SPAMIX for spatial localization of admixed individuals

A new preprint on the bioRxiv suggests that it is possible to geographically localize the location of a person's four grandparents. This is often a problem for persons of mixed ancestry who often tend to plot in PCAs in some average location between their ancestors (so someone who is Swedish+Italian+Spanish+Russian might end up somewhere in central Europe even though none of his ancestors are central European).

This has appeared shortly after the GPS method of Elhaik et al. (2014) which presents evidence of being more accurate than SPA, so it will be interesting to see a comparison between SPAMIX and GPS. My experience in the Dodecad Project suggests that this is a useful feature (the Dodecad Oracle could sometimes be used for this purpose and e.g., could infer that a person that had one Ashkenazi Jewish grandparent and 3 English ones was a ~3/4 British+~1/4 Jewish mix, but it is limited to mixtures of two populations, so it could not cope with the case of 3-4 grandparents with different origins). There is an under-appreciated pool of adoptees who would love a tool like that, and there are also obvious forensic implications if something like this really works.

bioRxiv doi: 10.1101/004713

Spatial localization of recent ancestors for admixed individuals

Wen-Yun Yang et al.

Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over non-model-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g. grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods using empirical data from individuals with mixed European ancestry from the POPRES study and show that our approach is able to localize their recent ancestors within an average of 470Km of the reported locations of their grandparents. Furthermore, simulations from real POPRES genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550Km from their true location for localization of 2 ancestries in Europe, 4 generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.

Link

Facial reconstruction of 5,600-year old Maltese woman

Source: Revealed...the face of a Maltese woman 5,600 years ago

Heritage Malta also launched a 3D virtual reconstruction of facial features based on one of the prehistoric skulls (over 5,000 years old) found at the Xaghra Stone Circle in Gozo. It revealed, for the very first time, what one of the earliest Maltese actually looked like.
It was a face which was much closer to what one would expect from a woman of our day and age rather than that of a person who lived on the islands over 5,000 years ago.

Crime and twins

Twins' DNA hinders France sexual assault investigation

Police who are investigating a series of sexual assaults in the southern French city of Marseille have arrested identical twin brothers.

The 24-year-old unemployed delivery drivers, named locally as Elwin and Yohan, were placed under investigation on Friday.

Officers say they are sure that one of the two men carried out the attacks, but that they do not know which.

Standard DNA tests are unable to differentiate between their DNA.

...

Police have been told it would cost upwards of 1m euros (£850,000) to conduct an ultra-sophisticated genetic test that would be able to tell one set of the twins' DNA from the other.


One expert told the French newspaper La Provence: "For a normal analysis, we would compare 400 base pairs [of nucleotides] which make up DNA."

In the case of identical twins, he added, "We would be looking at billions."

I wonder what is the ultra-sophisticated genetic test they are referring to; presumably no genetic test can be any more sophisticated than a whole genome sequence at very high coverage, and that does not cost a million euros anymore.

The closest I could find on the topic of twin genetic similarity is the following reporting on an ASHG 2012 abstract:

They then calculated the frequency with which these mutations occurred. Only two sets of twins had such mutations, which translates to a DNA change occurring once for every 10 million to 10 billion bases that are copied every time a cell divides. While that may seem like a high accuracy rate, cells in the body divide trillions of times. So that would mean an average twin pair carries 359 genetic differences that occurred early in development. 

One limitation of the study is that they could only estimate the mutation rate based on blood cells, but some cells in the body divide much more frequently and so may rack up many more mutations. Other cells, like brain cells, don't regenerate much and would probably remain stable.

Beware of who you kiss

Forensic Sci Int Genet. 2013 Jan;7(1):124-8. doi: 10.1016/j.fsigen.2012.07.007. Epub 2012 Aug 20.

Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

Kamodyová N, Durdiaková J, Celec P, Sedláčková T, Repiská G, Sviežená B, Minárik G.

Abstract

Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence.

