All About mtDNA in Genetic Genealogy

WHERE DID mtDNA COME FROM?

Roland Henry Baker, III: Most human DNA is contained in 23 chromosomes inside the nucleus of the cell. The mitochondria were once separate cells (bacteria) that entered the cytoplasm of a host cell and they had their own circular DNA molecule. They lived in a symbiotic relationship with the host. They conferred a selective advantage to the host which allowed the host to process oxygen to produce energy.
Previous to the period the atmosphere of earth was reducing and the cells we evolved from used reduction of substrates like sugar (glycose) to produce energy via glycolysis much like yeast cells do today through fermentation. The early atmosphere of earth contained lots of methane and little oxygen – much as you find today on Jupiter or Saturn for example. So our ancestors – single celled organisms evolved in an oxygen poor environment. In fact oxygen was toxic to them. They lived by reducing molecules like glucose into two molecules of pyruvate.
Cyanobacteria evolved and started to capture the energy of sunlight and as a byproduct released oxygen via photosynthesis. Over time this changed the composition of the atmosphere such that it became very oxidative and toxic to many organisms. We talk about global climate change today but this event was on a whole different scale.
By incorporating these symbionts our cells gained the ability to process oxygen for metabolism so they could adapt to the new environment. The endosymbiotic bacteria took the byproduct of glycolysis i.e. pyruvate and converted it to CO2 as a byproduct via oxidative phosphorylation. That’s why humans can eat carbon food sources extract the energy and exhale the carbon waste product as CO2. Over many generations these symbiotic cells lost most of their original DNA and became organelles in the cytoplasm called mitochondria. But they still carry a ring of DNA that is just over 16,000 base pairs long. It is circular in structure just like most bacterial genomes – it is not packaged in a chromosome. There are many mitochondria in each cell’s cytoplasm and each mitochondria contains a single circular strand of DNA.

WHY DO ONLY WOMEN PASS mtDNA ON TO THEIR KIDS?

Roland Henry Baker, III: During reproduction the human sperm does not transmit mitochondria to the zygote. Therefore all the mitochondria and therefore all the mitochondrial DNA in the zygote is from the mother.
Mitochondrial DNA unlike nuclear DNA never exchanges DNA. It remains the same from generation to generation unless there is a mutation.

HOW ARE MUTATIONS USED TO DISTINGUISH mtDNA HAPLOGROUPS?
(PLEASE USE Francoise Martinet, SM/PROG - WHO WE THINK IS U5B AS A RESULT OF A MOTHERLINE DESCENDANT ON THE GENI TREE -Private User - BEING GOOD ENOUGH TO POST HER DNA results.)

Roland Henry Baker, III: About 24,000 years ago a mutation occurred in the mitochondrial genome of a single female. That mutation is diagnostic for the U5b mtDNA haplogroup. All living people (male or female) today within the U5b are descendants of that single female who lived 24,000 years ago.

DO YOU MEAN THAT EVERYBODY WITH THE U5B mtDNA HAPLOGROUP HAS THE SAME FEMAL ANCESTOR FROM 24,000 YRS AGO?
Roland Henry Baker, III: Yes all people with the U5b mtDNA haplogroup share the same maternal ancestor. But they may have different maternal lineages to that same female ancestor. Since that time there have be other single base-pair mutations in single females. All descendants of these females can unambiguously be distinguished from the descendants from all other females because they carry this mutation plus all previous mutation of U5b. Subsequently more mutations occurred over time. And you can see how this forms a phylogenetic tree with a terminal set of mutations identical to the tester in question. This is a fact and can be proven.

The person who tested posted some markers:
mtDNA Markers
16,224 C
16,270 T
16,311 C
73 G
150 T
263 G
279 C
315 CC
517 T
But they didn’t post which reference they were from. We have two major references for a “standard” mtDNA sequence. Without knowing which one these data are useless. So that’s another thing we need to include. What these tell us is at base-pair 517 the person who tested has a mutant-type T instead of the value of the reference. At 315 you can see they have a C instead of the wild type reference plus an insertion of an extra C. etc.
So our job is to take the genealogical tree based on paper records and overlay it onto the phylogenetic tree.

