Tuesday, 9 December 2014

Richard III and the use of DNA as evidence

The long-awaited scientific paper with details of the Richard III DNA analysis has finally been published. Twenty-two months have passed since the memorable press conference at the University of Leicester in February 2013 when Richard Buckley, the lead archaeologist on the Richard III dig, declared that "It is the academic conclusion of the University of Leicester that beyond reasonable doubt the individual exhumed at Greyfriars in September 2012 is indeed Richard the III, the last Plantagenet king of England." However, at that time most of the DNA work had yet to be done and none of the findings had been written up and published in peer-reviewed journals, though the evidence already seemed to be overwhelming. Since then five peer-reviewed papers have been published on different aspects of the study (see the list below). The DNA paper by Turi King et al “Identification of the remains of King Richard III” has been published in the journal Nature Communications and can be found here:


It is accompanied by 56 pages of supplementary material with all the technical details about the DNA testing (including Richard III's Y-DNA and mtDNA haplogroup assignments) and extensive genealogical information. This is perhaps the first time that a scientific paper has included such detailed genealogical content. It is well worth reading the paper in its entirety together with all the accompanying material. It is a masterclass in how to do ancient DNA research and how to correlate DNA with genealogical evidence. In addition, the University of Leicester have issued an official press release and this includes further information about the study as well as links to a number of interesting videos showing how the genetic and genealogical research was done.

The DNA results have been extensively covered in the media, with most reports, such as this one from the BBC, focusing on the lack of  a Y-DNA match and the possible implications for the monarchy, though many people have also commented that it might perhaps have been more of a surprise if the Y-DNA had matched!

In what is believed to be the first analysis of its kind, the authors brought together the genetic and genealogical evidence, along with previously reported non-genetic evidence, and used a probabilistic assessment to determine whether or not the remains found in the Leicester car park were actually those of Richard III. Such analyses are often presented in courtrooms but have never previously been used to answer genealogical and historical questions. I wonder if this might be the start of a new trend!

The statistical analysis was done by my colleagues at University College London, Professor Mark Thomas and Professor David Balding, working alongside Turi King. Two competing hypotheses were investigated:

                                       Hypothesis 1 (H1) Skeleton 1 is Richard III
                                       Hypothesis 2 (H2) Skeleton 1 is not Richard III

The analysis took into account the genetic evidence from the Y-DNA and mtDNA testing and the previously reported non-genetic evidence (radiocarbon data, estimated age at death, sex, presence of scoliosis, and presence of wounds suffered around the time of death). People always tend to over-estimate the importance of DNA test results which is why in genetic genealogy we always emphasise the need to use DNA in combination with genealogical evidence. DNA can effectively prove that two people are not related on a specific line, and it can generally be used to confirm relationships with very close blood relatives. However, for more distant relationships DNA can only indicate that two cousins share a common genetic ancestor. DNA cannot give us the precise date when that ancestor might have lived and there is always a very wide range of possible dates. Consequently DNA evidence can broadly support a hypothesis but is generally not conclusive in its own right. This is particularly the case with mitochondrial DNA testing. Although it is now possible to sequence the whole mitochondrial genome, mtDNA has a low mutation rate and two people can have an identical mtDNA sequence yet sometimes share a common ancestor who lived several thousand years ago.

The same limitations apply to the case of Richard III. Contrary to popular belief, the mtDNA match on its own did not "confirm" Richard III's identity; it was merely one of a number of pieces of supporting evidence which had to be considered in combination with the conflicting evidence from the lack of a Y-DNA match. Here's an extract from the UCL press release:
Contrary to what many may have expected, the genetic evidence alone is not conclusive, partly because only the mtDNA and Y chromosome are suitable for comparing distantly related individuals. In fact, the Y chromosome, did not match presumed male-line relatives of the king, and so counted against Hypothesis 1. However, this non-match could be explained by one or more false-paternity events (where the biological father is not the father recorded in family history) over 19 generations; such events are not uncommon so the male-line data only weakly favoured Hypothesis 2. The mtDNA evidence was found to support Hypothesis 1, but overall the genetic evidence was not enough to confidently identify Skeleton 1 as Richard III. 
However, when combined with the non-genetic evidence, even after making assumptions intended to count against Hypothesis 1, the authors obtained an overall likelihood ratio of 6.7 million. Even a sceptical translation of this likelihood ratio corresponds to a 99.9994% probability that ‘Skeleton 1’ is the remains of King Richard III, which the scientists believe puts the matter beyond reasonable doubt.
It would have been interesting to see how the probabilities would have worked out if there had also been a Y-DNA match. There is still scope for further DNA testing on descendants of other Y-lines from the higher branches of the tree if suitable candidates can be identified. Now that the Y-DNA results are in the public domain it's also possible that someone might take a DNA test and discover that he matches the Richard III Y-DNA signature which could perhaps encourage genealogical research to determine whether or not there is a connection.

