July 18, 2019

Kemper's visit to iNat HQ!

It was a treat to meet Yann (aka @kemper) and his little brother during a visit to iNaturalist HQ at the California Academy of Sciences. Yann's in the top 500 observers and top 50 identifiers on iNaturalist and he only just turned 15 today - pretty cool!

Posted on July 18, 2019 20:10 by loarie loarie | 2 comments | Leave a comment

July 11, 2019

Visit to the Lepidoptera Society Meeting

It was an honor to present iNaturalist at the 2019 Lepidoptera Society Meeting yesterday. I got to hear about the very cool work that @marcepstein and @ivonnegarzon are doing incorporating iNaturalist into their research.

I also got to meet some personal informatics hero's: ie Jon Pelham (right) of Butterflies of America, Markku Savela (middle) of Funet.fi, and Steve Nanz of Moth Photographer's Group

Many thanks to Michael Collins (middle) from the Carnegie Museum of Pittsburgh for helping organize and it was a treat to mee Bob Pyle (left), the founder of the Xerces Society!

Posted on July 11, 2019 22:04 by loarie loarie | 2 comments | Leave a comment

July 03, 2019

Visit to Minnesota

It was really nice getting a chance to catch up with @rager001 and @alstrauss from the University of Minnesota Extension on Monday at the Minnesota Landscape Arboretum. Great to hear about all the cool stuff happening with iNaturalist in Minnesota from Master Naturalist to City Nature Challenge to @jwalewski's efforts up at the Wolf Ridge Environmental Learning Center!

Posted on July 03, 2019 19:19 by loarie loarie | 0 comments | Leave a comment

May 01, 2019

Visit to Big Rock Ridge for CNC (Trip)

I took the girls to Big Rock Ridge to do my part for CNC. The goldfields were in full form

Posted on May 01, 2019 19:12 by loarie loarie | 44 observations | 0 comments | Leave a comment

April 18, 2019

Ring mountain afternoon survey (Trip)

I stopped by Ring Mountain on the way to pick my daughter up at school and thought I'd keep my eye out for a few things

Posted on April 18, 2019 22:42 by loarie loarie | 51 observations | 5 comments | Leave a comment

April 13, 2019

New World Tylos

I've been looking (and bugging other people to look) for Tylos for a while with no luck. So I was super stoked to find some yesterday in Mexico. Since there's more than one species here, I did some research on New World species. I was able to convince myself I that what I found was T. niveus from the ventral view of the fifth pleonal segments. Referring to Schultz's 1970 A Review of the Species of the Genus Tylos Latreille from the New World (Isopoda, Oniscoidea) there are 5 new World Species:
T. latreille (Widespread)
T. niveus (Widespread)
T. wageneri (Widespread)
T. punctatus (Pacific)
T. spinulosus (Southern Chile)
And in his followup 1974 Terrestrial Isopod Crustaceans (Oniscoidea) mainly from the West Indies and adjacent regions 1. Tylos and Ligia, published in STUDIES ON THE FAUNA OF CURAÇAO AND OTHER CARIBBEAN ISLANDS he added T. marcuzzii which is at least in the West Indies.
But luckily the shape of the fifth pleonal segments as seen from the ventral view is pretty distinct. I've pasted in Schultz's illustrations of this character for all 6 species from these two papers and taken the liberty of coloring them in red. I also included and colored a photo from my observation which matches T. niveus well and none of the other species. (note T. wageneri's fifth pleonal segments don't even curve under enough to be visible ventrally so I colored in them on the dorsal view illustration and added a red line pointing to the ventral view illustration where they are missing.

Posted on April 13, 2019 01:50 by loarie loarie | 1 comments | Leave a comment

April 02, 2019

Hike on Ring Mountain (Trip)

I took a walk around Ring Mountain with my daughters. I was looking for herps and kept my eye out for California Golden Violet and Brownies

Posted on April 02, 2019 20:27 by loarie loarie | 6 observations | 0 comments | Leave a comment

January 29, 2019

How to work with Taxon Framework Relationships

If a Taxon Framework has a source and covers downstream taxa, then it can have Taxon Framework Relationships. These taxon framework relationships are created and edited by iNat curators and describe the mapping between internal taxa on iNaturalist and the external taxa in the reference.

