Journal archives for June 2019

June 09, 2019

Feather Stars and the Wonderful Weirdness of Marine Invertebrates - Observation of the Week, 6/8/19

Our Observation of the Week is this feather star, seen in Indonesia by @maridom!

“When I began diving some 25 years ago, I marveled at the beauty of sea life and was astonished to discover so many colors and forms, so many animals never seen on land,” says Maridom. “Then I became interested to learn more about the ecosystem and biology.”

And while she says most new divers think mainly about seeing fish, she likes to emphasize the beauty and diversity of marine invertebrates in when teaches marine biology courses. “I mostly am interested in phyla which seem weird to us terrestrial beings, such as Cnidaria and Echinodermata,” she says. “And during my last trip to The Philippines, I jokingly became known as ‘Queen of Ascidiacea’!

As soon as I see something beautiful under the sea, I point my camera to it and sometimes I come away with a successful photo! The photo of this Comatula this one of those: the colors are nicely contrasted and the shape of its arms are so delicately drawn.”

While sea stars and sea urchins are more familiar members of the Phylum Echinodermata, feather stars like the one Maridom photographed belong to a totally different subphylum called Crinozoa, which are also called sea lilies. They often have ten or more arms surrounding the mouth, and capture planktonic organisms with tube feet on the arms, moving the food down the arm in a blob of mucus.

Maridom (above, in Egypt) has been taking photographs on her dives for the last decade, and she tells me “it changed my way of diving and looking at living beings, even the small and weird ones, and I could not do without it now. Then, at home, trying to identify the species in my photographs brings back happy memories of the trip. I like to call things by their name while diving, as if I was part of their world.”

She discovered iNaturalist about three months ago, and has been uploading photos from her archive. “Each morning when I open my computer, the first thing I do is see if my unidentified strange things have now received an ID. Many thanks to all identifiers!

I love the way iNaturalist works, where all over the world, people keep connected and give from their personal time to help identify observations from others. I think, probably, when I was in The Philippines  last month, it changed my way of taking pictures and looking at unknown things.”

- by Tony Iwane. Some quotes have been lightly edited for clarity and flow.


- Feather stars can swim and crawl, both of which look really cool and strange.

Posted on June 09, 2019 00:06 by tiwane tiwane | 2 comments | Leave a comment

June 14, 2019

Rhino vs Elephants in Namibia - (belated) Observation of the Week, 6/13/2019

Our Observation of the Week is this confrontation between a Black Rhinoceros and a group of African Elephants, seen in Namibia by @jerrythornton!

Jerry Thornton, who grew up next to the Wichita Mountains National Wildlife Refuge but now resides in southern California, describes himself as “an amateur naturalist with a lifelong love of both nature and photography.” His wife, who is a freelance wildlife writer, will often research a topic and Jerry comes along to photograph her trip. They’ve been to Africa and South America, and also go scuba diving, “which we like to view as underwater safaris,” he says.

The dramatic series of photos you’ll see in this post were taken by Jerry during a tour of Nambia he and his wife went on back in 2014. They had stopped at the Moringa waterhole in Etosha National Park to and at first saw pretty standard waterhole behavior. However, after about half an hour a Black Rhinoceros approached. I’ll let Jerry take it from here.

The elephants began to get agitated as soon as the rhino arrived, even before it stepped into the water, with the elephants rapidly backing out of the water, ears fully extended, and bellowing much more than they had been just five minutes before. And they became even more agitated as soon as the rhino stepped into the water, forming the wall of elephants seen in the first of the photos.

As the rhino stayed longer and longer other elephant family groups would approach and then back off after seeing the rhino, sometimes their young males trying their luck at intimidating the rhino through bellows, ear waving, and as in the photo, even trying to blow water at them. Eventually one of the young males got too close and the rhino decided it had taken enough harassment, chased the offending elephant off in a cloud of dust, and then returned to the waterhole.

Unfortunately we could only watch this for about another hour, but the rhino was still soaking in the waterhole when we left and we had to assume it left on its own terms.

While it’s difficult to know exactly what motivated these behaviors, Jerry tells me he’s learned “elephants hate and fear rhinos, since they are one of the very few animals that can by themselves cripple or kill an adult elephant rather easily, and having a rhino so close to their young brought out their worst/most interesting behavior.”

