BSP Not converging

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Abid Ali

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Feb 7, 2024, 1:23:20 AMFeb 7
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Dear Beast Community,

I am running in BSP analysis in BEAST version 1.10.4 using CO1 and CYTB concatenated datasets to explore clade-specific demography. Despite extensive efforts, which involved running billions of chains and testing variations in the number of groups (ranging from 4 to 15 consecutively), I have been unable to obtain ESS.

For the clock rate, I utilized a value of 0.0476, derived from a time divergence tree using a constant coalescent population model. Additionally, I applied a strict clock, and the evolutionary model, detailed below, remains consistent with the methodology used for the entire dataset to estimate the MRCA under the constant coalescent population model suggested by Partitionfinder. However, none of the four clades show convergence.


 Please, see the information below,

image.png

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I am looking forward your kind suggestion and help in this regard, thank you!
Abid

HS

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Feb 7, 2024, 2:20:25 AMFeb 7
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Hi,

One thing that may help to improve ESS, might be using Gamma instead of Gamma+Invariants. You may find explanations in this group of why the Gamma+Invariants model might be problematic.

Best,
Hovhannes

Abid Ali

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Feb 11, 2024, 1:42:14 PMFeb 11
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Dear Havhannes,

Thank you so much for your insight. Well, I tried the one you are suggesting and still failed to get convergence on the data. I then ran Partitionfinder on each corresponding lineage dataset to find a model, however, still did not work after having a separate model.

I'm wondering what might help to increase the ESS value.

Thanks


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