Mammal Taxonomy Help Wanted

Hi folks interested in mammal taxonomy,

This discussion https://www.inaturalist.org/taxon_splits/3993#activity_comment_1105895
has revealed that we probably need to get our act together with mammal taxonomy.

Right now we're supposed to be following IUCN. But things are a bit out of sync. I'd like to either:
1) sync up to IUCN
or
2) be a bit more rigorous about how iNat's mammal taxonomy differs from IUCN (e.g. iNat differs from IUCN in these ways for these reasons)

Moving towards either will require sorting out a bit of a mess. If any of you are interested in helping, I could totally use your help. This spreadsheet includes columns for iNat and IUCN. Everything should match up but theres ~300 species that are only in iNat (e.g. unmatched in IUCN) and vice versa. If anyone has time to kill and wants to help match these taxa up that would be super helpful:
https://docs.google.com/spreadsheets/d/1-7qEhmDuqutwPi2K4MeLUhOTiHMs6eDRCxXEX_h61I4/edit?usp=sharing

For example, jakob if you could help connect up some of the mismatched bats that would be awesome.

Once all these unmatched taxa are accounted for we can do the next step of deciding whether to swap/split/merge everything over to IUCN or more explicitly keep a few discrepancies.

Does this sound good?

FYI @jakob, @sea-kangaroo, @aguilita

-=UPDATE=-
See comment below. Similar to Odes, Reptiles, Amphibians etc, Mammals on iNat are now marked as Complete from class to species. iNat uses IUCN as its taxonomic reference except for these explicit discrepancies (and also bats which is a total mess still)