SO,
GENEALOGICAL TREE= A PERSON”S FAMILY TREE eg on Geni
PHYLOGENETIC TREE=A SPECIES’ FAMILY TREE

SO, ON THE GENI TREE, WILL ALL THE DESCENDANTS OF Francoise Martinet, SM/PROG’s DAUGHTER’S DAUGHTER’S ETC ALSO BE U5B?
Roland Henry Baker, III: If the genealogical tree is certain then Francoise Martinet will have carried mitochondrial DNA with the same mutation as carried on the U5b haplogroup plus the terminal mutations of the person tested (possibly minus one), then all other matrilineal descendants will also be in the same U5b haplogroup. (However, they may be found to carry a new single point mutation. That can’t be ruled out. Mutations are natural. They just occur rarely in mitochondrial DNA. But we compare these mutations to the known tree to make sure this is a new mutation. That’s pretty simple.)

BUT THAT RELIES ON THE ASSUMPTION THAT THE GENI TREE IS ACCURATE, DOESN’T IT?
Roland Henry Baker, III: We can’t assume the genealogical (GENI) tree is certain. And we can’t assign it an arbitrary value of certainty from 0% to 100% at least not scientifically. The tree is a model and we find evidence to support or disprove the model. We use samples to scientifically prove the phylogenetic tree.

SO WHAT ABOUT IMPROVING THE CERTAINITY BY TESTING ANOTHER MATRILINEAL (MOTHERLINE) DESCENDANT OF Francoise Martinet, SM/PROG ON THE GENI TREE? Daan Botes IS A DESCENDANT FROM HIS MOTHER TO HER MOTHER, ALL THE WAY BACK TO ANOTHER DAUGHTER OF FRANCOISE’S THAN THE ONE Private User TRACKS DOWN FROM.
Roland Henry Baker, III : If a second tester has the exact same mutations as the first tester we can determine that they shared the exact same maternal ancestor. There would be no other samples necessary to reach this conclusion. That is to say they share the same maternal ancestor on the phylogenetic tree. And by testing more people we can refine the date for the emergence of the female who had the last mutation that formed the terminal branch in the phylogenetic tree.

SO, IF TWO MATRILINEAL DESCENDANTS ON OUR GENI TREE TEST WITH THE SAME mtDNA – IS THAT CONCLUSIVE PROOF OF THEIR FEMALE PROGENITOR’S mtDNA HAPLOGROUP?
Roland Henry Baker, III: Can we say with any certainty based on mtDNA genetics alone that the first two people who have matching results are both descendants of Francoise Martinet, SM/PROG? No not really. For example her husband could have had an unrecorded first wife – the married date could have been recorded wrong or forged, etc. (In other words we could have had a green fish from Nevada). Or they may have both descended from a female who lived before Francoise Martinet back in France. And there is no additional number of tests that will ever prove it.

But we have a model and we look at the data we use in genealogy to construct this model and DNA is probably the strongest evidence we have to support it. (WE DISCUSSED THAT AT LENGTH HERE: http://www.geni.com/discussions/152268?msg=1063707&page=1). We reason that there was a founding population with very few women and one of these women was Francoise Martinet, SM/PROG. This was a bottleneck (IN SA) as Sharon pointed out. If two people who claim to be descendants have the same mtDNA mutations that’s darn strong evidence that their genealogies are correct! It is better evidence that most of us will ever have for an ancestor this ancient.

So part of this is possibly how a biochemist like me uses the words “proof, support, predict” and how they are used in the social sciences and genealogy. I think most genealogists would call that “proof.” I prefer the words “strongly supports” this model. The bottleneck makes it almost undeniable but scientists don’t like to use the word “prove” unless we really mean it. Like I can prove 2+2 =4. I can prove energy is conserved when a photo elevates an electron to a higher energy orbital. That’s why we call evolution the “theory of evolution” – it is a model like genealogy and it is highly supported by the evidence. I use the word “disprove” much more often. If I can find a fact from DNA analysis that is not consistent with your genealogy I have disproven the model. DNA can be used to disprove genealogies easily. So I much prefer to disprove things than to try to prove things. But I do like evidence that supports a model too.
I agree with a lot of things Jan is saying – a negative match *is* data. That’s where the fun begins and we get to start testing our model. Usually a weak point will be found quickly.
So we use the DNA samples to prove the phylogenetic mtDNA tree. We overlay the genealogical tree onto the phylogenetic tree in order to support out model. We look for evidence that doesn’t match our model. Say we get a third person who doesn’t match? We start from the bottom of their genealogy and work our way up looking for an error. Alternately we use mtDNA, autosomal DNA and Y DNA testing to prove or disprove their genealogy a few generations at a time. Eventually we will find the error at least in many cases.

