Journal archives for December 2020

December 14, 2020

A Fish Isopod Photographed by a Free Diver - Observation of the Week, 12/14/20

Our Observation of the Week is this Fish Isopod (likely Genus Anilocra), seen off of Greece by @vasilis_stergios!

“The sea is where I really feel at home, unburdened by gravity, exploring a space with such biodiversity that you can always count on spotting something new every time you look below the surface,” says Vasilis Stergios. And he spotted this bright red isopod while free diving in the Saronic Gulf, where he says “[we] get to witness an abundance of planktonic life, from the common Leucothea multicornis ctenophore, to the rarely seen moray eel larva!” But it took a few tries with his camera.

On one of these dives, I spotted this free-swimming Anilocra isopod at almost zero depth, probably looking for a host fish to attach to. Must have taken at least 50 shots with my compact Olympus TG-4 in microscope mode to produce this one almost clear shot of a tiny, less than 1cm long, constantly moving creature, with a clear focus on the compound lenses of its eyes. Thankfully this was a day with zero wind or current, otherwise I wouldn’t have even bothered to try in the first place.

As Vasilis mentioned, isopods in this family (Cymothoidae) generally parasitize fish. Once they find a host, they will attach and feed on the fish’s blood. Many are seek out specific host species as adults, and often attach to certain parts of the host’s body (eg gills, behind the eyes, etc). Fascinatingly, they are protandrous hermaphrodites - juveniles start out as males, but will become female if no other females are around. Fish parasitized by these isopods will often visit shrimp that will remove and feed on the isopods.

Vasilis (above) grew up hiking the mountains and snorkeling and fishing by the sea, and tells me he likes to spend “every moment of my spare time away from work.”

He first found iNat via the Smithsonian’s Instagram account. “What really surpassed my expectations when I started using the site, is the image identification algorithm, which I have been using ever since as an invaluable tool on the field,” he says.

Being able to quickly pinpoint genus, or even species of any plant or animal I encounter, has really widened my focal range! While I originally would take shots of my favorite plants or animals, I now take time to photograph and identify any creature that draws my attention (rarely or first seen being my number one criteria), in an attempt to aid in recording the diversity of Greek flora and fauna.

- Speaking of Instagram, you can check out Vasilis’s Instagram account here!

- Vasilis posted the first observation of an Oceania armata hydroid to iNat a few weeks ago, it’s quite stunning.

- This is not the first Observation of the Week that documented a fish isopod. 

Posted on December 14, 2020 22:39 by tiwane tiwane | 11 comments | Leave a comment

December 15, 2020

Exploring fine scale geographic patterns on iNaturalist

One of my favorite things to do on iNaturalist is to look at fine scale geographic patterns of individual species. Yellow spotted millipede (Harpaphe haydeniana), for example, has specific habitat requirements and in the San Francisco Bay Area and is restricted to the forests around Mount Tamalpais in the North Bay and the Santa Cruz Mountains in the South Bay with relict populations on San Bruno Mountain and possibly in the Berkeley Hills.

Unfortunately, the way iNaturalist displays obscured observations and inaccurate observations can add noise to these maps which makes it more difficult to see the biogeographic patterns. Remember that for obscured locations iNaturalist displays a stemless marker randomly located within a 0.2 × 0.2 degree grid cell containing the actual location. Similarly, observations may have accuracies that are too inaccurate for the scale you’re exploring.

We don’t have filters in the menu for these yet, but we do have URL parameters that will let you construct URLs that exclude obscured and inaccurate observations from your searches. To ignore observations where the user has chosen to obscure location information (geoprivacy) and also observations automatically obscured via conservation statuses (taxon_geoprivacy), add parameters for geoprivacy=open&taxon_geoprivacy=open. To ignore observations with coarse accuracy circles, include the acc_below parameter and a value in meters. For example, adding acc_below=1000 will ignore observations with accuracy circles with radii larger than a kilometer. Compare the default search for Ensatina (Ensatina eschscholtzii) salamander observations around the Bay Area with one that includes these parameters. From the search on the right, its more clear that Ensatina's avoid urban areas in the South Bay and San Francisco.

