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

["David Marjanovic" <david.marjanovic@gmx.at>]

Gesendet:ÂMontag, 02. Dezember 2019 um 00:37 Uhr
Von:Â"David ÄernÃ" <david.cerny1@gmail.com>

> > 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.
>
> 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 ÂCT 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" â 
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?
>
> 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 â 
> characters for which every taxon has the same state â 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.