Re: [dinosaur] Phylogenetics in general was Re: Placental Mammal Diversification Across the K-Pg Boundary (free pdf)

Gesendet: Montag, 02. Dezember 2019 um 00:37 Uhr
Von: "David Černý" <[email protected]>

> > That said, I wonder how expensive it really is. It costs a lot more in person-hours; but the work itself is much cheaper: no expensive machines, no expensive chemicals, no unbelievably expensive electrophoresis gel every week, no ultrafreezers, not even liquid nitrogen. Just pay someone's costs of living and a few travels, and the work will get done.
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> That's only true for some types of data collection; high-throughput CT scanning, for example, is not exactly cheap, and judging from a couple of recent papers, the next big thing in morphological data collection may well be neutron tomography, where that holds to an even greater extent.

True. Neutron tomography, though, is rather specifically for specimens that can't be X-ray-scanned because they have too little density contrast between bone and rock, for example. And even there you can do it for free if you belong to the right institution; time remains a limiting factor, however.

> On the other hand, calling sequencing supplies "unbelievably expensive" does a disservice to just how insanely cheap sequencing has gotten over the last 20 years.

Fair enough; it was about 15 years ago that I was told a small amount (1 ml?) of electrophoresis gel cost 80 US$, and you needed that much every week in some fields.

> The amount of data stored in GenBank has been growing at a superexponential rate, which is simply not true for morpho phylogenetic datasets, where even a well-studied group like the tetraodontiforms can have over a decade's worth of studies recycling the same ~200-character matrix.

As I said, morphological phylogenetics costs a lot more in person-hours. Plus, the very fact that it's cheap and "boring" in terms of not needing the latest exciting methods works against getting it funded: there is _so much_ work that could and should have been done 20 years ago. Even without braincases and other character complexes that aren't generally accessible without µCT or whatever, a _lot_ could be done, but it's not fancy enough to be funded. Full disclosure: I'm employed right now because I won a grant from an "innovation fund" – projects the committee doesn't find "innovative" aren't funded, no matter how much future research could build on them.

We need a lot of giants on whose shoulders to stand. Right now, few people can grow to become giants, because they need to do other things to pay their rent.

> > Does anybody understand what this "ascertainment bias" is, and if it applies to anything but maximum likelihood?
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> It applies to all model-based phylogenetics (ML, Bayesian inference, and distance methods insofar as they use models to correct the raw, observed distances) and it refers to a situation where constant characters – characters for which every taxon has the same state – are not included in the dataset [...]

Ah, that! Thanks.

> Therefore, starting with Lewis's (2001) paper, most attempts to estimate phylogenies from discrete morphological characters in a model-based framework have relied on corrections implemented using Felsenstein's method. RAxML, MrBayes, BEAST 2, and RevBayes all do it that way, sometimes with the extra option of specifying whether to condition on variable characters or on parsimony-informative characters only.

Yes, MrBayes says it uses such a correction and can therefore deal with matrices that consist only of parsimony-informative characters.