OK, HOW DO YOU USE AUTOSOMAL DNA TO DIS/PROVE THEIR GENEALOGY? I THOUGHT THAT COULD ONLY BE MATCHED TO 4 GENERATIONS?
(AUTOSOMAL DNA = THE 22 OTHER CHROMOSONES THAT AREN’T THE X & Y SEX CHROMOSONES. UNLIKE mtDNA & Y DNA, THE PARENTS’ AUTOSOMAL DNA IS (PRETTY?) RANDOMLY RECOMBINED IN EVERY NEW BABY)
Roland Henry Baker, III: I’m not sure where this idea came about that autosomal DNA is only good for four generations. It can be critical in a case like this where we may get a third person who doesn’t match on a mtDNA test. Then we can use autosomal DNA to work our way up all three trees to look for evidence that doesn’t match.
Autosomal DNA can go back much further than four generations but not for all of our ancestors – only for some of our ancestors. But I have DNA that I can trace all the way back to the Mayflower. Each generation back the match gets smaller and smaller but it’s the same segment getting passed down. But I can’t trace autosomal segments back to other ancestors in my tree. Why? because I either don’t carry any DNA from those ancestors or the DNA I do carry from them either is no longer carried by any of my cousins or none of the cousins who do carry this same segment have taken a DNA test.

SO, HOW FAR BACK DOES AUTOSOMAL TESTING WORK?
Roland Henry Baker, III: How far back does autosomal testing work? The answer is it depends on which part of your tree you are looking at. It will vary from branch to branch.
It is important when reading about autosomal matching to make the distinction between:
1) the probability of your personal DNA sample matching a specific remote cousin via your MRCA
2) the probability of your DNA matching *any* remote cousin via that same MRCA
3) the probability of any two cousins matching via that MRCA.
That’s really, really important because you don’t have to match a specific person to prove your MRCA. For example you might match their second cousin. Alternately that specific person may not match you but they may match your second cousin. And that’s all that is needed to prove the relationship assume you get enough matches to triangulate. You can prove you share a very recent common ancestor with a 2nd cousin and then use your 2nd cousin’s DNA to prove a relationship to a more distant ancestor using that closer ancestor as a gateway. So if you think about it you can “walk” your way from ancestor to ancestor! But only if you can share matches with multiple cousins! And that’s why we need DNA sharing on GENI. Because we can all use other GEDMATCH kits to walk our ancestors. This becomes a very powerful tool to track down mismatches in mtDNA or Y DNA. And in some cases it can be used to go very far back.

Roland - you mention that in order for mtDNA markers to be useful (I presume for the purposes of comparing results to see if they match?), we need to indicate which one of two references the markers are from. Are you referring to HVRI or HVRII variations?

Perhaps you could give us an example (template) of a standard/useful way to present mtDNA results.

How far back does autosomal testing work?

Mathematically, this type of test cannot guarantee a match beyond 6 generations, however common ancestors between matches have been found further back than this. As technology improves, the capability of reaching farther back is very probable.

Say your 4th great grandparent gave his child 50% of his DNA, then the grandchild of the 4th grandparent would have 25% of the grandparent's DNA. In only a few generations the percentage of DNA from any 4th great grandparent is reduced. A person may not carry DNA from all of their ancestors 10 generations back, though they may carry DNA from some ancestors 10 generations removed.Here is a reason for getting as many people as we can to take genetic tests!

You can go further back in time with certain branches of your family tree. If your ancestors married cousins, then you would have a higher percentage of DNA from their ancestors than from you other ancestors in the same generation. So you would have more DNA from that line and you would be able to trace that line further with genetics.

