Hi Joe, The fossil version of BAMM can handle extinct clades and shifts in rate regime on branches, but I am not sure if the developers have implemented trait-dependent speciation and extinction. You can check out this paper and maybe follow-up with the developers:
https://academic.oup.com/sysbio/article-abstract/68/1/1/4999317?redirectedFrom=fulltext Pyrate may be able to do all you need. There are a lot of papers that use this tool, and I don’t have the details at hand, but check out the Google Scholar page of its developer, Daniele Silvestro: https://scholar.google.com/citations?user=X1jlzMoAAAAJ&hl=en&oi=ao Pyrate is a python program (no R interface), but Daniele is known to be helpful to users if they have questions. If the taxa have stratigraphic ranges (rather than all being restricted to a single interval), you can use non-phylogenetic approaches to look for an association between stratigraphic range and body size. If your hypothesis about extinction is correct, large-bodied taxa should have longer stratigraphic ranges. The simplest approach would be correlation or regression but you can switch to Pyrate (which also run on strat range data, rather than a phylogeny) or Capture-Mark-Recapture if you want to have a more flexible modeling framework. Those latter approaches can handle, for example, temporal or taxonomic variation in preservation and/or extinction. I can send references for these approaches to you separately if you’d like. The non-phylogenetic approaches are less suitable for trait-dependent speciation, however, because you have to make assumptions about transitions between traits (e.g., that small bodied taxa always arise from other small-bodied taxa). Best, Gene Gene Hunt (he/him) Curator Department of Paleobiology w 202.633.1331 [email protected]<mailto:[email protected]> web<https://naturalhistory.si.edu/staff/gene-hunt> SMITHSONIAN INSTITUTION NATIONAL MUSEUM OF NATURAL HISTORY Facebook<https://www.facebook.com/nmnh.fanpage/> | Twitter<https://twitter.com/NMNH> | Instagram<https://www.instagram.com/smithsoniannmnh/> From: R-sig-phylo <[email protected]> on behalf of Joseph Keating via R-sig-phylo <[email protected]> Date: Tuesday, December 3, 2024 at 3:21 AM To: [email protected] <[email protected]> Subject: [R-sig-phylo] Trait-dependence for an extinct clade External Email - Exercise Caution Dear All I�m hoping you can advise me on an appropriate test of trait-dependence for an entirely extinct clade. I want to look at the evolution of body size in ostracoderms - the palaeozoic armoured jawless fish. A number of ostracoderm clades show an apparent increase in body size through the Devonian. This is taken as a classic example of 'Cope's Rule' and has also been linked to competition with / predation by jawed vertebrates. I have some dated trees for a couple of the most diverse ostracoderm clades. Each tree consists of around 100 taxa (this might not sound like a lot, but is actually around 25% of the total known diversity). I've also got a keen MSc student ready to collect body sizes for these groups, potentially using some nice 3D models to get volume estimates. I had initially thought to use �quasse� to model body-size dependent speciation and extinction rates, but after some digging it seems like this only works for ultrametric trees. Is there a nice statical way of testing whether bodysize is correlated with extinction or speciation given a tree comprising 100% fossils? My hypothesis is that extinction is more likely in ostracoderms with small body sizes. Any help you can provide would be hugely appreciated! All the best Joe Keating Dr Joseph Keating Palaeobiology Research Group University of Bristol Bristol Life Sciences Building 24 Tyndall Avenue Bristol BS8 1TQ [[alternative HTML version deleted]] [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
