2021 Clements Update and Continual Concerns

Have added quite a few more maps, will try to do the remainder next week

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thanks so much for your help with this! This work is definitely the bottleneck for moving this forward but no pressure to do it all yourself.

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@ rjq (and others) thanks for all your hard work on these - how are things looking? Are we ready to move forward?

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All mapped, ready to go. Though atlases may need a bit more detail than is present in some of the maps

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It’s impressive all this taxonomic harmonization work, well done Loarie and all the helpers.

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Ok - thanks again to rjq et al. for helping clarify the splits again. I’ve now made draft splits for each. The next steps are to create atlases for each split so we can move as many IDs of the input as possible to the proper output (as opposed to coarsening them to the common ancestor of the outputs).

It would also be nice to update (rather than loose) the taxon ranges, and I find that this really helps create the atlases. However, I realize updating the taxon ranges takes some GIS skills, so if its not possible, just creating atlases still helps.

I’m going to describe the steps I took for split#3 - Anthus similis to update the ranges, create atlases, and then check that most IDs were being properly reassigned to an output taxon. If you can help do these steps to any of the other splits I pasted at the bottom many many thanks for your help!

(also, while I usually prefer using a split input as an output I didn’t do that here because it doesn’t lend itself as well to keeping changes in draft mode for a while and then committing everything at once which is the plan here)

(also, these are just the split, it ignores the ones where a split was not deemed necessary above, and I also went ahead and manually made/committed the Glaucidium brodiei change because its complex involving a species split and a genus split)

Step 1. Editing the ranges
To download a taxon range to edit it, navigate to the taxon range page by clicking on the “link” symbol next to “Range” in the “Overlays” menu


Then clock on the kml file to download it. If the iNat taxon doesn’t have a range and there is one on the IUCN Red List you can download it directly from IUCN. Also, its worth checking the IUCN Red List because they may have already split the taxon and if thats the case they might already have narrowed ranges for the output taxa available saving the step of manually creating them.

Open the downloaded range in your favorite GIS software - I use QGIS which is free. jwidness made a great tutorial for editing ranges you can find here. I usually make a new temporary shape to create a clipping mask outline (blue shape) and then first do a Vector->Geoprocessing Tools->Intersect with this shape and the original shape to create one narrowed range (purple) and then a Vector->Geoprocessing Tools->Difference on the same two shapes to create the other narrowed range (green). Then I save each out as a kml.

Next, edit each of the inactive output taxa and add the ranges you created. Make sure to indicate that they are not IUCN Red List ranges. One is a narrowed version of the IUCN Red List range (ie the IUCN Range map is unsuitable - namely because its too broad)

And the other is not in the IUCN Red List (ie its lumped into the broad taxon)

Making atlases
Making atlases is easier if the output taxa have ranges, but if you really don’t want to make ranges you can skip to this step. If a taxon is split on iNaturalist without atlases, all IDs on the input taxon will be replaced with IDs of the common ancestor of the output (e.g. the genus Anthus). This can result in a lot of coarsened data and can and should be minimized with atlases. We’ve made a handy tool on splits called “Analyze IDs” where you can see what the destination of IDs on the input taxon will be based on how the split is set up. Without any atlases, all IDs of the input (in this case 254) will be replaced by IDs of Anthus. With atlases we can reduce this.


To create/edit an atlas click on where it says “Not Atlased” next to one of the output taxa. Your atlas should be as simple as possible while still doing a good job of capturing the distribution.

Analyzing the fate of the Split input taxon’s Identifications
Once all the output taxa have atlases (the red “Not Atlased” will be replaced by green “Atlased” labels) rerun the “Analyze IDs tool”. If you’re atlases don’t overlap most of the IDs should have distinct output taxa as destinations. If you still have lots of IDs outside of atlases or in overlapping atlases, you can click on them to inspect them, alter the atlases accordingly, and rerun the tool. In this example, the 2 outside of atlas IDs are misIDs on observations far outside of range and coarsening them is not a problem

Once you’ve added atlases (and ideally taxon ranges) to the extent that the Analyze IDs tool thinks most IDs are going to distinct outputs, please cross the split off the list below. Once they are all ready, we’ll be able to commit them all at once. Thanks again for your help!