There are some tools in the genetic genealogist toolkit that can help us use genetics to find ancestors. One is called chromosome mapping. During meiosis (formation of sperm and egg), the DNA goes through a recombination which results in DNA segments that are somewhat different for each child. To illustrate this, consider a deck of cards,where the red cards are on one side and the black on the other, then shuffle the deck. Deal 26 cards face up in a vertical row. Do the same with the second half of the deck in a separate row. Consider these two rows of cards as pairs of chromosomes. Notice how many cards next to each other are red. Notice how many cards next to each other are black. Each red card or series of red cards are segments of DNA which come from one parent and segments of black cards come from the other parent. Say the black cards represent your father's contribution. We cannot determine which DNA segment came from his father, or his mother.The same is true for our mother's lines. By mapping our chromosomes and getting cousins to test, we can determine which ancestor gave us which segment of DNA.

Another useful tool is phasing. Using a process called phasing, we can determine which base pairs come from which parent. Phasing can be valuable genealogically because matches with a phased data set can be assigned to a paternal or maternal genealogical relationship.

Another tool to use to evalulate your matches is the centimorgan To evaluate the probability of sharing DNA with relatives, we can use something called a centimorgan. This is a measurement of how likely a DNA segment is to recombine from one generation to the next. As a general rule, 1 centimorgan corresponds to a million base pairs, though this can vary. Base pairs provide a linear measurement, whereas the centimorgan provides a weighted measurement. For the autosomal tester, the centimorgan value attached to a matching segment can be considered as a measurement of the quality of the match. Generally, the higher the value, the closer will be the relationship. (Though there are uncertainties in any estimate of the relationship)

So, chromosome mapping is a multi-step process that begins with testing yourself and various relatives. Phasing your data before mapping your chromosomes to particular ancestors helps to avoid mistakes in your chromosome map. Short matching segments from unphased data sets run a higher risk of being pseudo matches, where the match switches back and forth between the pair of chromosomes, which is not a match at all.

Here is an advantage of GEDmatch. They allow uploading of phased data sets. Their comparison tools work equally well with phased or unphased data.

Please have a look at the following links to learn more:

http://isogg.org/wiki/Autosomal_DNA_tools

http://www.isogg.org/wiki/Phasing

Wow: Phasing. Costly, though I imagine?

So now that they've mapped markers connected to intelligence on the X chromosome - you'd be able to figure out which granny your brains came from, if you used phasing?

Phasing is not necessarily costly. There are some phasing tools out there. What most genealogists need is guidance for how to best use the available tools.

Phasing also has medical applications. If one of your grandparents has an inherited disease, you can determine if that grandparent has passed that section of the chromosome containing the suspected gene to you. Eventually, we may be able to use phasing and recombination analyses to develop smart medical histories.

Wow! Thanks for sharing this Sharon! I’m glad my comments were helpful!

It really is too bad GENI does have a way to post images because biochemistry and molecular genetics is much easier to understand if you can visualize the mechanisms and molecules involved.

Ian, there are two ways to share an mtDNA sequence. You can publish the entire sequence or you can just post the difference of your markers against a reference sequence. Doing both is best. But just posting the markers that are different from a reference along with the reference name should be good enough (see below).

The gold standard for sharing mtDNAdata is to publish your complete DNA at NIH’s GENBANK. For example here is my complete mtDNA sequence:
http://www.ncbi.nlm.nih.gov/nuccore/KR072973

Then you can post the URL in the above format with your results.

For this you’ll need to download your FASTA file from FTDNA, YFull, FullGENOMES or wherever you had the sequencing done and convert it to an SQN file and send it in an email to the NIH. If you email your FASTA file to Ian Logan <ianlogan22@btinternet.com> he can prepare the SQN file for you and help you with the email free of charge. Then you just need your accession number to post the URL for your complete sequence. GEDBANK will display not only the entire sequence but also the translation of coding regions into amino acid sequences and it will define other functional units such as tRNA, ribosomal units and the D-Loop region. The site also has a set of tools such as BLAST/BLAT to work with these data. So it is an educational experience which is a lot of fun!