Link

Upcoming Richard III documentary

From Channel 4:

With the support of historians, the University of Leicester's archaeologists identified a possible location of the monastery as the car park for Leicester City Council's Social Services department. However as Richard Buckley, Head of the University of Leicester's Archaeology Services tells the programme: "...the chance of finding Richard was, I don't know, a million to one." Yet the dig commenced and on the very first day a male skeleton was discovered - which careful examination would later reveal to have curvature of the spine and battle injuries including a head wound.

For the last three months, the remains has been subjected to some of the most cutting edge technology and forensic testing in existence - with Channel 4 capturing every moment. In specialist labs in Leicester and across the country, the bones have been subjected to CT scans, they have been carbon-dated, DNA has been extracted to be compared to that of one his living descendants, the source of the spinal curvature has been investigated - and the entire body has been subjected to rigorous testing to reveal blow-by-blow how this individual died and how he was buried.

Perhaps most fascinating of all, using technology developed to identify human remains in crime investigations, scientists have been busily re-creating the face these bones belong to - this image will be revealed exclusively in the programme the night it airs. And of course, Richard III: The King in the Car Park will reveal the results of what could be one of the most astonishing archaeological discoveries in recent history - whether England's missing king has indeed been recovered.

This will air on Feb 4.

Progress in the Y-chromosome phylogeny

There is much of interest in the abstracts of the DNA in Forensics 2012 conference which will start very shortly, including news on the Tyrolean Iceman (he belonged to G-L91; and G2a "featured unexpectedly high densities within or near the Ötztal Alps."), speculations about a trans-Pacific spread of a lineage found in South Americans, and many other topics besides.

But, for me, the most interesting abstracts relate new developments in the Y-chromosome phylogeny world. The titles of the 3 abstracts are:

Y-chromosomal insights from large-scale resequencing

A calibrated human Y-chromosomal phylogeny based on resequencing

Insight into human Y chromosome variation from low-coverage whole-genome resequencing

and, they all seem to be from authors working at The Wellcome Trust Sanger Institute.

Researchers used 1000Genomes low coverage data (2x) and high coverage Complete Genomics data to untangle the Y chromosome phylogeny. As expected, the 1000Genomes data weer of poorer quality, and had a large number (~14-17%) of false negatives, i.e., SNPs that were actually present in the samples were not discovered. 

I list the main findings from the three abstracts:

The TMRCA of the entire tree was ~115 KYA (thousand years ago), and of the lineagesoutside Africa ~60 KYA, both as expected. Additional insights included a rapid expansion of hg F~40 KYA, and of R1b in Europe ~5-10 KYA. The archaeological counterpart of the former isunclear, but the latter is likely to represent a Neolithic expansion of this lineage

The GENETREE TMRCA for the complete set of chromosomes examined was 105-125KYA; times for the out-of-Africa movement were 62-79 KYA, a Paleolithic expansion 37-48KYA, and the expansion of R1b in Europe 7-10 KYA; rho times were broadly similar.

It confirmed Hg E (Bantu), O (China) and R1b (Europe) expansions associated with the Neolithic transitions in different parts of the world, and revealed that the expansion in Europe was the most extreme. One novel finding was a striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement, suggesting a previously unknown event of importance to male demography at this time.

I would say that these results are consistent with my "two deserts" theory and the climatic history of Africa and the Near East. Of course, I don't think there was a 60ky Out-of-Africa event, for a number of different reasons that I've written about to death. With respect to Y chromosome phylogeny, it is important to highlight one more time where I'm coming from:

The major African Y-haplogroup E belongs to the DE subclade of the CT clade:

I have color-coded the Eurasian lineages as "green", and the African ones as "red". Now, those who think that the age of CT corresponds to Out-of-Africa believe that this event was accompanied by a massive bottleneck which is responsible for the reduced genetic diversity of Eurasians compared to Africans.

But, the question is obvious: if there was such a massive bottleneck in Eurasian ancestors, then how come it is the Eurasians (the bottlenecked population) that ended up with most of the CT descendants?

