Tallying observed Vertebrate species with "complete taxa"

As a community, we've observed 1/3 of all known vertebrate species on iNaturalist! Plus, we're ticking an additional 5 to 10 new species each day. How do we know this? We're introducing new functionality that allows us to mark a taxonomic clade on iNaturalist as "complete" and then keep track of how many species on that list are ticked off with observations over time. Below I'll explain how we're using "complete taxa" tools to tally vertebrate species.

Marking a clade as complete means that all extant species in the clade are included in the iNaturalist taxonomy - no more and no fewer. Since vertebrates are marked as complete, you'll now notice new decorations under the taxonomy tab indicating this on taxon pages that fall within it. There is also a section listing "Taxon Curators" who are now the only curators with permissions to edit members of a complete clade.

Because complete taxa give us a clearer understanding of all the potential species in a clade, they allow us to track some interesting stats about progress the iNaturalist community has made in ticking these off of the list. At the top of a taxon page that falls within a complete taxon, you'll see a new "Total Species Observed" stat which, at the time of this writing, is "22,538 of 68,295" for vertebrates. The denominator is defined by the "complete" iNaturalist taxonomy and the numerator counts the subset of these species that have been observed. It's kind of remarkable that we've collectively observed 1/3 of all vertebrate species. Considering the thousands of rare deep-sea fishes, tropical herps with tiny ranges, and nocturnal bats and rodents that this number includes, this is a pretty amazing accomplishment!.

Under the trends tab, below the "Trending" feed there are two new feeds. The first is "Discoveries." This shows the most recent newly-identified species in the taxon. The second is "Wanted" which shows species in the taxon that have not yet been observed.

I did a quick analysis of the vertebrate discoveries from the last 38 days and I count:

91 reptiles

43 amphibians

56 birds

19 mammals

78 ray-finned fishes

3 other fishes
Here's how those discoveries over the last 38 days stack up over time. It's pretty exciting to see that we're getting about 5-10 new vertebrates added to iNaturalist each day. At that rate it will take us about 4 more years to reach half of all vertebrates. It will be interesting to see if that rate gets damped by increasingly hard-to-get species or boosted by a growing iNaturalist community.



You can click through to see the actual observations responsible for the growth in Discoveries. Mapping them reveals that most of these discoveries are coming from the tropics of the world. For example,
here's a map of the bird, mammal, reptile, and amphibian discoveries from the last 38 days. This should come as no surprise since the tropics harbor the richest biodiversity on the planet and also represent some of the least-explored areas by the iNaturalist global community.

Two caveats: first, the discovery feed pulls from verifiable observations. Some are the result of mis-IDs. But they disappear from the feed as they get corrected. Second, some of the entries in the discoveries feed are triggered by taxonomic changes. For example, if the scientific name of a species changes, then the first identification of the output species will trigger an entry in the feed even though there were already identifications of the input taxon. We're working on a solution to keep these out of the feed, but in the meantime I tried to manually exclude these cases from the numbers above, but there are less than 5 complex cases that remain (e.g. when a species was in the system as two active synonyms representing the same taxa and then swapped together).

Taxonomic Details


Taxonomy is still very much a work in progress. It may come as surprise to some that we don't yet have a global list for plants or even butterflies. This means that the taxonomy for many branches of the tree of life for iNaturalist will inevitably be messy. Some taxa will be missing, while others will be duplicated as "synonyms" (different names that all refer to the same taxon). Fortunately, the branch of life representing we humans and our closest relatives, the vertebrates, is relatively well-known. For each of the 10 classes making up this subphylum, there are relatively well-maintained and continually updating checklists that list all extant species members globally. iNaturalist has adopted several of these lists as external taxonomic references. They are: FishBase for the 6 fish Classes, Amphibian Species of the World for amphibians, the Reptiles Database for reptiles, the Clements Checklist of Birds of the World for birds, and the IUCN RedList itself for mammals.