Jerry (above) discovered iNaturalist recently, when trying to identify butterflies and flowers brought around by southern California’s rainy winter. “As I realized its potential for more accurately identifying all types of plants and animals,” he explains, “I began to post my past observations, with the goal of learning, and providing observations and photos for others.”

- by Tony Iwane


- Here’s an annotated video showing a Rhino and an Elephant with a bit of a misunderstanding.

- The New York Times has a nice article and video about an elephant’s amazing nose.

Posted on June 14, 2019 06:01 by tiwane tiwane | 7 comments | Leave a comment

Vision Model Updates

iNaturalist currently uses vision models in two main places: 1) a private web-based API used by the website and the iNaturalist iOS and Android apps, and 2) within the recently updated Seek app. When Seek 2.0 was released in April, it included a different vision model than we were using on the web. At that time the web-based model was a third-generation model we started using in early 2018. That web-based model was trained with the idea it would be run on servers, and servers can be configured to have far more computing power than a mobile device. As a result that model was far too large to be run on mobile devices.

Early this year, with an updated Seek in mind, we started another training run with two main goals: shrinking the file size of the model, and allowing it to recommend taxonomic ranks other than species (e.g. families, genera, etc.).

Smaller

The mobile version of the model needs to be small in terms of file size to minimize the amount of data app users would need to download. Smaller models can also be used by more devices as they need fewer resources to run (e.g. memory, battery), and can generate results faster, which is important for Seek's real-time camera vision results. These models take a lot of time and money to train, so we also wanted a model that could be simultaneously trained to produce a large web-based version and a smaller version for use in mobile devices.

Unfortunately, shrinking the file size like this slightly decreased model accuracy compared to the larger web-based version (kind of similar to image compression), and we found that was an unavoidable tradeoff. We take this into account when processing the model results, and on average for a similar error rate, the mobile version might recommend a taxon at a higher taxonomic rank than the web-based version. The taxon results we show to users shouldn't be less accurate, but they may be less specific.

More Species Represented

We wanted the model to include more species data, even when some species don't have enough photos to be recognized as species level. There are some species with a small amount of photos that, if we trained on that small set of photos, likely wouldn't have enough information for the model to reliable recognize those species.

Our 2018 model only included taxa at rank species. We set a threshold for number of photos, and species below the threshold were not included. We could still recommend higher taxa by doing some post-processing of results, but the model itself would only assign scores to species. In our latest training run we allowed the photos from species under the threshold to be rolled up into their ancestor taxa until the threshold was reached, and we allowed the model to assign scores to these non-species nodes. This allows more species to be represented in this newer model, sometimes at the genus level mixed up with photos of other species in the genus under our threshold. Now instead of not knowing anything about these species, the model can at least identify the genus or family, etc.

Replaced Web-Based Model

On May 24 we replaced the existing web-based model from 2018 with the web-based version of the 2019 model used by Seek. You may have noticed taxa higher than species starting to appear in vision suggestions, and this is why. That means the iNaturalist iOS and Android apps, and web vision suggestions have all been using this new model for the last few weeks. As of right now we are using the same model everywhere. The model has a web-based version (used by the website and iNaturalist apps) and a mobile version (used by Seek). The two versions are from the same training run, but can produce slightly different results because of compression in the smaller mobile version, and because the web-based version can weight results based on nearby species occurrences.

Evaluating

By adding photos of more species, we hoped to see an increase in accuracy for observations for species less represented in iNaturalist observations. One way we thought to get insight into that is to look at identifications made through vision suggestions that are current or improving (good) vs withdrawn or maverick (maybe less good). Here's a chart of such identifications for flies (Diptera) and spiders (Arachnida). The dotted red line represent with the web-based model changed. The difference isn't glaring, but it does look like for these groups vision-based IDs are sticking more.


The model was also trained more recently, so we hoped to see an increase in accuracy for observations in countries that have added a lot of observations since 2018. Here's a chart comparing the accuracy of the older model to the new model for a sample of random observations in California, Europe, Oceania, and South Africa (we could/should have included more countries with different observation and species densities, but these still show the trend). In this chart, "Right" means the model's best suggestion was consistent with the actual observation taxon (it suggested the right taxon or its ancestor), "Wrong" means the best suggestion was inconsistent with the actual taxon, and "Unable to determine" means the model was not confident enough to make a suggestion.