Richard III's DNA
Richard III belongs to Y-DNA haplogroup G2 (G-P287). His 23-marker Y-STR profile has already been uploaded to the public ySsearch database and is available via two different ySearch IDs:

Richard III ySearch ID 45AER

Richard III ySearch ID B8YDF

I presume that the authors followed the NIST standards for reporting STR markers. There are different ways of counting the markers and different companies have reported results in different ways. Family Tree DNA have not yet converted their database to the NIST standards. When comparing the Richard III signature on Ysearch with FTDNA results an adjustment would need to be made to the STR marker known as GATA H4.1. See the Marker Standards page on the Sorenson Molecular Genealogy Foundation website for a conversion table:


Richard III's mtDNA places him in haplogroup J1c2c3, a new branch of J1c that is defined by the mutation A12397G. This new subclade was added to the mtDNA tree with the latest build of Phylotree thanks to the work of Ian Logan (see his posting on the Genealogy DNA mailing list). Richard III's mtDNA profile (control region only) has been uploaded to Mitosearch:

- Richard III's  Mitosearch ID T227G

All the mitochondrial sequences generated from the Richard III study have been deposited in GenBank under the accession codes KM676292 to KM676294. I cannot find the sequences on GenBank and presume they must have only been submitted very recently so it will take time for them to appear. In the meantime Ian Logan has provided a list of all publicly available J1c2c sequences that have been uploaded to GenBank and www.openSNP.org.

Other peer-reviewed papers on Richard III
The DNA paper is the sixth in a series of papers resulting from the Richard III study. The other papers are:

2)  Mitchell PD et al. The intestinal parasites of King Richard IIIThe Lancet 2013; 382 (989): 888.

4)  Lamb AL et al Multi-isotope analysis demonstrates significant lifestyle changes in King Richard IIIJournal of Archaeological Science 2014: 50: 559-565.

5) Appleby J et al. Perimortem trauma in King Richard III: a skeletal analysisThe Lancet, Early Online Publication, 17 September 2014.

© 2014 Debbie Kennett


Brian Swann said...

I guess if there is no possibility in getting any further modern Y-DNA to triangulate on from any collateral descendants of any other male lines from John of Gaunt, as they do not survive, then the only other strategy I could foresee is something like this.

If Turi King sequenced in great detail by next-generation sequencing both the Y-DNA of Richard III and ideally two of the four modern descendants of the 5th Duke of Somerset then, longer-term, as we get enough samples from Y-DNA next-generation sequencing, you might be able to draw more conclusions about the ancestry of each from the analysed Y-SNP branching patterns.

This may take many years to achieve, but when you have gone to the effort to collect these samples it would be a shame to throw them away without this information being gleaned from them (especially the 4 matching samples from the 5th Duke of Somerset).

As such, I'm not sure if the Leicester group would spend their money to get these modern descendants sequenced. The Y-DNA of Richard III is likely to get sequenced in enough detail if they have the money to do the whole genome. Maybe we can discuss with Turi next time any of us sees her, unless you can do this via your UCL contacts?

This is very far from ideal but it is better than nothing. I am sure John Ashdown-Hill will have thought about this too.

Debbie Kennett said...


I'm not sure that Y-chromosome sequencing of the Somerset descendants is going to help given that they're from a different haplogroup altogether. There are now plans to sequence Richard III's whole genome and that will presumably include his Y-chromosome:


However, the connection is probably too distant for autosomal DNA to provide any answers.

Turi King, Kevin Schurer and Richard Buckley were interviewed by Adam Rutherford on Inside Science this week:


They did discuss the possibility of doing additional Y-chromosome testing to solve the riddle of the NPE, though I suspect tracing those male-line descendants will be a major challenge.

Joe Flood said...

One has to wonder given the inconclusive nature of the result whether the large effort put into this project was worth it. Do we have any actual matches to the Y- haplotype? G is not common in Britain and is usually associated with Roman remains.

However, I expect one way or another, the study will eventually pay off.

Brian Swann said...

I don't think we know at this stage where the NPE(s) could lie in this family. It could be that it lies between King Edward III and King Richard III, with some fingers pointing at Richard, Duke of Cambridge, who died in 1415, as the most likely possibility in that descent line.

So it could still be that the descent to the 5th Duke of Somerset is completely valid in Y-DNA terms.

At the other extreme there could be NPEs in both lines, which short of getting a sample of the Y-DNA from King Edward III himself, becomes almost impossible to investigate.

Debbie Kennett said...

Joe, It's only the Y-DNA result that was inconclusive. The statistical analysis of all the other evidence was about as conclusive as you can possibly get. DNA always seems to answer some questions but pose other questions at the same time.