Hi Jon, There are now comparative methods that can use admixture graphs (or phylogenetic networks), beyond trees. See this tutorial: https://cecileane.github.io/networkPCM-workshop/topic-overview.html or the software documentation section on comparative methods: http://crsl4.github.io/PhyloNetworks.jl/latest/man/trait_tree/
Here are papers that used these methods (among others): Pavón-Vázquez, Brennan & Keogh (2021)https://doi.org/10.1093/sysbio/syaa102 Rurik et al. (2024) https://doi.org/10.1111/tpj.16630 Cécile --- Cécile Ané, Professor (she/elle) Departments of Statistics and of Botany University of Wisconsin - Madison www.stat.wisc.edu/~ane/<http://www.stat.wisc.edu/~ane/> statistical consulting: https://stat.wisc.edu/statistical-consulting/ On Mar 19,2024, at 12:36 pm, Jon <jonsmit...@gmail.com<mailto:jonsmit...@gmail.com>> wrote: Hello all, I've become involved in a small student project looking at spatial variation in a very, very young group. There's discordance between the mtDNA and nDNA trees, and good estimates of admixture based on population genetic studies, between the different lineages (both mt and n lineages). I'm modeling size differences between lineages and attempting to detect clear shifts in both average body size and sexual dimorphism. I don't see any reason *per se* that a covariance structure based on admixture rates (rather than strictly from the tree) wouldn't work, and it would *seem*to allow for a not-strictly-bifurcating population history I suspect is the case here...but I can't find anyone who has done something similar! Am I blind and there's some obvious paper I'm missing where covariance between lineages was determined from something like admixture rates, or is it a silly idea and I should just use the tree as an "average" covariance and call it a day? Thanks! --Jon -- Jonathan S. Mitchell <https://urldefense.com/v3/__http://jonsmitchell.com__;!!Mak6IKo!Lh7vQMPyaY0U_spRXkqStOHgek-hllxtAbir7CFnuuBjmcUg1qJoaff7tl9KG7xGoVyXLA11qXBSLTJhvByI$ > Assistant Professor Coe College [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-sig-phylo__;!!Mak6IKo!Lh7vQMPyaY0U_spRXkqStOHgek-hllxtAbir7CFnuuBjmcUg1qJoaff7tl9KG7xGoVyXLA11qXBSLTqW8BBq$ Searchable archive at https://urldefense.com/v3/__http://www.mail-archive.com/r-sig-phylo@r-project.org/__;!!Mak6IKo!Lh7vQMPyaY0U_spRXkqStOHgek-hllxtAbir7CFnuuBjmcUg1qJoaff7tl9KG7xGoVyXLA11qXBSLcKTMl0m$ [[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/
