tipdatingbeast: an r package to assist the implementation of phylogenetic tip‐dating tests using beast

Abstract

Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast, an r package built to assist the implementation of various phylogenetic tip-dating tests using beast. tipdatingbeast currently contains two main functions. The first one allows preparing date-randomization analyses, which assess the temporal signal of a data set. The second function allows performing leave-one-out analyses, which test for the consistency between independent calibration sequences and allow pinpointing those leading to potential bias. We apply those functions to an empirical data set and supply practical guidance for results interpretation.

Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan

“…Sampling times of the sequences were used to calibrate the molecular clock. Date-randomization tests (DRTs) were performed in R 3.3.1 using the Tip Dating Beast package (Rieux & Khatchikian, 2016) to determine the temporal signal in data sets. A data set was considered to have an adequate spread in sampling time if its average rate did not fall within the 95% confidence intervals (CIs) generated from 20 replicates of randomized dates (Ramsden, Holmes, & Charleston, 2009;Duchêne, Duchêne, Holmes, & Ho, 2015).…”

Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood

“…We 246 used a clustered permutation approach in BEAST [49,50] (available from 247 http://beast.bio.ed.ac.uk/), asking whether the correlation was stronger 248 than expected if sampling dates were randomly assigned among clusters 249 of sequences sampled on the same date [51]. Clustered permutation tip 250 date randomization [51,52] was performed in R using the TipDatingBeast 251 package for 5 replicates [53] and used for Bayesian evolutionary reconstruc-252 tion in BEAST assuming the uncorrelated, relaxed molecular clock [54] 253 and Bayesian skyline demographic models [50]. Markov chain Monte Carlo 254 sampling of parameters and tree topologies was performed for 500 million 255 generations or until effective sample sizes (ESS) reached values greater 256 than 200 (after burn-in of 10%).…”

“…Analysis of time-dependent phylogenetic clus-387 tering of sequences revealed significant genetic distinction between the two 388 different time points (S1 Table), indicating viral population turnover and 389 sufficient evolution during the sampling time interval, despite initiation of 390 therapy. Date randomization tests [51][52][53] were also performed to determine 391 if greater evolutionary change was occurring over the 12-month period 392 than would be expected by random sampling of available dates, confirming 393 measurable evolution between sampling time points (S8 Fig). Temporal 394 reconstruction in P01 indicated that the median time of transmission for 395 each of the well-supported transitions occurred prior to administration 396 of cART, although extending well into the first year post-therapy in this 397 individual (S7 Fig). Despite potential sampling variation that can accom-398 pany the spatial sampling strategy described for these individuals, temporal 399 inferences of the well-supported dispersion patterns in P01 overlapped by 400 as much as 100% among the three replicates of sequence sub-sampling (S7 401 Fig), indicating the robustness of the molecular clock analysis and BSSVS 402 approach.…”

“…In 52 addition, 10 HIV-uninfected controls (CL) were enrolled. HIV-infected 53 volunteers were categorized as NL or having NCI, with nine volunteers 54 meeting criteria for Asymptomatic Neurocognitive Impairment (ANI), nine 55 -for Mild Neurocognitive Disorder (MND), and nine having HIV-Associated 56 Dementia (HAD) based on a clinical assessment/ neuropsychological testing. 57 Clinical examination included a neuropsychological testing battery [22], the 58 International HIV Dementia Scale [23], a macroneurological examination, 59 and brain magnetic resonance imaging/spectroscopy (MRI/MRS).…”

“…Participant gp120 sequence 548 data were re-sampled thrice (with replacement) according to the minimum 549 number of sequences in one of the three anatomical compartments, taking 550 into consideration both sampled time points -0 and 12 months post-cART. 551 Clustered permutation randomization [51,52] of the true sampling dates 552 (red), was performed in R using the TipDatingBeast package for 5 replicates 553 (Rep, black) [53] and used for Bayesian evolutionary reconstruction in 554 BEAST [49,50], assuming the uncorrelated, relaxed molecular clock [54] 555 and Bayesian skyline demographic models [50]. Mean evolutionary rate 556 (substitutions/site/month) and 95% high posterior density intervals (error 557 bars) are reported.…”