Relaxed phylogenies and dating with confidence entiredating com

The lab files you will need can be downloaded here: BEAST lab zip file. You will need to download it if you are using the cloud as it uses a graphical user interface and thus does not work on the cloud.

You may wish to download it for your own operating system even if you have the ubuntu virtualbox as java creates some difficult behaviour in BEAST on Ubuntu.

With recent advances in Bayesian clock dating methodology and the explosive accumulation of genetic sequence data, molecular clock dating has found widespread applications, from tracking virus pandemics and studying the macroevolutionary process of speciation and extinction to estimating a timescale for life on Earth.

We analyzed both simulated and real sequences to evaluate dating methods in phylogenies with mid–late Miocene roots.

To date, the suitability of Bayesian relaxed clock analyses of divergence times in shallow phylogenies has not been rigorously assessed. Most previous investigations of relaxed clock Bayesian dating have used longer more divergent sequences in which the likelihood has a greater influence on the posterior.

Divergence events since the mid–late Miocene generally correspond to lower taxonomic levels, such as the genesis of new intrageneric or intraspecific lineages (Avise 2000). Simulations indicate that global clock analyses perform relatively poorly when the clock is violated but relaxed clock analyses can work well for clock-like trees (Ho et al. Little is known about the sequence information content required for accurate recovery of divergence times.

We investigated Dirichlet and BDS priors because different specifications of these priors may be suited to particular node age distributions, for example, when most cladogenesis events are ancient and clustered near the root.

The probability density function of the Dirichlet is unimodal, symmetrical, and located centrally when the parameter α .

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A large number of data sets (5000) with 10 taxa each were simulated under a rate-drift model for trees with 2 topologies (balanced or unbalanced) and with different sets of divergence times (characterized by long or short external branches).

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