High-altitude Andean rodent Phyllotis vaccarum absent from COL / CLB / GBIF

[kcopas]

This Nature news article mentions a genomic study of mummified specimens of Phyllotis vaccarum (O. Thomas, 1912), a tiny Andean rodent that’s still around and allegedly “the highest-altitude mammal ever reported.” P. vaccarum appears to be absent from GBIF and ChecklistBank. ...

Literature references: Unknown (issue submitted by non-specialist)

[mdoering]

NCBI, ENA, iNat and the Mammals Diversity Database apparently has this species: https://www.checklistbank.org/nameusage/search?q=Phyllotis%20vaccarum&rank=species

@yroskov @dhobern has there been a discussion started whether to switch to MDD? See https://github.com/CatalogueOfLife/data/issues/408

[yroskov]

@yroskov @dhobern has there been a discussion started whether to switch to MDD?

As soon as we get Taxonomy Group decision, CoL will switch to a new provider.

[DaveNicolson]

In ITIS' last update of this mammal genus vaccarum was in synonym under P. xanthopygus (listed in synonymy as Phyllotis darwini vaccarum Thomas, 1912, which should be in COL too).

Have the issues with MDD synonymy been resolved yet? E.g., lack of explicit rank and combinations for ALL synonyms (they're just given as an unranked epithet & authorship with parens as if it had been published in combination with the current genus, rather than simply having been synonymized)? Until that issue is resolved, switching from ITIS will get you much quicker current data, but you'll sacrifice a lot on synonymy. That's a trade-off, so the question is whether synonymy based on names published in the literature is "more valuable" than always having more current valid names, I guess, FWIW.

[DaveNicolson]

NominalNames entry for this species lists: vaccarum O. Thomas, 1912|ricardulus O. Thomas, 1919|oreigenus Cabrera, 1926|wolffhuegeli Mann, 1944

Anyone want to provide actually published combinations, or even the original combinations for these?

How about these, under another congener? darwinii (Waterhouse, 1837)|melanonotus (R. A. Philippi & Landbeck, 1858)|boedeckeri (R. A. Philippi, 1900)|campestris (R. A. Philippi, 1900)|dichrous (R. A. Philippi, 1900)|griseoflavus (R. A. Philippi, 1900)|illapelinus (R. A. Philippi, 1900)|megalotis (R. A. Philippi, 1900)|melanotis (R. A. Philippi, 1900)|mollis (R. A. Philippi, 1900)|platytarsus (R. A. Philippi, 1900)|segethi (R. A. Philippi, 1900|fulvescens Osgood, 1943

[dhobern]

@DaveNicolson Your point is fair - cutting straight over to MDD would be lossy, and our classical approach to filling the gaps would be fraught. However, it is perhaps time for us to have a reasoned discussion about how to maintain each COL sector.

The answer to your first question is:

• Phyllotis vaccarum O. Thomas, 1912
• Phyllotis ricardulus O. Thomas, 1919
• Phyllotis oreigenus Cabrera, 1926
• Phyllotis wolffhuegeli Mann, 1944

The original combinations in answer to your second question are:

• Mus darwinii Waterhouse, 1837
• Mus melanonotus R. A. Philippi & Landbeck, 1858
• Mus boedeckeri R. A. Philippi, 1900
• Mus campestris R. A. Philippi, 1900
• Mus dichrous R. A. Philippi, 1900
• Mus griseoflavus R. A. Philippi, 1900
• Mus illapelinus R. A. Philippi, 1900
• Mus megalotis R. A. Philippi, 1900
• Mus melanotis R. A. Philippi, 1900
• Mus mollis R. A. Philippi, 1900
• Mus platytarsus R. A. Philippi, 1900
• Mus segethi R. A. Philippi, 1900
• Phyllotis darwini fulvescens Osgood, 1943

In all cases, I know this because ITIS has already exported these to CLB. The MDD parentheses are compatible with these interpretations.

That means that we could have a pipeline that uses MDD for current concepts and taxonomy and uses preferred nomenclatural sources in CLB to fill out the gaps. The current ITIS version would be at or near the top of the preferred list and we would then work down to others we might wish to flag as tentative.

We can't cut over now, but we could build a pipeline to do so pretty quickly. This is a key value in having CLB in place.

[DaveNicolson]

Re discussions of "how to maintain each COL sector", it sounds like this is quite a bit beyond how to maintain a given sector, unless the sector is to be built by COL staff from multiple sources. Since mammals are at hand in this thread, if COL decides to undertake this maintenance directly or to funnel data to MDD that is a new direction. Improving the data by combining multiple sources is certainly a good possibility, as long as someone somewhere is making it happen. ITIS' workflows don't allow us to do what you seem to be proposing here. ITIS updates are undertaken in taxonomic chunks that are smaller than "Mammalia" (or "Aves" for that matter), and they take the time that they take, given ITIS' limited staff & resources. So I guess cut over when you have your pipeline working. I'm not sure what else to say.

[dhobern]

Thanks, @DaveNicolson - it probably merits a bigger discussion on all our pipelines (and this issue is not the place where I should be dumping my musings). You could imagine a bot-like tool using components in CLB to augment sparse data sources with the objective fact-based assertions from elsewhere and then making it accessible in a form which could be imported directly into ITIS once an editor looked it over. As we get more of the data into a FAIR and intercompatible form, we have more options.