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*To*: dinosaur@usc.edu*Subject*: Re: Rép : Post–K-Pg Radiation of Placentals -- open access!!!*From*: David Černý <david.cerny1@gmail.com>*Date*: Wed, 13 Feb 2013 21:18:02 +0100*In-reply-to*: <CA+nnY_Ej7JpdDy67vGU548kO1gTdyA0Uxk5mTu0OUuYsD78nhA@mail.gmail.com>*References*: <F18B5DA5-466D-4C95-AB6B-5AC7C04EB2BA@mac.com> <CF796BB3-1699-4B8C-AF76-3A98550067CD@mac.com> <CAFGhNbP7dqGKx9zeVDMeFiHdEMoi5eWXMK+wwa48JRETxJ6JJQ@mail.gmail.com> <CA+nnY_Ej7JpdDy67vGU548kO1gTdyA0Uxk5mTu0OUuYsD78nhA@mail.gmail.com>*Reply-to*: david.cerny1@gmail.com*Sender*: owner-DINOSAUR@usc.edu

Tim Williams <tijawi@gmail.com> wrote: > Yes; although apparently this topology is sensitive to the analysis > used. Bayesian recovers these two (_Icaronycteris_ and > _Onychonycteris_) as stem-chiropterans (stem-bats). > > A similar thing happens to _Archaeopteryx_ vis-a-vis avialans (birds) > when Bayesian analysis is used, IIRC (from one study, anyway). AFAIK there have been only three Bayesian phylogenetic analyses of non-neornithine coelurosaurs (Snively et al. 2004; Clarke & Middleton 2008; Lee & Worthy 2011), and all of them found _Archaeopteryx_ in its usual position (as a sister group to all remaining avialans) despite some strange results in other parts of the tree. One of these analyses (Lee & Worthy 2011) supported a topology that was, if anything, even more pectinate than usual, with _Wellnhoferia_ more closely related to avebrevicaudans than to _Archaeopteryx_. Something analogous to the situation with _Icaronycteris_ and _Onychonycteris_ (a clade comprising _Archaeopteryx_ and _Jeholornis_) was recovered by Prieto-Márquez et al. (2011), but that was a parsimony analysis. David Marjanović <david.marjanovic@gmx.at> wrote: > That may be due to the known tendency of Bayesian inference, when given a > flat prior on tree shape, to gather basal twigs into larger clades to make > the tree more symmetric. I don't think that's correct -- flat priors are "flat" precisely because they assign the same probability to every possible topology (tree shape), be it symmetric or not. If a prior biases the analysis in favor of more symmetric trees, it's no longer flat. It's true, though, that priors that place equal probability on all _labeled histories_ (= topologies with internal nodes ordered in time), such as the Yule process, give more probability to symmetric trees than to asymmetric ones -- that's because the former are compatible with more labeled histories than the latter (Velasco 2008). But that's a property of a particular prior probability distribution, not of Bayesian inference as such. Unfortunately, O'Leary et al. don't mention their choice of priors in the supplementary information, but with such a large amount of data it may be irrelevant anyway. Refs: Clarke JA, Middleton KM 2008 Mosaicism, modules, and the evolution of birds: results from a Bayesian approach to the study of morphological evolution using discrete character data. Syst Biol 57(2): 185-202 Lee MSY, Worthy TH 2011 Likelihood reinstates _Archaeopteryx_ as a primitive bird. Biol Lett 8(2): 299-303 Prieto-Márquez A, Minjin B, Horner JR 2011 A diminutive deinonychosaur (Dinosauria: Theropoda) from the Early Cretaceous of Öösh (Övörkhangai, Mongolia). Alcheringa 36(1): 117-36 Snively E, Russell AP, Powell GL 2004 Evolutionary morphology of the coelurosaurian arctometatarsus: descriptive, morphometric and phylogenetic approaches. Zool J Linn Soc 142(4): 525-53 Velasco JD 2008 The prior probabilities of phylogenetic trees. Biol Philos 23: 455-73 -- David Černý

**References**:**Rép : Post–K-Pg Radiation of Placentals***From:*Paula Gaubert <paulawilder@mac.com>

**Fwd: Rép : Post–K-Pg Radiation of Placentals***From:*Paula Gaubert <paulawilder@mac.com>

**Re: Rép : Post–K-Pg Radiation of Placentals -- open access!!!***From:*Mike Keesey <keesey@gmail.com>

**Re: Rép : Post–K-Pg Radiation of Placentals -- open access!!!***From:*Tim Williams <tijawi@gmail.com>

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