fossil calibration

[Fatemeh Salabi]

Hello every body

We want to implement a Bayesian evolutionary analysis of molecular sequence variation in combination with a molecular clock analysis using the Bayesian Evolutionary Analysis Sampling Trees (BEAST) program package v1.10.4 with 23 species include scorpions, spiders, mite, tick and flies. we try to use the relaxed clock with a Skyline model for tree prior parameter. Branch lengths will be calculated using the Maximum Likelihood (ML) method and LG model. The 2 scorpion fossil records and dates will be used to calibrate the scorpion's tree of life. For this analysis, we will apply the calibrations in two nodes that they are the focus of research. We want to calibrate the one node at 98.17 million years ago (Ma) and one at 313.7 million years ago (Ma). Please help me to do that. I don’t know how to calibrate?

[Pratanu Kayet]

To calibrate the node go set a taxa and Set taxa.. Species those belongs to your desire node take them as include taxa and give it a name.. Then enforce monopoly on it..leave all other taxa as it is. 

After that go to prior option and use uniform prior in TRMCA of your created taxa  ans set it upper value that is your fossils date and lower  value 0..and take mutation rate in millions of year to get a million years result in figtree..

That's all you need to do

Good luck 

On Mon, Mar 1, 2021, 23:03 Fatemeh Salabi <fatemehsa...@gmail.com> wrote:

Hello every body

We want to implement a Bayesian evolutionary analysis of molecular sequence variation in combination with a molecular clock analysis using the Bayesian Evolutionary Analysis Sampling Trees (BEAST) program package v1.10.4 with 23 species include scorpions, spiders, mite, tick and flies. we try to use the relaxed clock with a Skyline model for tree prior parameter. Branch lengths will be calculated using the Maximum Likelihood (ML) method and LG model. The 2 scorpion fossil records and dates will be used to calibrate the scorpion's tree of life. For this analysis, we will apply the calibrations in two nodes that they are the focus of research. We want to calibrate the one node at 98.17 million years ago (Ma) and one at 313.7 million years ago (Ma). Please help me to do that. I don’t know how to calibrate?

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[Pedro Bond Schwartsburd]

Don't forget to check if the fossil belongs to the crown or to the stem of your selected clade. Dependening on what you choose, you may get different results.

Pedro 

Prof. Dr. Pedro Bond Schwartsburd Departamento de Biologia Vegetal Universidade Federal de Viçosa D.S. Pedro Bond Schwartsburd Teacher and researcher at Federal University of Viçosa, Brazil

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[Fatemeh Salabi]

Hello Dear Pratanu Kayet

Thanks a lot for your good guidance, I now understand what I should do, but I'm not sure about the time set, I'm doing the right thing, so I shared an image that you can confirm if possible. I'm going to set the node to 317 million years ago.

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[Pratanu Kayet]

IF you are using clock rate per units of years then this is correct.. But if you are using clock rate per million years then just put 317 in upper value..

Isuggest you read Ho and Phillips 2009 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times; in this paper you will observe the differences between parametric distributions that can be used as priors on nodes.

Maybe, you would also like to read Barba-Montoya et al. 2017 Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating; or Saquet 2013 A practical guide to molecular dating.

Good luck

On Tue, Mar 2, 2021, 13:57 Pratanu Kayet <pratan...@gmail.com> wrote:

Can you tell me the value of clock rate you are using?

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[Pratanu Kayet]

Can you tell me the value of clock rate you are using?

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