discrepancies = [
#domestic species in iNat, not in IUCN, leaving them
{iucn: [], inat: ["Equus caballus"]},
{iucn: [], inat: ["Equus asinus"]},
{iucn: [], inat: ["Canis familiaris"]},
{iucn: [], inat: ["Felis catus"]},
{iucn: [], inat: ["Bos taurus"]},
{iucn: [], inat: ["Ovis aries"]},
{iucn: [], inat: ["Capra hircus"]},
{iucn: [], inat: ["Bubalus bubalis"]},
{iucn: [], inat: ["Bos indicus"]},
{iucn: [], inat: ["Lama glama"]},
{iucn: [], inat: ["Vicugna pacos"]},
{iucn: [], inat: ["Camelus dromedarius"]},
{iucn: [], inat: ["Camelus bactrianus"]},
{iucn: [], inat: ["Cavia porcellus"]},
#newly described species added to iNat not yet in IUCN, leaving them
{iucn: [], inat: ["Monodelphis pinocchio"]},
{iucn: [], inat: ["Monodelphis saci"]},
{iucn: [], inat: ["Euroscaptor orlovi"]},
{iucn: [], inat: ["Euroscaptor kuznetsovi"]},
{iucn: [], inat: ["Gracilimus radix"]},
{iucn: [], inat: ["Neusticomys vossi"]},
#iNat would merge
{iucn: ["Sciurus vulgaris"], inat: ["Sciurus meridionalis","Sciurus vulgaris"]},
{iucn: ["Glaucomys sabrinus"], inat: ["Glaucomys sabrinus","Glaucomys oregonensis"]},
{iucn: ["Ictidomys mexicanus"], inat: ["Ictidomys mexicanus", "Ictidomys parvidens"]},
{iucn: ["Otospermophilus beecheyi"], inat: ["Otospermophilus beecheyi","Otospermophilus atricapillus"]},
{iucn: ["Thomomys umbrinus"], inat: ["Thomomys umbrinus", "Thomomys sheldoni", "Thomomys atrovarius"]},
{iucn: ["Proechimys trinitatis"], inat: ["Proechimys urichi","Proechimys trinitatus"]},
{iucn: ["Proechimys guairae"], inat: ["Proechimys poliopus", "Proechimys guairae"]},
{iucn: ["Clyomys laticeps"], inat: ["Clyomys bishopi", "Clyomys laticeps"]},
{iucn: ["Trinomys setosus"], inat: ["Trinomys myosuros", "Trinomys setosus"]},
{iucn: ["Lagidium viscacia"], inat: ["Lagidium peruanum", "Lagidium viscacia"]},
{iucn: ["Dasyprocta leporina"], inat: ["Dasyprocta cristata", "Dasyprocta leporina"]},
{iucn: ["Coendou quichua"], inat: ["Coendou rothschildi","Coendou quichua"]},
{iucn: ["Heterogeomys lanius"], inat: ["Orthogeomys lanius"]},
{iucn: ["Heterogeomys dariensis"], inat: ["Orthogeomys dariensis","Orthogeomys thaeleri"]},
{iucn: ["Heterogeomys cherriei"], inat: ["Orthogeomys matagalpae","Orthogeomys cherriei"]},
{iucn: ["Chaetodipus ammophilus"], inat: ["Chaetodipus dalquesti","Chaetodipus ammophilus"]},
{iucn: ["Dipodomys merriami"], inat: ["Dipodomys merriami", "Dipodomys insularis", "Dipodomys margaritae"]},
{iucn: ["Monodelphis glirina"], inat: ["Monodelphis maraxina","Monodelphis glirina"]},
{iucn: ["Monodelphis scalops"], inat: ["Monodelphis theresa","Monodelphis scalops"]},
{iucn: ["Monodelphis americana"], inat: ["Monodelphis rubida","Monodelphis americana","Monodelphis umbristriatus"]},
{iucn: ["Thylamys cinderella"], inat: ["Thylamys sponsorius","Thylamys cinderella"]},
{iucn: ["Chaetophractus vellerosus"], inat: ["Chaetophractus nationi","Chaetophractus vellerosus"]},
{iucn: ["Loxodonta africana"], inat: ["Loxodonta cyclotis","Loxodonta africana"]},
{iucn: ["Alces alces"], inat: ["Alces americanus","Alces alces"]},
{iucn: ["Sminthopsis fuliginosus"], inat: ["Sminthopsis fuliginosus","Sminthopsis aitkeni"]},
{iucn: ["Crocidura poensis"], inat: ["Crocidura fingui","Crocidura poensis"]},
{iucn: ["Sorex antinorii"], inat: ["Sorex arunchi","Sorex antinorii"]},
{iucn: ["Ochotona roylei"], inat: ["Ochotona roylei", "Ochotona himalayana"]},
{iucn: ["Ochotona dauurica"], inat: ["Ochotona dauurica", "Ochotona huangensis"]},
{iucn: ["Ochotona gloveri"], inat: ["Ochotona muliensis", "Ochotona gloveri"]},
{iucn: ["Ochotona forresti"], inat: ["Ochotona forresti", "Ochotona nigritia", "Ochotona gaoligongensis"]},
#inat would split
{iucn: ["Urocitellus brunneus","Urocitellus endemicus"], inat: ["Urocitellus brunneus"]},
{iucn: ["Hylobates muelleri","Hylobates abbotti","Hylobates funereus"], inat: ["Hylobates muelleri"]},
{iucn: ["Lutreolina massoia","Lutreolina crassicaudata"], inat: ["Lutreolina crassicaudata"]},
{iucn: ["Marmosops caucae", "Marmosops impavidus"], inat: ["Marmosops impavidus"]},
{iucn: ["Monodelphis peruviana", "Monodelphis adusta"], inat: ["Monodelphis adusta"]},
{iucn: ["Ochotona pallasii", "Ochotona opaca"], inat: ["Ochotona pallasi"]},
{iucn: ["Ochotona hyperborea", "Ochotona coreana", "Ochotona mantchurica"], inat: ["Ochotona hyperborea"]},
{iucn: ["Pithecia chrysocephala","Pithecia pithecia"], inat: ["Pithecia pithecia"]}, #IUCN wants to split P. pithecia into P. pithecia and P. chrysocephala, but currently have just added P. chrysocephala with no range
{iucn: ["Cebus albifrons","Cebus cuscinus","Cebus aequatorialis","Cebus cesarae","Cebus malitiosus","Cebus versicolor"], inat: ["Cebus albifrons"]}, #IUCN wants to split C. albifrons into C. albifrons,cuscinus,aequatorialis,cesarae,malitiosus, & versicolor, but currently have just added the additional taxa with no ranges and not reassessed C. albifrons
#inat would swap
{iucn: ["Cebus brunneus"], inat: ["Cebus olivaceus"]}, #IUCN wants to split C. olivaceus into C. brunneus & C. olivaceus but currently have just pulled C. olivaceus (sensu lato) and just added C. brunneus with no range
{iucn: ["Pithecia milleri"], inat: ["Pithecia monachus"]}, #IUCN wants to split P. monachus into P. monachus,milleri,hirsuta,inusta,napensis,isabela, & cazuzai, but currently have just pulled P. monachus (sensu lato) and just added P. milleri with no range
{iucn: ["Pithecia vanzolinii"], inat: ["Pithecia irrorata"]}, #IUCN wants to split P. irrorata into P. vanzolinii,rylandsi,mittermeieri, & pissinattii, but currently have just pulled P. irrorata (sensu lato) and just added P. vanzolinii with no range
{iucn: ["Neotamias minimus"], inat: ["Tamias minimus"]},
{iucn: ["Neotamias merriami"], inat: ["Tamias merriami"]},
{iucn: ["Neotamias amoenus"], inat: ["Tamias amoenus"]},
{iucn: ["Neotamias townsendii"], inat: ["Tamias townsendii"]},
{iucn: ["Neotamias umbrinus"], inat: ["Tamias umbrinus"]},
{iucn: ["Neotamias dorsalis"], inat: ["Tamias dorsalis"]},
{iucn: ["Neotamias speciosus"], inat: ["Tamias speciosus"]},
{iucn: ["Neotamias sonomae"], inat: ["Tamias sonomae"]},
{iucn: ["Eutamias sibiricus"], inat: ["Tamias sibiricus"]},
{iucn: ["Neotamias quadrimaculatus"], inat: ["Tamias quadrimaculatus"]},
{iucn: ["Neotamias quadrivittatus"], inat: ["Tamias quadrivittatus"]},
{iucn: ["Neotamias panamintinus"], inat: ["Tamias panamintinus"]},
{iucn: ["Neotamias durangae"], inat: ["Tamias durangae"]},
{iucn: ["Neotamias siskiyou"], inat: ["Tamias siskiyou"]},
{iucn: ["Neotamias canipes"], inat: ["Tamias canipes"]},
{iucn: ["Neotamias bulleri"], inat: ["Tamias bulleri"]},
{iucn: ["Neotamias obscurus"], inat: ["Tamias obscurus"]},
{iucn: ["Neotamias rufus"], inat: ["Tamias rufus"]},
{iucn: ["Neotamias senex"], inat: ["Tamias senex"]},
{iucn: ["Neotamias ruficaudus"], inat: ["Tamias ruficaudus"]},
{iucn: ["Neotamias cinereicollis"], inat: ["Tamias cinereicollis"]},
{iucn: ["Neotamias alpinus"], inat: ["Tamias alpinus"]},
{iucn: ["Neotamias palmeri"], inat: ["Tamias palmeri"]},
{iucn: ["Neotamias ochrogenys"], inat: ["Tamias ochrogenys"]},
{iucn: ["Gyldenstolpia fronto"], inat: ["Kunsia fronto"]},
{iucn: ["Tanyuromys aphrastus"], inat: ["Sigmodontomys aphrastus"]},
{iucn: ["Otomys karoensis"], inat: ["Otomys saundersiae"]},
{iucn: ["Gerbillus mackilligini"], inat: ["Gerbillus mackillingini"]},
{iucn: ["Micaelamys namaquensis"], inat: ["Aethomys namaquensis"]},
{iucn: ["Micaelamys granti"], inat: ["Aethomys granti"]},
{iucn: ["Nannospalax ehrenbergi"], inat: ["Spalax ehrenbergi"]}, 
{iucn: ["Nannospalax leucodon"], inat: ["Spalax leucodon"]},
{iucn: ["Nannospalax xanthodon"], inat: ["Spalax nehringi"]},
{iucn: ["Toromys rhipidurus"], inat: ["Makalata rhipidura"]},
{iucn: ["Brassomys albidens"], inat: ["Coccymys albidens"]},
#mysteriously removed from IUCN for seemingly no good reason, leaving them
{iucn: [], inat: ["Alouatta seniculus"]},
{iucn: [], inat: ["Mico manicorensis"]},
{iucn: [], inat: ["Cacajao melanocephalus"]},
{iucn: [], inat: ["Cebus capucinus"]},
{iucn: [],  inat: ["Cercopithecus pogonias"]},
{iucn: [], inat: ["Dipodomys ornatus"]},
]

