Diario del proyecto iNaturalist Cephalopod Working Group

20 de noviembre de 2018

Resolving discrepancies using iNaturalist's "Framework Relationships"

A new feature has been added to iNaturalist that replaces "complete" taxonomies with Taxonomic Frameworks. (You can read more about them here.) This is a very helpful tool for taxon curators because it allows them to follow flags and immediately locate taxonomic discrepancies between iNaturalist and our authorities. Using this new tool, @loarie was able to identify a number of issues between the cephalopod taxonomy on iNaturalist and WoRMS / MolluscaBase. He resolved most of them himself, but for the outstanding issues remaining, I have addressed them and have outlined the changes below:

Swap Argonauta nodosa (iNat) with Argonauta nodosus (WoRMS) [ref]
Swap Graneledone verrucosa media (iNat) with Graneledone verrucosa (WoRMS) [ref]
Parateuthis tunicata (iNat/WoRMS) is an accepted species on WoRMS and should be left alone; its parent genus Parateuthis (iNat) is nomen dubium on WoRMS [ref]
Swap Idioteuthis magnoteuthis (iNat) with genus Magnoteuthis (WoRMS) [ref]
Swap Eogonatus tinro (iNat) with Gonatopsis okutanii (WoRMS); while the parent genus Eogonatus is active on WoRMS, it has no active children and has consequently been swapped with Gonatopsis on iNaturalist [ref]
Swap Histioteuthis corona inermis (iNat) with Histioteuthis inermis (WoRMS) [ref]
Swap Cirroctopus antarctica (iNat) with Cirroctopus antarcticus (WoRMS) [ref]
Pterygioteuthis giardi giardia (iNat) is not on WoRMS; it is an EOL import; on WoRMS, the parent species Pterygioteuthis giardia has no attributed subspecies on WoRMS; tentatively swapping it into its parent
Swap Rondeletiola capensis (iNat) with Inioteuthis capensis (WoRMS) [ref]
Swap Idioteuthis idioteuthis (iNat) with Idioteuthis (WoRMS) [ref]
Swap Graneledone verrucosa verrucosa (iNat) with Graneledone verrucosa [ref]
• Genus Polypus (WoRMS) has no valid children; it should not be integrated into iNaturalist [ref]
• Section(?) glaukopis-group has no descendants and is unreviewed on WoRMS; it likely represents either Mastigoteuthis glaukopis as a species complex or a subtribe-esch group; it should not be integrated into iNaturalist [ref]

Despite being a complete taxon, there were a few issues with iNaturalist's cephalopod taxonomy. This is in part due to the fact that cephalopod taxonomy is frequently in flux (and thus changes frequently) and that WoRMS adopts new taxonomic schemes uncritically. One of the consequences of the lattermost point is that a singular species is recognized under two separate, valid names on WoRMS, but that is a mater to address in a later journal post. I think further review is necessary to mitigate these developments, but the issues explicitly outlined on the Framework Relationships have been resolved. I think the tool has a lot of potential, and I look forward to using it more in the future.

Publicado el 20 de noviembre de 2018 02:36 por bobby23 bobby23 | 7 comentarios | Deja un comentario

9 de agosto de 2018

ALL of Cephalopoda has been reviewed – it is ready for 'completion'

I originally wanted to complete this in sections throughout the course of the week. I instead went all in and reviewed all remaining non-Octopodiformes cephalopods at once. Every squid, cuttlefish, nautilus, and related mollusc is now in-line with WoRMS. Cephalopoda in its entirety is ready to be considered a complete taxon. I hope @loarie will mark the node as such and incorporate the Cephalopod Working Group into the Taxonomic Working Groups umbrella project. The changes I have committed can be viewed here under the group name "Cephalopod Working Bee". Known discrepancies are as follows:

deviations from WoRMS:
• Several extinct nautiluses on iNat are not in WoRMS, namely Nautilus alumnus, N. costellatus, N. discors, and N. trochlea. The names were imported from uBio, and I found some of the same taxa on other authorities like FossilWorks. Their absence on WoRMS is unusual because they do include other extinct nautiliods, just not these ones specifically. This is a low-priority discrepancy due to their extinct status.
Chiroteuthoides is an accepted genus on WoRMS I deactivated on iNaturalist . Like Polypus, it has no valid children. Its only child is taxon inquirendum.
Tankaia borealis and Leachia rynchophorus are unreviewed taxa on WoRMS. I deactivated them on iNaturalist and I recommend waiting on clarification from WoRMS.

