Welcome to the iNaturalist Fish Taxonomy Working Group

iNaturalist currently has 33,814 active, extant species of 'fish' (the 6 classes of fish-like vertebrates). This project is a continuation of the discussion started here: https://www.inaturalist.org/posts/13324-fish-taxonomy.

We follow Fishbase taxonomy with a select set of 'explicit deviations' that map exactly how iNaturalist deviates from Fishbase via 1-to-1 swaps, splits, lumps, or newly described species not known to Fishbase.

These are the current set of explicit deviations from Fishbase (e.g. Fishbase -> iNaturalist) as of 6/6/2018:
Hippocampus alatus, Hippocampus spinosissimus -> Hippocampus spinosissimus
Hippocampus procerus, Hippocampus whitei -> Hippocampus whitei
Hippocampus waleananus, Hippocampus satomiae -> Hippocampus satomiae
Hippocampus biocellatus, Hippocampus trimaculatus -> Hippocampus trimaculatus, Hippocampus planifrons, Hippocampus dahli
Hippocampus fuscus, Hippocampus borboniensis, Hippocampus kuda -> Hippocampus kuda
Pegasus volitans -> Pegasus tetrabelos, Pegasus volitans
Cheilinus fasciatus -> Cheilinus quinquecinctus, Cheilinus fasciatus
Chrysiptera brownriggii -> Chrysiptera leucopoma, Chrysiptera brownriggii
Poecilia sphenops -> Poecilia thermalis, Poecilia sphenops
Synodus variegatus -> Synodus houlti, Synodus variegatus
Antennatus coccineus -> Antennarius nummifer, Antennatus coccineus
Lethrinus lentjan -> Lethrinus punctulatus, Lethrinus lentjan
Pagrus auratus -> Chrysophrys auratus
Acanthurus nigricansm -> Acanthurus nigricans
Zebrasoma veliferum -> Zebrasoma velifer
Synchiropus rameus -> Orbonymus rameus
Crenimugil seheli -> Moolgarda seheli
Helotes sexlineatus -> Pelates sexlineatus
Schistura denisoni -> Nemacheilus denisoni
Planiliza haematocheila -> Liza haematocheila
Dajaus monticola -> Agonostomus monticola
Chelon ramada -> Liza ramada
Chelon aurata -> Liza aurata
Pelates octolineatus -> Helotes octolineatus
-> Dellichthys trnskii (newly described species)
-> Trachelochismus aestuarium (newly described species)
-> Hippocampus casscsio (newly described species)

These are names that iNaturalist thinks are active, extant fish that aren't in Fishbase* and aren't accounted for by our explicit deviations from FishBase above. If you can account for the status of these names (e.g. what names they should be synonomized, how they should be added as explicit deviations, or any other issue), thanks you as we need your help!

