Dear Emmanuel, Thank you very much for the explanation and example! This works just as I expected. When I divide the divergence rate by 2 (i.e., .0221 / 2 = 0.01105) and use it as "mu", like you showed, I get a tree that has node dates pretty close to what I get when using BEAST with a strict molecular clock.
I will also investigate chronoMPL(), but I think the estimate.dates() and compute.brtime() functions are exactly what I was hoping for. Thanks again. I really appreciate your input and also the input from Liam and Klaus. Best wishes, Vincenzo On Thu, Mar 7, 2024 at 5:58 AM Emmanuel Paradis <emmanuel.para...@ird.fr> wrote: > What about this (after reading 'tree' using your code): > > n <- Ntip(tree) > dates <- estimate.dates(tree, rep(0, n), .0221) > plot(compute.brtime(tree, -dates[-(1:n)])) > axisPhylo() > > ? > > E. > > ----- Le 6 Mar 24, à 2:50, Vincenzo Ellis vael...@udel.edu a écrit : > > > Dear Klaus, > > > > Thank you for your response. I was wondering if you could expand on how > to > > do this with phangorn::pml_bb(). Here's a small tree I made in Raxml with > > the cytochrome b gene of a few species of birds: > > library(ape) > > tree <- read.tree(text = > > > "(Nesillas_typica:0.04793543089316195,(((A_schoenobaenus:0.043980600360374364,A_melanopogon:0.06481521246716708):0.022244127250028972,(((I_caligata:0.08810019775981455,I_pallida:0.062476654152826855):0.017350459234948976,(((A_newtoni:0.033344055105229795,A_sechellensis:0.01792648331103279):0.021283417245643144,(A_rufescens:0.05238658747602984,A_gracilirostris:0.044877312044462714):0.013125661916305195):0.022403450749406223,((A_arundinaceus:0.04093765705229456,A_stentoreus:0.01826146619561772):0.015107695382970854,A_griseldis:0.0972067122912957):0.011211088579910683):0.02819743631258305):0.007869067285886489,(H_icterina:0.058362559770475525,H_polyglotta:0.033259000190850735):0.05342630181117944):0.005148698839842897):0.006239321505491391,((A_palustris:0.05185723350471064,(A_scirpaceus:0.014053067606248151,A_baeticatus:0.008365145972302118):0.045911856091680914):0.023773812432215297,(A_dumetorum:0.08560190754497965,A_agricola:0.07765117111045171):0.000001):0.013260470881828468):0.04793543089316195);") > > > > If we assume that the divergence rate for cytochrome b for these species > > is 2.21% per million years, how could we rescale the tree with a strict > > clock? Do we need to start with a DNA alignment and re-estimate the tree > > topology or can this be done just with the ML tree I already estimated > and > > the rate? > > > > Thank you, > > > > Vincenzo > > > > On Mon, Mar 4, 2024 at 7:57 PM Klaus Schliep <klaus.schl...@gmail.com> > > wrote: > > > >> Dear Vincenzo, > >> For ML estimates the edge length are the expected number of > substitutions > >> per site, which depends on the product of rate and time. So you need > either > >> a rate estimate or calibration points to estimate the time. If you > divide > >> the edge length by the rate the edges should be proportional to time. > >> With pml_bb you can estimate ultrametric or tip dated trees with a > strict > >> molecular clock model. > >> Kind regards, > >> Klaus > >> > >> > >> > >> > >> Von meinem iPhone gesendet > >> > >> > Am 04.03.2024 um 21:06 schrieb Vincenzo Ellis <vael...@udel.edu>: > >> > > >> > Dear Liam, > >> > > >> > Thank you for your answer. Yes, I have a hypothesized average clock > rate > >> > and no explicit calibration points. > >> > > >> > If I use ape::chronos() with default values it gives me a depth of 1 > at > >> the > >> > root. So I suppose to rescale the branch lengths I just need to > multiply > >> > all of the branch lengths by a value (i.e., tree$edge.length * > value), is > >> > that right? > >> > > >> > Thanks again, > >> > > >> > Vincenzo > >> > > >> >> On Mon, Mar 4, 2024 at 11:43 AM Liam J. Revell <liam.rev...@umb.edu> > >> wrote: > >> >> > >> >> Dear Vincenzo. > >> >> > >> >> If I understand your problem problem, you do not have any explicit > >> >> calibration points -- but you have a hypothesized average clock rate? > >> >> > >> >> If so, then you can obtain an ultrametric tree from* ape::chronos* > for > >> >> any value of the smoothing parameter (*lambda*) and then simply > re-scale > >> >> it to have the desired total depth (based on your hypothesized clock > >> rate). > >> >> > >> >> To choose a "correct" value of *lambda* one can use cross-validation > as > >> >> described in Sanderson (2002; > >> doi:10.1093/oxfordjournals.molbev.a003974). > >> >> > >> >> Others should feel welcome to weigh in if this is not right. > >> >> > >> >> 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 3/4/2024 11:09 AM, Vincenzo Ellis wrote: > >> >> > >> >> [You don't often get email from vael...