Please look at the URL above for a second. There are about 200,000 mtDNA molecules in an egg found inside of mitochondria which are located outside the nucleus in the cytoplasm. A mature human cell has less than half that number. Mitochondria contain multiple copies of the mtDNA molecule. The mtDNA molecule in humans is a simple double stranded loop about 16,000 base-pairs long similar to a bacterial genome and isn’t organized into a chromosome but is packaged with proteins. The mtDNA molecule encodes 22 transfer RNAs (tRNAs) and 13 protein-encoding regions, two ribosomal subunits (rRNAs) and well as a control region called a d-loop which takes on interesting 3-demenional conformations. The coding regions for the tRNAs, proteins and rRNAs are highly conserved meaning they don’t mutate often because they are crucial to survival and random changes can be fatal or at least be deleterious to survival. However there are two portions of the control region which have a high mutation rate which makes them very interesting for genealogy and these are called hypervariable regions (HVR). HRV1 is at the end of the loop at base-pairs 16001-16568 and HVR2 is located at the start of the look at base-pairs 001-574. But there are also mutations found in the coding regions mentioned above. So mutations are usually categorized by their location in HVR1, HVR2 or the coding region.

The proteins encoded by mtDNA include subunits important in oxidative metabolism: Cytochrome b, NADH dehydrogenase, Cytochrome Oxidase and ATP Synthase. If you look at the URL above under “product=” you’ll see what each gene codes for. These genes are all of a very ancient origin. When nature discovers a key molecule it conserves it and copies it and modifies it for a variety of uses. But the fundamental design and chemistry remain the same in all organisms. Cytochrome is one of the most interesting molecules. It includes a porphyrin ring with highly mobile conjugated electron orbitals bound to an iron ion which is easily oxidized and reduced and is used to pump positively charged protons across the mitochondrial membrane creating an electrical potential across the membrane. This electrical potential is used to generate ATP from ADP. And ATP transfers energy to drive reactions all over the cell. Porphyrin comes from the Greek word for purple because the mobile field of electrons is able to absorb and emit light in the visible spectrum and is therefore a pigment. Related porphyrin and corrin ring structures conjugated to a metal ion are used in the heme containing groups of red blood cells, chlorophyll groups which absorb photons in plants, Vitamin B12, and also in the process of nitrogen fixation. Similar systems of conjugated electron orbitals are also used in vision.

So the mitochondria take over where anaerobic metabolism leaves off. It takes the left over pyruvate and converts it to CO2 generating ATP in the process. Have you’ve ever felt that burning in your legs while you are running? That pyruvic acid building up because your mitochondria aren’t keeping up!

The second way to report mtDNA sequence data is by taking your specific sequence and comparing it to a reference sequence and then only reporting the nucleotides that are different from the reference squence. This gives you a much shorter list to post. You’ll also use this technique if you want to have your sequence analyzed by a doctor.

There are two primary reference sequences:

1) The revised Cambridge Reference Sequence (rCRS) – this is the older of the two reference sequences and you’ll see it cited in the medical literature frequently. It represents and arbitrary sequence published by Dr Sanger (of Sanger sequencing fame) in the 1970s. Some errors were fixed and the updated rCRS (r for revised) was published in 1999.

2) The Reconstructed Sapiens Reference Sequence (RSRS) is a much newer reference which is intended to represent the genome of Mitochondrial Eve from whom we all descend. This is probably more interesting for genealogy because differences from the RSRS represent derived SNPs in your sequence compared to the wild type in the reference.

If you tested at FTNDA you’ll notice that they have already posted RSRS and rCRS reports with your results. So you can download your certificate in PDF and that will have all the information you need. You’ll notice the reports break down the markers by HVR1&2 and Coding region (see above). So this is a very compact way to share your results and it is easy to read. You’ll see three types of items in the list. For example:

16069T
523-
315.1C

The first item means that at base-pair (bp) 16,069 my genome contains a T instead of the wild-type C. The second item means that I have a deletion at bp 523. The third item means after 315 I have an insertion of a C.

The import thing to remember if you post these lists of values is always state if they are compared to the rCRS or the RSRS. That way we know what we’re looking at.

Along with the report should be:
The name of the person who tested,
What test they took,
The company they tested with
Their pedigree to the ancestor in question.
Contact information or a link to your profile is a plus.
Also include your haplotype if it is known.