Rhinogobius nganfoensis ???
Rhinogobius vinhensis ???
Cryptocentroides argulus ???
Pseudogobius melanosticta ???
Oxyurichthys zeta ???
Hazeus diacanthus ???
Egglestonichthys ulbubunitj ???
Pseudocaranx georgianus ???
Teleocichla preta ???
Percina apina ???
Pomadasys approximans ???
Mullus barbatus ???
Ozichthys albimaculosus ???
Dentex carpenteri ???
Scorpis hectori ???
Scorpis boops ???
Scorpis australis ???
Parascolopsis rufomaculata ???
Nemadactylus carponotatus ???
Nemadactylus concinnus ???
Cheilodactylus antonii ???
Cheilodactylus aspersus ???
Cheilodactylus carmichaelis ???
Microdesmus longispinnis ???
Gobiomorphus gobiodes ???
Ditrema temminckii ???
Boroda malua ???
Eucinostomus californiensis ???
Pseudocalliurichthys goodladi ???
Bathycallionymus bifilum ???
Bathycallionymus kailolae ???
Calliurichthys afilum ???
Calliurichthys australis ???
Calliurichthys ogilbyi ???
Foetorepus apricus ???
Foetorepus grandoculis ???
Pterosynchiropus occidentalis ???
Repomucenus filamentosus ???
Repomucenus keeleyi ???
Repomucenus meridionalis ???
Repomucenus sublaevis ???
Repomucenus belcheri ???
Stichaeus punctatus ???
Heteropriacanthus carolinus ???
Heteropriacanthus fulgens ???
Olisthops brownii ???
Sillago burra ???
Uranoscopus terraereginae ???
Hypopterus macroptera ???
Aurigequula longispinis ???
Psenes hillii ???
Emmelichthys nitidus ???
Matsubaraea fusiformis ???
Puntius euspilurus ???
Dionda flavipinnis ???
Scaphesthes tamusuiensis ???
Anabarilius liui ???
Sarcocheilichthys variegatus ???
Physoschistura chulabhornae ???
Orthrias angorae ???
Beaufortia schaueri ???
Beaufortia orbifolia ???
Beaufortia micrantha ???
Meuschenia scabra ???
Aluterus abassai ???
Acanthostracion bucephalus ???
Chilomycterus spinosus ???
Scorpaena africana ???
Scorpaena aculeata ???
Sebastolobus varispinis ???
Trachyscorpia cristulata ???
Onigocia macrocephala ???
Platycephalus angustus ???
Platycephalus australis ???
Liparis madrensis ???
Liparis makinoana ???
Notoliparis stewarti ???
Paraliparis copei ???
Kanekonia leichhardti ???
Hoplichthys mimaseanus ???
Doryrhamphus excisus ???
Phyllopteryx dewysea ???
Halicampus ensenadae ???
Pseudoxiphophorus jonesii ???
Allodontichtys hubbsi ???
Allodontichtys polylepis ???
Allodontichtys tamazulae ???
Ariosoma hemiaspidus ???
Chaetostoma anomala ???
Olyra taquara ???
Oreoglanis hponkanensis ???
Engyprosopon osculum ???
Monolene maculipina ???
Etropus delsmani ???
Brachirus breviceps ???
Brachirus fitzroiensis ???
Pardachirus rautheri ???
Pseudaesopia callizona ???
Symphurus sitgmosus ???
Paraplagusia bleekeri ???
Clupea pallasii ???
Gephyrocharax atricaudatus ???
Saccoderma falcata ???
Pygopristis denticulatus ???
Leporinus enyae ???
Pterodiscus cookei ???
Galaxias arcanus ???
Galaxias mungadhan ???
Galaxias aequipinnis ???
Galaxias brevissimus ???
Galaxias gunaikurnai ???
Galaxias lanceolatus ???
Galaxias longifundus ???
Galaxias mcdowalli ???
Galaxias oliros ???
Galaxias supremus ???
Galaxias tantangara ???
Galaxias terenasus ???
Mallotus philippinensis ???
Argentina tapetodes ???
Nansenia boreacrassicauda ???
Dolicholagus longirosytis ???
Platybelone argalus ???
Strongylura notata ???
Hyporhamphus roberti ???
Cheilopogon pinnatibarbatus ???
Menidia alchichica ???
Menidia ferdebueni ???
Menidia labarcae ???
Menidia letholepis ???
Menidia promelas ???
Menidia squamata ???
Menidia bartoni ???
Menidia charari ???
Menidia riojai ???
Menidia aculeatum ???
Atherinella pellosemion ???
Atherinosoma elongatum ???
Pseudomugil luminatus ???
Porophryne erythrodactylus ???
Kuiterichthys pietschi ???
Antennarius steffifer ???
Chaunacops spinosus ???

*one caveat is that we're comparing iNat with Fishbase using an API here https://fishbase.ropensci.org/ whichuses database copy from http://www.fishbase.org/ and thus has a few errors. So if any of the mystery taxa are on Fishbase.org thats because of differences between the Fishbase API database and the 'true' Fishbase database. Please let us know if you find these.

Posted by loarie loarie, June 07, 2018 04:44

Comments

Thumb

Maybe there's a case for using regional guides for fishes, when appropriate, to make up for the numerous shortcomings of Fishbase. For Australian taxa the Australian Faunal Directory (AFD) or the more accessible "Fishes of Australia" http://fishesofaustralia.net.au/ which follows the AFD would be appropriate. Here are some recently described taxa from your mystery list that are listed as valid in the AFD and FoA.
Galaxias arcanus ???
http://fishesofaustralia.net.au/home/species/5121
Galaxias mungadhan ???
http://fishesofaustralia.net.au/home/species/5128
Galaxias aequipinnis ???
http://fishesofaustralia.net.au/home/species/5122
Galaxias brevissimus ???
http://fishesofaustralia.net.au/home/species/5123
Galaxias gunaikurnai ???
http://fishesofaustralia.net.au/home/species/5124
Galaxias lanceolatus ???
http://fishesofaustralia.net.au/home/species/5125
Galaxias longifundus ???
http://fishesofaustralia.net.au/home/species/5126
Galaxias mcdowalli ???
http://fishesofaustralia.net.au/home/species/5127
Galaxias oliros ???
http://fishesofaustralia.net.au/home/species/5129
Galaxias supremus ???
http://fishesofaustralia.net.au/home/species/5130
Galaxias tantangara ???
http://fishesofaustralia.net.au/home/species/5131
Galaxias terenasus ???
http://fishesofaustralia.net.au/home/species/5132

