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IGBB / D_Cottons_USDA

Gossypium D Subgenomes - USDA, MSU, ISU Collaboration
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Phylogenetics of the D-genome #1

Closed iamcorrinne closed 7 years ago

iamcorrinne commented 7 years ago

We need to revamp the phylogeny of the D-genome, minimally for ancestral state reconstructions. Introgression among members of the D-genome and with other cottons complicate this, mostly for G. gossypioides. I cannot use the cpDNA phylogeny because it has chloroplast introgression from G. raimondii.

Nuclear phylogeny of the D-genome: RaxML + Astral: does astral actually give branch lengths (required for ancestral state reconstruction)?

MrBayes+TICR: can I get this pipeline to work....??

iamcorrinne commented 7 years ago

Also, I should do a concatenated nuclear tree. I think that is what we need for ancestral state reconstructions

iamcorrinne commented 7 years ago

concatenated nuclear tree is being a pia; waiting for snp data for snp tree

iamcorrinne commented 7 years ago

running the concatenated nuclear tree using Raxml; should be done by Monday

iamcorrinne commented 7 years ago

Tree is done! Miracle!!!

The old D10-8 is still wonky -- this should be removed from all analyses @jconover11 @maa146 . Otherwise, the tree looks as expected. RAxML_bestTree.all.GTRGAMMA.raxml.pdf

I'm going to drop this tip from the tree before doing any ancestral state reconstructions. Now this can proceed. We need to decide how far down the phylogenetic rabbit hole we want to go... This tree tells us nothing novel, so do we want to do anything more complicted, e.g., concordance? Could be done, but will take a while, especially since the program doesn't seem to want to work well. Concordance, however, will give us an indication of conflict in the tree....

Thoughts?

iamcorrinne commented 7 years ago

Guys, unless anyone has a problem with it or a different/better suggestion, I will just be using the concatenated nuclear tree and SNP tree (unless there is conflict). We can address more about placement laterof the colima aridum (the only weird thing imo) in a later paper.

conJUSTover commented 7 years ago

I am not using D10-8 for CNV or Ks. Using D10-7 instead.