Journal archives for March 2023

March 08, 2023

A Freshwater Crustacean That's a Work of Art - Observation of the Week, 3/7/23

Our (belated) Observation of the Week is this Freshwater Anomuran (likely in the genus Aegla, known as Pancoras in Spanish), seen in Uruguay by @danielamartinezz!

“The story of this little crustacean began on a walk through Minas (Lavalleja), in the middle of summer,” says Daniela Martínez.

While many others took the opportunity to carry out recreational activities at the San Francisco stream, my first instinct is always to go straight to observe what surrounds me and look for which beings are around, going unnoticed by most human eyes. The first thing I noticed was a large number of dragonfly nymphs in the water, accompanied by adult dragonflies fluttering across the landscape above the water. 

Then my father showed me the Aegla crustacean he found (he is also passionate about getting lost in nature). I’ve rarely seen them before, since they are very elusive, and I immediately took some photos of it. I love nature photography and recording everything I see to be able to share it with the rest in order to make the little creatures that live with us more visible.

Something curious I realized is that despite the fact that the crustaceans of the genus Aegla are native to my country, many people who saw the photo told me that they had never seen this animal, and couldn’t believe the strange shape it has, as if time had not passed for it, with its great armor that reminds us of the ancient creatures that inhabited the Earth.

While they may look like true crabs at first glance, anomurans belong to a separate infraorder that contains familiar crustaceans such as hermit crabs, king crabs, and porcelain crabs (yes, those all have English common names that contain “crab”). Often, the hind-most pair of legs of an anomuran are hidden under the carapace and used the clean the gills. The genus Aegla currently contains about seventy species, all of which live in South American freshwater habitats.

Daniela (below) says she’s always had a passion for nature, and 

the mere idea of such different beings living with us with their great variety of shapes, colors, and lifestyles has always captivated my attention. Which led me to want to know more, because I think that our world can be so different depending on which species is seeing it. Which led me to enroll in the University of Sciences of UdelaR, and become the biologist I am.

Daniela joined iNat in 2019 and especially enjoys looking at observations from different parts of the world, which she says is “a great activity for me since I am passionate about biogeography. I even did my degree thesis in the study of the factors that model the geographical patterns of native continental mammals of Uruguay.”

[iNaturalist] is a good citizen science tool, which allows everyone to contribute to the knowledge of the world that surrounds us, regardless of whether they have a scientific background or not. Because in the application there are many experts willing to help quickly with the identification. I always jokingly tell my friends that it's like a kind of "Pokemon Go", that game where people were looking for fictitious creatures, but in real life, hoping with this comparison to encourage the use of the application.

(Some quotes were lightly edited for clarity.)


- The Aegla painting you see above was made by Daniela!

- Check out the various colors of different Aegla on iNat!

- Here’s some footage of an Aegla walking about.

- iNatUY site admin @flo_grattarola and iNatUY user @jumanbar made this really cool interactive tool to find iNat data gaps in Uruguay.

Posted on March 08, 2023 01:01 AM by tiwane tiwane | 22 comments | Leave a comment

March 14, 2023

Facebook Login may be going away

Facebook is threatening to remove the ability to sign in to iNaturalist with a Facebook account on March 20. We're not sure if that will happen or not, but if you regularly sign in to iNaturalist with your Facebook account, please follow these steps to make sure you can sign in without Facebook (if you never sign in with Facebook you can ignore this):

  1. Go to https://www.inaturalist.org/users/edit#profile
  2. Change your password; you will be signed out after doing so
  3. Go to https://www.inaturalist.org/login and sign in with the password you just entered
  4. Always sign in with your username and password in the future

If you have any problems, please email help@inaturalist.org (we will not reply to direct messages on iNat).

THE DETAILS

Facebook has increasingly stringent security requirements for applications that access data from their platform, which includes any application that supports signing in with a Facebook account. Most of these requirements are good ideas, but they can be difficult to implement, and only 2-3 people on our team are able to do so. Just assessing their requests and replying to them can take days. We are hoping to meet their requirements by the deadline, but you should take the steps above to ensure you are able to sign in to your iNat account no matter what. We are also not committed to supporting Facebook Login in the future, so it's doubly worth making sure you have a working password.

