tag:blogger.com,1999:blog-8499895524521663926.post7015603177917320294..comments2019-01-23T15:37:10.562-05:00Comments on Phylogenetic Tools for Comparative Biology: Fitting a variable-process model of discrete character evolution on the tree using phytoolsLiam Revellhttp://www.blogger.com/profile/04314686830842384151noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-8499895524521663926.post-84354833914131979732018-12-28T20:29:36.869-05:002018-12-28T20:29:36.869-05:00Before have a
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I believe this is what Beaulieu et al. ...Hi John. <br /><br />I believe this is what Beaulieu et al. (<a href="https://donoghuelab.yale.edu/sites/default/files/beaulieu_systbiol_2013_0.pdf" rel="nofollow">2013</a>) published, and they specifically point out that it is a generalization of the covarion model. <br /><br />Please correct me if I'm wrong, of course, but this is not the same, so far as I can tell - in the sense that the regimes we are computing the likelihood over are fixed. That means, for instance, that we might have one time period (from t=0 to t=0.25, say) on the tree that we permit to evolve under one process, than a second under a different process, and so on. That is - the regime 'paintings' are observed or specifically hypothesized a priori. By contrast in the covarion model & its guild we have an unobserved set of regimes & we compute the likelihood by integrating over the probability that each datum comes from each regime.<br /><br />Note that this is not better or more sophisticated than the covarion or 'hidden-rates' model - in fact, it is less! However, it does suit a specific class of hypothesis that is common in phylogenetic comparative biology - for instance that trait evolution differs between clades or among geological eras, and allows us to contrast that hypothesis against one in which it does not differ or varies in a different way.<br /><br />Thanks for pointing out the relationship to the covarion model. This is a very important literature, of course!<br /><br />- LiamLiam Revellhttps://www.blogger.com/profile/04314686830842384151noreply@blogger.comtag:blogger.com,1999:blog-8499895524521663926.post-87092644678930735852017-12-05T21:56:54.078-05:002017-12-05T21:56:54.078-05:00This seems like an overly complicated solution. Wh...This seems like an overly complicated solution. Why not just make a covarion-like model? That is to say, you embed different 2 X 2 rate matrices into a (2 X N) X (2 X N) rate matrix, where N is the number of "regimes." The 2 X 2 rate matrices go along the diagonal. Along the off diagonal 2 X 2 areas, you have a rate of switching from one regime to another. As an aside, this is not new at all. It's an extension of the covariant model. My colleagues and I did something identical, though computationally more intensive, for selection regimes: we embedded three codon models into a 183 X 183 rate matrix, allowing switching among selection regimes. <br /><br />Guindon, S., A. G. Rodrigo, K. A. Dyer, and J. P. Huelsenbeck. 2004. Modeling the site-specific variation of selection patterns along lineages. {\it Proceedings of the National Academy of Sciences, U.S.A.} 101(35):12957--12962.John Huelsenbeckhttps://www.blogger.com/profile/02319608745646179087noreply@blogger.com