For observations from California, the models get nearly the exact same number right, with the older model making more specific suggestions. For observation from Europe, again the two models get nearly the same amount right, but this time the new model makes the more specific suggestions. In Oceania, the new model is getting more right and is more specific. And looking in South Africa, the new model gets a lot more right, with nearly double the amount of correct species recommendations (and fewer wrong).

Finally, the new model can now suggest taxa higher than species beyond the suggested common ancestor we've always had. This means the vision suggestions will be a mix of species and higher taxa. Here's a chart of the rank of all vision-based identifications over the last month or so. Nothing really stands out in this view of the data - there are maybe more identifications recently, and you can maybe see more at rank genus (the larger yellow bar).

By removing identifications at rank species, it’s clearer there have been more vision-based identifications of higher taxa since the new model went into effect.

By going even further and remove ranks below order, it's clear that there's been a vast uptick in vision-based identifications at these ranks. It should be noted that on May 31 the Seek app started to allow observations to be submitted to iNaturalist, and as explained above Seek will tend to recommend taxa at higher ranks than the web-based vision of the model, and we can see these higher taxon identifications really pick up after that. Better to have accurate but broad identifications, than inaccurate species identifications.

So that's an update on iNaturalist's vision models, and why some things may have appeared to change recently, like the addition of non-species recommendations. We think these changes are overall for the better, and hopefully you agree. We're interested to hear you thoughts. Did anyone notice the change? Now that you know the model should perform better for less observed species, I'd be interested to hear people's experiences with different taxa, or in different places.

Posted on June 14, 2019 19:07 by pleary pleary | 16 comments | Leave a comment

Clarifying Ancestor Disagreements

What is the Community Taxon?

Every observation with at least one identification has what we call an Observation Taxon. This is the label shown at the top of the observation page and is the taxon that the observations is "filed under" on the tree of life.

The Community Taxon (also sometimes called the Community Identification) is a way to derive a single identification from multiple identifications provided by the community. If an observation has more than one identification, it will also have a Community Taxon. The Observation Taxon will match the Community Taxon unless: (a) the observer has opted out of the Community Taxon, (b) there is an identification of a finer taxon that hasn’t been disagreed with (more on disagreements shortly).

Identifications hang on nodes on the tree of life. An identification adds an agreement with that node and also all of that nodes ancestors back to the root of the taxonomy.

If two identifications are on different branches of the tree of life, they each count as an agreement for the branch they are on and a disagreement for every node on the other branch back to the common ancestor of the two branches.

Each node is scored with the cumulative number of Agreements (i.e. the identifications on it or its descendants), the total number of Disagreements (from identifications on other branches), and something called "Ancestor Disagreements" which we’ll describe shortly.

The Community Taxon is the finest ranked taxon with at least two agreements where the ratio of the number of agreements to the sum of agreements, disagreements, and ancestor disagreements is greater than ⅔.

In contrast, the Observation Taxon will always match the Community Taxon unless:
a) there is just a single identification, then the Observation Taxon will be defined by that identification
b) the observer opts out of the Community Taxon, then the Observation Taxon will be defined by the observers identification
c) there are no disagreements and there is an identifications of descendants of the Community Taxon, then the Observation Taxon will be defined by the finest such identification (because the community likes that a single non-controversial identification being able to ‘move the ball forward’)*

*if that finest identification is of infra-species rank (eg subspecies), the Observation Taxon won't roll forward to that rank from the Community Taxon if that identification was added later (because the community doesn't like what would be Research Grade observations at species rank being rolled forward to Needs ID observations at infra-species rank). However, if the Observation Taxon was initially set at infra-species rank from a single identification, a non-disagreeing identification of an ancestor won't roll the Observation Taxon back to the Community Taxon.

What are Ancestor Disagreements?


So what are Ancestor Disagreements? If one person adds an identification of one node and another person thinks it’s not that but can’t provide an alternative on another branch, they might add an identification of an ancestor of that node. For example, I might add an identification of Seven-spotted Lady Beetle, but you might add an identification of the family lady beetles, which contains that and many other species.

When the Community Taxon was first implemented, any identification made after previous finer identifications in time was implied to be a disagreement with these finer taxa. These ‘implicit ancestor disagreements’ are now labeled as such.

