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Latimeria chalumnae not extinct #537

Closed obgiorgetti closed 3 months ago

obgiorgetti commented 2 years ago

Dear OToL community, I am currrently working on a project regarding the evolution of the vertebrate immune system. I constructed a subtree of many species including Coelacanth, but unfortunately, I am told by Francois Michonneau, this both living species of Coelacant have been marked as "extinct" in the taxonomy, and therefore cannot be included in the tree. I would like you to consider addressing this issue. Thanks for your help and the amazing resource!

Best Regards,

Orlando Giorgetti

Postdoc at Boehm lab, MPI Freiburg

snacktavish commented 2 years ago

Hello Orlando, Thank you! Yes - we have a few issue with tracing of which taxa are and are not extinct. In this case though I think the issue causing the Latimeria to get pruned is actually not their being labelled as extinct - but their being labelled incertae sedis, which means that we do not have good placement information for them. It looks like we do have some phylogenies that have placements for them - I will add these to the synthetic tree so that Latimeria will be in the next update.

jar398 commented 2 years ago

The biggest issue with extinctness flagging - at least a few years ago - was that often IRMNG did not have species-specific extinctness information, so there was confusion if a genus (such as Equus or Homo, both of which I patched) contained both extinct and extant species. More here, which is going to be more reliable than my current memory...