Note that the acc_below param also ignores observations without unknown accuracies. There’s currently no way to search for observations with accuracies that are unknown OR below some threshold. But you can search for observations with unknown accuracies by constructing a URL with acc=false

As you’re exploring these fine scale geographic patterns, please help mark locations that don’t look reasonable. For example, the presence of forest and mountain loving Pacific Trillium in the middle of Santa Rosa (flat and suburban) looks suspicious.

Mark these observations by voting no to "Location is accurate" under the "Data quality assessment"

Please don’t vote no to "Location is accurate" if somewhere within the accuracy circle could be suitable. For example this Common Cowparsnip with a marker centered on the ocean but with an accuracy circle that encompasses suitable habitat on land.

But if all of the area within the accuracy circle is unreasonable in your judgement, as in the case of the Pacific Trillium described above, it’s fine to mark the location as inaccurate.

In addition to voting no to "Location is accurate", it’s a good practice to also leave a comment in case you’re wrong (which may means its a very interesting observation) or is captive (which means you should remove your "Location is accurate" vote and replace it with a no vote to "Organism is wild").

If an observation has an unknown accuracy and the marker is centered on a very unreasonable location (e.g. this flowering plant in the middle of the ocean) its fair game to vote no to "Location is accurate".

Thanks for your help curating these data. They're only as useful as they are well curated. Assuming we as a community can keep on top of bad IDs and suspect locations, these maps are becoming more and more interesting each day as they fill in with new observations.

Posted on December 15, 2020 23:44 by loarie loarie | 19 comments | Leave a comment

December 18, 2020

Special tax incentives in 2020 for charitable gifts from U.S. taxpayers

Every day in 2020, iNaturalist connected people around the globe to biodiversity around them and to each other. iNaturalist fostered connections and meaning for over a million people during a time of isolation and suffering. With your support, iNaturalist will continue to put biodiversity on the map for years to come. Has iNaturalist helped you this year? If so, can you help iNaturalist?

Just for 2020, there is a new tax deduction for taxpayers in the United States as part of the CARES Act to encourage philanthropic giving to causes such as iNaturalist (via a qualified charity, the California Academy of Sciences). This year, households taking the standard deduction can take an additional tax deduction of up to $300 (total for both individual and joint filers). Normally, only those who itemize deductions receive a tax benefit from charitable gifts, so this new deduction can benefit the 87% of filers who take the standard deduction. Those who itemize also benefit this year—they may be able to deduct up to 100% of their adjusted gross income.

There has never been a better time to make a generous charitable gift to support iNaturalist. Donate to iNaturalist before the end of the year to take advantage of this special tax deduction for 2020.

If you want to support iNaturalist by check, an IRA Qualified Charitable Deduction, a Donor Advised Fund, grants, employer matching, or employer volunteer hours, we have more details here. iNaturalist is a not-for-profit joint initiative of the California Academy of Sciences and the National Geographic Society, and all donations are received by the California Academy of Sciences (Tax ID: 94-1156258).

Disclaimer: We are not qualified to provide tax/financial advice and encourage you to ask your tax-advisor how a gift of cash, appreciated stock, or a qualified charitable distribution from your IRA can benefit you.



Posted on December 18, 2020 06:07 by carrieseltzer carrieseltzer | 6 comments | Leave a comment

Bridging museum characters and field characters: a case study in Ghost Crabs

Growing the community’s identification expertise is core to iNaturalist. Often the scientific literature is the best or only source of information for how to distinguish species. But the scientific literature often references “museum characters” that are convenient when dealing with preserved specimens but less convenient for naturalists. Naturalists often prefer “field characters” that can be seen externally and macroscopically - ideally without having to hold the organism in hand. Field characters may include colored markings, living posture, vocalizations or other characters that aren’t preserved in dead specimens. For example, in the Ghost Crabs (Genus Ocypode) the purple leg joints in mature Pink Ghost Crabs (Ocypode ryderi) and the H-shape back markings in mature Horned Ghost Crabs (Ocypode ceratophthalmus) are very useful field characters that are rarely referenced in the scientific literature.

An important outcome from iNaturalist is the development of reliable field characters for poorly studied groups that are readily visible in observation photos. One useful step towards this goal is to help create iNaturalist observations documenting both museum characters and field characters. These observations allow us to ground-truth their identification via the museum characters and develop convenient and reliable field characters on this foundation. But to generate such observations, observers need to know what characters to photograph.

