Journal archives for November 2018

November 02, 2018

A Colorful Oyster in Fiji - Observation of the Week, 11/2/18

Our Observation of the Week is this Thorny Oyster, seen in Fiji by @desertnaturalist!

Always fascinated by nature - “high school science projects involving insect collections and frog dissections cemented that interest” - Joe Thompson eventually ended forging a career in medicine but says

my twin hobbies of scuba diving and birdwatching spurred me to travel extensively to over 100 countries. While I have always been interested in nature photography, it was always frustrating to not have the ability to ID and catalog sightings. But now, with the advent of web-based programs like iNaturalist for aid in identification, I've been stimulated to broaden my photographic interests to other aspects of my travel like botany.

As you might expect, Joe has travel experience in the South Pacific and says “we were fortunate to spend 9 days recently on the island of Qamea in Fiji, where we did 10 dives and enjoyed quite a variety of marine life, especially the invertebrates. The people on Qamea were absolutely the friendliest people imaginable!”

And while diving there one of the invertebrates Joe encountered was the colorful thorny oyster pictured above. The thorny oysters, of the genus Spondylus, are actually not true oysters at all, but along with scallops are members of the superfamily Pectinoidea. Their common name comes from their incredible shells, which are often adorned with spiny growths - helpful for defense. Joe’s photo shows the colorful interior mantle of this species (S. varius), and if you look closely you can see its tiny eyes just inside the edges of the shell, reflecting the camera flash and almost sparkling. This is the largest Spondylus species, reaching about 20 cm in size.

I asked Joe (above, at the Eaglenest Wildlife Sanctuary in Arunachal Pradesh, India this past April) for any tips he’d like to share about traveling to see wildlife, and he told me “One key to travel, I think, is to just enjoy different cultures and focus on all of the interesting differences there are between the various areas of our planet…

Secondly, and most importantly, I think that by far the best way to travel is to get into contact with local travel agencies and nature guides that live in the country you want to visit.  Some of them often guide part-time for large international companies but are available for local guiding as well.  By booking trips with local companies, not only do the profits go directly back into the local economy, but you often get to have a much meaningful cultural experience as part of your travel.

Joe has a diving trip planned for Raja Ampat, Indonesia, and “upcoming birdwatching trips include Guyana, Colombia, and Sri Lanka, but there will be a lot of focus on butterflies and dragonflies on those trips as well! I'm sure that iNaturalist will help me with my identifications.”

- by Tony Iwane


- Those are a whole lot of green areas on Joe’s travel list, so why did he choose desertnaturalist as his iNat handle? Well, when he’s not traveling, Joe resides in the deserts of southern California and enjoys observing the wildlife and flowers in the spring, but says “I'm quite happy to leave the desert during our hot summers and go scuba diving, though!”

- Spondylus were used in various ways by many native cultures throughout the Americas and the Mediterranean, according to this article.

- Check out this Thorny Oyster, which also look to have a cool purple tunicate (among other lifeforms) on its shell.

Posted on November 02, 2018 10:31 PM by tiwane tiwane | 7 comments | Leave a comment

November 11, 2018

Mysterious Identifications

Some of you may have noticed some mysterious identifications created over the past day, or some identifications mysteriously disappearing. I've been running a script to get past observations to conform with the change we made last February that allows observations to be associated not with the community taxon but with the most advanced proposed taxon that is a descendant of the community taxon. Unfortunately, I messed up my script and it's been adding identifications on behalf of the observers that match the new observation taxon, which added up to a lot of identifications, a lot of notifications, and many observations that were Research Grade when they shouldn't have been.

I stopped the script and am currently cleaning things up. This affected observations between 8621916 and 9700842, so roughly those created between Oct 30, 2017 and Feb 1, 2018. I am deleting the identifications that were probably created by this problem, i.e. identifications created by the observer between 2018-11-09 12:00 PST and 2018-11-10 14:00 PST on observations created between Oct 30, 2017 and Feb 1, 2018. This means I may have deleted some identifications that were genuinely created during that time period, but I figured that was a smaller price to pay than a lot of erroneously Research Grade observations. My spot checking suggested there were very few genuine identifications among those deleted, but if you think you may have been affected, let me know and I can try and get you a list of affected observations created by you in the relevant time period. Again, you would have to have been intentionally adding identifications to observations you created between Oct 30, 2017 and Feb 1, 2018, between the hours of 2018-11-09 12:00 PST and 2018-11-10 14:00 PST.