Also here's the top mammal IDers figure referred to in that comment:


Posted by loarie loarie, October 05, 2017 01:02

Comments

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As mentioned in the Cervus thread linked above, the American Society of Mammalogists (ASM) has an online mammal taxonomy in the making. The IUCN Red List has never been a taxonomic authority in the first place, so using that list in the absence of an up-to-date (and regularly updated) mammal taxonomy is understandable but certainly not ideal.

As far as I know, the ASM database should become available pretty soon, so why don't we wait with an overhaul until their DB is released rather than now trying to align iNat's mammal taxonomy with what is a compromised species list (IUCN), and then having to deal with a major revision again (ASM).

Posted by jakob almost 2 years ago (Flag)
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Repeating my comment from the recent butterfly discussion here (www.inaturalist.org/observations/6429457):

@loarie I'd be very much in favour of using global lists wherever these are available (and where global lists fulfil some criteria that might need to be carved out). Maybe we should create a new subpage under the curator guide where we could list & link taxa with global and/or regional lists. My previous post was trying to add a bit in this direction www.inaturalist.org/journal/jakob/10253-taxonomic-backbones-for-europe-plus-some-others.

I'm not sure where GBIF's backbone taxonomy currently stands (I should have a close look at their taxonomy of African bats vs the one we're curating here on iNat). Maybe their approach is already good enough, and iNat could adopt GBIF's taxonomy for most if not all taxa.

I find stitching approaches not really adequate for data management in 2017, but maybe integrative taxonomies such as the one by GBIF are not there yet.

Posted by jakob almost 2 years ago (Flag)
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This kind of thing is so interesting to me. I wish I had taken mammalogy in colllege now. Too much time spent on plants and birds.

Posted by vermfly almost 2 years ago (Flag)
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nutcracker - would be great to keep this thread focused on mammal taxonomy. Generally policy questions are best for the google group. (but I guess you've got me since humans are mammals - posting humans is ok - iNat makes them always quality grade 'casual')

Jakob - that interesting about ASM - would be awesome if they released a well curated list.

In the meantime, thanks for those who are helping with the Mammal spreadsheet. I suspect most of the issues (along with most of the species) are going to be in Chiroptera and Rodentia. So maybe we can pick off some of the non-controversial orders first. Lets start alphabetically with Afrosoricida which IUCN lists as having 54 species. iNat currently differs in 2 places. Everyone okay with bringing iNat in line with IUCN on this front by making the following 2 changes:
1. swap Calcochloris leucorhinus with Huetia leucorhina
2. split Microgale brevicaudata into Microgale brevicaudata & Microgale grandidieri
?

Posted by loarie almost 2 years ago (Flag)
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@loarie why not hold on until ASM releases the database? I've tried to explain above why I don't think that aligning iNat's mammal taxonomy with the IUCN Red List is a good idea at this point.

And any thought re my suggestion using GBIF's backbone?

Posted by jakob almost 2 years ago (Flag)
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jakob - we've been using IUCN as the reference for mammals (see curator guide). I've just been lazy at enforcing it because of your concerns with bats. But now there's urgency to be more rigorous about this because:
a) we're working to release features that rely on well referenced taxonomy for Birds, Mammals, Reptiles, Amphibians, and Fishes.
b) as the site scales issues like the Elk issue that result from taxonomic confusion are becoming a bigger problem
So we need to do something now whether thats:
1) start enforcing the IUCN reference
2) explicitly deviating if theres a need to as I hope we can discuss here
3) switch to another reference (e.g. ASM or GBIF)

You can help with (3) by getting a timeline on ASM and adding GBIF cols to the spreadsheet I attached (one col for name and one col for GBIFID).

But for now we need either to align with IUCN or we need to explicitly lay out how iNat differs. For example, if we choose to deviate from IUCN by using Calcochloris leucorhinus rather than Huetia leucorhina we need to explicitly describe that we're doing that and why. Does that make sense?

So using Afrosoricida as an example. Why would you not support:
1. swap Calcochloris leucorhinus with Huetia leucorhina
2. split Microgale brevicaudata into Microgale brevicaudata & Microgale grandidieri
to bring Afrosoricida in line with IUCN?

Posted by loarie almost 2 years ago (Flag)
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@loarie what if a mammalian species is present on both iNaturalist and IUCN, but have different subspecies? I understand that subspecies are probably less pressing than true species at the moment, and there isn't any real specific guideline for what makes a subspecies a subspecies among taxonomists, but it is generally being driven by genetics now a' days and the IUCN is lagging on the incoming research, particularly with pantherines (big cats). For example, the IUCN recognizes 9 subspecies of tiger, but the SCC IUCN Cat Specialist Group and IUCN Cat Task Force now only recognize two.

Posted by bobby23 almost 2 years ago (Flag)
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bobby - same rules would apply. The reference would either be IUCN or the discrepancies would need to be explicitly stated (e.g. split ssp X into ssp Y and ssp Z for such-and-such reason).

But I should mention that while I'm very supportive of you or someone else actively curating mammal ssp taxonomy, I'm not going to be able to personally help too much. My priority is to help clean up and maintain extant species cleaned up for Mammals and a few other other major clades (e.g Birds etc.)