Posted by rfoster about 1 year ago (Flag)
Thumb

Additional taxa from FoA

Kuiterichthys pietschi ???
http://fishesofaustralia.net.au/home/species/4902

Atherinosoma elongatum ???
http://fishesofaustralia.net.au/home/species/4632
(long recognised so not sure why this one is a mystery unless it's present as the synonym A. elongata)

Posted by rfoster about 1 year ago (Flag)
Thumb
Posted by rfoster about 1 year ago (Flag)
Thumb

I added Gymnura lessae which seems to be in Fishbase but not in the Fishbase API https://www.inaturalist.org/observations/1900717#comment-1923100

Posted by loarie about 1 year ago (Flag)
Thumb

I have a question about fish taxonomy.
Stomias boa species don´t exist in iNaturalist: https://www.inaturalist.org/observations/9660923
I tried to make a new species (from Curator) but a message advice me that Actinopterygii is locked-down taxa.
You can check the species status in fisbbase:
https://www.fishbase.de/summary/stomias-boa.html
or IUCN red list:
http://www.iucnredlist.org/details/198563/0
Could we create this species for iNaturalist?

Posted by gmucientes about 1 year ago (Flag)
Thumb

Meuschenia scabra = mispelling of M scaber (Atlas of Living Aus has this mistake)

Platycephalus australia = mispelling of P australis

Platycephalus angustus - see http://fishesofaustralia.net.au/home/species/4861 also valid in AFD

Doryrhamphhus excicus - see http://fishesofaustralia.net.au/home/species/1525 BUT not listed in AFD. @humuhumufish maybe you can shed some light?

Posted by sascha_schulz about 1 year ago (Flag)
Thumb

You’re correct, only the genus Doryrhamphus is listed in AFD despite the known species occurrence of D. excisus in WA, NT, and QLD.

https://biodiversity.org.au/afd/taxa/Doryrhamphus

This is incorrect:

Hippocampus waleananus, Hippocampus satomiae -> Hippocampus satomiae

These two species of pygmy seahorses have not been formally synonymized. It was suggested in Lourie et al 2016 that the two species are one and the same, however meristics, morphology, and behavior don’t agree with this assessment.

Posted by humuhumufish 12 months ago (Flag)
Thumb

Hi there,
there are quite a few missing species and genera in Loricariidae, many taxa maintained here resp. at fishbase are since long synonyms, assigned to different genera, etc.
The taxon Ancistrinae for instance is no longer valid, the assignment of genera to Ancistrinae and Hypostominae is not at all in congruence with currently accepted phylogeny (if you compared with current definition of the tribes Ancistrini & Hypostomini). Fishbase seems to be quite incomplete or not up to date, at least for Loricariidae and Callichthyidae.
I would be willing to support here as a curator.
However, I feel that it would be a good move to change to Eschmeyer's catalog as the primary reference. It is to my experience always up to date and according to the latest accepted phylogeny. With fishbase there would be always conflicts when introducing newly described species if those belong to genera which are not up to date at fishbase. The only drawback of Eschmeyer's catalog could be that they don't publish the phylogeny below subfamily rank that they follow afaik (which anyway changes quite often it seems).
What do you think ?

Posted by karsten_s 6 months ago (Flag)
Thumb

I would completely support a shift to Eschmeyer's Catalog. Fishbase is so far behind current thinking, error ridden and only seems to be going backwards. A move to a reliable frequently updated authority would be a very good one.

Posted by rfoster 6 months ago (Flag)
Thumb

there's no way to export data from Eschmeyer which is a big big minus in my book

Posted by loarie 6 months ago (Flag)
Thumb

let me think about it, many years back I did some programming with Tcl scripts and I'm sure it should be easily possible to extract all required data in an iterative manner. Basically input could be a list of genera and output a structured list of all included species with current status in whichever format it's required. I'm very optimistic that this would be quite easy to code for an expert, I'm a bit out of exercise, but this would be a nice exercise...
In the same way you could also check the status of a single species, like this:
input: "Brochis multiradiatus" => output: "Current status: Corydoras multiradiatus (Orcés V. 1960), Callichthyidae: Corydoradinae"
Is this what you would expect or what kind of data do you export from fishbase ?

Posted by karsten_s 6 months ago (Flag)
Thumb

I'm just realising that with this approach you could also retrieve the assignment of genera to families and subfamilies.
You only need a complete list of genera to start with or even a list of all families seems to be sufficient if families and subfamilies are always maintained in the data sets of the species.

Posted by karsten_s 6 months ago (Flag)
Thumb

the funny thing is that Eschmeyer is run out of the California Academy of Sciences where iNat is also based. But the only way to get an export of it is to ask Jon Fong to query the database directly.