I'm sorry about this, folks.

Posted on November 11, 2018 01:08 AM by kueda kueda | 1 comments | Leave a comment

Mudskippers in an Indian Creek - Observation of the Week, 11/10/18

This group of Boleophthalmus dussumieri mudskippers, seen in India by @anil_kumar_verma, is our Observation of the Week!

“I believe we are all born in love with nature,” says Anil Kumar Verma. “Who among us doesn’t like to be in peaceful environment of forests, mountains & lakes. While I was a kid, used to live near ‘Western Yamuna’ canal in Yamuna Nagar, Haryana, India. This canal was dotted with trees on banks and we would go chasing butterflies & birds. Somewhere in search of a good life, this got left behind. This interest got re-kindled in 2012, when I got my DSLR. This gave me the power to capture in a good way whatever I observed.”

Anil now often goes out to photograph wildlife in the Yeeor Range as well as the Nagla Range in Sanjay Gandhi National Park and makes other excursions with groups of fellow nature photographers. He has also made several visits to the bank of the Vasai Creek near Kolshet village at dawn to capture the sunset (see below), and this is where he’s seen mudskippers mucking about. However, Anil has often lacked the proper lens with which to photograph them.

This time [however], I had a visit along with photo enthusiast buddies and had the luxury of a 100-400mm lens. And after so many years, I finally captured my observation of mudskippers...This was the last observation to be made and captured. Loved the way these creatures were present in hundreds and moving around in mud. The shining blue eyes catch one’s attention and it took quite some time getting it right.

Anil posted his mudskipper photos to iNaturalist and Gianluca Polgar (@gianlucapolgar), a mudskipper specialist from Italy, idenitfied as Boleophthalmus dussumieri. I asked Gianluca about this species, and he tells me it’s one of three fascinating species that live along the coasts of the Persian Gulf and the Arabian Sea, feeding on “microscopic and filamentous algae on the surface of the mud during low tide, scraping the mud surface using their comb-like lower-jaw teeth and characteristic side-to-side head movements.”

They make burrows in the mud (as do other mudskippers) which can be over a meter deep; useful for hiding during high tide. But at low tide the fish come out and, according to Gianluca, “dig a shallow pool around one of the openings that does not dry out during low tide, and where the concentration of microscopic algae happens to be higher... therefore, they appear to cultivate small muddy gardens!” The mudskippers also engage in territorial disputes, especially in areas of high density, such as Kuwait Bay, and Gianluca tells me

apparently due to these high densities, the mud dug by each individual and accumulated around the defended area builds up with the mud dug by the neighbours and is ‘cooked’ under the strong sun, thus creating a peculiar pentagonal pattern on the mudflat which resists to flood tide currents and is visible at a large distance.

Anil (above) first learned about iNaturalist in a Facebook post by Roger Kendrick (@hkmoths) and says “now, I’m trying to put most of my observations here. This is helping me put all of them in one place. Before this, I had so many pictures without species or family name. The iNaturalist community has helped me document most of it...iNaturalist’s efforts in building a community of observers and identifiers has brought a renewed focus in my observations.

I would say, I started my journey as a photographer, somewhere, somehow getting to know what I’ve captured. iNaturalist is giving me a direction towards being a naturalist, making me understand the natural world, its diversity.

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


- Amazing footage of mudskippers fighting, burrowing, and more.

- Check out Gianluca’s mudskipper website.

- Here are the most-faved mudskipper observations on iNat.

Posted on November 11, 2018 01:28 AM by tiwane tiwane | 7 comments | Leave a comment

November 17, 2018

A Melanistic Serval Cat in Kenya - Observation of the Week, 11/17/18

This melanistic Serval, seen in Kenya by @srullman, is our Observation of the Week!

“I’d like to be a biologist because I like to study life. I like to cut off bark of trees with my pocketknife. I like to study plants and things. I like [to] study animals, especially raccoons, foxes, and all living things.”

