Human environmental genome recovered in the absence of skeletal remains Date: July 12, 2021

[Patrick]

Human environmental genome recovered in the absence of skeletal remains

https://www.cell.com/current-biology/fulltext/S0960-9822(21)00818-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982221008186%3Fshowall%3Dtrue

[thoughtful (Valerie (non-scientist))]

I wonder how many in the scientific community are skeptical and think human contamination is likely? This dirt stuff is pretty nuts.

[Patrick]

The researchers doing this work are professionals. Honest skepticism is warranted but as more and more results keep coming in with this method, it will become mainstream science. I see this work as ground breaking research.

[T_aquaticus]

@thoughtful

I wonder how many in the scientific community are skeptical and think human contamination is likely?

Human contamination is always a possibility which is why they look at the length of the DNA they find. DNA fragments over time, so any modern DNA will have long fragment lengths while ancient DNA will have short fragments. If I am understanding the biochemistry correctly, naked DNA is deaminated in the environment over time, so an additional check is to look at the amount of deamination in the recovered DNA. Deamination is the process of removing an NH3 group from cyotisine and replacing it with an O (which is uracil).

Next, we assessed whether modern contamination could explain the detection of mitochondrial polymorphism in the sample (Table 1). Modern sequences are expected to be less fragmented, but we find no difference in the length distribution between deaminated and other reads (method details). Manual inspection of phylogenetically diagnostic positions suggests the presence of minority sources in the human data, including in the deaminated reads (Table S1). However, these variants are present at very low frequencies, in line with the estimated low proportion of minority sources (Tables 1 and S1). All human reads support haplogroup N, suggesting any minority sources would not be from haplogroup M and derivatives. Similar detailed inspection of the wolf data shows that the evidence of substantial polymorphism persists when restricting to deaminated reads (Figure S2B). The bison data are too limited to allow for a similar robust assessment. The diversity signal in the SAT29 sample is thus consistent with DNA deriving from multiple human and wolf individuals, rather than reflecting modern contamination. The contDeam.pl tool from Schmutzi estimates 0% contamination for all three species; in the three files, we have obtained values of 0, which indicates that there is no evidence of contamination based on deamination patterns.21
https://www.cell.com/current-biology/fulltext/S0960-9822(21)00818-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982221008186%3Fshowall%3Dtrue

They also found bison DNA which isn’t a species currently living in that region.

[RonSewell (RonS)]

I found the actual paper to be more clear and better written than the ScienceDaily summary.

@thoughtful

I wonder how many in the scientific community are skeptical and think human contamination is likely?

Certainly a legitimate concern. The authors maintain:

the results of the population genetics analyses are in accordance with those published by other studies on skeletal genomes from the same region and time period. These observations thus suggest that the DNA has not been significantly affected by modern contamination or leaching through archaeological layers.

Time will tell, but the technique is generating interesting results.

You seem to be intrigued by mtDNA. You will have to add this paper to your files.

[thoughtful (Valerie (non-scientist))]

@T_aquaticus yes, that they can also have some confidence to identify animal species seems to give weight to the science being valid, as well as being able to identify the mtDNA haplogroup. That is interesting.