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This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole genome/core-genome phylogeny?

For instace, I am drawing a core-genome phylogeny of Staphylococcus aureus genomes taken from NCBI as well as from my own sequenced ones. Now, my isolates have grouped with several isolates from NCBI (Bottom four greens with four red ones). I want to know, weather these isolates are actually closely related to NCBI ones or they are just those strains themselves?

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Thank you all in advance!

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  • $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Commented Nov 10, 2023 at 10:41
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    $\begingroup$ Please edit and tell us what you are doing, what kind of data you are working with etc. $\endgroup$
    – terdon
    Commented Nov 10, 2023 at 10:56
  • $\begingroup$ Can you provide a tree that represents your data? If you do that I'll explain how to interpret it. $\endgroup$
    – M__
    Commented Nov 10, 2023 at 18:03
  • $\begingroup$ Thank you very much for the reply! I have tried to add details to the best of my understanding! $\endgroup$
    – prekij
    Commented Nov 15, 2023 at 5:12

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Your isolates are both robustly part of the NCBI lineage of 4, i.e. now making a lineage of 8 taxa and genetically very close to it, but slightly distinct.

The robustness is given by the bootstrap values (100) and the genetic proximity is given by the genetic distances for each branch. What you want to do is look at the epidemiological information for your strains and those in Genbank, there should be some sort of recognised association, e.g. country, possibly locality, anything else?

The association has epidemiological significance, thus it's not random, if that is your question. There will definitely something connecting this lineage of 8.

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    $\begingroup$ Yes, they indeed are from same country. Thank you very much!! $\endgroup$
    – prekij
    Commented Nov 15, 2023 at 11:32

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