Relaxed phylogenetics and dating with confidence plos biology Sex chats no verify
For now, let us assume that the data take the form of a bifurcating rooted phylogeny with branch lengths in units of substitutions per site and that all tip dates are known.
We will subsequently relax the assumption that the input tree is rooted and that all tip dates are known. 2015), we index nodes such that is the negative binomial density.
Optimising this likelihood is straightforward using gradient-descent or simplex strategies; the computational cost of a likelihood computation is linear in sample size. We therefore adopt a fast heuristic iterative approach described in algorithm 1.
This algorithm can be repeated for multiple starting conditions of the initial substitution rate to improve the quality of the estimate. The slope of the regression line is an estimate of the mean rate of substitution per unit time where the correlation due to shared ancestry has been neglected.
This has led to the development of computationally-intensive Bayesian approaches, which assume an underlying model for how evolutionary rates vary across the phylogeny (Drummond et al. With the growth in the size of pathogen sequence datasets, it is becoming increasingly difficult to apply Bayesian relaxed-clock methods.
There have been several recent developments in fast, approximate methods for generating time-trees from sequence data (To et al.
I am particularly interested in integrating data from DNA sequences, ecology and fossils to better understand the origins and maintenance of mammalian biodiversity.
We assume that the length of the sequence alignment, denoted , and the position of the root of the phylogeny.
We demonstrate these features using a large ( = 1,610) genome-scale dataset of Ebola virus sequences from the West African Ebola epidemic (Dudas et al.
2015) and compare the performance of the new method with other state-of-the-art methods.
Background Much of my earlier research focused on developing phylogenetic methods to resolve evolutionary relationships, usually among mammals or birds.
Although I continue this work, my research now primarily involves using molecular and morphological phylogeny to infer macroevolutionary patterns and processes.