@udel.edu. Learn why this is > >> important at https://aka.ms/LearnAboutSenderIdentification ] > >> >> > >> >> CAUTION: EXTERNAL SENDER > >> >> > >> >> Dear Emmanuel, > >> >> > >> >> Thank you very much for your response. I cannot see how to provide > the > >> >> substitution rate to the phangorn::pml_bb() function, but I was > looking > >> at > >> >> the ape::node.dating() function and it appears that I could provide > the > >> >> substitution rate to the "mu" argument and then set the "node.dates" > >> >> argument to NA or zero for all tips (I'm not sure if NA or zero > would be > >> >> preferable to force the tips to all be from a single time point). Do > you > >> >> think that would work? I'm not sure how to make ape::node.dating() > >> accept a > >> >> substitution rate rather than try to estimate one. Maybe an option > >> could be > >> >> added to allow mu to equal a user-specified number rather than the > >> output > >> >> of ape::estimate.mu()? > >> >> > >> >> Another option might be to calculate an estimated age for every node > >> >> connecting sister taxa in the tree by converting the genetic > distances > >> >> between sister pairs to divergence times using the substitution rate > and > >> >> then use those as priors in ape::chronos(). I suppose I could also > apply > >> >> that logic to date all of the nodes by using the mean pairwise > distances > >> >> between taxa on either side of a node and converting that to > divergence > >> >> times (although the R code for such a calculation would likely take > me a > >> >> while to figure out). Would that be another option? > >> >> > >> >> Thanks again, > >> >> > >> >> Vincenzo > >> >> > >> >> On Sat, Mar 2, 2024 at 5:44 AM Emmanuel Paradis < > >> emmanuel.para...@ird.fr> <emmanuel.para...@ird.fr> > >> >> wrote: > >> >> > >> >> > >> >> Hi Vincenzo, > >> >> > >> >> There's no direct way to do this with ape::chronos(). You may have a > >> look > >> >> at the function phangorn::pml_bb() but I'm not sure it can estimate > the > >> >> dates if the rate is provided in a model object given as main > >> argument(?) > >> >> > >> >> That said, I expect that estimating so many dates to be very > challenging > >> >> (unless you have a lot of known dates for calibration). This implies > >> that > >> >> you are certainly right to look for an approach where you don't need > to > >> >> estimate the rates. > >> >> > >> >> Best, > >> >> > >> >> Emmanuel > >> >> > >> >> ----- Le 27 Fév 24, à 22:40, Vincenzo Ellis vael...@udel.edu a > écrit : > >> >> > >> >> > >> >> Dear R-sig-phylo members, > >> >> > >> >> I've made a maximum likelihood tree in Raxml for several thousand > taxa > >> >> using a single gene that has an estimated substitution rate of 0.006 > >> >> substitutions/nucleotide/My. Is there a way to use chronos in ape to > >> >> > >> >> apply > >> >> > >> >> that substitution rate as a fixed clock rate and generate an > ultrametric > >> >> time-scaled version of the tree? > >> >> > >> >> Thank you, > >> >> > >> >> Vincenzo > >> >> > >> >> [[alternative HTML version deleted]] > >> >> > >> >> _______________________________________________ > >> >> R-sig-phylo mailing list - R-sig-phylo@r-project.orghttps:// > >> > nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193183565%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wV2IJEHNPpbc2a7Erg%2F14jVmDcIqLshVohWaKa6vG6U%3D&reserved=0 > >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > >> >> Searchable archive at > >> >> > >> >> > >> > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193196126%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=d4fLpFetiQDBjHKTmdlDijgx%2F360Z2oPddHLdCqrrUQ%3D&reserved=0 > >> <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.orghttps:// > >> > nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193201324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=XV4ICgm3xswIObonT8pYZcEHsQVSImxPcKHqefo8zuk%3D&reserved=0 > >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > >> >> Searchable archive at > >> > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193205831%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=dbdnzYPubwMiyqGLncCCl8P5bPDQ%2Bn3QPUUEAt4sQZQ%3D&reserved=0 > >> <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/
