Tsar Nicolas II and the curious case of the mismatched bases in his maternal mitochondrial DNA – was Tsar Nicolas II really killed in a cellar in 1917?

The Death of the entire ruling Romanov Family in 1917

In 1917, Tsar Nicolas II, together with his wife, the Tsarina Alexandra, their five children (Maria, Anastasia, Olga, Tatiana and crown prince Alexei), and four servants, was executed and hastily buried in non-marked graves. His death ended the monarchic rule of House Romanov in Russia; no Tsar would ever sit on the Imperial throne again. A house which included famous Tsars Peter the Great and Catherine the Great was literally eradicated overnight.

However, the myth of at least one Romanov escaping the slaughter persisted and has captured the world for generations – Anna Anderson claimed famously that she was Anastasia, the tsar’s youngest daughter, for decades until DNA testing revealed her to be a Polish factory worker; Ingrid Bergman won an Academy Award for her portrayal of Anastasia in “Anastasia”. The movie was so successful that Disney used the storyline for its own animated adaption and the musical “Anastasia.”

However, the Russian Government was not so romantically inclined – any surviving Romanov (and their potential claims) was a threat to the established order. So, when in 1991, when 11 bodies presumed to be the tsar’s, his family’s and the servants’, were excavated from a mass grave near Yekaterinburg, the Russian government wanted to make sure that the Royal Family really died.

How?

Science!

Let me take you on a (albeit simplified) journey of identifying the remains of one of the most powerful royal dynasties of the previous century…. and without further ado ….

We need to prove (or disprove) that the skeletons in the mass grave are members of the House Romanov (and if they are, that they are the Tsar and his family)

What do we know?
1. We know that 11 bodies were found, which would correspond to the reports that the Tsar was killed with his wife, their 5 children and 4 servants.

2. Children inherit the maternal mitochondria from their mother. As it passes unchanged from mother to children, mitochondrial DNA (mtDNA) can be used to establish lineage using the females in one’s family.

3. Similarly, the Y chormosomes passes from father to son and can be used to establish a paternal line.


How we will proceed

  1. We need to establish through the mtDNA that the Tsarina was the mother of the five younger skeletons, thereby constructing a maternal lineage
  2. We need to establish that one of the male skeletons is related to the skeleton of the boy. If so, this would be an indication that they are father and son, and thus potentially Nicolas II and his son, fourten-year old Crown Prince Alexei.
  3. Assuming that we managed to establish a maternal line through mtDNA for six of our skeletons, we can use the mtDNA of a known relative to establish that one of the older female skeleton is Tsarina Alexandra.
  4. If we managed to establish the paternal line, we can, again using mtDNA of a known relative, establish that one of the male skeletons is Tsar Nicolas II.

And then we solved the mystery of the last remains of the Romanov Family. Let’s proceed:

Step 1 and 3: Establish the maternal line !

We researchers quickly establish that 6 people shared the same mitochondrial DNA – one of the older female skeletons and all of the 5 younger skeletons. This points to the possibility that the older female skeleton is the one of Alexandra.

We now need a known relative for the comparison of mtDNA with the skeleton we assume to be Alexandra’s. Fortunately for us, Royals have well-kept family trees, which allows us to easily identify living close relatives who would be willing to provide samples.
As luck would have it, we see that HRH Prince Phillip is a close living relative of Alexandra’s through her mother.

So, let’s quickly go to Buckingham Palace and ask whether he is willing to provide a sample…. and yay! We have a sample of a close maternal relative of Alexandra’s.

After comparing the mitochondrial DNA, it is now obvious that Prince Philip is related with the female skeleton, thus identifying her als Alexandra (and in turn, the 5 younger as the five Romanov children). It is highly unlikely (and not documented anywhere) that another close relative of Philip’s was killed near Yekaterinenburg at the same time, together with her 5 kids, also said kids would have had to have been 4 female and one male child….

So, we have just managed to identify Alexandra and her 5 Romanov children!

Step 2 and 4: Establish the paternal line, identify Tsar Nicolas II!

