The dangers of publishing partial taxonomic revisions...

iNat relies on the IUCN RedList as the taxonomic authority for mammals. The downside of taxonomic authorities are that they lag a bit from the primary literature - so maybe we're not quite as up-to-the-minute-informed as we could be about where species boundaries are and what our set of species should be as we could be. But the upside is we have a clear sense of the taxonomic concepts we should be following when we identify species (e.g. lets all agree to call fuzzy brown things from this are this name and fuzzy gray things from over here this other name). All being on the same page when it comes to taxonomic concepts is critical to organize conservation efforts, or inventory efforts like iNaturalist. And I'd argue that its more important that we are all on the same page regarding taxonomy even if our concepts don't represent up-to-the-minute bleeding edge taxonomy in the primary literature.

With that, IUCN during the 2004 Global Mammal Assessment used the current taxonomy that considered the 'Desert Woodrat group' as having five species: Neotoma lepida on the mainland, Neotoma bryanti known only from Cedros Island off Baja CA, and 3 other now extinct Baja Island endemics:

Figure 1.

Enter Patton et al.'s excellent revision in 2014. This study determined that the mainland woodrats, Neotoma lepida (sensu lato), actually should be split into 3 groups: a coastal species, an Arizona species, and the remaining species in between. Re: the former Baja island species, Patton et al. determined that they are all part of the coastal species except rats on Isla Ángel de la Guarda which are their own species. Patton re-used the name N. bryanti (senus lato) for this coastal species, and named the Arizona species N. devia, N. insularis for the Isla Ángel de la Guarda and reused Neotoma lepida (sensu stricto) for the remaining rats:

Figure 2.

What bothers me is that, in my opinion, IUCN should have held updating the RedList until they were ready to revise this entire group. Specifically by updating the existing assessments of N. bryanti and N. lepida, removing N. bunkeri, N. anthonyi, & N. martinensis from the list and adding N insularis and N devia. But what IUCN published in 2016 only included the addition of N. devia without addressing these other species (e.g. N. devia now overlaps with the range of N. lepida):

Figure 3.

Now the RedList gives the impression that N. lepida and N. devia co-occur in Arizona. Perhaps to address this, they yanked the map of N. lepida (sensu lato) but this just adds a lot of confusion making it impossible to understand what they mean by the names N. lepida with regard to the other taxa in the group.

If anyone from the RedList is listening, in my opinion its critical not to only partially incorporate taxonomic revisions into the published RedList. The N. lepida group should have been tackled in its entirety or not at all. In the meantime this puts us here at iNat in an awkward situation. Should we:

  1. leave out species coming from our taxonomic authority (specifically N. devia rolling things back to Fig 1.)
  2. or should we imply that they meant to incorporate all the revisions from Patton et al. and move things forward to Fig. 2 ahead of the published RedList?
  3. or should we follow the Published RedList exactly (Fig. 3) even though it leaves us in an ambiguous state that partially follows Patton et al. in an unclear way?

Publicado por loarie loarie, 23 de diciembre de 2016

Comentarios

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Thanks @loarie ! Amazing work and yes, what a mess. Looking forward to see where this takes us.

Publicado por patsimpson2000 hace casi 4 años (Marca)
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I've read several of Patton's papers when I was deep into the gopher taxonomy studies... He's done extensive work on Thomomys and the umpteen batrillion subspecies... I really enjoyed them, but as I tried to digest the practical applications of seperating species/subspecies, I would get more and more confused. Isolated populations form distinct lineages because of the lack of gene flow, so I guess it makes sense that we call them something else. How would that effect conservation of those gene pools? Beats me.

Anyways, I do understand the frustration and confusion on what to consider a taxonomic authority, especially when it comes to 'new' publications. I used to get really worked up about all of this, but I've mellowed out a bunch (maybe I'm just paying less attention to taxonomy papers these days!). Personally, I just think that every taxonomic authority is forever temporary. This is the nature of my understanding of what a species even is -- just a 'human recognizable unit of evolution.'

I don't have any real suggestion on what iNat should do with this -- I'm just ranting a bit too. :) Take my two cents for the 1.5 cents it's worth! :)

Publicado por sambiology hace casi 4 años (Marca)
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My preference is to move towards (2) but in the meantime follow (1). To move towards (2) I made these draft taxon changes to migrate http://www.inaturalist.org/taxon_changes?change_group=Neotoma+lepida+split
But to put us back on solid footing (1) for now, I inactivated N. devia (it has no obs), and am advocating that these be considered N. lepida for now. This will resolve the 'out of range' flags these San Diego obs are triggering for N. bryanti (sensu stricto)

Once the taxon changes are committed, things will get automatically moved from (1) to (2) and all will be right with the world. I'm waiting to commit the change until this ticket is closed though https://github.com/inaturalist/inaturalist/issues/1233

Publicado por loarie hace casi 4 años (Marca)
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Tagging my self into this discussion for obvious reasons, @loarie.

I've argued before that IUCN is not only a little bit but very much lagging behind current mammal taxonomy - what we're currently seeing is a taxonomic revolution, and that's not because every genetically distinct population is now split from broader taxonomic concepts, but because mammal taxonomy was dominated for several decades by lumpers who have synonymized clearly recognizable species into species waste baskets. With the help of genetics and several other tools (e.g. bioacoustics, morphometrics) we can now employ integrative taxonomy to revise these species baskets, and to eventually recognize highly distinct species that have been buried for a long time (not to mention the many unique new mammals that were simply discovered by recent field work). Some taxa have been / will be probably oversplit, but in general I'm convinced that we're moving towards the real mammalian diversity rather than away from it.

Publicado por jakob hace casi 4 años (Marca)
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nice to hear your thoughts on this jakob - I think we have slightly different opinions on the pros/cons of super dynamic taxonomies (I'm a bit more conservative than you I think), but we're definitely on the same page that its critical to have an explicit taxonomy that that we can all reference if we want to use iNat data to surface cool discoveries - otherwise we just surface taxonomic messes rather than interesting observations

Publicado por loarie hace casi 4 años (Marca)
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I'm probably less in favour of super dynamic taxonomies than you think, Scott ;-) However, the increase in mammal species over the last decade or two has been frequently perceived as an artificial inflation by oversplitting well-defined taxa, and that's definitely not the case. The group I know best - African bats - will probably see a 1.5 to 2-fold increase in species, many of which are diagnosable by classic methods.

Publicado por jakob hace casi 4 años (Marca)
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Re evolving mammal taxonomy: you might want to look into www.nsrl.ttu.edu/publications/opapers/ops/OP269.pdf

The 2nd edition of MSW (1993) recognized 925 bat species while the 3rd edition (2005) recognized 1116 species. The paper linked above, based on rates of discoveries, estimated that there are further 71 bat species to be discovered. We're now standing at 1300+ species.... Also worth reading is http://dx.doi.org/10.1007/978-3-319-25220-9_16

Publicado por jakob hace casi 4 años (Marca)
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Update: I committed the taxon changes to move towards (2) migrate https://www.inaturalist.org/taxon_changes?change_group=Neotoma+lepida+split

Publicado por loarie hace más de 3 años (Marca)
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ugh, i feel like taxonomy is a train wreck in general and the people researching it and tracking it pay little if any heed to the fact that others need to use these names for something. But that's just me. I'd prefer to wait several years to change anything, and to shake my fist and grumble at all of them

Publicado por charlie hace más de 3 años (Marca)

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