This is where you can help. Specifically, we’d like to encourage you to adopt a group of organisms, do the research to learn the most useful museum characters for a group, and share a jargon-free, visual explanation for how observers can capture these characters in their observations. There have already been some great examples of this kind of work including @gcwarbler’s guide to Cisthene Moths (which we highlighted in this blog video), @edanko's fly resources, and @dan_johnson’s guide to photographing crayfish. Here’s a journal post I wrote on identifying Cycadians. We’d like to find ways to encourage more of this kind of content. Many thanks if you've already authored and shared information like this or are willing to try doing so. And please let us know if there’s anything we can do to help streamline or facilitate the development and sharing of this kind of content.

In this spirit, I’ve given it a shot at this with Ghost Crabs (Genus Ocypode). Ghost Crabs are a good example of a clade where in many cases iNaturalist observations don’t get identified beyond genus. I’ve included sections that provide a brief overview of Ghost Crabs, an explanation of useful museum characters, and a few words on distribution. Again, it’s my hope that this post will encourage more observers to document these characters in their Ghost Crab observations which will facilitate identifying them to species. Ultimately that will result in our community better grasping field characters and distribution details for some of the less well known Ghost Crab species. Any feedback on the usefulness of this content would better facilitate those goals would be much appreciated.

What are ghost crabs, what segment of the population to focus on, and how to find them?

This post is aimed at moving identifications from the genus level (Ocypode) to species as the community seems to have little trouble identifying Ghost Crab observations to genus. But briefly, Ghost Crabs can be distinguished from their relatives by their very large eyes which are held vertically atop prominent stalks and their preference for sandy beaches. In most of the world, their only close relatives are the fiddler crabs (Subfamilies Ucinae and Gelasiminae) which have smaller eyes (more similar in width to the stalks they sit on) and males have one very large claw. The Mangrove Ghost Crabs (Subfamily Ucidinae) are more likely to be confused with land crabs or other crabs of the Superfamily Grapsoidea than ghost crabs. In the Western Pacific and Indian Ocean there are several other crabs with prominent eyestalks and beach habits that share a superfamily with the Ghost Crabs and might be confused - e.g. the Sand Bubbler Crabs (Family Dotillidae) - but like fiddlers they can be readily distinguished from ghost crabs with a bit of practice.

While Ghost Crab species often have distinctive adult coloration, juveniles tend to have similar sand-camo coloration and they lack the pointy eye projections distinctive of many species. So if it’s possible to find an adult crab it’s much more likely that it can be identified to species.

The museum characters I’ll refer to here work on both males and females but knowing the sex will help control for some variation. The best way to sex Ghost Crabs, like all crabs, is by looking at the shape of the pleon (abdomen) on the underside of the crab. It is narrow and triangular in males and broad and round in females.

.Like this abdomen character, most of the museum characters I’ll describe shortly are easier to photograph with a crab in hand. Before trying to catch a crab make sure you follow local regulations about handling wildlife and try to understand and minimize the ethical and conservation impact your handling of these organisms may have. A good rule of thumb: don’t handle wildlife unless you’ve done your homework and know what you’re doing. That said, a great way to catch crabs is by going out at night with a flashlight. I’ve found that adults are often easier to find using this technique, they are more likely to be outside of their burrows, and the light distracts them and makes them easier to catch. During the day, digging them out of their burrows by hand can sometimes be effective.

Museum characters
Here, I attempt to visually explain the characters used in the key in Sakai, K.; Türkay, M. (2013). Revision of the genus Ocypode with the description of a new genus, Hoplocypode (Crustacea: Decapoda: Brachyura). Memoirs of the Queensland Museum — Nature. 56(2): 665-793. But based on my research, these characters are widely used in the scientific literature on Ghost Crabs.

Eyestalks prolonged distally
Adults of some species of Ghost Crabs have pointy projections on top of their eyes (“eyestalks prolonged distally”). Generally, this is a projection of the eyestalk itself but in Tufted Ghost Crab (Ocypode cursor) it is made of a tuft of hair (“Setal brush”). This is a great character because it can generally be seen without having the crab in hand. But unfortunately, it only works on mature adults. So to take advantage of this character try to find an adult member of the population to photograph.