Now we still have unidentified male skeletons in that mass grave – and we need to find the father of the family.
As we now know that the boy is Prince Alexei, we can compare his Y chromosome to all male skeletons in the grave to identify his father. So let’s do it!

Ok. Results are back in.

One of the male skeletons has a perfectly matching Y chromosome to the young boy, thus tentatively identifying him as Tsar Nicolas II, Alexei’s father.
However, the same Y chromosome simply signifies that these two share a common male ancestor; technically speaking, these two skeletons could also be uncle and nephew. And are we also sure that these are Romanov?
Comparing their Y chromosomes to the Y chromosome to a known cousin of Nicolas II’s, it was quickly established that the Y chromosomes of the two male skeletons are related in the male line to the Romanov Family.

Unfortunately we are not done, however…

The Russian Government also wants us to compare the mtDNA of the Tsar to known maternal relatives…. We would expect them to match, thus allowing us to leave work early and go to the pub….

And now the lab comes back and we have a Problem: the mitochondrial DNA extracted from the Tsar did match his two maternal relatives except for one single position. Here, at position 16169, the bone sample has a mixture of matching (T) and mismatching (C) bases.

OK …… Well, it’s just one position, so what’s the harm in that? Well, our employers, the Russian Government, are not happy. They want to be 100% certain that the tsar is really dead. So, what was it: was the original sample contaminated? Did the tsar escape, but someone else with the same Y-chromosome, but mtDNA with one differing position is somehow lying in his grave?

Just as we are about to get really, really drunk, a nice scientist from a fellow lab sends us a few publications about the so-called “Heteroplasmic mtDNA” with a friendly smiley. We read and learn that sometimes, a mutation can occur in the mtDNA of the mother, which is then inherited by her children.

So, we have to go and find a male relative of Tsar Nicolas II to check whether heteroplasmic mtDNA variants occur in the Tsar’s maternal line, and since we don’t want to work double shifts, we need a very close relative to Tsar Nicolas II, preferably a brother or sister since they would share the same DNA as Nicolas’s mother,

Fortunately for us, Nicolas’s brother Georgij Romanov is buried in the St. Peter and Paul Cathedral in St Petersburg. So let’s grab a shovel and exhume him to get a DNA sample.

If this skeleton is really the one of Tsar Nicolas II, then we would expect that Georgij’s DNA contains the same heteroplasmic variant at exactly the same position … which would confirm the occurence of mtDNA sequence heteroplasmy in the Tsar’s lineage.

So, it’s back to the lab ….. and look and behold – the two have the same missmatch at position 16169 ….

Yay !

We can now conclude with certainty that the Tsar, his wife and all five kids were killed in 1917, having scientifically proven it with mtDNA and nuclear DNA. We can also write a paper about how Tsar Nicolar is one of the most prominent examples of Mitochondrial DNA sequence heteroplasmy.

Unfortunately, we also have to conclude that all the legends of a surviving Romanov Member were just – legends.

Are you interested in more reading material?

Ivanov, Pavel & Wadhams, Mark & Roby, Rhonda & Holland, Mitchell & Weedn, Victor & Parsons, Thomas. (1996). Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgi Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nature genetics. 12. 417-20. 10.1038/ng0496-417.
Link: https://www.nature.com/articles/ng0496-417

Coble, Michael. (2011). The identification of the Romanovs: Can we (finally) put the controversies to rest?. Investigative genetics. 2. 20. 10.1186/2041-2223-2-20.
Link: https://investigativegenetics.biomedcentral.com/articles/10.1186/2041-2223-2-20

Coble, Michael & Loreille, Odile & Wadhams, Mark & Edson, Suni & Maynard, Kerry & Meyer, Carna & Niederstätter, Harald & Berger, Cordula & Berger, Burkhard & Falsetti, Anthony & Gill, Peter & Parson, Walther & Finelli, Louis. (2009). Mystery Solved: The Identification of the Two Missing Romanov Children Using DNA Analysis. PloS one. 4. e4838. 10.1371/journal.pone.0004838.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0004838

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