Thanks Eliot and Brian, It is encouraging to see the amount of resources available and realize different ways to compute and achieve the desired measurement. This way, my learning curve become a little easily to climb. Thanks for sharing. Cheers,
Bruno Em qua, 6 de fev de 2019 às 18:56, Brian O'Meara <omeara.br...@gmail.com> escreveu: > Hi, Bruno. It's also possible that there are other ways of getting at the > biological question you're going after, since others also examine how > phylogenetic relatedness affects overlap (my apologies for the redundancy > if you know about this already, just a teachable moment, as they say). An > early, key review of this is Webb et al., (2002): > https://doi.org/10.1146/annurev.ecolsys.33.010802.150448 and a more > recent review is Cavender-Bares et al. (2009): > https://doi.org/10.1111/j.1461-0248.2009.01314.x. The literature blossoms > from there, but those should give a feel for the approaches. > > Here's some packages used for things like overlap in species in areas > [stolen from the task view > <https://cloud.r-project.org/web/views/Phylogenetics.html>]: > > *Community/Microbial Ecology *: picante > <https://cloud.r-project.org/web/packages/picante/index.html>, vegan > <https://cloud.r-project.org/web/packages/vegan/index.html>, SYNCSA > <https://cloud.r-project.org/web/packages/SYNCSA/index.html>, phylotools > <https://cloud.r-project.org/web/packages/phylotools/index.html>, PCPS > <https://cloud.r-project.org/web/packages/PCPS/index.html>, caper > <https://cloud.r-project.org/web/packages/caper/index.html>, DAMOCLES > <https://cloud.r-project.org/web/packages/DAMOCLES/index.html>, and cati > <https://cloud.r-project.org/web/packages/cati/index.html> integrate > several tools for using phylogenetics with community ecology. HMPTrees > <https://cloud.r-project.org/web/packages/HMPTrees/index.html> and > GUniFrac <https://cloud.r-project.org/web/packages/GUniFrac/index.html> > provide > tools for comparing microbial communities. betapart > <https://cloud.r-project.org/web/packages/betapart/index.html> allows > computing pair-wise dissimilarities (distance matrices) and multiple-site > dissimilarities, separating the turnover and nestedness-resultant > components of taxonomic (incidence and abundance based), functional and > phylogenetic beta diversity. adiv > <https://cloud.r-project.org/web/packages/adiv/index.html> can calculate > various indices of biodiversity including species, functional and > phylogenetic diversity, as well as alpha, beta, and gamma diversities. > entropart <https://cloud.r-project.org/web/packages/entropart/index.html> can > measure and partition diversity based on Tsallis entropy as well as > calculate alpha, beta, and gamma diversities. ecospat > <https://cloud.r-project.org/web/packages/ecospat/index.html> can also > examine phylogenetic diversity. metacoder > <https://cloud.r-project.org/web/packages/metacoder/index.html> is an R > package for handling large taxonomic data sets, like those generated from > modern high-throughput sequencing, like metabarcoding. > > > Best, > Brian > > _______________________________________________________________________ > Brian O'Meara, http://www.brianomeara.info, especially Calendar > <http://brianomeara.info/calendars/omeara/>, CV > <http://brianomeara.info/cv/>, and Feedback > <http://brianomeara.info/teaching/feedback/> > > Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville > Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville > > > > On Wed, Feb 6, 2019 at 3:07 PM Eliot Miller <eliot.is...@gmail.com> wrote: > >> The amount of time two taxa have been evolving independently from one >> another is, barring some complex introgression, independent of other >> species in the tree. Pruning the tree from however many species to 700 >> won't affect the distances between those 700. After pruning, use >> cophenetic() to nearly instantly calculate the relevant distances between >> taxa. All the values you need are in the matrix. Access the evolutionary >> distance between any two taxa by pulling the relevant element of the >> resulting cophenetic matrix, e.g. copheneticMatrix["sp1", "sp2"]. If you >> are interested in the time since two taxa shared a common ancestor, >> assuming the tree is ultrametric and in units of time, that value is the >> distance between those two taxa divided by 2. >> >> Cheers, >> Eliot >> >> On Mon, Feb 4, 2019 at 5:30 PM Bruno Garcia Luize <luize...