October 26, 2013

New aDNA capture method (plus some data on ancient individuals from Bulgaria, Denmark, and Peru)

This seems to present an alternative method for capture of ancient DNA libraries than the one used on the Tianyuan individual. It is mostly a methods paper, but also has some initial analysis of some ancient individuals. From the paper:
We were able to tentatively call mtDNA haplogroups for these samples (Table S1). The two Bulgarian Iron Age individuals (P192-1 and T2G5) fell into haplogroups U3b and HV(16311), respectively. Haplogroup U3 is especially common in the countries surrounding the Black Sea, including Bulgaria, and in the Near East, and HV is also found at low frequencies in Europe and peaks in the Near East.41 The three Peruvian mummies fell into haplogroups B2, M (an ancestor of D), and D1, all derived from founder Native American lineages and previously observed in both pre-Columbian and modern populations from Peru. 
P192-1 was an Iron Age Thracian; T2G5 was from an Iron Age Thracian tumulus burial.

For the Peruvian mummies, we also included 10 Native American individuals from Central and South America in the PCA (Figures 3E and 3F). Interestingly, all of the mummies fell between the Native American populations (KAR, MAY, AYM) and East Asian populations (JPT, CHS, CHB), as would be expected for a nonadmixed Native American individual (Figures 3E, 3F, and S2). These mummies belonged to the pre-Columbian Chachapoya culture, who, by some accounts, were unusually fair-skinned,39 suggesting a potential for pre- Columbian European admixture. However, based on our preliminary results, these individuals appear to have been ancestrally Native American. 
The Peruvian mummies were from 1000-1500AD, so it's not very surprising that they don't appear to have European admixture and to be "ancestrally Native American".

Hopefully a more complete analysis of this data and production of more data with this method will follow in the future.

The American Journal of Human Genetics (2013), http://dx.doi.org/10.1016/j.ajhg.2013.10.002

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Meredith L. Carpenter et al.

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain less than 1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

Link (pdf)


Krefter said...

I heard about this bronze age DNA from hair in Denmark. This person is from very early Germanic Nordic bronze age culture. Do they have any type of results in mtDNA and autosomal DNA.

genefan said...

So much the mtDNA U3b is a Gypsy haplogroup, it is in fact old Thracian on the Balkans. It is now around 2% among modern Bulgarians.
Most HV's (3,5%) in the Karachanak's mtDNA Bulgarian study have the 16311 mutation as well.
The new aDNA Capture study has a Figure 2 with Principle Component Analysis based on autosomal SNPs.
The first 2 images - A and B are for the Bulgarian Bronze age Thracian sample, then the Danish Bronze Age and the Peruvian.
Unfortunately the choice of colours does not distinguish very well where exactly the Thracian stands among modern Europeans - maybe closer to the Tuscans.
The Danish is sort of closer to the Finns.

Unknown said...

So the ancient Bulagarian sits in the middle of the modern Germans.

The ancient Dane sits in with the modern Finns (Hmmm).

The ancient Incan? sits darned close to the modern Aymara.

Pretty good continuity for a few thousand years.

ZeGrammarNazi said...

They did not list the Danish sample's mtDNA haplogroup, but when plotted over modern populations, the sample is closest to Finns and Northeast Euros.

http://images.cell.com/images/EdImages/AJHG/ajhg1537.pdf <- See figure three for details.

eurologist said...

I wonder to what extent the "bait" method introduces bias, based on what is pre-selected.

Also, intuitively, it seems to me that Fig. 3 exaggerates the improvement of the new method. I have always liked the projection method (in which a DNA sample does not enter the PCA, instead is just projected onto that orthogonal space), but shouldn't it be possible to create this space with a large sequence, and then project the small a-DNA subset of that onto that space? (Here it seems that the space was created from both small a-DNA sequence subsets). The results then likely would be some probability distribution around a single point, but it seems to me that would be a fairer representation.