There really is no archaeology to support a 62-79ky Out-of-Africa, the only archaeology (and anthropology) in support of Out-of-Africa relates to the pre-100ky period, with things like the Nubian complex, the Mt. Carmel hominins, Jebel Faya, and others links between Africa and the Near East.

There are no genetics to support it either: track every paper that has argued for ~60ky Out-of-Africa, and you will invariably find a 2.5x10-8/bp/generation or similar mutation rate and/or a recent human-chimp calibration hiding somewhere in the details. While the mutation wars rage, it is not certain how they will be resolved, but I would put money on the true mutation rate ending up much lower than the one dominating the literature, and, consequently, Out-of-Africa being much earlier.

Getting back to the topic, the "striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement" corresponds to the UP Revolution in west Eurasia. So, to recapitulate my thinking in bullet form:

1. Pre-100ky Out-of-North Africa (Mt. Carmel, Nubian, Jebel Faya?)
2. c. 70ky climate crisis in North Africa-Arabia. Reduction of Y-chromosome diversity: CT founder.
3. 70-50ky. Modern human biocultural evolution accelerates as they (i) face climate crisis, (ii) face new environments as they move out of North Africa-Arabia, (iii) face archaic humans in Eurasia and Africa.   Haplogroup DE is group of "southern"  Out-of-Arabians heading east (D) or west (E); Haplogroup CF is group of "northern" Out-of-Arabians, some of which head east (C) or stay around (F).
4. 50-40ky. Culmination of the process leads to UP/LSA Revolution: 

• In East: some F descendants come to dominate over the early D and C settlers
• In West Eurasia: other F descendants break through the Neandertal bottlecap and invade Europe with UP technologies
• In Africa: E descendants (descended from DE back-migrants) kick-start the Lower Stone Age.

.

Y-chromosome admixture in self-identified Australian Aboriginals

Forensic Sci Int Genet. 2012 Jan 30. [Epub ahead of print]

An investigation of admixture in an Australian Aboriginal Y-chromosome STR database.

Taylor D, Nagle N, Ballantyne KN, van Oorschot RA, Wilcox S, Henry J, Turakulov R, Mitchell RJ.

Abstract

Y-chromosome specific STR profiling is increasingly used in forensic casework. However, the strong geographic clustering of Y haplogroups can lead to large differences in Y-STR haplotype frequencies between different ethnicities, which may have an impact on database composition in admixed populations. Aboriginal people have inhabited Australia for over 40,000 years and until ∼300 years ago they lived in almost complete isolation. Since the late 18th century Australia has experienced massive immigration, mainly from Europe, although in recent times from more widespread origins. This colonisation resulted in highly asymmetrical admixture between the immigrants and the indigenes. A State jurisdiction within Australia has created an Aboriginal Y-STR database in which assignment of ethnicity was by self-declaration. This criterion means that some males who identify culturally as members of a particular ethnic group may have a Y haplogroup characteristic of another ethnic group, as a result of admixture in their paternal line. As this may be frequent in Australia, an examination of the extent of genetic admixture within the database was performed. A Y haplogroup predictor program was first used to identify Y haplotypes that could be assigned to a European haplogroup. Of the 757 males (589 unique haplotypes), 445 (58.8%) were identified as European (354 haplotypes). The 312 non-assigned males (235 haplotypes) were then typed, in a hierarchical fashion, with a Y-SNP panel that detected the major Y haplogroups, C-S, as well as the Aboriginal subgroup of C, C4. Among these 96 males were found to have non-Aboriginal haplogroups. In total, ∼70% of Y chromosomes in the Aboriginal database could be classed as non-indigenous, with only 169 (129 unique haplotypes) or 22% of the total being associated with haplogroups denoting Aboriginal ancestry, C4 and K* or more correctly K(xL,M,N,O,P,Q,R,S). The relative frequencies of these indigenous haplogroups in South Australia (S.A.) were significantly different to those seen in samples from the Northern Territory and Western Australia. In S.A., K* (∼60%) has a much higher frequency than C4 (∼40%), and the subgroup of C4, C4(DYS390.1del), comprised only 17%. Clearly admixture in the paternal line is at high levels among males who identify themselves as Australian Aboriginals and this knowledge may have implications for the compilation and use of Y-STR databases in frequency estimates.