These are the attributes from Facebook that we store and why we store them:

  • user ID (to keep track of whether you've signed in with Facebook before)
  • name (to create your initial username)
  • email address (to contact you and let you recover a forgotten password)
  • profile image (to create your initial iNat profile image)

The Facebook user ID and email address are as private and secure as any other private data on iNat, and depending on your Facebook preferences, we may never have accessed anything other than your user ID.

You can learn more about Facebook’s data security requirements for developers at https://developers.facebook.com/docs/development/maintaining-data-access/data-protection-assessment.

Posted on March 14, 2023 10:01 PM by kueda kueda

Yes, There Are Two Vipers Here - Observation of the Week, 3/14/23

Our Observation of the Week is this pair of Wagler's Pit Vipers (Tropidolaemus wagleri), seen in Singapore by @limhongyao!

Like many of us, the seeds of Lim Hong Yao’s interest in nature were planted in his childhood, when he watched documentaries on TV. “However,” he says,

it was only years later, during my undergraduate studies, when I realised that nature was all around me and not just those far away places on TV (Africa, Madagascar, the deep sea, etc.). I started out with birdwatching and bird photography and subsequently grew into a general naturalist, finding beauty in all sorts of animals. Currently I am still heavily invested in bird watching, but am also very keen to seek out butterflies, odonates, herpetofauna and mammals (in no order of interest).

So when Hong Yao heard about a pair of Wagler’s pit vipers seen in the area of a planned night hike, he had to stop by and take some shots. “I had not expected to see them though, as I heard that they were first seen over a week ago,” he says.

I wasn’t able to find any information on the reproductive behavior of these venomous snakes (if you know anything, please share in the comments!) but it’s pretty cool that the snakes look to have stayed together for at least a week. What’s really amazing is the sexual dimorphism here. The female in this photo is quite large and has black, yellow and white coloration, while the male is much smaller, pale green and white, and has a stripe over each eye. 

Like many arboreal snakes, individuals of this species don’t move much and rely on ambush to capture prey. They range throughout much of southeast Asia, both on islands and the mainland.

Hong Yao (above, eating a meal after birdwatching), joined iNat in 2018 and says

I mainly use iNaturalist to look for existing observations of animals I am interested to seek out, to share my sightings in general, as well as to get help with identifying subjects that I am not familiar with. I believe that using iNaturalist has led me to gain a better appreciation of the distribution of many animals, and the importance of habitats and microhabitats. Being able to look at the spatial distribution of a species on a map serves as a great starting point for learning more about a species and its ecology.

(Photo of Hong Yao by Goh Cheng Teng.)


Check out the beauty and diversity of temple vipers on iNat!

- A different temple viper species was Observation of the Week waaaay back in 2017!

Posted on March 14, 2023 10:33 PM by tiwane tiwane | 11 comments | Leave a comment

March 18, 2023

Thank you for helping generate most GBIF records for most species since 2020

GBIF (the Global Biodiversity Information Facility) is an online archive that brings together global biodiversity data from over 81,000 datasets by thousands of publishers. These publishers include natural history museums like the Smithsonian museum and also citizen science sites like iNaturalist. GBIF provides essential monitoring capacity to inform biodiversity conservation. Over time, iNaturalist has become an increasingly significant contributor to GBIF. In fact, since 2020, most GBIF records for most species have come from iNaturalist.

Only about 8% of the GBIF records since 2020 are from iNaturalist, so how can this be true? The answer is that most GBIF records represent a relatively small number of species (records of birds from popular bird-focused citizen science publishers such as eBird and records of common European species from popular European-focused citizen science publishers such as Artportalen). iNaturalist is unique as a GBIF publisher because it has generated tens of millions of records distributed across hundreds of thousands of species. This is important from a conservation perspective because unless we rely on a relatively small number of species such as birds (~11k species globally) as proxies for global biodiversity, reducing extinction rates is going to require insights across a large portion of the ~2M named species.

Selecting 2020 as a cutoff is arbitrary, but biodiversity records that can be generated and mobilized on short time scales (e.g. years rather than decades) are particularly important from a conservation perspective because they give scientists a real-time picture of the status of biodiversity in response to rapidly changing in climate and land use.