While new species of vertebrates are being described each day, these external taxonomic references at least strive to be relatively complete and to keep relatively up to date. Keeping iNaturalist in sync with these lists should, in theory, reduce curation work and taxonomic confusion for everybody

However, it's difficult to get the entire iNaturalist community onboard with a single external taxonomic reference. The inevitable errors, lag-time in adopting new species, and subjective taxonomic opinions in any list will frustrate some members of the iNaturalist community. When this happens, we can make an exception against using the external taxonomic reference for the controversial taxon/taxa in question by making an explicit discrepancy. For example, the Reptile Database considers just one species of Mountain Kingsnake in California, Lampropeltis zonata sensu lato (meaning in the broad sense). However, the most widely used regional reptile reference in California considers these snakes to represent 2 species, Lampropeltis multifasciata and Lampropeltis zonata sensu stricto (meaning in the narrow sense). It might therefore make sense for iNaturalist to make an explicit discrepancy to avoid following the Reptile Database's decision to merge Lampropeltis multifasciata & Lampropeltis zonata sensu stricto into Lampropeltis zonata sensu lato.

I've created journal posts to serve as discussions for proposing and making decisions about explicit discrepancies for
reptiles, fishes, mammals, and amphibians. Please contribute to those conversations if you'd like to discuss explicit discrepancies for each of these clades.

Posted by loarie loarie, December 27, 2017 07:42 AM

Comments

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Two thoughts that I think could help:

1. Change the Aves authority from Clements to IOC. I'm guessing this has been discussed before, but worth raising again as I think it will bring a substantial increase in global acceptance and usage; Clements is not liked by many birders in Europe, Australia, etc.

2. Is it permitted to add other peoples' observations, where they are available for use under a creative commons licence? Example: if a species not represented on iNat has reliably identified, dated & geolocated photos on Wiki Commons, can they be added here? There is no bar from the Wiki Commons end on doing so. I don't know offhand if this could add any vertebrates (though it probably can), but I'm aware of quite a few plants that could be added this way.

Posted by nutcracker 7 months ago (Flag)
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Interesting summary, Scott! Adopting as global a taxonomic backbone as possible would fit with iNat‘s scope of being a global platform, hence adopting IOC sounds appropriate.

Posted by jakob 7 months ago (Flag)
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jakob and nutcracker:I made a post here to discuss explicit discrepancies from Clements https://www.inaturalist.org/journal/loarie/13385-explicit-discrepancies-from-clements-for-birds

nutcracker: if you had a license to republish the media and knew the location/date and were willing to steward the data, there aren't any problems with posting observations you didn't personally observe. But is there really much existing data out there that fits all those criteria?

Posted by loarie 7 months ago (Flag)
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This is great Scott! And showcasing the recent vertebrate 'discoveries' (hoping for the rate note to go down too fast yet) is a great way to highlight the importance of iNat as a global platform!

Amael

Posted by amarzee 7 months ago (Flag)
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The other post says that it isn‘t a place to discuss switching from Clements to IOC, but I wonder what iNat‘s rationale for sticking to Clements is.

Posted by jakob 7 months ago (Flag)
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@loarie - yes, there's a lot on Wiki Commons; for example, Pinus pumila (no observations here!), Wiki Commons has 58 photos showing the species in the wild, most of which have usable location data (if not exact geotags, then place names which can be converted to approximate geotags). For adding them here, the important factor is citing the original observer, and doing so in a way that the observation does not appear to be in my name even though I might have added it to iNat. Something in the Upload form saying "Credit this observation to anonther observer: [add name & link here]".

@jakob - I guess inertia / tradition? It is true that conversion over to IOC would require quite a lot of work.

Posted by nutcracker 7 months ago (Flag)
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I never really had the chance to look over this. It looks wonderful, and see the percentage of species observed gives a lot of perspective to what's being seen and uploaded to the site (75% of all birds observed? That's amazing!).

Posted by bobby23 6 months ago (Flag)
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@loarie I would still appreciate a reply why iNat isn't adopting IOC. Wherever possible, we're moving towards global taxonomies, but birds seem to be exempted from that. Is it because of US users? If so, then let's be explicit about it.

Posted by jakob 6 months ago (Flag)
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jakob - in case you missed my reply https://www.inaturalist.org/posts/13377-tallying-observed-vertebrate-species-with-complete-taxa#activity_comment_1254150 Clements is a global taxonomic reference for birds so I'm not sure what you mean there. But happy to discuss more on the bird post I made specifically for this issue.

Posted by loarie 6 months ago (Flag)
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The other post says "This is *not* a place to propose switching to the IOC World Bird List", which is why I commented here. So: proposal for a complete switch to IOC here or on the other post?

Posted by jakob 6 months ago (Flag)
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I'm not sure I understand but I tried to respond on the bird thread

Posted by loarie 6 months ago (Flag)

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