That’s what Dr. Stan Rullman wrote while in second grade, when responding to the question What do you want to be when you grow up? While he denies debarking trees with his knife (and now wonders why a second grader was allowed to run around with a pocket knife), Stan does “recall prying off the bark of fallen trees to look for critters and see the intricate patterns of bark beetles underneath.”

Stan’s second grade essay proved prescient, as he earned a PhD in Urban Ecology and worked as a Wildlife/Conservation Biologist and Educator on Washington State’s Bainbridge Island before his current position as Research Director for Earthwatch Institute. “I help oversee our support of research projects in about 30 countries around the world, most of which have something to do with wildlife and conservation,” he explains. “I am very interested in human-wildlife conflict issues, which seem to be increasing as wild creatures find the space allotted them to be more and more restricted, and primary food resources shrinking, prompting their forays into the human realm.”

It was on a trip with students from the North Hollywood High School Zoo Magnet that Stan encountered the melanistic serval you see pictured here. Thanks to funding from Linda Duttenhaver, several students and zoo staff get to participate in an Earthwatch project each year, and in 2017 they traveled to Kenya and took part in a project “assessing the efficacy of various deterrents deployed to keep elephants out of the crops that local community members struggle to grow in the increasingly dry, arid conditions.”

While in the field, the group noticed hornbills and White-bellied Go-Away-Birds mobbing an animal. At first they figured it was a black dog, but it soon became clear that the animal was a felid, “though the black color was throwing all of us off.”

I was in the front of the bush vehicle with Dr. Bruce Schulte, the principal investigator for the elephant project, with a crew of the students standing up and observing the creature’s progress through the pop-top, open-air roof. We kept as quiet as we possibly could, with the only noise being the digital clicking from the cameras...Finally, when it was about 40 meters away, it stopped— suddenly aware of something blocking its progress down the road. Equally nervous and curious, it slunk off the road, skirting around our vehicle about 30-35 meters away through the grass and brush.    

If you’re familiar with servals, you’ll know why the group was at first taken aback by the black fur of this melanistic individual - the coats of most servals have a yellowish ground color spangled with black dots and stripes. A medium sized cat (they weigh 8-18 kg (18-40 lbs) and reach a height of about 54-62 cm (21-24 in) at the shoulder), the serval is a solitary predator that generally eats small prey such as rodents, birds, insects, and snakes. They’re known for their incredible leaping ability, which they can use to knock down larger birds.

Stan waited over a year to post this observation because he was concerned about bringing attention to such an uncommon individual cat, but after seeing an article about melanistic leopards he got in touch with the article’s author, Dr. Lucas Gonçalves, a Brazilian wildlife biologist. “I sent him some photos of the Tsavo serval, and he indicated 16 records of such creatures, primarily from the Mt. Kenya area (where they are fairly well known) as well as the Pare Mountains of northern Tanzania - just across the border from the Tsavo complex. That really sparked my interest in this topic, and eventually, wore down my concerns regarding ‘outing’ this fabulous cat.”

Stan (pictured above) has “been promoting iNaturalist as a bridge between observers and the highly participatory (and certainly not passive) nature of collecting and posting of their observations - making them available to the larger scientific community,” and is currently suggesting iNaturalist could be used “to engage our local residents in collecting observations of obligate vernal pool species (e.g. fairy shrimp, wood frogs/blue-spotted salamanders/spotted salamanders (eggs), etc.) that could then be provided to the Massachusetts Natural Heritage & Endangered Species Program” to help protect the vernal pools in and around his township. He sees data created by citizen scientists as a powerful way to engage with policymakers.

And Stan tells me that using iNaturalist “has rekindled my interest in what E.O. Wilson calls ‘the little things that run the world,’...

Though much of my professional career as a naturalist first and ecologist later has shifted my focus to birds and carnivores, I still find myself looking under logs and bark, especially if I’ve got my macro lens with me to document such observations on iNaturalist.

- by Tony Iwane.


- After an inspiring National Moth Week event, Stan has now started Project Porchlight on iNaturalist, check it out!

- Stan sent me to this interesting paper about citizen science and conservation decision-making.