Posted by loarie almost 2 years ago (Flag)
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@loarie I'd like to focus on www.inaturalist.org/posts/10253 for a bit to see what iNat's overall strategy is. Can we resume this discussion then? I'm all for updating iNat's mammal taxonomy where it lags behind IUCN's Red List. However, I don't think the reverse should be done for the said reasons, ie merging stuff that isn't recognized by the IUCN Red List yet, and suggest to wait for the release of the ASM database.

Posted by jakob almost 2 years ago (Flag)
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Woop!!!
Mammal list is game on! See: https://mammaldiversity.org.

@loarie, time to be happy and update the Curator Guide?

From the 2017 MSA meeting minutes:
"The Mammal Biodiversity Committee stewards the Mammal Diversity Database (MDD), an ASM-based, readily updatable, and online database of mammal taxonomic and biodiversity information hosted at http://mammaldiversity.org/ [beta version; official launch in July 2017]. This database aims to serve the global mammalogy community by providing the latest information on species-level and higher taxonomic changes, thereby promoting more rigorous study of mammalian biodiversity worldwide. The initial objective for this online database is to aggregate, curate, and compile new citations on species descriptions and taxonomic revisions into regular releases in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data, and an online forum for discussing mammalian taxonomy and systematics. By serving as both a platform and forum, this initiative aims to stimulate interest in mammals and promote the ASM’s role as a leader in high quality research on mammalian biology. "

Interestingly, "we have unified the majority of listing to now include 6,162 extant valid species, 83 recently extinct species, and 41 synonyms from that union. A total of 834 new species are new since MSW3, along with 267 species transferred in genus."

From:
https://www.mammalsociety.org/uploads/report_files/Mammal%20Biodiversity%20Committee%202017.pdf

Posted by johnnybirder almost 2 years ago (Flag)
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Hurray!

Posted by jakob almost 2 years ago (Flag)
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nice - ok step 1 can we fill in the columns I added for ASM here https://docs.google.com/spreadsheets/d/1-7qEhmDuqutwPi2K4MeLUhOTiHMs6eDRCxXEX_h61I4/edit?usp=sharing so we can get a sense for how different iNat currently is from ASM? Note: there's already columns for comparing iNat to IUCN, these new columns are for comparing iNat to ASM - thanks!

Posted by loarie almost 2 years ago (Flag)
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Hi folks,

I spent some time working on mammals. Here's a ruby script that compares whats currently on iNat with whats. I punted on bats which is a mess (@jakob can you help me sort them out here). But for all other orders, I explicitly listed the discrepancies between IUCN and whats currently on iNat. I added them to the top of this thread. Let me know if there's any additional discrepancies we should add or any of these we should remove.

Also, if there's disagreement, here's who I propose we have as a mammal working group to resolve any disputes (top global and regional mammal IDers - I also pasted a figure at the top of this thread):
@johnnybirder, @sea-kangaroo, @markuslilje, @bobby23, @joachim, @jmaughn, @asemerdj, @jakob, @sequeirajluis, @emilianomori, @oebenin, @calebcam, @jadonald, @adammyates, @tony_wills, @biohexx1, @john8, @joshuagsmith, @ariel-shamir, @pfaucher, @kokhuitan, @camilojotage, @pantanaldouglas

Posted by loarie over 1 year ago (Flag)
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Everything looks good so far, but I won't be able to give an in-depth look at this until morning. (It's late where I live.) However, here's a few quick thoughts.
- Unlike iNat, the IUCN distinguishes wild yak (as Bos mutus, which is on iNat) from domestic yak (as Bos grunniens, which is not on iNat) and wild gaur (Bos gaurus) from domestic gaur (Bos frontalis which, again, is not on iNat). Given that the wild populations of both species are threatened with extinction, I think it is an important distinction that iNaturalist should also adopt.
- Pongo tapanuliensis is another recently described species added to iNat that is not yet acknowledged by the IUCN.
- I strongly advise against merging Loxodonta africana and Loxodonta cyclotis. IUCN's African Elephant Specialist Group only recognizes them as one species to avoid placing hybrids in any kind of legislative or conservation limbo. A fair amount of research has been carried out that strongly supports distinguishing them as distinctly separate species (example texts: Rohland et al. [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000564] Callaway article [https://www.nature.com/news/elephant-history-rewritten-by-ancient-genomes-1.20622]).
- I'm not sure it's a good idea to merge Alces americanus with Alces alces either, but I'm not too familiar with recent research investigating their potential speciation. A lot of work that the IUCN cites for the merge seems to be over a decade old. I think @nutcracker had more concrete opinions on the matter.
- I would gladly be part of the Mammal Working Group.

Posted by bobby23 over 1 year ago (Flag)
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thanks bobby23, but I don't see Bos grunniens or Bos frontalis in IUCN http://www.iucnredlist.org/search
and I do see Pongo tapanuliensis in IUCN http://www.iucnredlist.org/details/120588639/0

Posted by loarie over 1 year ago (Flag)
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Neither species receive their own assessment pages because they are domestic species, but they are acknowledged in the assessments for the wild yak and gaur. This mirrors how they treat Bos taurus and like species.
To quote:
"The International Commission on Zoological Nomenclature (2003) ruled that the name for this wild species is not invalid by virtue of being antedated by the name based on the domestic form. Therefore, IUCN considers the wild species of yak under Bos mutus, while the domestic form is considered under Bos grunniens (see Gentry et al. 1996)." (http://www.iucnredlist.org/details/2892/0)

"IUCN considers the wild species of Gaur under Bos gaurus, while referring to the domestic form (Mythun, Mithan or Gayal) as Bos frontalis Lambert, 1804 (see Gentry et al. 2004)." (http://www.iucnredlist.org/details/2891/0)

The Tapanuli organgutan was a personal oversight - it lacked a assessment page last time I looked and I assumed it had yet to receive one still.

Posted by bobby23 over 1 year ago (Flag)
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Hi guys...

In Italy we have some new mammal species:

1) All the Italian water voles (Arvicola amphibius) are now Arvicola italicus: http://www.italian-journal-of-mammalogy.it/article/view/11588
2) The Microtus voles in Sicily are "Microtus nebrodensis".