How to set them up


Suppose our external reference had 4 species (Species A, B, C, & E) and internal to iNaturalist we had 4 species (Species B, C, D & E). Without any additional information, iNaturalist will naively map these two sets of species as follows. Species with the same name, rank, and parent will 'match'. Whereas species in one but not both of the sets will be described with 'not internal' or 'not external' relationships. Relationships other than 'match' are collectively known as 'deviations'

The problem is that true 'not external or 'not internal' deviations are actually quite rare. One-to-one, Many-to-one, and One-to-many deviations are much more common (e.g. splitting a ssp off as a species in the external reference would be a 'many-to-one'). But for iNaturalist to understand these more complex mappings, taxon curators need to provide them.

This is done by creating and editing Taxon Framework Relationships. For example, search for Taxon Framework Relationships with relationship 'not internal' associated with the Rodentia Taxon Framework. At the time of this writing, there is a 'not internal' Taxon Framework Relationship linked to the external taxon Marmota kastschenkoi.

A little research reveals that Marmota kastschenkoi was previously considered a subspecies Marmota baibacina kastschenkoi and comprises the northern populations of Marmota baibacina 'sensu lato' (ie 'in the broad sense') .

Its clear that by Marmota baibacina, iNaturalist intends to means this broader 'sensu lato' concept that includes M. kastschenkoi. This is evident by inspecting the distribution (e.g. observations, taxon range map, atlas etc.) and also the taxonomy itself (e.g. Marmota baibacina kastschenkoi exists as a ssp of Marmota baibacina). This means that both the 'not internal' Taxon Framework Relationship for Marmota kastschenkoi and also the 'match' Taxon Framework Relationship for Marmota baibacina (since one is 'sensu lato' and one is in the narrow sense: 'sensu stricto' ) are misspecified.

The former should be deleted, and the latter should be expanded from a 'match' to a 'many to one' by editing the Taxon Framework Relationship and adding Marmota kastschenkoi as an additional 'external taxon'

There are cases when 'not internal' and 'not external' deviations are legitimate. They are used for obscure nodes (e.g. tribes) or ranks (e.g. hybrids) that might be missing from either iNaturalist or the external sources by design. But they also should be used for species 'wholly new to science'.

For example Svensson et al., 2013 describe a new galago from Angola. This species is sympatric with its closest relatives (G. thomasi and G. demidovii) and is much larger. This distinction between "a change in views of what a species is, that is, dependent on which species concept is adopted" and species "wholly new to science" is often blurry. When its not a clearcut case of the former, discerning when it is indeed the latter from the literature can be aggravating. This is made worse by the fact that journal articles tend to try to hype the 'new species discovery' parts of their paper for greater impact even if they are just reshuffling species. There's some nice text on the distinction in Svensson et al., 2013:

"Most new primate species recognized in the 21st century are the result of the taxonomic elevation of previously known subspecies to species (Groves, 2001; Macaca spp.: Kitchener & Groves, 2002; Aotus spp.: Defler & Bueno, 2007; Nomascus spp.: Thinh, Mootnick, Thanh, Nadler, & Roos, 2010; Microcebus spp.: Hotaling et al., 2016). Taxa wholly new to science, however, are also being described (e.g., Rungwecebus kipunji: Davenport et al., 2006; Jones et al., 2005; Tarsius tumpara: Shekelle, Groves, Merker, & Supriatna, 2008; Rhinopithecus strykeri: Geissmann et al., 2010; Nycticebus kayan: Munds et al., 2013)." Legitamite 'non-internal' Taxon Framework Relationships should include information on why the taxon is 'wholly new' and doesn't risk impacting neighbors (e.g. for Galagoides kumbirensis)

For iNaturalist's purposes. this distinction is important to the extent that we can:
1) avoid changes in the interpretation of past identifications
2) avoid associated meta-data with taxa (distribution information, default taxon photos, names etc.) from becoming misspecified

For example, in the Marmota kastschenkoi case, if we failed to alter the Taxon Relationship Framework mapping from 'non internal' to a 'many-to-one' relationship involving Marmota baibacina, then the proper coarse of action for adding Marmota kastschenkoi would be to create a new taxon. This would mean that the existing taxon range and atlas for Marmota baibacina would become misspecified (since they would continue being 'sensu lato' but the existence of Marmota kastschenkoi as a sibling would change the interpretation to 'sensu stricto'). Similarly, existing identifications of Marmota baibacina - which were intended to be interpreted as Marmota baibacina 'sensu lato' would start being interpreted as Marmota baibacina 'sensu stricto' and would result in the appearance of disagreements where none exist.

