Duplicate scientific names in tree

[Yan Wong]

Just thought I'd flag this up, but in a rough attempt to find hemihomonyms, I took a quick look at names that appear twice in draftversion4. A rough and ready perl script, which isn't by any means perfect, found quite a few:

perl -e "\$/='_ott'; while(<>) {m/([-\w']+)_ott\$/; print qq{\$1\n};};" OpenTree/draftversion4_no_subsp.tre | sort | uniq -d | less

I suspect this is known, but this rough first pass finds cases where whole genera seem to have been duplicated in different places.

Bifidobacterium_angulatum

Bifidobacterium_animalis

Bifidobacterium_bombi

Bifidobacterium_breve

Bifidobacterium_catenulatum

...

Burkholderia_cepacia

Burkholderia_glumae

Burkholderia_graminis

Burkholderia_multivorans

Burkholderia_oklahomensis

Burkholderia_phymatum

...

Byssus_aeruginosus

Byssus_aluta

Byssus_antiquitatis

Byssus_aquatica

Byssus_argentea

Byssus_atra

Byssus_aurantiaca

Byssus_barbata

Byssus_botryoides

...

Drosophila_badia

Drosophila_fragilis

Drosophila_kikkawai

Drosophila_opaca

Drosophila_palustris

....

and so on. I wonder if some of these should be investigated in a little more detail?

[Jonathan A Rees]

Agreed, these could all use some attention.

I see no automated fix, so each case will require TLC. Our source taxonomies are fighting with each other, and someone needs to decide which one is correct on a case by case basis.

E.g. the Drosophila problem is due to errors in Index Fungorum, which were copied to GBIF. There is a genus Drosophila in fungi, but it does not contain those species, which are flies.

Tracking at https://github.com/OpenTreeOfLife/reference-taxonomy/issues/181

Any volunteers? We have a tool (taxonomy browser) coming out that should help make the job easier.