I do not know if they are already on IUCN,

Emiliano

Posted by emilianomori over 1 year ago (Flag)
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From : https://groups.google.com/forum/#!topic/inaturalist/Nmuge1WPyLc

Proposed higher classification of the Mammals following latest DNA results:

Class Mammalia

Subclass Prototheria
= Order Monotremata

Subclass Theria
Infraclass Metatheria
= Order Dasyuromorphia
= Order Didelphimorphia
= Order Diprotodontia
= Order Microbiotheria
= Order Notoryctemorphia
= Order Paucituberculata
= Order Peramelemorphia

InfraClass Eutheria

SubinfraClass Afrotheria (Afromammals)
Clade (or Superorder?) Afroinsectiphilia
= Order Afrosoricida
= Order Macroscelidea
= Order Tubulidentata
Clade (or Superorder?) Paenungulata
= Order Hyracoidea
= Order Proboscidea
= Order Sirenia

SubinfraClass Xenarthra
= Order Cingulata
= Order Pilosa

SubinfraClass Boreoeutheria
* SubsubinfraClass Euarchontoglires
Superorder Euarchonta
= Order Dermoptera
= Order Primates
= Order Scandentia

Superorder Glires
= Order Lagomorpha
= Order Rodentia

* SubsubinfraClass Laurasiatheria
= Order Eulipotyphla

Clade (SuperOrder?) Ferungulata
= Order Artiodactyla
= Order Cetacea

Clade (SuperOrder?) Pegasoferae
= Order Chiroptera
= Order Perissodactyla

Clade (SuperOrder?) Ferae
= Order Carnivora
= Order Pholidota

Posted by tonyrebelo over 1 year ago (Flag)
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Or in tabular form

Class Subclass Infraclass SubinfraClass SubsubinfraClass Superorder Order
Mammalia Prototheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . Monotremata
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Dasyuromorphia 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Didelphimorphia 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Diprotodontia 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Microbiotheria 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Notoryctemorphia 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Paucituberculata 
Mammalia Theria  Metatheria  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Peramelemorphia
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Afroinsectiphilia  Afrosoricida 
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Afroinsectiphilia  Macroscelidea 
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Afroinsectiphilia  Tubulidentata 
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Paenungulata  Hyracoidea 
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Paenungulata  Proboscidea 
Mammalia Theria  Eutheria Afrotheria . . . . . . . . . . . . . . . . Paenungulata  Sirenia
Mammalia Theria  Eutheria Xenarthra  . . . . . . . . . . . . . . . . . . . . . . . . . . Cingulata 
Mammalia Theria  Eutheria Xenarthra  . . . . . . . . . . . . . . . . . . . . . . . . . . Pilosa
Mammalia Theria  Eutheria Boreoeutheria  Euarchontoglires  Euarchonta  Dermoptera 
Mammalia Theria  Eutheria Boreoeutheria  Euarchontoglires  Euarchonta  Primates 
Mammalia Theria  Eutheria Boreoeutheria  Euarchontoglires  Euarchonta  Scandentia
Mammalia Theria  Eutheria Boreoeutheria  Euarchontoglires  Glires  . . . Lagomorpha 
Mammalia Theria  Eutheria Boreoeutheria  Euarchontoglires  Glires  . . . Rodentia
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  . . . . . . . . . . Eulipotyphla
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Ferungulata  Artiodactyla 
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Ferungulata  Cetacea
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Pegasoferae  Chiroptera 
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Pegasoferae  Perissodactyla
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Ferae  . . . . . Carnivora 
Mammalia Theria  Eutheria Boreoeutheria  Laurasiatheria  Ferae  . . . . . Pholidota

Posted by tonyrebelo over 1 year ago (Flag)
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Hi @loarie, will finish what I've started re bat taxonomy, but not before early January.

I also think that a modern classification of mammals is desirable for various reasons - as mentioned a couple of times, the IUCN Red List was never meant as a taxonomic reference, and this is all the more true for the higher classification of organisms. Not sure how many taxonomic levels are needed or preferable in the context of iNat, but something similar to what is proposed above looks good.

Posted by jakob over 1 year ago (Flag)
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very nice, I propose that we should split the Giraffe into several spp as displayed on GCF (giraffe conservation fund).

Posted by calebcam over 1 year ago (Flag)
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iNat allows that. If merged into one species the vernacular would be Elk and assigned to the European and Asian subregions, and WhateveritisthatyoucallitinAmericathatyoupresumedthatIshouldknow in the North American subregion.
What the global name would be I dont know: I presume that there would not be one, or more correctly that both subregions would consider their name to the be global one.

Posted by tonyrebelo over 1 year ago (Flag)
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Giraffe: link please
how does that differ from
https://www.inaturalist.org/taxa/42157-Giraffa-camelopardalis

Posted by tonyrebelo over 1 year ago (Flag)
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4 species instead of one: ah OK: Missed that - it is the subspecies I am interested in, and that does not change so much.

Posted by tonyrebelo over 1 year ago (Flag)
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But iNat can make the European name the Elk and the north American name the Moose. The Americans need never ever know that the Europeans are calling Mooses something else (I think they are wee timorous beesties in Scotland) because they wont bother to look, and Europe has long given up with America calling everything something else.

In addition there are a dozen? subspecies - just assign the appropriate name to each of them (and throw in some Asian names too).

Posted by tonyrebelo over 1 year ago (Flag)
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They call the moose Eurasian elk? LOL! That's so weird.

Posted by vermfly over 1 year ago (Flag)
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hey folks lets please steer clear of the common names debate here. Quite enough of that here https://groups.google.com/forum/#!topic/inaturalist/toBKglDiG1g
This thread is for discussing explicit discrepancies in iNaturalist extant species mammal taxonomy from the IUCN redlist

Posted by loarie over 1 year ago (Flag)
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Its quite easy to create an account, you should be able to hook up to FB or gmail (right?)

Posted by calebcam over 1 year ago (Flag)
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Okay, never mind. Sorry for getting off-topic myself!

Posted by calebcam over 1 year ago (Flag)
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Yes, let me know how I can help.

