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Pacific redfin wrongly marked as extinct_inherited #458

Open hyanwong opened 4 years ago

hyanwong commented 4 years ago

Weirdly, Tribolodon brandtii is marked as extinct_inherited in the taxonomy file. I suspect there is another, fossil Tribolodon species (?IRMNG?) with which this has been confused.

================================================ Metadata Do not edit below this line
Author Yan Wong
Upvotes 0
URL tree.opentreeoflife.org/opentree/argus/opentree12.3@ott535876/Tribolodon-brandtii
Target node label Tribolodon brandtii
Synthetic tree id opentree12.3
Synthetic tree node id ott535876
Source tree id(s)
Open Tree Taxonomy id
Supporting reference https://www.fishbase.de/summary/Tribolodon-brandtii.html
hyanwong commented 4 years ago

Also marked as extinct_inherited is the southern water shrew, Neomys anomalus (see https://www.iucnredlist.org/species/29657/115169785 to see it is not), and Archaeoprepona amphimachus, the white-spotted prepona.

I have been finding these when looking for subspecies marked as extinct, which brings up a number of others, as well as some positive hits (e.g. Elephas antiquus falconeri really is extinct)

grep 'subspecies.*extinct' ott3.2/taxonomy.tsv
mtholder commented 3 months ago

https://github.com/OpenTreeOfLife/edOTTs/commit/c98bfa37aac1a28a56901f313a3bb683990ae00c will fix the Tribolodon issue

mtholder commented 3 months ago

other examples to be fixed by https://github.com/OpenTreeOfLife/edOTTs/commit/a330c5e6d639de0806cdcd99899525036c5691f6 still need a general solution.