Splits needing atlases
split#2 - Zosterops senegalensis
split#3 - Anthus similis
split#4 - Arremon flavirostris - using IUCN maps
split#5 - Basileuterus rufifrons
split#6 - Bubo africanus
split#7 - Catharus dryas - using IUCN maps
split#9 - Cistothorus platensis - using IUCN maps
split#10 - Colluricincla megarhyncha
split#11 - Cyornis banyumas
split#12 - Cypsiurus parvus - using IUCN maps
split#13 - Alophoixus bres - using IUCN maps
split#14 - Alophoixus ochraceus - using IUCN maps
split#15 - Pyriglena leuconota
split#17 - Pyrocephalus rubinus - using IUCN maps
split#18 - Pyrocephalus erythaca
split#20 - Rhynchospiza strigiceps
split#21 - Saltator coerulescens - using IUCN maps
split#22 - Saxicola maurus
split#23 - Sclerurus mexicanus
split#27 - Strix aluco
split#28 - Strix varia
split#29 - Synallaxis stictothorax - using IUCN maps
split#30 - Thalasseus maximus
split#31 - Cynanthus latirostris - using IUCN maps
split#32 - Euphonia affinis
split#33 - Zosterops abyssinicus
split#36 - Eremalauda dunni - using IUCN maps
split#37 - Euscarthmus meloryphus - using IUCN maps
split#38 - Ficedula narcissina - using IUCN maps
split#39 - Formicarius analis - using IUCN maps
split#40 - Forpus xanthopterygius
split#41 - Gallinago paraguaiae
split#42 - Grallaria rufula
split#43 - Herpsilochmus rufimarginatus
split#45 - Lanius sphenocercus - using IUCN maps
split#46 - Larus canus
split#47 - Lophornis chalybeus - using IUCN maps
split#51 - Oenanthe hispanica
split#52 - Ortalis motmot
split#53 - Otus scops - using IUCN maps
split#54 - Penelope obscura
split#55 - Phylloscopus maforensis - using IUCN maps
split#56 - Pitta elegans
split#57 - Polioptila plumbea
split#58 - Prinia crinigera
split#59 - Prinia gracilis
split#60 - Prinia polychroa
split#61 - Alaudala rufescens
split#62 - Pachycephala pectoralis
split#63 - Bradypterus baboecala - using IUCN maps
split#66 - Lonchura tristissima - using IUCN maps
split#67 - Sylvia cantillans
split#68 - Trichoglossus flavoviridis- using IUCN maps
split#69 - Meliphaga gracilis- using IUCN maps
split#70 - Turdinus crispifrons
split#71 - Campylopterus largipennis

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I went through and cleaned up the observations and added common names and pictures to the taxa.

Also, can only curators do these parts?

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only curators can upload ranges, but anyone can create the kmls
only curators can make/edit atlases

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Thanks! So if I create the kmls, how will they be added (since I’m not a curator)?

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If there’s a public place you could post them - like a dropbox folder or something - you could provide the links here

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Would it be possible for all of the requested hybrid bird taxa to be added at this time, too?

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my understanding of hybrid taxa is adding them isn’t the only issue, its that having a taxonomy complicated with an unbounded set of hybrid combinations isn’t something everyone is onboard with (as opposed to using things like observation fields or some new feature to keep track of hybrids). Lets keep this thread to the Clements update, but maybe we should discuss hybrid policy on iNat in a separate thread.

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@loarie would it be possible to automatically pull in the IUCN maps for the 19 splits that they’ve already processed?

sure - thanks for annotating the list above so people can focus on the other ones

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Split #6: https://www.dropbox.com/sh/r4tyrgnvxle01z7/AACw317h9afxLnng2Z6TS80Ja?dl=0
Split #27: https://www.dropbox.com/sh/u146z19hv8nkgeh/AAB_FN7Wetu7T8YXS8ncaK_pa?dl=0
Split #28: https://www.dropbox.com/sh/8xynx35zbkju945/AABPntViapRIB50TUaIQNHsaa?dl=0

A note for Split #53- O. scops migrates through Cyprus (https://www.inaturalist.org/observations/39573720); however, the 3 observations of O. scops on Cyprus are all probably O. cyprius.

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I uploaded the kmls and added the atlases. Maybe you can double-check them?
It would probably also be good to add the source for the map and a description of how you made them. (I usually do the citation of the paper describing the split as the source, and then for the description something like "modified IUCN map following Smith et al. 2020.)

Thanks! I’ll take a look at them now.

Did you want me to add this as comments to the splits?

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Sure, I can copy them from there to the taxon range edit page.

Thanks!

Everything looks good! I also added sources and a description.

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