They only disagree with taxa associated with previous finer identifications. Also some bugs were fixed in how the Community ID charts on the observation page handle "implicit ancestor disagreements".

What are Explicit Disagreements?


Because of confusion about whether people were disagreeing or not, we later made ancestor disagreements "explicit". When an identification is made that is an ancestor of the Community Taxon (or the Observation Taxon if there’s only one identification), the identifier is now presented with a choice to indicate whether they are disagreeing with the Community Taxon or not.

If they are not disagreeing, their identification does not count as an ancestor disagreement for the taxon that was the Community Taxon.

And the identification is not labeled as a disagreement:

However, If they are disagreeing, their identification counts as an "explicit ancestor disagreement" with the Community Taxon.

And the identification is labeled accordingly:

Two ways to disagree...


When we implemented this, we thought that ancestor disagreeing should disagree with the entire branch below the disagreeing identification i.e. “I disagree that this is Seven-spotted Lady Beetle *and* all taxa on the branch between Seven-spotted Lady Beetle and the taxon I have proposed”. Let’s call this the “Branch Disagreement” way to disagree.

We’ve since come to realize that our communication about this was inconsistent and confusing, based on numerous discussions with community members in person and in the Forum. Furthermore, these discussions suggest the community interprets disagreeing as just with the Community Taxon i.e. “I disagree that this is Seven-spotted Lady Beetle but not the whole branch below the taxon I have proposed”. Let’s call this the “Leading Disagreement” way to disagree. We’ve also since realized from the Forum that Leading Disagreement is a more common and less controversial way to disagree than Branch Disagreement.

At the end of this post, we’ll discuss planned changes to improve things moving forward. But for now, let’s try to clarify our communication describing how things are currently behaving to all get on the same page.

Imagine the following sequence of identifications:

Branch Disagreement tallies disagreements as follows:

Which differs from how one would tally disagreements for the Leading Disagreement case:

Notice that this can impact how the Community Taxon is calculated. In this example, Branch Disagreement computes the Community Taxon as Lady Beetles Family:

While Leading Disagreement would compute it as Asian Lady Beetle:

The site is currently assuming Branch Disagreement as it calculates the Community Taxon. We tried to capture the language for the Potential Disagreement question to distinguish "not disagreeing" with "branch disagreeing" as:

To more precisely capture how the Community Taxon was being calculated this could have been worded something like:

Likewise, Ancestor disagreement identifications could have been more precisely labeled something like the following to reflect how the Community Taxon is being calculated.

Planned changes to distinguishing the two ways to disagree

While we hope the above description will help clear up much of the confusion with how iNaturalist is handling explicit ancestor disagreements, we’ve also learned that these two ways of disagreeing (branch and leading) are distinct and both useful. While "leading disagreement" is clearly the most commonly-used way to disagree, we still think that "branch disagreement" is useful, particularly in enabling the community to stop observations from becoming too finely identified beyond where the community can be certain.

We’re working on changes that would enable identifiers to indicate which way (leading or branch) they are disagreeing. The Potential Disagreement prompt will have three questions:

Here the first orange button would mean a "leading disagreement" and the second would mean a "branch disagreement".

Likewise, "leading disagreement" identifications will be decorated as:

and "branch disagreement" identifications will be decorated as:

Apologies for the length of this post, but we hope it clarifies some of the confusion about how the "ancestor disagreement" functionality is currently working and planned improvements to address concerns expressed in the forum.

Posted on June 14, 2019 21:10 by loarie loarie | 16 comments | Leave a comment

June 19, 2019

A Chilean Flamingo and an America Flamingo Meet in Mexico - Observation of the Week, 6/18/19

Our Observation of the Week is this unlikely pair - a Chilean Flamingo on the right and an American Flamingo on the left - seen in Mexico by @luisave!

About three years ago, an American Flamingo arrived in the Mexican city of León, Guanajuato, establishing itself in Metropolitan Park. It was around this time that Luis Mauricio Mena Páramo (luisave) began his bird inventory of the city. Since then, Luis has documented 188 species in the city (Mexico’s fourth largest), and on May 29th of this year he photographed a second flamingo in Metropolitan Park.

