node dating

[…] of ancestral nodes were estimated using lsd. branch lengths were also obtained using abs-rel to account for the effect of variation in selective pressure along branches and to re-estimate ancestral node dating. the cutthroat trout virus sequence was used to root the phylogeny., to obtain an overview of the geographic distribution of orthohepevirus a genotypes, we combined data from human […]

[…] built 1,000 bootstrap phylogenetic trees with raxml v8.2.10 () and a gtr + γ model of nucleotide substitution. each tree was rooted with the rtt function of the r package ape () and time scaled with node.dating ()., we simultaneously reconstructed the ancestral sequences and country of origin using beast v1.8.3 () markov chain monte carlo with two parallel runs per data set each with 10 million […]

[…] with half gaps and without gaps and four datasets without bias screened from 129-gene datasets after sequence bias detection., beast v1.8.3 was used to estimate a time-calibrated tree with a node-dating strategy. a beast xml file was generated by beauti v1.8.3 using an uncorrelated log-normal-distribution relaxed-clock model and a yule speciation process as the tree prior. […]

[…] and keeuna do not appear to be members of dasyuromorphia, whilst barinya and mutpuracinus are of uncertain relationships within the order. divergence dates calculated using total evidence tip-and-node dating are younger than both molecular node-dating and total evidence tip-dating, but appear more congruent with the fossil record and are relatively insensitive to calibration strategy. […]

[…] on the total evidence dating (ted), , under the fossilized birth- death (fbd) process model and the sensitivity analyses performed, see supplementary materials. in all analysis, ted as well as node dating, topology and divergence times were inferred simultaneously, hence our inferred divergence times are not dependent on a topology presumed to be known without error. to set a prior […]