Stridulating ridge
On their larger claw’s palm surface (the inner side facing the crab), some species of Ghost Crab have a line of bumps called the “Stridulating ridge”. The presence (or absence) of this ridge and details of its shape are probably the most commonly referenced museum character for Ghost Crabs. Unfortunately, this character is very difficult to photograph unless you have the crab in hand and have a nice macro lense. But on the flip side, this is the most reliable museum character for identifying juveniles.

Setae on P2 and P3 prodopus
Some species of Ghost Crab have hair (setae) on their legs. The key specifically refers to the presence of setae on the P2 and P3 prodopus. The P2 legs are the ones just behind the claws and the P3 legs are the ones behind those. The prodopus is the segment of the leg just before the tip.

Chelipeds pointed distally
The final character referred to in the key is whether the claws (chelipeds) are squared-off (truncate) or pointed at their tips (distally).

Distribution is extremely helpful for identifying Ghost Crabs. It should be noted that relying too much on distribution can obscure finding unusual observations such as this Pink Ghost Crab in Madagascar and this Painted Ghost Crab as far north as El Salvador. Nonetheless, here’s a few words on the distributions of Ghost Crabs.

In the Eastern Pacific and Atlantic the situation is relatively straightforward with just 5 mostly allopatric (non-overlapping) species. In the Eastern Pacific there’s a non-pointy eyed ghost crab ranging from Mexico down to around Costa Rica (Gulf Ghost Crab) and a pointy-eyed ghost crab (Painted Ghost Crab)ranging from around El Salvador to Peru. They overlap in much of Central America. In the Western Atlantic there’s just one ghost crab (Atlantic Ghost Crab) ranging from Massachusetts to Uruguay. In the Eastern Atlantic there’s a pointy eyed species (Tufted Ghost Crab) with a disjunct population in the Eastern Mediterranean and along the coast of Africa. Here it overlaps with a non-pointy eyed species (African Ghost Crab).

In the Indian Ocean and Western Pacific the situation is much more complex with multiple overlapping species. Some, like Horned Ghost Crab are very wide ranging while others like Red Sea Ghost Crab have very restricted distributions. But in nearly all areas more than one species occur and the exact limits of the ranges are poorly known.

I've created a forum thread to accompany this post in order to take advantage of the iNaturalist's forum's superior tools for supporting discussion. Please comment there if you have feedback/ideas/thoughts on the more general topic on how to better support and encourage the creation and sharing of this kind of content. Feel free to comment directly on this post below if you have thoughts on identifying Ghost Crabs.

Posted on December 18, 2020 07:15 by loarie loarie | 7 comments | Leave a comment

December 21, 2020

Oh, Just a Blue-winged Kookaburra with a Sea Snake in its Beak - Observation of the Week, 12/21/20

Our Observation of the Week is this Bar-bellied Sea Snake, snagged as prey by a Blue-winged Kookaburra! Seen in Australia by @joswan12.

Walking one’s dogs is often a pretty mundane activity, but in 2015 Jo Duncan’s morning dog walk included a venomous snake dangling over her head. “I was taking my dogs for an early morning walk at the beach, also hoping to get some sunrise photos, when I saw what I thought was a dead snake,” she says.

I then realised there were about 4-5 kookaburras in the tree eyeing me and the snake. The dogs and I kept walking, and when we strolled by again about half an hour later, this particular kookaburra had the still writhing snake in its beak, and it was whipping it against the branch to finish it off. I kept creeping closer to get a better shot, but eventually I guess I got too close and he (or she) flew off with the snake! A flying snake over my head! 

Jo recently posted her photos of this encounter to iNat and the community identified the snake as a bar-bellied sea snake, one of many species in the genus Hydrophis. A member of the Elapid family of snakes (which includes cobras), they are quite venomous but like many other sea snakes are not known to be particularly aggressive. Bar-bellied sea snakes have quite narrow mouths and are known to prey on snake-eels in the sand flats. In her study [PDF] of this species in Shark Bay on Australia’s west coast, Megan Kerford noted that bar-bellied sea snakes in that area preyed exclusively on them, and foraged for them in the sand flats during low tide. 