Link

Forensic analysis of King Tut and his relatives

DNA Tribes has released an analysis, based on 8 forensic autosomal STR markers, of the "Amarna Pharaohs". The analysis is based on data from Ancestry and Pathology in King Tutankhamun's Family.

The results of the DNA Tribes analysis can be seen below:

They seem to indicate that there is something definitely "African" about this collection of mummies. I have previously used PopAffiliator and STRUCTURE with CODIS markers. The results of that analysis suggest that even this small number of markers is sufficient to place a sample in a continental group with high accuracy, but insufficient to estimate levels of admixture. There is a new version of PopAffiliator, which, unfortunately, does not allow for incomplete data entry, and hence cannot be used to verify the results of the DNA Tribes analysis.

The DNA Tribes results are interesting, but may hinge upon a few marker values that are more prevalent in Africa than in Eurasia. Also, it is not clear which population(s) make up the "North African" group. It would be interesting to extract full genome sequences from Egyptian mummies in order to properly place them in the global genetic landscape.

Pictorial evidence in Egyptian art, as well as the statements of classical Greco-Roman authors strongly suggest that the ancient Egyptians occupied an intermediate position in the phenotypic continuum between Near Eastern and "Ethiopian" people. It is also clear that there was variation within ancient Egypt itself: geographic, temporal, and even perhaps social aspects of this variation may have existed. But these qualitative observations are no substitute for the harder type of evidence that can be provided by authentic ancient DNA.

Hopefully, the debate on the genetic identity of the ancient Egyptians can proceed on the basis of new data, although I am not holding my breath that this will happen anytime soon, both because of the fluid state of politics in Egypt itself, the existence of various fringe theories outside of Egypt, and, the rather controversial state of mummy DNA analysis itself.

Reconstruction of 7,500 years old forager from Norway

Source (in Norwegian)

FOTO: ARKEOLOGISK MUSEUM/UNIVERSITETET I STAVANGER

Rapidly mutating Y-STR panel

This should also be of interest to genealogists, as the ability to tell apart very closely related individuals is essential to proving a genealogical link, rather than a more general link of an individual to a broader patrilineal kinship group.

Forensic Sci Int Genet. 2011 May 23. [Epub ahead of print]

A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages.

Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, de Knijff P, Kayser M.

Abstract

The panels of 9-17 Y-chromosomal short tandem repeats (Y-STRs) currently used in forensic genetics have adequate resolution of different paternal lineages in many human populations, but have lower abilities to separate paternal lineages in populations expressing low Y-chromosome diversity. Moreover, current Y-STR sets usually fail to differentiate between related males who belong to the same paternal lineage and, as a consequence, conclusions cannot be drawn on the individual level as is desirable for forensic interpretations. Recently, we identified a new panel of rapidly mutating (RM) Y-STRs, composed of 13 markers with mutation rates above 1×10(-2), whereas most Y-STRs, including all currently used in forensics, have mutation rates in the order of 1×10(-3) or lower. In the present study, we demonstrate in 604 unrelated males sampled from 51 worldwide populations (HGDP-CEPH) that the RM Y-STRs provide substantially higher haplotype diversity and haplotype discrimination capacity (with only 3 haplotypes shared between 8 of the 604 worldwide males), than obtained with the largest set of 17 currently used Y-STRs (Yfiler) in the same samples (33 haplotypes shared between 85 males). Hence, RM Y-STRs yield high-resolution paternal lineage differentiation and provide a considerable improvement compared to Yfiler. We also find in this worldwide dataset substantially less genetic population substructure within and between geographic regions with RM Y-STRs than with Yfiler Y-STRs. Furthermore, with the present study we provide enhanced data evidence that the RM Y-STR panel is extremely successful in differentiating between closely and distantly related males. Among 305 male relatives, paternally connected by 1-20 meiotic transfers in 127 independent pedigrees, we show that 66% were separated by mutation events with the RM Y-STR panel whereas only 15% were with Yfiler; hence, RM Y-STRs provide a statistically significant 4.4-fold increase of average male relative differentiation relative to Yfiler. The RM Y-STR panel is powerful enough to separate closely related males; nearly 50% of the father and sons, and 60% of brothers could be distinguished with RM Y-STRs, whereas only 7.7% and 8%, respectively, with Yfiler. Thus, by introducing RM Y-STRs to the forensic genetic community we provide important solutions to several of the current limitations of Y chromosome analysis in forensic genetics.