@gmail.com> >> wrote: >> >> > Thank you Liam, >> > >> > For sure it is a lot of computational time. I'm only interested in a >> subset >> > of species, lets say close to 700 species in a regional species pool. I >> did >> > the computations using fastDist and it take almost 7 hs to complete in a >> > windows based 16 Gb RAM. The function was realy useful for my propose. >> > Another doubt that came is if I prune the bigger tree with my species >> list >> > and apply the ape::cophenetic the distances will remain the same or the >> > prunning will change the tree edges lengths and consequently the >> patristic >> > distances. But, by the way I see that fastDist did the work I want. >> > >> > Best regards, >> > >> > Bruno Garcia Luize >> > >> > PhD candidate Ecology and Biodiversity – São Paulo State University >> (Unesp) >> > >> > >> > >> > Em seg, 4 de fev de 2019 às 16:53, Liam Revell <liam.rev...@umb.edu> >> > escreveu: >> > >> > > Dear Bruno. >> > > >> > > > To estimate species divergence time between pair of species, I'm >> using >> > > > the phylogeny in Smith & Brown 2018 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. >> > > >> > > To get this straight, do you want to compute pairwise distances from a >> > > tree containing over 353 thousand taxa? One problem that immediately >> > > arises is the memory that would be required to store such a matrix. If >> > > we assume that each element of the matrix occupies 8 bytes of memory, >> > > and that we are economic & record only the upper or lower diagonals of >> > > the matrix, we would still need about 500 GB to store the matrix. >> > > >> > > Maybe it would be sufficient to write each distance to file, so you >> > > don't have to worry as much about memory (just enough disk space to >> > > store the file). In that case, you could use fastDist to compute each >> > > distance, but this would take a while as there are 62,369,645,520 >> > > non-trivial distances between taxa (that is, excluding the distance of >> > > each taxon to itself and remembering that Dij=Dji). fastDist can >> indeed >> > > calculate distances between tips on such a large tree, but (on my >> > > computer) it takes about 0.5s per tip. At that rate it would take >> about >> > > 10 years to compute all these distances. >> > > >> > > Perhaps you actually only need to compute the distances between a >> subset >> > > of the taxa on your tree, like a few hundred up to a couple of >> thousand. >> > > If that is the case, you should be able to use fastDist; however, for >> > > cases in which all distances (not just one or a few) are required then >> > > cophenetic (which computes all distances between all tips in the tree) >> > > will be much faster than fastDist. fastDist is really only useful if >> one >> > > or a small number of distances are required in which case it can be >> used >> > > to compute these without calculating all patristic distances from the >> > tree. >> > > >> > > > As I see in Revell's blog "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 define as a patristic >> > > > distance: "A patristic distance is the sum of the lengths of the >> > > > branches that link two nodes in a tree"? >> > > >> > > Yes, these distances are the same. The patristic distance is the sum >> of >> > > the edge lengths that connect a pair of taxa, but this value can be >> > > computed by taking the sum of the total distance from the root to each >> > > taxon, and then subtracting two times the distance from the root to >> > > their common ancestor. >> > > >> > > > Furthermore, I'm wondering if the results of the >> phytools::fastDist is >> > > > interchangeable with the adephylo::distTips(method="patristic")? >> > > >> > > I can't comment on that function, but the distances from fastDist are >> > > the same as in ape::cophenetic. >> > > >> > > > Finally, is the patristic distance the right choice for my propose >> or >> > > > should I use another phylogenetic distance? >> > > >> > > I don't know. >> > > >> > > All the best, Liam >> > > >> > > Liam J. Revell >> > > Associate Professor, University of Massachusetts Boston >> > > Profesor Asistente, Universidad Católica de la Ssma Concepción >> > > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org >> > > >> > > On 2/4/2019 12:41 PM, Bruno Garcia Luize wrote: >> > > > 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/ >> > > > >> > > >> > >> > [[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/ >> > >> >> [[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/ >> > [[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/