Kookaburras (Genus Dacelo) belong to the Kingfisher family and sport large heads and beaks which they use to hunt prey. Blue-winged kookaburras are quite large, measuring about 40 cm (16 in) in length, and hunt insects, frogs, invertebrates, lizards, and yes, snakes. According to The Australian Museum, “they show extra care when snakes are the prey.”  

Now a high school English teacher in the Northern Territory, Jo’s sunrise photography habit naturally turned into curiosity about wildlife on the beach. When putting together a photo book for her nephew, she started looking up the names of the birds she photographed, which she says led to her learning insect, reptiles, frogs, and more. “Wildlife and landscape photography is a great hobby for me,” she explains. “I can recharge my soul and my mind ready for the classroom again.”

She joined iNat in April of this year, and uses it as a way to share her photos and identify their subjects, as well as add IDs to other users’ observations (“particularly frogs, butterflies and birds”), peruse photos, and to contribute species occurrence data. She tells me, “I believe it's important for communities to know what animals share their space, and know their names, so they feel more connected to their own environment and feel invested in protecting what we have.”

- Here’s some footage of a blue-winged kookaburra trying to swallow a python. It’s not easy.

- Let us go back in time to 2018, and another Observation of the Week involving a flying bird and its elapid prey.

Posted on December 21, 2020 23:10 by tiwane tiwane | 9 comments | Leave a comment

December 23, 2020

Year In Review 2020

It's the end of the year and here at iNat that means another Year in Review (don't forget, you can make your own, too). Of course, 2020 wasn't a typical year, so this go around I figured I'd spend a little time trying to answer the question many people asked us this year: how is COVID-19 affecting iNaturalist?

When lockdowns and stay-at-home orders started going into effect around the world in March, there was a lot of speculation about what would happen on iNat. Would we see less activity because people couldn't travel as far or as much as they used to? Would we see more because people were spending even more of their lives on the Internet? There was even an early and largely falsified series of social media posts out there about nature "returning" to the world now that humans had supposedly abandoned it, so some journalists were wondering if we were seeing that in iNat data.

That last question is the easiest to answer: no, we didn't, not because the behavior of all the other organisms changed (or not), but because for most of them we simply don't have the amount or regularity of data to detect changes like that. Even if we did, that data is entirely dependent on people, particularly people behaving consistently in the aggregate, and 2020 was just not the year to assume that people were behaving the same as they were last year.

So let's try a question that we might have a shot at: did people use iNat more or less when the pandemic set in? Answer: they used it more... but maybe not more than they would have without a pandemic:

That's verifiable observations by week of the year observed from the last four years (week of year is a bit weird but it makes it easy to compare years with a little more resolution than months). You can see people observed more than ever before in 2020, but maybe not quite as much more than the difference between 2018 and 2019. Plus you can see that City Nature Challenge (the big spike in Spring) took a serious hit, only barely exceeding its 2019 numbers (City Nature Challenge isn't organized by iNat, but it's regularly the biggest single event on iNat).

The number of people making those observations shows a similar pattern:

Early in the pandemic we were observing minor shifts in intra-week activity, i.e. people seemed to be making more observations during weekdays than on weekends than they did in 2019, but that pattern seemed to go away after a few weeks.

One of my favorite metrics of COVID's impact on iNat behavior is unfortunately also one of the hardest to explain, but in short: people traveled less to make observations in 2020. Surprise! The way we looked at this was to draw a rectangle around all the obs each person made each month and measure that rectangle's diagonal as an estimate of how far they traveled, and then calculated some stats on those numbers. Here's what that looks like for each month in 2019 and 2020:

It's definitely a bit zany, but you can see steep upticks around the solstices in 2019, which I would expect for summer/winter holiday travel, and then a big dip when COVID sets in and people stopped traveling. Those of you who remember your geometry and think about my description of this metric will realize that it's only a rough estimate, but it's a lot quicker to compute than measuring the actual maximum distance between observations.

Newly-added species also took a hit, as you can see in the YIR chart.

We also wondered if more of the observations added this year were actually observed in prior years, so we calculated these percentages for each year of iNat's life ("backlog" observations):

So... we're not seeing any major shift in backlogging, and in fact it seems to be stabilizing over time.