In contrast, by properly mapping Marmota kastschenkoi with a 'many-to-one' this would indicate that Marmota kastschenkoi should be added through a split and that additional work will be required to properly curate the distribution, identifications and explain to the community what the change means.

In the galago case, the new galago Galagoides kumbirensis can be simply added without any adverse impacts on its relatives.

Who can edit them?


Any taxon that is covered by a sourced Taxon Framework should have a Taxon Framework Relationship. Only curators can create, edit, or destroy Taxon Framework Relationships. If the Taxon Framework has Taxon Curators, only these taxon curators can create, edit or destroy them.

Good housekeeping of Taxon Framework Relationships


Generally, sourced Taxon Frameworks are initially populated through the back end of iNaturalist via a script that reads in the external taxa from the external reference and compares them to the internal iNaturalist taxa covered by the framework. The purpose of the script is to determine which species in iNaturalist aren't in the external reference (and vice versa) once all the deviations are taken into account. The script makes use of the Taxon Framework Relationships to do the mapping and will fail if there are issues with the Taxon Framework Relationships. Therefore its very important that curators take care when creating/editing/destroying Taxon Framework Relationships. Please do not leave loose ends around. For example, in curating Marmota kastschenkoi so that it is mapped through a many-to-one rather than a 'not internal' you need to do two steps (1) delete the 'not internal' Taxon Framework Relationship involving Marmota kastschenkoi and (2) edit the 'match' Taxon Framework Relationship involving Marmota baibacina by adding Marmota kastschenkoi to make it a 'many-to-one'. Just doing one of these two steps will corrupt the Taxon Framework Relationships.

Likewise, if you were to split Marmota baibacina (sensu lato) into Marmota baibacina (sensu stricto) and Marmota kastschenkoi, once the split is committed, remember your work is not done until you remove the many-to-one Taxon Framework Relationship on the inactive Marmota baibacina (sensu lato) and add new 'match' Taxon Framework Relationships to the outputs Marmota kastschenkoi and Marmota baibacina (sensu stricto).

Posted on January 29, 2019 18:38 by loarie loarie | 0 comments | Leave a comment

January 10, 2019

Identifying Cycadians (Genus Eumaeus)

I spent a little time looking into the Cycadians (Genus Eumaeus). Its a pretty easy group because there are only 6 species and they're pretty distinct visually from other Hairstreaks in the Lycaenidae. Their distributions are also mostly allopatric. The exceptions are the 2 Mexican species Eumaeus toxea and Eumaeus childrenae which luckily look very different. And also the 2 South American species that occur East of the Andes which are Eumaeus minyas and Eumaeus toxana. This genus is endemic to the America's so Butterflies of America's has complete info on taxonomy and distribution.

I found some helpful notes from Kim Garwood's discussion board here on distinguishing Eumaeus minyas from Eumaeus toxana which make sense to me after examining some photos. They are:

Also, it wasn't mentioned in the post, but to me Eumaeus toxana's wings look more pointed and Eumaeus minyas's more rounded.
I haven't spent too much time looking at the dorsal sides of the wings because 90% of the photos are of perched individuals with their wings closed. But here's a shot of Eumaeus atala in flight © Joseph MDO:

The larvae feed on Cycads - hence the common name Cycadians - and their larvae are quite distinctive. Here's a shot of Eumaeus godartii © Alessandro Bartolo. I haven't looked into how to identify caterpillars to species where more than one species overlap.

Hope this helps, and let me know if I've gotten anything wrong!

Posted on January 10, 2019 08:46 by loarie loarie | 1 comments | Leave a comment

August 16, 2018

Talking Plant Phenology with Alison Northup!

Was awesome to have @alisonnorthup visit iNat HQ today all the way from Austin Texas! We had some cool discussions about plant phenology

From left to right @loarie @kueda @alisonnorthup @tiwane

Posted on August 16, 2018 04:01 by loarie loarie | 4 comments | Leave a comment