The graph below shows all GBIF records from 2020 pooled by species and arranged in descending order by number of species. On the left hand side, American Robin (Turdus migratorius) has more GBIF records since 2020 than any other species. While the GBIF records since 2020 span 325,558 species, the distribution is very unbalanced. Even plotting the y-axis on a log scale, the number of observations per species drops off rapidly. Most GBIF observations are from a relatively small number of species. The moth Pidorus atratus which is positioned near 30,000th place for most records, has just 292 records. Near the 100,000th place, the plant Stigmaphyllon ellipticum has just 16 records on GBIF. This is out of 2M named species and likely many more waiting to be discovered.

The next graph is nearly identical except that the GBIF records are split into two groups: those published by iNaturalist in green and those from all other publishers in black. While both lines are unbalanced, notice that the green iNaturalist line is less unbalanced and crosses the black line around the 22,700th place for most records. These first ~20k species with the most records are mostly birds and common European species with many tens of thousands of records from publishers to GBIF such as eBird (a birds-only, global citizen science site) and Artportalen (an all-taxa, Sweden-only citizen science site). But for most species, most of the data on GBIF is from iNaturalist.

The next graph displays this in another way by plotting these GBIF records since 2020 as the percent of species versus the percent of records published by iNaturalist. 42% of the species have 100% of their records from iNaturalist. 58% of species have at least 58% of their records from iNaturalist. In other words, since 2020, most GBIF records for most species have come from iNaturalist.

There is likely error in these graphs from taxonomic and identification issues among the various GBIF datasets, but its difficult to know how this error would influence these statistics. The bias towards a relatively small number of well-studied species like birds in GBIF is striking. Birds represent about 0.6% of named species, but represent about 83% of all GBIF records since 2020. The iNaturalist GBIF subset since 2020 is still skewed towards birds (21%), but also has a large proportion of records from the most speciose groups: insects (22%), plants (39%) and other species (10%). Excluding iNaturalist, over 88% of GBIF records since 2020 are of birds.

I mentioned that only 8% of the GBIF records since 2020 are from iNaturalist. This is mostly because of the tremendous number of bird records coming to GBIF through platforms such as eBird. The graphs below show the relatively small bird contributions of iNaturalist to GBIF since 2020 relative to other publishers (including eBird). The data from the top 2 graphs below are identical to those above for all GBIF records since 2020 except the graphs in the left columns have log scale x-axis. These log-log graphs are more confusing to understand but they reveal differences in the lines more clearly. The bottom two graphs show just birds. Note that only 10% of bird species have at least 10% of records from iNaturalist (due to the data volume of other publishers like eBird) compared to the equivalent 58% statistic across all species.

The graphs for other terrestrial vertebrates are very different from birds. Across all GBIF records since 2020, 63% of mammal species have at least 63% of records from iNaturalist; 81% of reptile species have at least 81% of records from iNaturalist, and 73% of amphibian species have at least 73% of records from iNaturalist.
.

The graphs for fish and the two most speciose groups (insects and plants) are also similar to terrestrial vertebrates. Across all GBIF records since 2020, 64% of fish species have at least 64% of records from iNaturalist; 64% of insect species have at least 64% of records from iNaturalist, and 62% of plant species have at least 62% of records from iNaturalist.

The unique diversity of species recorded on iNaturalist reflects the unique diversity of the iNaturalist community. The iNaturalist community brings together people posting observations from all parts of the globe and people with identification expertise on all parts of the tree of life. Thank you for all your efforts to create and sustain this truly unique snapshot of the Earth’s biodiversity.

GBIF will only receive your observations if your observation license has a CC0, CC-By, or CC-BY-NC license
You can set your observation license separately from your photo license if you wanted to, for example, allow GBIF to harvest your observations but not your photos or sounds. From your Account settings -> Content & Display -> Licensing, separately set observation license, photo license, and sound license to your preferences.

Currently on iNat there are 58.5M research grade observations with observation licenses that are CC0, CC-BY, or CC-BY-NC. This is the subset that goes into the archive that iNat makes available for GBIF to harvest. There are currently 145.4M observations total (casual + needs id + research grade) on iNaturalist. Of these, 81.4M are research grade and 99.6M have CC0, CC-BY, or CC-BY-NC observation licenses.

