Genetic Study Identifies Three Variants of SARS-CoV-2 Coronavirus | Genetics,

That study is getting savaged by phylogenetics experts and its conclusions should not be trusted. See for example this twitter thread from a prominent phylogenetic methods developer:

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Wow that thread is damning.

Beware of COVID-19 carpet baggers.

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For those who don’t know, Andrew Rambaut is pretty much the guy when it comes to viral phylogenetics.

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In other words, trust the twitter thread more than the PNAS article…

In this case, absolutely.

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It gets worse in their interview:

Totally appalling!

Yeah, it’s really bad. The only possible good thing that I can envision coming out of this is that maybe if enough attention is brought to this debacle, PNAS might be shamed into finally getting rid of their “Contributed” papers altogether?

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I thought they already got rid of that, or at least severely limited it? This is not only PNAS’s fault. The authors themselves bear resposibility.

It’s never gone away, but their site claims that 75% of published papers are now “direct submissions.” Contributed papers, then, are still 1/4 of the journal. Note that authors choose their own reviewers in those cases.

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I don’t know all the details, but I believe that the “Contributed” avenue for publication at PNAS has been scaled down and/or subjected to more scrutiny but not removed. This particular paper was contributed by an NAS member.

Certainly the authors are very much at fault too. But without this paper being contributed it would presumably have been published somewhere with a lower media profile, where it would likely have done less damage. I do blame PNAS for that.

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It used to be more common, but 1/4 of the journal is still via that route. The authors choose reviewers as I mention above, but the reviewers are identified on the article. I haven’t checked to see if that is true of all papers in PNAS; maybe it is. Info on submission routes here.

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Thanks. Even 25% seems way too high. What a ridiculous and corrupt system.

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There were two rather strongly worded letters published in PNAS this week that describe severe methodological and interpretation problems with the study referenced in the OP:

https://doi.org/10.1073/pnas.2007062117

https://doi.org/10.1073/pnas.2007295117

The conclusion from one of the letters is rather damning:

The authors’ misinterpretation of MJNs [Median-joining Networks] fosters misconceptions, inaccuracies, and misrepresentations of fundamental phylogenetic principles. Thus, unfortunately, Forster et al.’s study (1) misleads more than illuminates an understanding of the evolutionary history of SARS-CoV-2 in humans.

Sadly, I suspect that these rebuttals will not garner nearly as much media attention as the original paper did.

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Now, someone needs to instruct us in what a MJN is, and why it is not a phylogenetic tree.

I had to look it up. Apparently Median-joining Networks is a distance-base method (i.e., comparing the overall similarity) use to infer relationships among intraspecific sequences.

The main problems seem to be:

  1. distance methods often produce unreliable phylogenies
  2. the resulting MJN is unrooted, making inferences regarding the order of evolutionary changes difficult.

I don’t normally read or recommend papers in Cladistics, but this paper (also cited in one of the letters above), goes into some nice detail regarding MJN and its shortcomings:

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