After discussions on both iNaturalist and in local birding fora, the second flamingo was confirmed as a Chilean Flamingo, a species that naturally ranges in the western and southern parts of South America and has been introduced in some parts of Europe. Luis’s photo is the first photo on iNaturalist of a wild Chilean Flamingo in Mexico (and Central America, for that matter), and well out of its normal range!

“So far,” explains Luis, “we have no knowledge or information about the possible origin and permanence of this bird

What we can know is that the American Flamingo that also inexplicably arrived at the park more than three years ago has given it an excellent welcome. Perhaps it is a historical record, in which two wild Flamingos of different species coexist together and are very well adapted to each other.

Like other flamingos, the Chilean Flamingo uses the filters in this beak to feed on algae and invertebrates, and the carotenoids in their food cause the pink coloration of the birds’ plumage. Just one egg is laid per mating pair, and it rests on a raised mud nest. Both parents are able to produce crop milk to feed the young bird after it hatches.

Luis (above, at Metropolitan Park with both flamingos in the background) is turning his bird inventory into a book titled PRIMERA GUÍA DE AVES DE LEÓN, and he tells me “I use iNaturalist virtually every day in order to learn more about the world around me and also to share my observations with a community of naturalists...It is clear that without the support of the iNaturalist platform I would not have gotten this far...in my fifties I think it's been the best way to invest my free time, doing what I really like. It's a good way to transcend.

To this day, both flamingos continue to reside in the Metropolitan Park of León, and I have practically watched and photographed them every day. It has been amazing this story of adaptation to the urban environment and I feel very fortunate to share it with all of you.

- by Tony Iwane. Some quotes have been edited for clarity.


- A group of Andean Flamingos “dance” in this video.

- Scientists have found that flamingos are more stable on one leg than two

Posted on June 19, 2019 03:02 by tiwane tiwane | 14 comments | Leave a comment

June 24, 2019

iNaturalist World Tour

We’re launching a new series today where each week we’ll focus on seven countries and feature one of them each day. We tried this a year and a half ago, but it was heavy on writing which made it a bit too staff intensive for us to maintain. We’re giving it another shot, but this time are going to let the figures speak for themselves.

As we’ve done before, we’ve sorted countries based on the number of observations and will proceed in descending order. This week we’ll start with the most active countries on iNaturalist. iNaturalist is still heavily biased towards the United States, its North American neighbors (Mexico and Canada), the United Kingdom, and her southern hemisphere Commonwealth sisters (Australia, South Africa, and New Zealand).

So without further ado, let’s kick things off with the United States. This figure shows the top 50 observers located near the median of their observations made within the country. Each user is scaled by the number of observations they’ve made. You can see the bias towards California, Texas, and New England where most of the top observers are based. These figures are static snapshots of iNaturalist from today (6/24/19).

Growth in number of observations per month looks a lot like growth on the site overall. Observations have been doubling annually and there’s a clear summer bias.

The figure below shows the most "observose" groups of organisms and the top identifier in each group. Also like the site as a whole, Plants, Insects and Birds are the three biggest groups.

We’ll be back tomorrow with Mexico!

@ck2az @finatic @srall @erikamitchell @sambiology @greglasley @aguilita @graysquirrel @john8
Posted on June 24, 2019 21:12 by loarie loarie | 94 comments | Leave a comment

June 25, 2019

A Parasitic Plant Rises from the Desert in Jordan - Observation of the Week, 6/24/19

Our Observation of the Week is this Cynomorium coccineum plant, seen in Jordan by @fragmansapir!

Currently the scientific director of the Jerusalem Botanical Gardens, Dr. Ori Fragman-Sapir works “on endangered plants, flower bulbs, doing ecological and taxonomic research.” He also leads tours in Israel, the Mediterranean, and the Caucasus. While on an excursion to the southern part of Jordan (for his birthday!) this past April when Dr. Fragman-Sapir came across the small plant seen above. “It was amazing to see this parasite coming out of the dry sands, as if it was a miracle,” he recalls.

Those red stalks are pretty much the only parts of the plant one can see above ground, and they’re source of this species’ myriad common names, such as red thumb, desert thumb, and the bizarre (and misleading) Maltese fungus. A completely parasitic plant, Cynomorium coccineum contains no chlorophyll and spends most of its existence as a rhizome (an underground stem - think ginger or lotus “roots”), leaching nutrients and water its host plant, or plants. In spring the plant will send up its inflorescence, which is covered in tiny flowers. Flies are attracted to the cabbage-like smell of these flowers, and serve as the plant’s main pollinators.