Posted on March 18, 2023 03:04 PM by loarie loarie | 53 comments | Leave a comment

March 21, 2023

Fluorescing Mushrooms! - Observation of the Week, 3/21/23

Our Observation of the Week is this group of Hypholoma acutum mushrooms, seen in New Zealand (Aotearoa) by @kathyliuliu!

A resident of Fox Glacier, New Zealand (Weheka), Liu Yang has been hiking at the nearby Lake Matheson (Te Ara Kairaumati) and found over one hundred species of fungus on the trail in the past year. “It is just amazing to mushroom hunt here,” she says. “So much fun.”

Her friend Joseph Pallante told her that some fungi, including the native Hypholoma acutum mushrooms, fluoresce under UV light. “It is a New Zealand endemic fungus and quite common in the forest,” she says. “I found those ones on dead wood around sunset time. So I still have some light to balance the UV lights and the day lights.”

A cosmopolitan genus, Hypholoma is often found in clusters on dead wood and common species like sulphur tuft have a greenish tinge to the gills. Hypholoma acutum is said to be poisonous and have a bitter taste.

Yang (above) has been on iNat for just over two years and tells me:

After I take photos, I always want to know what I was photographed. So iNaturalist is quite a handy website for getting help from experts and learning the value of each species. It makes me more open-minded and definitely more interested in nature!

(Photo of Yang by Moto Ye. Some quotes have been lightly edited for clarity)


- Take a look more than 3k+ observations in the UV fluorescent organisms project!

- The $50 New Zealand banknote includes an image of the native blue pinkgill mushroom
(Entoloma hochstetteri, Werewere-kokako).

Posted on March 21, 2023 06:17 PM by tiwane tiwane | 15 comments | Leave a comment

March 30, 2023

Identifier Profile: @jurga_li

This is the fifteenth entry in an ongoing monthly (or almost monthly!) series profiling the amazing identifiers of iNaturalist. 

Lichens! These symbiotic organisms occur all over the place but are often overlooked by many people. However, to Jurga Motiejūnaitė, iNat’s top identifier of common lichens,  

there are many exciting things about lichens: they are very colourful, they grow practically anywhere, some (like Ramalina menziesii [California’s state lichen! - Tony], or Pulchrocladia, or Stellarangia, or Eremastrella) have really crazy forms. Another pleasant thing is that they are not seasonal - one can find and enjoy them all year round (unless they are under deep snow cover). Some are very long lived and one can visit the same thallus for a number of years (if the habitat does not change dramatically). And even more interesting, lichens have parasites - lichenicolous fungi, which are spectacular by themselves.

Jurga lives in Lithuania and works at the Mycology Laboratory at the Nature Research Centre in Vilnius, where she studies lichens and lichenicolous fungi. She remembers catching pond organisms as a child, and collecting and identifying mushrooms and herbs with her parents and grandparents. When attending university, she studied plant communities and, after getting a job at the Botanical Institute, she started researching lichens.

When identifying on iNaturalist, Jurga often starts out  by filtering for fungi, Lecanoromycetes, or other taxa, and “for identification I use either personal knowledge, or consult extensive lichen literature that I own. For quick checks, especially for morphological variations of lichens, I use several reliable internet resources (e.g. ITALIC, Lichenportal, Lichens marins, etc.). Regretfully, online resources tend to disappear, change addresses and create inconveniences, so recommending them to other users is difficult…

Identification is part of my job, and identification from photographs gives me a different skill set from that required for specimen identification. As with any researcher, I like things to be as correct as possible, especially because Research Grade observations go to GBIF. I respect cleanliness of the data. I do not add comments to all observations. Many users seem to not be very interested, but when people ask questions, I always respond. I am particularly pleased when iNaturalist users take an interest in lichens and make obvious progress in their knowledge.

While Jurga’s focus is mostly on lichen and fungi in northern Europe, she’s helped out with identifications in southern Africa “because previously there was no one identifying lichens there, and I had gathered some identification material. But now I can almost resign from that position, because @ian_medeiros has taken over, and he is working directly on the lichenoflora of that region. I am very happy about this, as well as the fact that more lichenologist colleagues have joined iNaturalist.”

