use of a genotyping pipeline poorly suited to ancient DNA which meant that 80% of the genetic variants they “analysed” were likely completely artefactual and did not exist.
Brutal!! I didn’t know this gotcha existed. I hope there aren’t too many papers silently gotch’d by it. Sounds like the type of error that could easily be widespread and unnoticed, if the statistical trace it leaves isn’t always obvious.
I don’t think that recent ancient DNA papers are affected by this issue, at least not to the same extent. Every aDNA researcher I know is extremely aware of the many pitfalls associated with sequencing ancient material and the various chemical and computational methods to mitigate them. Checking for signs of systematic artifacts in your aDNA data is very routine and not especially difficult.
To provide some brief speculation, I think a major explanation for this paper’s errors is that aDNA lab that did the sequencing was quite old, under-staffed, and did not have much recent experience with sequencing human nuclear aDNA, so they had not kept fully abreast of the enormous methodological improvements in this area over the past twenty years.
Brutal!! I didn’t know this gotcha existed. I hope there aren’t too many papers silently gotch’d by it. Sounds like the type of error that could easily be widespread and unnoticed, if the statistical trace it leaves isn’t always obvious.
I don’t think that recent ancient DNA papers are affected by this issue, at least not to the same extent. Every aDNA researcher I know is extremely aware of the many pitfalls associated with sequencing ancient material and the various chemical and computational methods to mitigate them. Checking for signs of systematic artifacts in your aDNA data is very routine and not especially difficult.
To provide some brief speculation, I think a major explanation for this paper’s errors is that aDNA lab that did the sequencing was quite old, under-staffed, and did not have much recent experience with sequencing human nuclear aDNA, so they had not kept fully abreast of the enormous methodological improvements in this area over the past twenty years.