- “The students from the zoo were absolutely amazing to work with,” says Stan. “Their passion for nature, their untarnished sense of wonder, and their interest in the research were inspiring. And several of the students were avid iNaturalists!” Here are @rynaturalist‘s posts from the trip.

Posted on November 17, 2018 11:17 PM by tiwane tiwane | 12 comments | Leave a comment

November 21, 2018

Introducing Taxon Frameworks

We're in the process of rolling out new functionality called Taxon Frameworks. Please read about them here. But in a nutshell, taxon frameworks allow us to track and communicate what we mean by a particular branch of the tree of life and thus what we're all agreeing to reference and curate towards. Taxon Frameworks can be sourced to external secondary authorities like the Reptile Database and deviations from the authorities can be explicitly mapped. We've also folded in the existing 'complete taxa' and 'taxon curators' functionality into taxon frameworks.

Some background: the core activity on iNaturalist is observing and identifying observations by hanging them on the Tree of Life. The tree of life on iNaturalist is a single global taxonomy that we all share. A big thank you to the few dedicated iNaturalist Curators who are responsible for maintaining this taxonomy.

The policy on iNaturalist has generally been to adhere to secondary taxonomic authorities (like the Reptile Database) for a number of reasons. However, as iNaturalist has grown, its been increasingly difficult to manage information about these secondary taxonomic authorities including what they are, when we defer to them, and when we deviate from them.

Over the last year, I've been experimenting with ways to better manage iNaturalist taxonomy with a few informal taxonomy working groups and some pilot features like 'complete taxa' and 'taxon curators'. These features allow branches of the tree of life to be curated only by a smaller subset of curators assigned to a particular branch and to make it clear that these branches have all taxa added.

While this pilot has been productive, using journal posts, projects, external spreadsheets, and flags hasn't been the best way to maintain, share, and communicate all of this information. Keeping track of 'deviations' - places where we wish to depart from whatever secondary taxonomic authority we're otherwise following - has been particularly difficult with the existing system.

We're still in the process of rolling out the Taxon Framework features including migrating over content managed by the old system and updating documentation. But I wanted to give everyone a heads up about this functionality incase you stumble across it. Also for the moment, only iNat staff can create/edit taxon frameworks and taxon framework relationships while we continue testing things and getting the bugs out.

As we continue experimenting with ways of leverage the Tree of Life on iNaturalist - from making computer vision suggestions and consensus identifications more sophisticated to tracking range extensions and other discoveries - its becoming increasingly important that we have a well formed and robust tree of life to build these systems on. While we recognize that the tree of life will always be constantly changing, we're striving towards systems where it changes in a more structured way. Taxon frameworks are a step in this direction by letting us explicitly lay out what taxonomy we're all agreeing to reference by stitching together secondary sources and the judicious use of deviations.

At the moment, we have about 25 taxonomic frameworks covering much of the tree of life:

When we scale the tree by the number of observations, about 75% of observations are covered by taxon frameworks. The major 'holes' in this coverage are Lepidoptera and several other insect orders (Diptera, Hymenoptera, Coleoptera, and Hemiptera), Fungi, and Bryophytes, and various marine invertebrates such as Malacostraca, Cnidarians, Echinoderms etc.

I believe the World Registry of Marine Species can be used as a basis of frameworks for many of these marine invertebrate groups. For Bryophytes, Goffinet, B., W.R Buck and A.J. Shaw (2008), Morphology and classification of the Bryophyta looks promising.

For Fungi, it would be great if Fungi leaders in the iNaturalist community could come together and provide some guidance. In the past we used Index Fungorum but there were too many instances where the community wanted to deviate from this reference so Fungi are currently a bit of a free for all. If we could use taxon frameworks and deviations to rein Fungus taxonomy in to something that would have broad buy in by the community that would be fantastic.

This leaves Lepidoptera and the other Insect orders. The Orthoptera Species Files and a few other "Species Files" exist for smaller orders but guidance on what to do about the large orders like Lepidoptera would be very helpful. Remember, while ideally taxon frameworks would extend all the way down to species, they can rather only extend down to coarser nodes. For example, even constraining Lepidoptera taxonomy down globally to tribe would be hugely helpful in terms of reining in taxonomic free-for-all.

