically, but no H13a1d.

 

One more resource I have – a screenshot I made in Mar-2016, and filename says it’s from SNPedia.com, but I can’t verify real URL to that image now. It’s somehow related to mutation i4000870 (G) which defines H13a1.

Open Question #2 – Where to find info about i4000870 and all nested mutations???

 

Phylotree.org

This is most updated, and most recent resource to get latest information about mtDNA phylogenetic tree.

By using archives on phylotree.org, I verified, that Build 15 (30 Sep 2012) DID NOT have H13a1d yet. But it appears in Build 16 (19-Feb-2014) and continue to be in Built 17 (18-Feb-2016).

Here is visualization of H13 tree as of Build 17 was released in February of 2016 (screenshot made Jul-02-2017):

Here is image I took from some web site about “African Genetics”, and now I can’t find it original URL. Anyway it was captured in Mar-2016, and H13a1d was there:

Open Question #3 – find original web resource of above tree???

 

 

FamilyTreeDna

Accounts

In 2014 year, I ordered simple “mtDNA Plus” test. At that time, I knew only a few about DNA analysis. The test is not very detailed, but so far I received preliminary haplogroup H. In fact I received set of numbers and ability to download it into csv file. But at that time, I had no idea what they mean. My list of matches based on HVR1 and HVR2 only.

Then, in feb-2016, I ordered “mtFull Sequence” mtDNA test for my mother (Kateryna Babij), which is now more detailed, and mother haplogrup defined as H13a1 (as for 2016). But in 2017 it has been changed to H13a1d. On behalf of mother’s FTDNA account, I have now ability to download *.FASTA file, which contains “ATGC” data of mtDNA analysis. Besides HVR1, HVR2, “mtFull Sequence” test gives ability to select/find matches based also on “Coding Regions” aka CR.

I follow FTDNA groups, for updates related to H and H13 haplogroups. But there are many others. Here is lis of them.

 

Detailed results analysis

FTDNA has a nice certificate with short info about results:

Here is my certificate/results, but it contains less info, and in fact my mother’s is much important for the research.

First, glossary note from FTDNA:

The Reconstructed Sapiens Reference Sequence (RSRS) is a mitochondrial DNA (mtDNA)reference sequence that uses both a global sampling of modern human samples and samples from ancient hominids. It was introduced in early 2012 as a replacement for the rCRS (revised Cambridge Reference Sequence). Because it is based on the likely modal haplotype of the common ancestor to both modern humans and such ancient groups as the Neanderthals, it shows an unbiased path back from any one modern mtDNA sequence to our distant common maternal ancestor.

 

FROM FTDNA FAQ question 1:

Mitochondrial DNA (mtDNA) testing covers both recent and distant generations.

  • Matching on HVR1 means that you have a 50% chance of sharing a common maternal ancestor within the last fifty-two generations. That is about 1,300 years
  • Matching on HVR1 and HVR2 means that you have a 50% chance of sharing a common maternal ancestor within the last twenty-eight generations. That is about 700 years
  • Matching on the Mitochondrial DNA Full Genomic Sequence test brings your matches into times that are more recent. It means that you have a 50% chance of sharing a common maternal ancestor within the last 5 generations. That is about 125 years.

The same here

FDTNA FAQ question 1 shows a table:

… table below shows the expected time to a common ancestor with your exact matches. This time span should be used alongside relevant genealogical information such as a known pedigree on the direct maternal line and geographic locations.

FTDNA FAQ question 2:

The control region is often called the hypervariable region (HVR). Hypervariable means fast changing. In mitochondrial DNA, the control region is the fast changing part. The control region may be further divided into two hypervariable regions, HVR1 and HVR2.

  • HVR1 runs from nucleotide 16001 to nucleotide 16569.
  • HVR2 runs from nucleotide 00001 to nucleotide 00574.

The coding region (CR) is the part of your mtDNA genome that contains genes. Because it does contain some genes, the coding region is believed to be slower mutating than the control region. Often, the mutations that are found in the coding region are used to define haplogroups.

  • The coding region runs from nucleotide 00575 to nucleotide 16000.

 

FTDNA Results page has 2 sections, with “kinda human-readable information”.

RSRS Values (my mother account)

rCRS Values (my mother account)

Similar dataset is for my personal account.

And for advanced users/customers, there is ability to download FASTA file, which is generated only for “mtFullSequence” (I have only for my mother). File is 17kB, which is extremely small comparing raw data (archived csv file) from FamilyFinder tests by FTDNA. Here is how FAST file looks like:

It is rather small, because as text file it contains only 209 lines in text editor. For comparison, CSV file for FF test contains 715980 lines !!!

FTDNA also has a map of matches, but I will analyze and publish my results in separate article. Soon 🙂

Further mtDNA research

ncbi.nlm.nih.gov

NCBI – The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. There is ability to upload DNA materials to GenBank, and scientists will be available to research it when they have time.

ianlogan.co.uk

Since 2016, I know there is also alternative variant. Here is instructions how data can be uploaded. Not yet tried. Jul-02-2017 sent an email to Ian to verify that instructions.

Here is info about some NCBI/GenBank publications related to H13a1d:

 

Jul-04-2017 I uploaded my mother’s mtDNA data to GenBank, and Jul-12-2017 it has been published.

Here is some quotes from discussion with Ian Logan:

… there are 37,432 complete sequences on the GenBank database – that have been fully processed.

Now there 4 sequences in H13a1d out of the 36,000+ sequences on the GenBank database.
And that is all the sequences I know about from this subgroup – so not a very big subgroup!

… there is nothing special about any of the mutations  – which is good, but makes things less exciting!

