Dear Phylo-community, I would like to acknowledge this channel that is extremely helpful for my education regard phylogenetic research in a broad sense. I can describe myself as an ecologist recently introduced to evolution.
As an enthusiast and moved by my curiosity and desire to better understand tropical tree ecology I'm now trying to include phylogenetic information for answer my research questions. Obviously, I'm stucked in a lot of doubts. I'm asking if the divergence time is corelated with the probability of a species pair positive or negative co-occurrence. I expect species pairs relatively more divergent show greater probability of positive co-occurrence, while close related species pairs show greater probability of negative co-occurrence. To estimate species divergence time between pair of species, I'm using the phylogeny in Smith & Brown 2018 (ALLOTB https://github.com/FePhyFoFum/big_seed_plant_trees) which is rooted and contain 353 185 seed plant species along with 85 679 nodes, branch lengths are dated. I'm applying the R function phytools::fastDist for a list of sampled species to achieve a matrix of patristic distance. I have doubt regard the values that the function fastDist is returning. May I consider those values as the divergence time between species? As I see in Revell's blog ( http://blog.phytools.org/2015/10/new-reasonably-fast-method-to-compute.html) "the patristic distance between them is simply the sum of the heights above the root for species i and j minus two times the height above the root of the common ancestor of i & j", is this the same that Fourment and colleagues (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1352388/) define as a patristic distance: "A patristic distance is the sum of the lengths of the branches that link two nodes in a tree"? Furthermore, I'm wondering if the results of the phytools::fastDist is interchangeable with the adephylo::distTips(method="patristic")? Finally, is the patristic distance the right choice for my propose or should I use another phylogenetic distance? I would like to thank in advance you all. With my best regards. Bruno Garcia Luize PhD candidate Ecology and Biodiversity – São Paulo State University (Unesp) [[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/