Link

The many faces of Moora

Here is a 2,600-year old bog woman from Lower Saxony, Germany as reconstructed by forensic scientists (Illustration courtesy Ursula Wittwer-Backofen, University of Freiburg).

And, here is a German language article on the same female which shows many different reconstructions.

By Caroline Wilkinson:

or, by Sabine Ohrlogge:

Embalmed head of Henry IV found

BMJ 2010; 341:c6805 doi: 10.1136/bmj.c6805

Multidisciplinary medical identification of a French king’s head (Henri IV)

Philippe Charlier et al.

From the paper:

Since the desecration of the French kings’ graves in the basilica of Saint-Denis by the revolutionaries in 1793, few remains of these mummified bodies have been preserved and identified. After a multidisciplinary analysis, we confirmed that an embalmed head reputed to be that of the French king Henri IV and conserved in successive private collections did indeed belong to that monarch.

and:

Now positively identified according to the most rigorous arguments of any forensic anthropology examination, the French king’s head will be reinterred in the royal basilica of Saint-Denis after a solemn funeral ceremony. Similar methods could be used to identify all the other kings’ and queens’ skeletons lying in the mass grave of the basilica, so that they can be returned to their original tombs.

Unfortunately, no "uncontaminated" mtDNA could be extracted. It would be interesting to compare his Y-chromosome to that of his descendant Louis XVI, but that doesn't seem to be possible.

Wikipedia article on Henry IV

(no abstract)

Link

Reconstruction of 2,500 year old Carthaginian

Racial Reality points me to this reconstruction. From the related story:

An anthropological study of the skeleton showed that the man died between the age of 19 and 24, had a pretty robust physique and was 1.7 metres (five feet six inches) tall, according to a description by Jean Paul Morel, director of the French archaeological team at Carthage Byrsa.

...

"We can clearly see that this exceptional witness to Carthage in the Punic era is a Mediterranean man, he has all the characteristics," noted Sihem Roudesli, a paleo-anthropologist at the Tunisian National Heritage Institute.

Y-STR mega-paper (Ballantyne et al. 2010)

This will be quite useful as a reference for Y-STR mutation issues.

The American Journal of Human Genetics, 02 September 2010
doi:10.1016/j.ajhg.2010.08.006

Mutability of Y-Chromosomal Microsatellites: Rates, Characteristics, Molecular Bases, and Forensic Implications

Kaye N. Ballantyne et al.

Abstract

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10−4 (95% credible interval [CI], 1.38 × 10−5 − 2.02 × 10−3) to 7.44 × 10−2 (95% CI, 6.51 × 10−2 − 9.09 × 10−2) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the father's age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Link

"Aunty": 600-year old Maori woman reconstructed

Iwi face to face with "Aunty"

The face of a Maori woman who died on the Wairau bar in Marlborough more than 600 years ago has been revealed using digital technology.

Skulls found on the Wairau Bar in 1939 have been used to help digitally recreate the faces of the people who once lived there.

Local iwi Rangitane have affectionately renamed the woman as "aunty".

Video from above story.

Maori ancestor face mapped

It's not easy to visualise what our ancestors might have looked like, but now digital technology has allowed a group of researchers to reconstruct the face of a Maori woman using her 600 year old skull.

The woman the local iwi Rangitane have come to call "Aunty" lived in New Zealand's Marlborough region. Her skull was recovered several decades ago, but it's taken until now to repatriate the remains and reconstruct her face.