And here is list of H13a1d members on Ian Logan website  “h13_genbank_sequences” page:

A simple breakdown of the CRS mutations (13):

T152C - mutation in HVR2 area
A263G - mutation in HVR2 area
309.1C - insertion in HVR2 area
315.1C - insertion in HVR2 area
A750G - mutation in 12S rRNA gene (MT-RNR1) . . . . . . . Common mutation near CRS
A1438G - mutation in 12S rRNA gene (MT-RNR1) . . . . . . . Common mutation near CRS
C2259T - mutation in 16S rRNA gene (MT-RNR2) . . . . . . . Defines Haplogroup H13a
A4745G - mutation in peptide NAD2 (MT-ND2) synonymous - no change in amino acid
A4769G - mutation in peptide NAD2 (MT-ND2) synonymous - no change in amino acid
A8860G - mutation in peptide ATP6 (MT-ATP6) non-synonymous 'T112A' Common mutation near CRS
G14858R - mutation in peptide CYTB (MT-CYB) Heteroplasmy G14858A is non-synonymous 'G38S'
G14858R is heteroplasmy of G14858G & G14858A
G14858A - mutation in peptide CYTB (MT-CYB) non-synonymous 'G38S' Found in several Haplogroups
C14872T - mutation in peptide CYTB (MT-CYB) synonymous - no change in amino acid
A15326G - mutation in peptide CYTB (MT-CYB) non-synonymous 'T194A' Common mutation near CRS
C16234T - mutation in HVR1 area

A few notes from Ian Logan (Jul-16-2017):

G14858R appears unique in the 36,000+ mtDNA sequences on the GenBank database.
And, the full mutation G14858A is actually quite uncommon, occurring only 7 times, so it is not surprising the heteroplasmic form is uncommon. ‘G14858‘ appears very stable; but it would seem the change G38S is not unduly troublesome.
(‘G’ often adds a bit of rigidity to the folded protein, and ‘S’ is a little less rigid and a bit larger – and G>S is not particularly uncommon.)

 

FTDNA as alternative #3

Jul-02-2017, I discovered (logged in to FTDNA withing mother’s account), that there is new feature – “mtDNA Full Sequence Release Survey”:

And there are fields to fill in:

I submitted that survey, and maybe in nearest future, some scientists will take a look 🙂 But there some doubts, defined by reply from Elena Kuyumdjian (Елена Куюмджиян) in email correspondence (Jul-02-2017):

“The survey is an alternative route that does not guarantee the submission to Genbank. With the support of Ian Logan you submit directly. Through the survey you wait your sequence to be selected and then as part of an academic study be submitted to Genbank. you may never be selected and then if you are selected you have to wait several years for the draft and the peer review and the submission … This could take years. “

Here is a few other quotes 🙂

Stanley Petrowski I am old. I submitted all of my data to genbank. I very much support science and citizen science even though I know the risks.

Eryk Jan Grzeszkowiak It is much better to submit your mitochondrial sequence directly to GenBank, you might end up waiting many years if you do it via FTDNA. 

 

mtDNA and modern person Ethnicity

Most probably, I will extend this article later with more details, but so far a few sections/quotes here.

In 2014, there was post on theapricity.com, where mentioned “Samples from southern Russia”:

PEJ2(EBA-Cat2, Peschanyi, Russia)=H(H), listed one HVR1 mutation (16234T) which is a defining HVR1 mutation in three H subclades: H1a1b, H13a1d, and H24a1. No pigmentation alleles listed.

Note: PEJ : Peschanyi, Rostov Oblast, Russia

According to “Genetic studies on Bulgarians” (wikipedia) with analysis of “MtDNA haplgroups of ~1000 Bulgarians”, HV haplogroup is on very top – 49%, with nested sub-branch H – 41%. No data for H13 percentage though. But this South European direction reminds me atDNA results of me and my parents. Details in my dedicated articles here on blog.

UPD, Jul-04-2017, from email with Ian Logan:

Another way of looking at the same problem is to consider the geographic spread; and in this case
it appears there might be diffusion over ‘Finland – Ukraine -Bulgaria’  – which would fit fairly well with either range. Not just a few centuries, and also not thousands of years.

 

2014 Updates

2014-07-17, Nelly Hymen from “The mtDNA H Haplogroup Project” wrote in email about my mtDNA results (mtDnaPlus test):

I see you only have your HVR1&2 regions tested. Your results are inconclusive to determine a sub branch 309.1C and 315.1C are not used for branch/subbranch determination. The only mutation used to determine a branch structure would 16234T.
– H1ab1  C16234T
– H13a1d  C16234T
– H24a1  G5261A  C16234T (you do not have A16293G which is the H24 branch defining mutation)

2016 Updates

  • Discussion with Elena Kuyumdjian regarding FTDNA algorithm and what haplogroup can assigned to my mother’s account.

2017 Updates

We’re excited to announce the release of mtDNA Build 17, the most up-to-date scientific understanding of the human genome, haplogroups and branches of the mitochondrial DNA haplotree. As a result of these updates and enhancements — the most advanced available for tracing your direct maternal lineage — some customers may see a change to their existing mtDNA haplogroup. This simply means that in applying the latest research, we are able to further refine your mtDNA haplogroup designation, giving you even more anthropological insight into your maternal genetic ancestry.

Build 17 was released in February of 2016. The previous version, Build 16, was released in February 2014 and Build 15 in September of 2012.

  • And on FTDNA page with results, there is note:

*Based on Build 17 from:
van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30(2):E386-E394. http://www.phylotree.org/ (Build 17)”

  • Jul-2017, mtDNA data of my mother was  uploaded to GenBank.
  • Jul-23-2017, on facebook group for H haplogroup, posted eupedia page by Faith Sentinel, and I questioned about H13a1d and I received answer, which reminded me the article I saw in 2014/2015, when I just performed mtDNA tests.

 

Resources

 

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