add support for matching names to phylogeny tips provided by Upham et al. 2019 #158
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Data supplements published via: Upham, Nathan S.; Esselstyn, Jacob A.; Jetz, Walter (2019), Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation, Dryad, Dataset, https://doi.org/10.5061/dryad.tb03d03 with 4GB zip file containing: with Data_S7_Mammalia_credibleTreeSets_tipDR.zip containing from which the following files appear to contain nexus trees of sorts - @n8upham - which resource should I use to have nomer map taxonomic names to their equivalent phylogenetic trees? |
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there is an effort among GBIF and phylogeny specialists, et open tree of life, to do this and make them accessible for use in GBIF and beyond:
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@myrmoteras thanks for sharing that GBIF and phylogeny specialists are working on linking specimen to their associated phylogenies. Can you point to the methods they use / or intent do use? Who's working on it? Where do they keep their source code? |
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@n8upham pointed to https://github.com/n8upham/MamPhy_v1/blob/master/_DATA/taxonomy_mamPhy_5911species_toPublish.csv to use for taxonomic alignment with Upham et al. 2019 mammal phylogeny. |
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@n8upham also https://vertlife.org/data/mammals/ is the easiest way to get the consensus tree. with related pubs https://github.com/n8upham/MamPhy_v1/blob/master/_DATA/MamPhy_fullPosterior_BDvr_DNAonly_4098sp_topoFree_NDexp_MCC_v2_target.tre |
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More details on how to align taxonomy file from the Mammalia phylogeny of Upham et al. 2019 (MamPhy v1.0) to the Bat Taxonomic Alignment
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Hi!
I won't be able to dive into this until early next week, but I'm not sure
if we want to match our taxonomy to the tree or just add character states
represented by a pie chart or symbol at the terminal nodes? I don't think
it matters that we have blank spaces at the terminal nodes for those taxa
not represented. It might be better to have the blanks so we can visualize
gaps in our data. If I remember correctly, constructing a partial tree will
take a significant amount of time that could be used in a more constructive
way. I value your input, so please let me know if this is a step you feel
strongly about. I realize we need to separate out Chiroptera from the rest
of the mammal tree, but narrowing down to our exact list of taxa might be
unnecessary. I have been out of the tree generating world since 2014. Do we
know if software outside of PAUP etc. is accurate enough to produce trees
for publication purposes? I assume Jorrit, you are asking in order to
produce trees with a software add-on? This might need a meeting. Also, I'm
very close to being done resolving for taxonomic names, so we will have
accurate valid names associated with the source taxa in the next hour or
so. Also, do we want to wait until I ingest the newest version of MDD names
into the BTA so we aren't working off an old version?
Thank you in advance,
Aja
…On Wed, Aug 30, 2023 at 12:22 PM Nate Upham ***@***.***> wrote:
More details on how to align taxonomy file from the Mammalia phylogeny of
Upham et al. 2019 (MamPhy v1.0) to the Bat Taxonomic Alignment
1.
Go to this file:
https://github.com/n8upham/MamPhy_v1/blob/master/_DATA/taxonomy_mamPhy_5911species_toPublish.csv
2.
Recommend doing the following to add this taxonomy to the BTA:
subset by "ord" = "CHIROPTERA"
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do an automated match to the BTA (I would use "left_join()" in the R
dplyr package, but there are many ways to do this)
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Keep all columns of the MamPhy taxonomy -- it is the "tiplabel" column
you will need to interact with the phylogenies themselves
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for those names that don't match
- In BTA, not MamPhy
- add entry for which BTA species (of which taxonomy) that
species is likely represented by in the MamPhy phylogeny
- can use the "MSW3_sciName_matched" column in MamPhy taxonomy
to assess if which MamPhy name matches to MSW3 (or if the name differs
since MSW3)
- In MamPhy, not BTA
- add row in the BTA (but perhaps this case doesn't exist?)
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As discussed with @ajacsherman et al. , we'd like to add support for matching names against phylogeny tips as published by:
Upham NS, Esselstyn JA, Jetz W. Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol. 2019 Dec 4;17(12):e3000494. doi: 10.1371/journal.pbio.3000494. PMID: 31800571; PMCID: PMC6892540.
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