Audio from above story.

Face of 11-year-old victim of the Great Plague of Athens

On the top left you can see a forensic reconstruction of an 11-year old girl (nicknamed "Myrtis") who died during the Great Plague in 5th c. BC Athens. You can probably get a basic understanding of the Greek article in Ta Nea, via Google Translate.

See also:

• Secret of Athens plague unravelled
• DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the Plague of Athens.

45 SNP universal genetic identification

Forensic geneticists currently use the highly polymorphic CODIS microsatellite markers for DNA sample identification. This paper shows that a unique DNA id for a human can be achieved by a panel of 45 SNPs.

Human Genetics doi:10.1007/s00439-009-0771-1

SNPs for a universal individual identification panel

Andrew J. Pakstis et al.

Abstract

An efficient method to uniquely identify every individual would have value in quality control and sample tracking of large collections of cell lines or DNA as is now often the case with whole genome association studies. Such a method would also be useful in forensics. SNPs represent the best markers for such purposes. We have developed a globally applicable resource of 92 SNPs for individual identification (IISNPs) with extremely low probabilities of any two unrelated individuals from anywhere in the world having identical genotypes. The SNPs were identified by screening over 500 likely/candidate SNPs on samples of 44 populations representing the major regions of the world. All 92 IISNPs have an average heterozygosity >0.4 and the F _st values are all less than 0.06 on our 44 populations making these a universally applicable panel irrespective of ethnicity or ancestry. No significant linkage disequilibrium (LD) occurs for all unique pairings of 86 of the 92 IISNPs (median LD = 0.011) in all of the 44 populations. The remaining 6 IISNPs show strong LD in most of the 44 populations for a small subset (7) of the unique pairings in which they occur due to close linkage. 45 of the 86 SNPs are spread across the 22 human autosomes and show very loose or no genetic linkage with each other. These 45 IISNPs constitute an excellent panel for individual identification including paternity testing with associated probabilities of individual genotypes less than 10⁻¹⁵, smaller than achieved with the current panels of forensic markers. This panel also improves on an interim panel of 40 IISNPs previously identified using 40 population samples. The unlinked status of the subset of 45 SNPs we have identified also makes them useful for situations involving close biological relationships. Comparisons with random sets of SNPs illustrate the greater discriminating power, efficiency, and more universal applicability of this IISNP panel to populations around the world. The full set of 86 IISNPs that do not show LD can be used to provide even smaller genotype match probabilities in the range of 10⁻³¹–10⁻³⁵ based on the 44 population samples studied.

Link

Ethnicity inference from DNA in Madrid terrorist attacks

In case there was any lingering doubt about the utility of inferring ancestry from DNA:

PLoS ONE 4(8): e6583. doi:10.1371/journal.pone.0006583

Ancestry Analysis in the 11-M Madrid Bomb Attack Investigation

Christopher Phillips et al.

Abstract

The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.

Link

The face of Oase 2

I had previously posted about an article on the Pestera cu Oase 2 cranium from Romania, a European from 35,000 years ago. Now, John Hawks points me to a new BBC series titled The Incredible Human Journey to begin airing this Sunday. and to a reconstruction of the Oase-2 cranium by forensic scientist Richard Neave. Prof. Hawks seems to approve of the way the reconstruction was done, pointing out that other Upper Paleolithic Europeans (e.g., Mladec) have a more modern European appearance.

(Image Copyright (c) BBC)

Forensic anthropology web comic: The Secret in the Cellar

A really nice pedagogical effort to demonstrate what forensic science (and other disciplines) can tell us about a centuries-old murder mystery. I'm not going to spoil the ending for you, so go ahead and read it for yourselves. From the Smithsonian:

The Secret in the Cellar, is a Webcomic based on an authentic forensic case of a recently discovered 17th Century body. Using graphics, photos, and online activities, the Webcomic unravels a mystery of historica, and scientific importance. Online sleuths can analyze artifacts and examine the skeleton for the tell-tale forensic clues that bring the deceased to life and establish the cause of death.