Posted by biohexx1 over 1 year ago (Flag)
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Update: I would keep Sciurus vulgaris and Sciurus meridionalis separate as well. The latter was only recently described as a distinct species. When the IUCN assessment for S. vulgaris was last updated (in 2016), they aknowledged that it was probable for S. meridionalis to be treated as it's own species in the future once a proper study looked into it.

UPDATE:
Article link (Wauters et al. http://www.italian-journal-of-mammalogy.it/article/view/12015)

Posted by bobby23 over 1 year ago (Flag)
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@tonyrebelo I agree that iNat's mammal taxonomy (and all life taxonomy) should reflect modern taxonomic schemes, but do you have a reason for why all of those levels you suggested are necessary or beneficial for iNaturalist? I feel that navigating all of those non-traditional categories might be confusing or daunting for those not as familiar with taxonomy beyond the basic order, family, etc. While there is no standard to follow, I've personally only have only included sub-categories if I felt it made the taxonomic branches easier to navigate (ex.https://www.inaturalist.org/taxa/42241-Bovidae). (I hope I don't come off as accusative - I don't have too strong of an opinion either way. I'm just curious about your reasoning.)

Posted by bobby23 over 1 year ago (Flag)
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also iNat doesn't support SubinfraClass + SubsubinfraClass ranks. Those nodes at the other ranks could be added. But they won't help move unidentified observations forward as few mammal obs are lingering between class and order. I don't feel strongly. Might warrant a separate discussion so we can stay focused on species here

Posted by loarie over 1 year ago (Flag)
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@bobby23 There are swathes of ranks beyond the handful of traditional ones. And different groups have traditionally focussed on different levels. So Echinoderms are very heavy in the upper ranks, and almost dont use the lower ones, but Entomology focusses primarily on those around family and tribe, and the Crustaceans focus in the middle levels. Each expands these regions with super and sub and infra and other odd rankings. The rankings SubinfraClass + SubsubinfraClass are not current ranks: but I saw that iNat did not want to use "Clades".

@loarie The purpose of using these classifications is to teach and learn the relationships. To be quite honest, I dont care very much for the Eurasian mammals, but the Australian Mammals (Metatheria), African Mammals (Afrotheria) and South American Mammals (Xenarthra) are key groupings, missing in the current classification in a meaningless mass of almost 30 Orders. This is an opportunity to highlight the spectacular findings of the past two decades and iNat is ignoring it.
I never intended them to move unidentified observations: that is not the sole reason of adding intermediate ranks, and not at all on the agenda when I first raised.

I dont think there is any reason to continue this thread. I have highlighted it and someone has to decide what to include. Anything is better than nothing, although if you are going there why not just do it completely? (The actual names of the ranks will take decades to stabilize and even longer if the cladists keep on pushing "clades" into the system, so just bite the bullet and set the trend: Oh dear this better be a new thread, but I would rather stay out of it).

(((Dare I risk some ire with some closing words? No - I will email you instead.)))

Posted by tonyrebelo over 1 year ago (Flag)
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Of the North American flying squirrels:
"#iNat would merge {iucn: ["Glaucomys sabrinus"], inat: ["Glaucomys sabrinus","Glaucomys oregonensis"]},"

I believe we should keep the two separate. When the IUCN released its current assessment on Glaucomys sabrinus back in 2016, its authors noted that it may represent a species complex, suggesting that some preliminary research suggests that there may be two or more species inncorectly asserted as one. In 2017, Arbogast et al. published a genetic study indicating that Glaucomys oregonensis (traditionally treated as a subspecies) was indeed a separate species, but it seems that the IUCN has lagged on the update. (ref: https://academic.oup.com/jmammal/article/98/4/1027/3807034)

FYI anyone is welcomed to express how they disagree or agree with anything I've assessed thus far.

Posted by bobby23 over 1 year ago (Flag)
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I'm late to the party, but:
I'm not seeing the columns for the ASM database in the spreadsheet in the link. Have we given up on that and are just going with IUCN? Did people have thoughts on the quality of the ASM database? I've only poked around in it a little bit and it certainly has more of the recently-split species than IUCN does (where "recently" is "within the last 12 years"), but is a bit sparse, with no name revision histories etc.

Also have we decided not to use GBIF in favor of IUCN?

Posted by sea-kangaroo over 1 year ago (Flag)
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I guess it wasn't posted here, but @jakob said ASM isn't ready for showtime. I know IUCN isn't perfect but it IS being actively updated. For example, they added tons of small mammals in their last update. My preference would be to do this 'explicit discrepancy' approach I outline here where we follow IUCN unless we want to make an explicit discrepancy from that list (ie split this, lump those, add these, remove these). I listed all the explicit discrepancies we're making (not by choice, just based on where things stand currently) above - please comment on whether we should keep making those or fall in line with IUCN and also please suggest any new discrepancies from IUCN not listed above we should consider - also remember bats are a still a real mess. We're waiting on Jakob to help make sense of where and how iNat should be deviating from IUCN on bats

Posted by loarie over 1 year ago (Flag)
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Ah, ok, thanks for explaining! I'm generally in favor of keeping discrepancies and erring on the side of splitting. (I'm a lumper personally but splitting seems to make less taxon change mess and be more-requested by users.) I was worried the discrepancies were all on the chopping block in favor of strict adherence, and had a vision of the mire that would make swapping in-use taxa back to old concepts only to have to switch them forwards again with an update (like Alces, nooo).

For Otospermophilus atricapillus I support these researchers' conclusion that it's not distinct from O. beecheyi, but not going to lose sleep if it stays as is.

Split for consideration: I had a wildlife guide request I split Petrogale brachyotis into P. brachyotis and P. wilkinsi, after a 2014 Australian Museum paper splitting them on the basis of morphological and genetic differences. The actual paper is behind a UC paywall, but here's the 2014 press release and here's the 2010 precursor to this change quantifying difference amongst populations. Atlas of Living Australian recognizes both species, and there are conservation implications since while P. brachyotis is Least Concern the populations of it that are now P. wilkinsi are much smaller and declining (Near Threatened), at least in part due to their ~1kg (25-40%) smaller size making the adults vulnerable to cat predation.