Noelle - I really like your card analogy - I'm going to have to steel that :) I hope you don't mind.

Sharon - if you have your DNA tested and one of your parents tested you can download your files and upload them to GEDMATCH. They have a phasing tool which is quick and free. You have 23 pairs of chromosomes and you get 23 from your mom and 23 from your dad. What this simple tool does is compare your DNA to one (or both) of your parents' DNA and it tells you which portions of your DNA come from your mom's side and which comes from your dad's side and it will even generate a kit for each so you can search for matches only one that one side. It is very easy to use.

Thanks:)
Suppose the new kit nr with P1 at the end is Paternal line and M1 is maternal line.
Waiting for batch process to complete.

100% correct.

My father has an especially rare mtDNA haplogroup: f1c1a.

He has no matches on FTDNA whatsoever.

His most distant maternal ancestor was from Kidderpore, Kolkata.

He has only one match on Genbank (FJ748720) which is from China (though Tibet is listed as ancestral origin).

I joke that he is a Gurkha, because he has legendary endurance. He has run the Comrades Marathon twice. Whilst I, with my h1ak1 mtDNA, would much rather drink wine and eat cheese...

That's pretty fascinating - f1c1a. I've never met anyone with that haplotype.

mtDNA Lineage Expansions in Sherpa Population Suggest Adaptive Evolution in Tibetan Highlands
http://mbe.oxfordjournals.org/content/early/2013/10/12/molbev.mst14...

I wonder if adaptation to high elevation somehow contributes to his endurance.

I've often wondered the same thing! Whatever contribution it has made to his endurance has come at the cost of his height. I'm 191cm tall, he's 175cm; comparably short.

I'd be very interested to hear from others with f1c1a haplogroup. As well as any other Anglo-Indian South Africans with ancestors who left India in the 1930s and 1940s.

Also, Roland, just noticed UC Berkeley! I can't get enough of Phil Broughton's Black Blood of the Earth. He is (was?) the Radiation Safety Specialist at UC Berkeley. (http://news.berkeley.edu/2012/11/13/persons-of-interest-extreme-sci...). Have a look at BBotE, it's incredible stuff.

Sharon Doubell I just sent you a private message.

Drummond - I had not read about Phil. The article says:

“Black Blood” is now available in a handful of varietals, including “Death Wish,” which his bean supplier boasts is the most highly caffeinated, dark roast, organic coffee in the world.

I may have to give that a shot :)

LOL

Thanks Roland - I'll go and take a look. Late afternoon here, and I'm supposed to be working on a report, not on GEni :-(

Ek het my Phasing kit op GEDMATCH ge run op n one to many.
Net so vir interressantheid sien ek n vd Walt met U5b2b3a mtDNA Haplogoup.

Dit is interesant. ek wonder of hulle op Geni is?

Please update the links to mtDNA projects to the Geni mtDNA projects.
Ive done some updates on the H mtDNA project.
https://www.geni.com/projects/mt-H/32567

So, clearly, something's happened with Geni.com's mtDNA results because I currently have 1014 mtDNA matches. From about 50 matches to 1014 matches overnight. Also, they're all HVR1, HVR2 matches. Is there no facility to compare Coding Regions to wither down this list of 1014 matches a little?

I don't know the answer. If you send your question to Customer Service; I'll see if I can find Curators who can reply.

Hi,
as far as I know what happend, is the ftDNA has this function under their Y DNA matches that is called ysearch and under their mtDNA matches is mitoSearch. When you use these functions, it upload your results onto or into an anonymous account on the internet to broaden your search for more matches. It only load your HVR1 +2 and not the coding regions as the might be some sensitive information in that data.
So Geni has loaded that data into Unnamed or Private profiles to get matches on the Geni site. That is also whey those profiles does not have any trees/ single persons.
Its more of an advertising plot (hooo look at the lot i got) than being helpfull.

Thanks C, you are a star :-)

C Barry, I was aware they had done that with Y-DNA (as I had a match to a Private CORRIE, that happened to be me). As you say, they've obviously done that with mtDNA too now. With H being such a common haplogroup, I can't say the HVR1, HVR2 matches really help me that much (unless we're talking ancient origins, in which case there sure are a lot of Scandinavians with H haplogroup!).