Finally it's important to remember that many of the benefits of iNat specifically and natural history more generally are impossible to measure and chart. Taking the time to slow down, consider another creature, and deliberately document the encounter has always been, for many of us, a source of solace in itself. It's an act that's just as grounding when you do it in a neighborhood park as when you do it in far-flung locales, a fact that has been crucial this year as we've all been spending more time at home. I know I personally cut way down on nature-related travel this year, but I think I also appreciated my local hikes even more. I distinctly remember the surprising sense of... unknotting I felt on the first long hike I went on with my partner during the pandemic. Just to be reminded that the sun was still shining and the plants were still growing seemed strangely revelatory, easing a tension I wasn't fully aware of.

I hope you've all managed to weather this terrible year as best as you can, that you've spent some time with friends and family, human and otherwise, in person or remotely, and that those encounters brought some some small degree of relief. As always, a huge thanks to all of you from everyone on the iNat team. While iNat has changed a lot over the years, it has always been an expression of the collective efforts of the people who use it. That means you! So to everyone who's added an observation, made an identification, or even told a friend about iNat, thank you. Here's to more time in nature in 2021.

Posted on December 23, 2020 04:44 by kueda kueda | 24 comments | Leave a comment

December 29, 2020

Colorful Calling Bullfrogs in India - Observation of the Week, 12/29/20

Our Observation of the Week is this pair of Indus Valley Bullfrogs (Hoplobatrachus tigerinus), seen in India by @vishalmistry!

“I am lucky that I have been born in an area bestowed with abundant natural beauty and wildlife diversity,” says Vishal Mistry, who hails from the Indian state of Gujarat. As a child he spent many days catching lizards and frogs, as well as looking for crocodile burrows and saving snakes and lizards. “I love observing nature, the species, the landscape, everything. 

Having a camera also made the task of capturing such natural beautiful moments easy and exciting. Initially I would just record photographs. However, the fascination with nature grew up, and I started identifying the species, to make a directory of species I encountered and share my observations.

In 2007, Vishal began working with the Voluntary Nature Conservancy (VNC), where he monitored mugger crocodiles in Gujarat and assessed the population and habitat status of the Indian wolf in the Kutch region. “This stint prepared me well and equipped me with the necessary training in wildlife research conservation,” he says, and currently still works with VNC,

where I am engaged in monitoring crocodile population, understanding human-crocodile relations and assisting in developing a program to build a community based crocodile monitoring program and involve the local community in conservation. I believe awareness is the best conservation strategy and spend a lot of time developing and conducting nature awareness and educational programs in school and colleges.

While visiting a nearby pond, Vishal came across some Indus Valley bullfrogs and made a note to return during the monsoon, when they were breeding. “This species is not so great in colours during other times of the year,” he says, “but during the monsoon, that’s when they breed and they attain greater size and the males develop the bright lemon yellow colour. That’s the time when they look like a bridegroom so eager to get married.” He found a group of about 25-30 individuals and photographed this pair of males calling for mates. 

Vishal tells me 

this species is mostly solitary and nocturnal in nature. They inhabit holes and bushes near permanent water sources. They do not stay in water for a long time, however, and spend most of their time hiding and feeding in the surrounding vegetation, where they catch anything they can and feed on it. This includes even small snakes and rodents.

He's been a long time eBirder, but Vishal (above) joined iNat only a few months ago after VNC created the Monitoring Butterflies in Gujarat project as part of Big Butterfly Month. “Sitting at home, that is not me. I am an outdoor person,” he says. 

Moreover, I love recording nature. This is something that is core to my heart. So, I have tonnes of pictures of numerous species I have encountered in my region. I did not know what to do with other groups of wildlife, other than birds. Nevertheless, my introduction to iNaturalist through the butterfly project opened up a new avenue for me, where I can contribute the information of other species as well. In addition, this app gives me information on the species found in my region that I have not seen. This makes my trips and exploration easy. I have been using iNaturalist ever since as an invaluable tool on the field. Knowing that people having proper training to contribute to the conservation of wild species will use my data is a consolation to my heart.

(Some quotes have been lightly edited for clarity)

- Vishal has uploaded several wildlife videos to his YouTube channel.

- In case you wanted to know what a group of calling Indus Valley bullfrogs look and sound like...

Posted on December 29, 2020 19:19 by tiwane tiwane | 9 comments | Leave a comment