Journal archives for October 2017

October 02, 2017

How to use iNaturalist for the upcoming Penang Bioblitz 2017!

We prepared a flyer here that explains the basics of using iNaturalist. If you're having trouble feel free to email me at sloarie at calacademy dot org.

Posted on October 02, 2017 21:20 by loarie loarie | 0 comments | Leave a comment

October 03, 2017

Prueba MX

Aquí es donde la gente está observando en MX - y quien está observando



Aquí es cuando la gente está observando en MX - y quien está observando



Esto es lo que la gente está observando en MX - y quién está identificando


Posted on October 03, 2017 23:30 by loarie loarie | 0 comments | Leave a comment

October 04, 2017

Canada Test

where:



when:



what:


Posted on October 04, 2017 03:37 by loarie loarie | 0 comments | Leave a comment

Prueba CO

Aquí es donde la gente está observando en CO - y quien está observando



Aquí es cuando la gente está observando en CO - y quien está observando



Esto es lo que la gente está observando en CO - y quién está identificando


Posted on October 04, 2017 04:05 by loarie loarie | 0 comments | Leave a comment

ZA test

where:



when:



what:


Posted on October 04, 2017 07:28 by loarie loarie | 0 comments | Leave a comment

AU test

where:



when:



what:




Posted on October 04, 2017 07:30 by loarie loarie | 0 comments | Leave a comment

October 05, 2017

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 on October 05, 2017 01:02 by loarie loarie | 60 comments | Leave a comment

October 07, 2017

Gymnosperms ready for global taxonomic consensus?

Hi folks,

For some groups like Odes and Amphibians, global taxonomic references are mature enough that iNat has pretty well curated and globally complete taxonomies facilitated by conversations like these:
https://www.inaturalist.org/journal/loarie/11694-world-odonata-list
https://www.inaturalist.org/journal/loarie/11101-internal-reference-taxonomies-amphibian-pilot

Unfortunately, for Plants and most other Insect orders (which are the 2 most 'observose' groups on iNat) global taxonomy simply isn't there yet. As a result, taxonomy on iNat for these groups is a bit looser with curators often adding species opportunistically, but as a result more synonymy and confusion across regions.

the 12 (or 13 depending on your taxonomic preference) families Gymnosperms represent a subset of plants that are probably mature enough for iNat to take a more rigorous global approach.

But to explore this further, we need to better understand where iNat is now in comparison to the various global references out there. To that end, I started this spreadsheet https://docs.google.com/spreadsheets/d/10e3QgCam8rikt_y17Wh3XvY2-auTFIyqwq_2tbME1oo/edit?usp=sharing
I added and filled out columns matching iNat to key (WCSP) and I added a blank column for conifersdotorg (conifersdotorg_name) that @nutcracker is going to help fill in. If folks want to consider other sources (e.g. the GBIF backbone) can you add columns and fill them in? This will allows us to fill in the surface specific discrepancies in the sources so we can contrast the sources with specific examples (extant species only please - e.g. no hybrids, extinct taxa, or ssp/var)

Just to give a sense for where we'd be going with this Gymnosperm exercise, I fully coded the family Araucariaceae for both WCSP and GD. So were we to adopt a global reference for that genus (rather than the regional stitching approach), whether we went with WCSP or GD we'd probably want to:
1. merge Agathis robusta (sensu stricto) & Agathis spathulata into Agathis robusta (sensu lato)
2. merge Agathis dammara (sensu stricto) & Agathis philippinensis into Agathis dammara (sensu lato)

However, the following 3 changes would bring iNat in line with WCSP but out of line with GD. So whether we were to make them or not would depend on which reference we would be using.
3. swapping Agathis labillardieri into Agathis labillardierei
4. merging Agathis borneensis (sensu stricto) & Agathis endertii into Agathis borneensis (sensu lato)
5. merging Agathis moorei (sensu stricto) & Agathis corbassonii into Agathis moorei (sensu lato)

Similarly, the following 1 change would bring iNat in line with GD but out of line with WCSP.
6. splitting Araucaria muelleri (sensu lato) into Araucaria goroensis & Araucaria muelleri (sensu stricto)

Thanks!

Posted on October 07, 2017 16:33 by loarie loarie | 1 comments | Leave a comment