Posted by loarie 6 months ago (Flag)
Thumb

Yes, that is ironic and it's odd that they still have the CoF locked up like that. Nonetheless the benefits of using CoF would be great. Couldn't it be done with the occasional big download of everything and a reliance on curators to keep everything tidy in the meantime? I'm way out of my depth with the technical aspects of this but as a fish taxonomist I find the reliance on Fishbase as an authority very frustrating. Ultimately it leads to a lot more curation with very large numbers of deviations from Fishbase required.

Posted by rfoster 6 months ago (Flag)
Thumb

I tried some semiautomatic procedure with Tcl (free SW & runs on every platform) and tested it on subfamily Hypoptopomatinae with 258 records in Eschmeyer's catalog.
Result: 257 species correctly processed, which means I have an array with original genus & species name, current genus & species name, family & sub-family as well as status (synonym or valid) and could save this in any format that could be read in and further processed here.
1 species is "Species inquirenda in Loricariidae", for this case I only read original genus and species name and dump out the complete entry.
"Semiautomatic" means I stored the result from interactive website manually as ASCII file which I read in, so there is no direct interface to the website, additionally I specify the family name.
Example output: "orig: Hemipsilichthys azygolechis, act: Pareiorhaphis azygolechis in Loricariidae : Hypoptopomatinae, Status: Valid"
There is certainly some more testing etc. needed but this should work both on subfamily level as well as family level.

Posted by karsten_s 6 months ago (Flag)
Thumb

That sounds very promising!! Nice work!

Posted by rfoster 6 months ago (Flag)
Thumb

I know that there are some extension to Tcl that would also allow to further automise it like based on a list of all families iteratively poll Eschmeyer's website for each family and process the output further with that script. You could even retrieve the family list from Eschmeyer website.
I cannot judge exactly hoch much additional effort this means as I never used these extensions but I'm quite sure most of it is just getting familiar with it, the coding itself will be just a matter of a few hours.
Is there somewhere a description which format can be imported here, is CSV or in general ASCII format possible ?
If it helps I could generate an example and send it to you.

Posted by karsten_s 6 months ago (Flag)
Thumb

Any progress on this?

Posted by rfoster 4 months ago (Flag)
Thumb

At that time I wrote the Tcl script and it works. As there was no further feedback I did not continue.
Before continuing I would like to know if this would really be useful.
If you are interested I can send the test files and the script if you send me your mail address.

Posted by karsten_s 4 months ago (Flag)
Thumb

let me know if there's anything in my court

Posted by loarie 4 months ago (Flag)
Thumb

I don't really know who could answer my above questions, like which format could be imported at iNat.
The core functionality (extracting taxonomic data from Eschmeyer's website) works in a semi-automated way and I'm very confident that it could be extended to a nearly fully automated tool with reasonable effort. However, I don't know enough about iNat system.

Posted by karsten_s 4 months ago (Flag)
Thumb

you mean were to switch from Fishbase to Catalog of Fishes as a source for the Fish Taxon Franemwork? We'd need every active fish taxon (including non-species ranks) in this format:
{name: name, url: url, rank: rank, parent_name: parent_name, parent_rank: parent_rank}
and it would need to be relatively straightforward to generate this list from publicly accessible websites/API's
We use https://fishbase.ropensci.org to generate this list from Fishbase

Posted by loarie 4 months ago (Flag)
Thumb

yes, right. I was refering to Eschmeyer.
With url you mean a link to a species or more generally a taxon page like this (https://www.fishbase.se/summary/Parotocinclus-britskii.html), right ?
Afaik Eschmeyer does not have anything like this.
All the other attributes are already available with my script for species and genus level. For higher ranks it should also be possible without much problems. This list should be complete: https://www.calacademy.org/scientists/catalog-of-fishes-classification/

Posted by karsten_s 4 months ago (Flag)
Thumb

not ideal that Eschmeyer (CoF) doesn't have URLs. Also CoF is run out of the California Academy of Sciences and I think there's some question about the longevity/sustainability of the project. Apologies if I'm misunderstanding/confused. But I'm not in favor of doing the work to shift from Fishbase to CoF if the latter isn't likely going to be maintained much longer

Posted by loarie 4 months ago (Flag)
Thumb

Ohhh that doesn't promising. As FishBase uses CoF as its checklist, the shutting down of the latter would really impact FishBase as they seem to lack the resources to do such work themselves.

Posted by sascha_schulz 4 months ago (Flag)
Thumb

From what I understand the longevity of Fishbase is similarly in doubt, due to lack of funding.

Posted by rfoster about 2 months ago (Flag)

Add a Comment

Sign In or Sign Up to add comments

Is this inappropriate, spam, or offensive? Add a Flag