Dr. Fragman-Sapir (above) has recently started posting his photos to iNaturalist, and hope it becomes a place where can have all of his “observations in one convenient place where others could enjoy and learn as well.”

- by Tony Iwane


- Dr. Fragman-Sapir has authored or coauthored several books, some in Hebrew and some in English, including Flowers of the Eastern Mediterranean.

- Many cultures have believed Cynomorium coccineum can cure multiple ailments, such as ulcers, anemia, hypertension, and impotence. It’s flesh is also edible as a food source.

- Check out this video about dodder, another type of parasitic plant, and watch it “choose” a host.

Posted on June 25, 2019 04:59 by tiwane tiwane | 5 comments | Leave a comment

Mexico - iNaturalist World Tour

The second most active country on iNaturalist is Mexico. This is due to the efforts of CONABIO who were the founding members of the iNaturalist Network with Naturalista.mx.


While growth has been steady since 2013, Mexico saw a huge bump April 2019 from the Mexico Reto Naturalista Urbano organized in conjunction with the 2019 City Nature Challenge.


Compared to the United States, there's a slightly larger proportion of bird and herp observations and slightly fewer insects and fungi.


We’ll be back tomorrow with Canada!
@momoto-erick @francisco3_tutor @juancarlosgarciamorales1 @blakesito @najera_tutor @ivanresendizcruz @alexiz @poncho @aztekium_tutor @pioleon

Posted on June 25, 2019 15:15 by loarie loarie | 26 comments | Leave a comment

June 26, 2019

Canada - iNaturalist World Tour

Canada is the third stop on the iNaturalist World Tour with over 1 Million observations. iNaturalist.ca became part of the iNaturalist Network in 2015 through the efforts of the Canadian Wildlife Federation, Royal Ontario Museum, Parks Canada and NatureServe Canada. @jpage_cwf deserves huge credit leading coordination of this effort. Like the United States, most of the top observers in Canada are based on the east or west coasts.


Canada is even more seasonal than the United States with observations peaking in July each year.


The distribution of observations across species groups is similar to the the United States with slightly more mammals than herps which also makes sense given the higher latitudes.


We’ll be back tomorrow with Australia!
@owenclarkin @jem9redwood @nanorca13 @johndreynolds @swampy @xyz @wdvanhem @gwynethgovers @alwoodhouse @danavan

Posted on June 26, 2019 15:01 by loarie loarie | 24 comments | Leave a comment

June 27, 2019

Australia - iNaturalist World Tour

Moving from North America to the Southern Hemisphere, Australia is the fourth stop on our iNaturalist World Tour. Here, most of the top contributors are based along the coast from Adelaide north to Brisbane. @coenobita's observations concentrated in northern Queensland, @gumnut's in Tasmania and @ryber& @daniel_heald near Perth help flesh out other parts of the country.



The number of observations per month has been growing steadily since 2016. Its not a coincidence that 2016 is also when the fantastic Australasian Fishes project (which fueled the hoodwinker discovery among many others) launched. Questagame (which is most popular in Australia) also started posting observations to iNaturalist in 2016. However, the dramatic jump in May 2019 was from the arrival of many members of the Bowerbird community (and our efforts to help them migrate their data over before Bowerbird closes down). iNaturalist is honored to help carry on the Bowerbird legacy! Much of the motivation for the Bowerbird community to migrate to iNaturalist is because iNaturalist contributes data to the Atlas of Living Australia. We're very excited to strengthen ALA-iNat collaboration with the Australia Node of the iNaturalist Network launching in August.


The increased number of insect observations relative to other countries we've looked at so far is likely due to @vicfazio3's prodigious efforts to grow the Lepidoptera community in Australia and the entomology expertise BowerBird has contributed. The large number of fish observations is due to the hard work of @markmcg and the Australasian Fishes community


We’ll be back tomorrow with South Africa!
@reiner @vicfazio3 @imcmaster @nicklambert @silversea_starsong @joshuagsmith @vicfazio3 @gumnut @sascha_schulz @jadonald

Posted on June 27, 2019 16:37 by loarie loarie | 38 comments | Leave a comment