People often get very passionate about taxonomy - which I guess is good. But as we work towards a consensus taxonomy that we all share, I'll close with a plea for a spirit of compromise and flexibility. The iNat tree of life exists in this weird place between phylogeny (a tree that exactly matches evolutionary history) and taxonomic nomenclature (a set of rules for categorizing things). The taxonomies behind Catalogue of Life, GBIF, the IUCN Redlist, EOL and others occupy similar spaces. This means that while most of the changes come from trying to make the trees reflect evolutionary history, they still have many useful but non-'natural' (non-monophyletic) groups like 'Reptiles'. iNat curators coming from more of the phylogenetic philosophy often want to totally restructure the tree with something that better reflects evolutionary history. While this is a critical component of guiding taxonomic decisions, other factors like stability and simplicity must also be considered too. At its core, the iNaturalist tree is still a Linnaean taxonomy and unnamed ranks such as 'clade' can't be accommodated by the system at the moment. Please try to be open minded and flexible as we compromise towards a consensus taxonomy even if it doesn't result in a perfect phylogeny.

Similarly, iNaturalist isn't built to accommodate all of the rules and metadata that have governed taxonomic nomenclature back to the days of Linnaeus. Some things like quadrinomials are allowed under the rules of nomenclature but can't be accommodated by the iNaturalist system at the moment. Please be similarly flexible regarding some of the strict rules of nomenclature and the omission of certain nomenclatural metadata like types and authors. Once taxon frameworks become editable by iNat curators, we hope they will be places for curators to add some of this metadata if they wish.

Posted on November 21, 2018 12:08 AM by loarie loarie | 52 comments | Leave a comment

November 24, 2018

Lichens in New Zealand - Observation of the Week, 11/24/18

This group of Placopsis lichens, seen in New Zealand by @linda_johnson, is our Observation of the Week!

Since she joined the Royal Forest & Bird Protection Society of New Zealand, Inc. (Forest & Bird  for short) a dozen years ago, Linda Johnson says “My interest and knowledge [in nature] has grown a lot.” She’s a coordinator for the Kiwi Conservation Club, a junior section of Forest & Bird, and “preparing nature-based activities for the KCC children has been a significant contributor to my increased knowledge about nature.” She also take part in pest control initiatives and restoration work.

Linda recently spent five days and four nights hiking The Old Ghost Road (OGR), an abandoned mining road in New Zealand’s Kahurangi National Park, and recounts

Whenever I'm out hiking I'm taking notice of what is around me and regularly stopping to get a better look around without falling over. The first day of the OGR was in beautiful beech forest and there was an abundance of bird life, especially NZ robins. On the second day we got up above the tree line and I was seeing plants I don't usually have an opportunity to see. The day was sunny and a section of the track had a rocky bank with grass and other low growing vegetation on it. There were some big boulders not covered by vegetation. The colours and shapes of the lichen on the rocks were eye catching so I stopped to take a photo.

The lichens she photographed are in the genus Placopsis, which are often referred to as “bullseye lichen” due to the their appearance. A crustose lichen, they grow tightly to their substrate (in this case a rock) and their more conspicuous structures are often grouped toward the center, with the thallus extending outward. Lichens can reproduce both sexually and asexually, and it looks like sexual reproductive structures called apothecia are the dark red dots fringed by lighter tissue. I’m not sure what the striking structures in the middle are - if you know, write in the comments!

Linda (above, on the OGR), mainly uses iNat for ID help and to make sure there are records for particular places. “For instance, I uploaded photos from my visits to the Chatham Islands (800km east of New Zealand), and subsequently was told I was the first person to submit data from there,” she says. “I actually started taking more photos on the OGR with iNaturalist in mind after taking the lichen photo.”

- by Tony Iwane


- Lichens have long been thought to be a symbiosis between a fungus and algae or cyanobactera, but recently a third partner has been found.

- Do lichens age? A Harvard mycologist has been studying lichens in a cemetery in an attempt to answer that question.

Posted on November 24, 2018 08:38 PM by tiwane tiwane | 4 comments | Leave a comment