Dear Laura. The marginal ancestral states that you obtained under the "ER" model are consistent with a very high backward/forward rate of transitions between the two states. If the best-fitting model implies a very high transitions rate between the two states, then we can say almost nothing about the character condition for internal nodes (hence the "50:50" results you see).
Sometimes the /cause/ of very high estimated transition rates in an M/k/ model can easily be pinpointed -- for example, a pair of sister taxa separated by a short evolutionary distance but with different states. In your case, however, I don't see it. Something I've seen on rare occasions is a /likelihood surface/ for the M/k/ model that has a sharp peak close to zero, but then monotonically increases towards infinite (but with a much lower likelihood). Optimization can miss this first peak and spuriously convergence on large values for the transition rate /q/. One way to identify this problem would be by visualizing the likelihood surface. This is pretty easy with /fitMk/ (as shown on my blog here <http://blog.phytools.org/2021/12/graphing-likelihood-surface-of-fitted-m.html>) -- but if you'd like help, please send me your tree & data (or, even better, a saved .RData workspace) and I will take a look at your problem. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022) On 7/28/2023 9:57 AM, Laura Schaedler wrote: > > > You don't often get email from schaedler.la...@gmail.com. Learn why > this is important <https://aka.ms/LearnAboutSenderIdentification> > > > CAUTION: EXTERNAL SENDER > Hello all, > > I am doing ancestral state estimation analyses with binary traits > (presence or absence of a behavior), and while doing so I ran into > something that is puzzling me. > > For one particular behavior, the results look wrong to me, although R > doesn't report any errors during the analyses. Assuming Equal rates is > the best model (which I previously assessed with /fitDiscrete/), no > matter if I use function /ace/, /make.simmap/, or /ancr/ after > /fitMk/, this behavior shows the same values of scaled likelihoods for > all ancestral states (0.5, figure attached). Setting marginal = T does > not change the results. > > When looking at this information plotted on my tree that just doesn't > feel right. > I would expect likelihood values to be greater in some ancestral nodes > (those immediately before groups of species where all of them have the > behavior) and smaller in others (those before groups without the > behavior), not the same likelihood for all of them. > > Now, if I choose to run analyses with model = ARD, for /ace /and > /ancr/ I get results that look similar to what I would expect > (although /make.simmap/ yields the same result as model = ER; figure > attached). However, as I have previously run /fitDiscrete/ to > determine what is the best model for this behavior, and it was ER, I > don't think it makes sense to just choose ARD instead because 'it > looks better' (AIC weight ER = 0.74 /vs./ AIC weight ARD = 0.25). > > As I have congruent results no matter which functions I use, I wonder > if this could be influenced by the way that this behavior is > distributed across the tree (too dispersed? - but not a 'problem' that > I could fix, it's just how my data is). > Does anyone have any thoughts on whether my results are correct or if > something might be off? > > I appreciate your time and effort. > Best, > Laura > > -- > Laura Maria Schaedler > Doutoranda em Ecologia > Laboratório de Biologia Evolutiva e Comportamento Animal > Instituto Nacional de Pesquisas da Amazônia > http://lattes.cnpq.br/5795430755021849 > <http://lattes.cnpq.br/5795430755021849> > > /PhD student in Ecology > Evolutionary Biology and Animal Behavior Lab > National Institute for Amazon Research > Manaus, AM, Brazil/ > > _______________________________________________ > R-sig-phylo mailing list -R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive athttp://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