Posted by sea-kangaroo over 1 year ago (Flag)
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Thanks, nutcracker!

Posted by sea-kangaroo over 1 year ago (Flag)
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Lets add Inia araguaiaensis!

Posted by calebcam over 1 year ago (Flag)
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thanks for everyone's (ongoing) help getting Mammal taxonomy in line. Here's some of the fruits of our labor: https://www.inaturalist.org/blog/13377-tallying-observed-vertebrate-species-with-complete-taxa

Posted by loarie over 1 year ago (Flag)
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Some new primate species have been described in the latest issue of Primate Conservation, including the Blue Nile Palas Monkey (Erythrocebus poliophaeus). Also included is, "a new dwarf lemur in Madagascar, two new tarsiers in Indonesia, and two new sub-species of slender loris in Sri Lanka". (http://www.bbc.com/news/science-environment-42720556)

Posted by bobby23 over 1 year ago (Flag)
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^I will try to find the primary source soon, if no else finds it before me.

Posted by bobby23 over 1 year ago (Flag)
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Articles of the issue 31 are available here: www.primate-sg.org/primatre-conservation-31

Posted by jakob over 1 year ago (Flag)
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Awesome, thank you! Based on the above info, the following species should be added to iNat's taxonomy (unless someone here has strong opinions on the contrary):

- Cheirogaleus grovesi (Groves' Dwarf Lemur)
- Erythrocebus poliophaeus ( Heuglin’s Patas Monkey)
- Tarsius spectrumgurskyae (Gursky’s Spectral Tarsier)
- Tarsius supriatnai (Jatna’s Tarsier)

Posted by bobby23 over 1 year ago (Flag)
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I do not have strong opinions against these particular new primate species, but it seems at odds with the statement "we explicitly do not track the taxonomy from the primary literature".

Posted by jwidness over 1 year ago (Flag)
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Well, I first learned of these changes from secondary literature, and some of these taxonomic revisions were issued by people affiliated with the IUCN (which is our primary reference for mammal taxonomy on iNat anyhow...).

Posted by bobby23 over 1 year ago (Flag)
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I found some issues with the IUCN taxonomy related to the fact that Cercopithecus pogonias is inexplicably missing from their data set. Specifically, there is some additional information written out in some of the entries that is not captured in their database.

From the page for Cercopithecus wolfi ssp. wolfi:
"Gautier-Hion (2013) treats C. denti and C. wolfi as a distinct species with elegans and pyrogaster as subspecies of the latter; this treatment is now followed here."

Based on that, I think iNat should revise C. pogonias to contain only the subspecies grayi, nigripes, and pogonias, and C. wolfi should be a separate species. If we keep the subspecies elegans, it should be moved under C. wolfi. This would bring iNat in alignment with the written IUCN taxonomy.

(I would draft up these potential changes for review, but I don't have curator status.)

Posted by jwidness over 1 year ago (Flag)
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Hi iNaturalistas! I found this post by accident but I better chime in here-- I'm the chair of the new American Society of Mammalogists’ effort to update mammal taxonomy, which is now displayed via the Mammal Diversity Database. Looks like you've already found our web-link (http://mammaldiversity.org)-- although note that we haven't yet publicly announced the web site! What you see now is our beta version, and the taxonomy hosted is going to change quite a bit (now up to 6399 extant species), so I’d recommend holding off before you make whole-sale changes. I’m glad to communicate with you on this more though. I think there are some major challenges for integrating the *spatial* components of each of these taxonomic changes (since there always is one), and it would be great to use some of the tools that you all have to help us do this. We are starting to work with Map of Life in this context, since we currently display their iframe maps on our species pages, but perhaps there is a way to harmonize with iNat as well. Who at iNat should be talking with more directly?

Big thanks—also note that our J Mammalogy article announcing the database should be online by Feb 6th, if not a bit earlier.

--nate
nathan.upham@yale.edu

Posted by nateupham over 1 year ago (Flag)
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Article summarizing the new taxonomic changes since MSW3 is now published here: https://academic.oup.com/jmammal/article/99/1/1/4834091

And the database is live, although we are still working out a few bugs: https://mammaldiversity.org/

Posted by nateupham over 1 year ago (Flag)
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Thanks for the update @nateupham. I'll make sure to check it out later when I get the chance, and hopefully others here will too.

Posted by bobby23 over 1 year ago (Flag)
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OK thanks for letting me know, nutcracker! I just filed an issue with our developer, which is open source and can be viewed on Github: https://github.com/tigerhawkvok/asm-mammal-database/issues

Posted by nateupham over 1 year ago (Flag)
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Hello, everyone! I hope all is well.
There is a discrepancy among some canine taxonomists, world authorities (including the IUCN and ASM), and users on iNaturalist concerning Canis lupus and related taxonomy, and I wanted to gauge all of your opinions on the matter.

Currently, iNaturalist acknowledges the following canine taxa:

Canis lupus (gray wolf, grey wolf, wolf) https://www.inaturalist.org/taxa/42048-Canis-lupus
Canis lupus spp. lycaon (Algonquin wolf, eastern wolf) https://www.inaturalist.org/taxa/234844-Canis-lupus-lycaon
Canis rufus (red wolf) https://www.inaturalist.org/taxa/42052-Canis-rufus
Canis latrans × lupus (coywolf, eastern coyote) https://www.inaturalist.org/taxa/567882-Canis-latrans-%C3%97-lupus

As I'm sure some of you know, there has been a lot of debate over the relatedness between these individuals and the validity of them as species. I'll try to outline some of the biggest conclusions out there that people will argue about, but please understand the nature of these issues makes consesnsus nearly impossible right now.