Introduced to iNat by Almantas Kulbis (@almantas), “a passionate promoter of iNaturalist in Lithuania, who works in non-formal education for students,” she says, Jurga joined in 2018. “By the way, it is especially thanks to him and his colleagues that iNaturalist is so popular in Lithuania.”

I use iNaturalist myself for many reasons. First and foremost, for entertainment and self-education. It is a wonderful tool to keep the mind and body (after all, you need to walk a lot!) active. It's also great fun to go back to my early experiences of trying to learn about different organisms in nature, not just the ones I study. Another area is education. I also encourage people to get involved in these activities when they have the opportunity - to look back at nature, to see its extraordinary diversity, to start respecting it more.

And finally, I use iNaturalist for work. Mycologists in Lithuania are few and far between, so citizen science is very useful for collecting the data on distribution of fungi and lichen species. Thanks to the iNaturalist community alone, one species that had not been found in Lithuania before and one that was thought to be extinct were found. Of course, IDing lichens from photos (even very good ones) is problematic, as most of them require microscopy or chemical tests (or at least reagent reactions and UV light). But it is still possible to ID some of them, so the iNaturalist community should not stop uploading observations of lichens, even if they can sometimes only be IDed down to the class level.

(Some quotes have been lightly edited for clarity.)


- Speaking of southern Africa, here’s an undescribed lichen from that region that Jurga helped get identified. Great discussion!

- When it comes to lichens, “Ramalina menziesii or genera Niebla and Pulchrocladia are my absolute favourites,” says Jurga.

- And finally, some adivce for finding and phtoographing lichens. “Lichens can indeed be found almost anywhere: even in water on the half or fully submerged rocks or on shells of barnacles. The only problem is that for many lichens a hand lens is required even to find them and a very good macro lens is needed to take a photo. For these which can be seen by the naked eye, my advice is to take several photos: one of general view of the thallus, one close up of any structures present on the thallus (ascomata, vegetative propagules, pseudocyphellae, etc.) and one close up of the edge of the thallus. For some foliose lichens (Peltigera, Nephroma, some others)  view of both sides of thallus is obligatory.”

- Check out the Lichenicolous Fungi of the World project!

Posted on March 30, 2023 09:15 PM by tiwane tiwane | 33 comments | Leave a comment

A new Computer Vision Model (v2.2) including 1,603 new taxa

We released a new computer vision model today. It has 72,511 taxa up from 71,286. This new model (v2.2) was trained on data exported last month on February 19th and added 1,603 new taxa.

Taxa differences to previous model

The charts below summarize these 1,465 new taxa using the same groupings we described in past release posts.

By category, most of these new taxa were insects and plants

Here are species level examples of new species added for each category:

Click on the links to see these taxa in the Explore page to see these samples rendered as species lists. Remember, to see if a particular species is included in the currently live computer vision model, you can look at the “About” section of its taxon page.

We couldn't do it without you

Thank you to everyone in the iNaturalist community who makes this work possible! Sometimes the computer vision suggestions feel like magic, but it’s truly not possible without people. None of this would work without the millions of people who have shared their observations and the knowledgeable experts who have added identifications.

In addition to adding observations and identifications, here are other ways you can help:

  • Share your Machine Learning knowledge: iNaturalist’s computer vision features wouldn’t be possible without learning from many colleagues in the machine learning community. If you have machine learning expertise, these are two great ways to help:
  • Participate in the annual iNaturalist challenges: Our collaborators Grant Van Horn and Oisin Mac Aodha continue to run machine learning challenges with iNaturalist data as part of the annual Computer Vision and Pattern Recognition conference. By participating you can help us all learn new techniques for improving these models.
  • Start building your own model with the iNaturalist data now: If you can’t wait for the next CVPR conference, thanks to the Amazon Open Data Program you can start downloading iNaturalist data to train your own models now. Please share with us what you’ve learned by contributing to iNaturalist on Github.
  • Donate to iNaturalist: For the rest of us, you can help by donating! Your donations help offset the substantial staff and infrastructure costs associated with training, evaluating, and deploying model updates. Thank you for your support!
Posted on March 30, 2023 10:56 PM by loarie loarie | 14 comments | Leave a comment