potential issues:
• WoRMS recognizes four extant Nautilus species: N. belauensis, N. macromphalus, N. pompilius, and N. stenomphalus. iNaturalist’s taxonomy currently matches this. However, I believe recent phylogenetic work suggests that only two are valid – N. macromphalus and N. pompilius.
• The iNat cuttlefish taxa Sepia bartletti and S. baxteri were deactivated because they are nomina dubia on WoRMS. Neither taxon had any observations attributed to them.

I will probably post a "master list" of discrepancies that includes the ones for Octopodiformes in the future for convenience. If there are any other discrepancies that come to mind, please convey them in the comment section below.

While Cephalopoda is ready to be made 'complete', I think it would be helpful to communicate with WoRMS to address the noted discrepancies. @anudibranchmom suggested @bernardpicton could be a mediator between us and WoRMS, and while I would appreciate his help, Scott also suggested that we contact Julian Finn and Bruce Hayward. They are the WoRMS Cephalopod editors. However, it was sort of ambiguous as to whether Scott was going to email them or I was...

Publicado el 9 de agosto de 2018 05:18 por bobby23 bobby23 | 2 comentarios | Deja un comentario

6 de agosto de 2018

Octopodiformes is now 'complete'

iNaturalist is working towards having complete taxon schemes and they are an important part of the site's future. (I'm particularly excited to see how many insect orders can be completed in the future.) In order to help get as many taxa complete as possible, I combed through Octopodiformes (the octopuses and vampire squid) to make sure our taxonomic backbone mirrors the World Register of Marine Species (WoRMS). I'm happy to report that we are now up-to-date, with the exception of the following discrepancies:

intentional deviations from WoRMS:
Japetella heathi is an unreviewed taxon on WoRMS. I did not add it to iNaturalist and I recommend waiting on clarification from WoRMS.
Eledone nigra is mysteriously not anywhere on WoRMS. It is not even a junior synonym. This taxon is not too obscure (it has its own Wikipedia page) and is acknowledged by SANBI. I think it should be considered valid here and left alone.
Polypus was not added to iNat. While it is an accepted genus on WoRMS, it has no valid children. Its only child is nomen dubium. All other members of Polypus have been moved elsewhere, primarily to Octopus or Muusoctopus.
Sasakinella was not added to iNat. It is another “accepted” genus on WoRMS with no valid children.

other potential issues:
Opisthoteuthis albatrossi is accepted on WoRMS, but its validity is dubious. It closely resembles Opisthoteuthis californiana and some people consider them synonymous. It has not been seriously reviewed since its discovery in 1920.
Octopus hongkongensis, an accepted taxon on WoRMS, was a junior synonym of Enteroctopus dofleini on iNat. I suspect this comes from EOL’s taxonomic backbone. I added it to iNat because we recognize WoRMS as an authority over EOL, which is not always the most accurate taxonomic resource. Additional authorities like SeaLifeBase treat O. hongkongensis as its own taxon and pictures of the octopuses do not resemble E. dofleini.
Octopus sinensis, an accepted taxon on WoRMS, was a junior synonym of Octopus vulgaris on iNat. Same issue as O. hongkongensis.
Octopus stictochrus, an accepted taxon on WoRMS, was a junior synonym of Octopus penicillifer on iNat. Same issue as O. hongkongensis.
Octopus warringa, an accepted taxon on WoRMS, was a junior synonym of Octopus huttoni on iNat. Same issue as O. hongkongensis.
Scaeurgus patagiatus, an accepted taxon on WoRMS, was a junior synonym of Scaeurgus unicirrhus on iNat. Same issue as O. hongkongensis.

While I love cephalopods, I would not call myself an expert on them, so please let me know if there are any other discrepancies and I will add them to the list above. I have tagged the relevant people below who I believe would be great taxon curators. The next course of action would be to curate and 'complete' Nautiloidea and Decapodiformes, the latter of which is a particularly large taxon and would benefit from multiple hands.

Publicado el 6 de agosto de 2018 21:53 por bobby23 bobby23 | 4 comentarios | Deja un comentario