1. The eastern wolf (C. l. lycaon) is a different species from the gray wolf (C. lupus).
2. The red wolf (C. rufus) is conspecific with the eastern wolf (C. lycaon).
3. Both the red wolf and eastern wolf are distinct evolutionary units, but are more closely related to each other than to other canids.
5. The "eastern coyotes" of eastern North America are truly hybrids between dogs and wolves, (C. latrans × lupus). Wolves used to live in the lower 48 U.S. states, but administrated extirpation efforts nearly wiped them all out. This allowed coyotes to greatly expand their range eastward. The eastern wolves that continue to live in eastern Canada, in response to the greater genetic isolation, started to mate with coyotes.
4. The eastern wolf and the red wolf are the products of coyote-and-gray wolf hybridization. They are not valid taxa.
5. Red wolves and eastern wolves do not actively hybridize with coyotes despite being sympatric with them, suggesting that their differentiation is valid.
6. The eastern coyote (C. latrans × lupus) should be acknowledged as its own species (C. oriens).
7. Gray wolves and eastern wolves have the largest hybrid zone of any large mammals, in the Great Lakes region, where the "wolves" are an admixture of western populations, eastern populations, and coyotes.

I personally don't agree with all of these points, and there are a lot of contradictions between these points.

While this is a complicated issue, I think it is important we discuss it because these discrepancies are starting to impact users and observations on the site. Now there are a mass of unverified "Coyote" and "Coywolf" observations on iNaturalist because people don't know what to do anymore. There are people in the position that all eastern "coyote" observations should be marked as "Coywolf", while other users feel like there have to be more explicit justification for a hybrid ID. I know at least one or two users who want the "Coywolf" to be its own species on iNat, while I personally think it's premature. In at least one encounter I tried to argue with a user that eastern wolves did not live in Massachusetts because he was operating under the assumption that coywolves and eastern wolves are synonymous.

Here are some particularly noteworthy observations that highlight these discrepancies; ones that generated healthy discussions or just inflated the issues.
https://www.inaturalist.org/observations/1909168
https://www.inaturalist.org/observations/6906723
https://www.inaturalist.org/observations/9762212
https://www.inaturalist.org/observations/10249977

I think it is important that we address these taxonomic issues to mitigate the issue with observations and to make our taxonomy more concise. I encourage others to share what they would do, what changes are to be made (if any), and how we go about those changes. I hope others are willing to provide insight even if they are not super familiar with the issue or don't live in the United States. Thanks.

Additional reading:
• DNA Study Reveals the One and Only Wolf Species in North America (https://www.nytimes.com/2016/07/28/science/red-eastern-gray-wolves.html)
• Why the eastern coyote should be a separate species: the ‘coywolf’ (http://theconversation.com/why-the-eastern-coyote-should-be-a-separate-species-the-coywolf-59214)
• The Wikipedia articles accessible through each taxon's page.

Tagged for their two cents: @jwidness, @oebarker, @sea-kangaroo, anyone else already following this discussion page

Posted by bobby23 over 1 year ago (Flag)
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I dont think we should be usurping the scientific process. Sorting out these issues can take decades in exceptional cases.

Until the issue is sorted the logical approach is to keep all options open: the route that in the worst case scenario will not lose any data.
The problem is that disciples of one school of thought wont play ball (and some possibly wont accept the final resolution if it goes the other way).
Also it may be a borderline case where both options are almost correct and one way or the other is probably just a matter of opinion.

Any decision will result in some people being unhappy. The approach that maximises content for all outcomes is the only logical way to sit on the fence and keep all options open, until the matter is adequately resolved. Meantime expect proponents to be forcibly expounding their views.

Posted by tonyrebelo over 1 year ago (Flag)
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I don't have a strong opinion other than wanting consistency -- it seems like a bad idea to have different people using different terminology for the same animals.

Posted by jwidness over 1 year ago (Flag)
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@tonyrebelo I'm not suggesting we usurp anything. I didn't bring these taxonomic issues here for consensus: I brought them here because observations are being left unverified because people don't know the discrepancy between coywolves and regular coyotes or don't think we should acknowledge the former.

Maybe I shouldn't have brought up all the issues involving the eastern wolf or the red wolf to the depths that I did, but I think the issues with those taxa are related because some people have tried to ID coyote-wolf hybrids as "eastern wolves".

Posted by bobby23 over 1 year ago (Flag)
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@bobby23 - if the issue is simply that some people are calling these populations "Eastern Wolves" and others as "CoyoteXWolf then this is easily accommodated by either making the hybrid a synonym of the Eastern Wolf, or the Eastern Wolf a synonym of the hybrid. Which is immaterial: they are equivalent.
I would prefer iNat to allow one to specify a synonym. So assuming we chose the "Eastern Wolf" as a synonym of CoyoteXWolf, if I was an "Eastern Wolf" proponent, I would want iNat to allow me to post "Eastern Wolf" as a name. If iNat 10 milliseconds later adds a "taxon update" to CoyoteXWolf , I would be happy, because iNat would allow me to express my view. Currently, if I enter Eastern Wolf, I am not allowed to have this opinion, and iNat immediately posts it as CoyoteXWolf. The problem with this current iNat process, is if scientists discover that mostly these are hybrids, but in northern California there is a population of "Eastern" Wolf which is not a simple hybrid, then it will not be possible to "revert" to the original identifications on iNat, and users who had this correct ID are not acknowledged.
The real problem is simply "there is valid different terminology for the same populations": taxonomists differ in opinion, with some recognizing species, others the same populations as subspecies, and some who dont recognize subspecies at all, even though some of these acknowledge that there is subspecific variation of conservation significance. This is the unfortunate reality.

Posted by tonyrebelo over 1 year ago (Flag)
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So what's the status with changing the mammal backbone from IUCN to MDD? Is that going to happen eventually, or are we going some other route?

Posted by jwidness over 1 year ago (Flag)
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jwidness - we asked ASM to provide a mapping between the two but still no word. Such a mapping would be useful to understand the degree and character of the discrepancies between the sources and would be critical were we to transition.

Also, I pulled in an another update from IUCN so we're now up to date aside from the 'explicit deviations' we're making and the bat free-for-all. Also I created a project with its own journal where we can continue these discussions - seems more appropriate than my personal journal here. Please follow the project if you want to be looped into Mammal Taxonomy Discussions

Posted by loarie about 1 year ago (Flag)

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