Five Things you live with as a Taxonomist! Taxonomist Appreciation Day!

What are taxonomists? 

Simply put, taxonomy is the subsection of biology that deals with assigning names to biological entities and arranging them in an orderly "system." Usually in describing new species or even new genera, families or higher depending on what you work on. 

Many names apply and different scientists focus on different areas of expertise: Systematist, evolutionary biologist, invertebrate zoologist, marine biologist, paleontologist, systematic biologist, entomologist, botanist, protistologist, herpetologist, etc., etc. 

Arrangements of organisms are known as classifications which are dictated primarily by the evolutionary relationships of the organisms in question..be they single celled amoebas, fungus, plants, or any number of animals..starfish, cats, water bears, fish, dinosaurs, etc. 

BUT the first part of that process is to figure out exactly WHICH species you are studying. What phylum of worm? What kind of single celled animal? What kind of plant?  Out of the hundreds to millions of known and unknown species in the world??  

Some species are well known, but others, especially those that live in poorly studied or out of the way habitats: the deep-sea, the distant tropics or even the microfauna and flora of your local pond these can be highly varied and you need a specialist to tell you what they are..(if you can't figure it out yourself!)

It was said for magic that knowing a demon or magical creature's name gave you power over it. This is the same for our knowledge of organisms. Knowing which genus, species, family, etc. allows you access to all the previously known knowledge about it. 

Do we have hundreds of articles on its biology? Or is it something completely unknown?

Thus: TAXONOMISTS! 

                      

What do I do??

Even though I know a little bit about everything, my expertise focuses primarily on the diversity of sea stars, especially those in the deep-sea but you can read about me here.  There are other scientists who work on sea stars of course. Marine biologists, paleontologists, ecologists, and so on..  But at the moment, I am one of the only people who specializes in the evolution and identification of living sea stars (aka starfish or asteroids).

So, that's my bias.   

That said, I've been doing this for awhile now so here's a five ups and downs that I think I've experienced in my career as a taxonomist/biologist/paleontologist/whatever that I thought might provide some insight into why you should support a taxonomist (and taxonomy!)

As a taxonomist, these are dynamics that one comes to accept as part of the profession. They are challenges and we always hope that things will be better. But for the moment, this is how they are.. Most folks in the taxonomy field live with these things every day.

These are my opinions/perceptions and not the perspective of any organization I am affiliated with. 

1.  Taxonomy is biological infrastructure: everybody wants/needs what you offer but its often (still) professionally taken for granted.

For many decades, taxonomy was considered as almost a service to the rest of the scientific community. Say, you had some scientific study X, that focused on a weird deep-sea worm..but you didn't know what it was!!  Send it off to the local museum. Or to the Smithsonian or wherever.
They would often identify these things (and yes, of course for free) and there was not even a suggestion that the name of the taxonomist would be included anywhere but in the acknowledgements.

So, the scientists were held in high regard but never got full credit.
This happened to me a lot early in my career. but not any more...

TODAY, I usually insist on co-authorship on anything that involves a significant amount of work. Credit where credit is due.  

But, its still commonplace for papers that use one or many species to omit the name of the scientist (or whomever) who described it in the paper's references.

Its often convention to list the author and date of description after the species name, especially if it was described recently (i.e., in the last 50 years or so). This is usually done only in formal taxonomic papers. But in journals which use taxonomy outside of "formal" use (e.g., in ecology, physiology, etc.), its not unusual for the author and date to not be cited and the reference (and thus the credit) for scientific papers is denied to taxonomists. Thus lowering their status in the scientific community. This paper documents this issue. 

2. You get to travel.....but then spend months to years writing up the results

This is a good problem to have. Being a taxonomist has taken me all over the world and to the bottom of two oceans. You've seen my travel posts about working in Japan, Paris and out on ships to the middle of the North Pacific among the many places I've experienced and shared on the blog.

BUT these trips last for only so long. The exotic adventure stuff gets balanced by the more mundane preparation and wrap up. Some expeditions or even just museum trips take months to YEARS to completely "finish".

Why?  Most day to day work involves a lot of standard office work. Papers have to be written. Specimens have to be cataloged. Reports have to be made on the expeditions. Receipts have to be tallied. Meetings and responsibilites have to be met. Sometimes classes have to be taught.  For new trips.. proposals have to be written and logistics have to be made. 

So yes. cool things to be done and seen but a lot of the time. Work. Meetings. Etc. 

3. Most discoveries happen in museums....

I've written about this dynamic in past posts (here). Some specimens await discovery for decades before being found by someone who writes it up. On average this turns out to be about 21 years from the time the specimen is discovered until the paper is published..

As much as I've gone to sea and travelled to exotic places, I find the most number of new discoveries in buckets and jars of preserved specimens.

The museum is practically the HABITAT for the taxonomist. So, like any endangered species, one needs to save it to save the species!  If you support natural history and taxonomy, support the museum!! 

A lot of museums with natural history collections have also been struggling. Funding is almost always below what is necessary to maintain a collection at optimal levels. Other challenges to museums I've observed

• Space! So many jars, specimens, etc. fit into a storage room and real estate can be expensive. Universities and private collectors are prone to give up their collections, which often end up at museums overwhelming the in-house resources.
• Personnel! People are one of the most important ingredients to a good museum collection. Specimens require upkeep. They have to be cataloged. Shipped. Mailed. Received. Sorted. Some materials are protected by law. Training museum professionals is now its own field separate from what scientists do. Collection management is a challenge.
• Resources! Specimens require material. Jars. Archival storage boxes. Tissue samples require freezers. Shelving. The list goes on. Individually, some of the items may not cost much..but remember these are used at a pretty regular clip.                                

and.. the resources above speak NOTHING of research materials.... DNA labs, microscopes, computers, etc. etc. which is another matter entirely.

4.  You belong to a small community which is growing smaller 

In this regard, taxonomy isn't all that much different from other academic fields or even other professional or business fields with a very specific focus.

Most taxonomists are unique experts in their group. As I said above, I am one of the world's only practicing taxonomists specializing in living sea stars (there are paleontologists around though). In the early 20th Century there were up to 5 to 7 sea star experts at any given time. Yes. there are people who work on regional faunas (i.e. starfishes of island X) but folks who work on all of them? That's me. 

For marine invertebrates, there is a perception that there is a serious lack of taxonomic expertise which I think bears some concern. You do get students who train and get degrees, but not a lot of jobs or positions are available. Some of us have gotten by but I've seen many of my gifted colleagues move on to other fields for lack of a stable position.

I've always seen the demand from other fields (ecology, physiology, oceanography etc.)  for MORE people who can ID or describe the "creature X" that they collected, etc.. but "Nobody works on those any more, since Dr. Y died..."

I briefly discussed this in a past post here.

Which is a segue to...

5. There are new discoveries to be made!! but where are the jobs?

There are many places where you can read about the "Biodiversity Crisis" and the corresponding "extinction of taxonomists". Wired did a nice bit on it here. 

One of the things I always clarify to folks is that even though there's always something to DO, there's not always someone who will hire you to do it. 

I love what I do. But I don't have a "proper job" (I get by on soft money and other funds) but I feel compelled to continue (and I continue to hope!). My career is a good one but I've been lucky. Its a difficult field to survive in.

So, yes. There's an avalanche of undescribed species awaiting description! But whether you are a classical (but modern!) taxonomist like me, a person working on protists, or a barcoding guru, these are all pretty specialized positions. And getting a job doing what we're trained for is, at best difficult.

What happens when the last person working on a big or important group retires or dies?

There's been an unfortunate decline in jobs for taxonomists in recent years. This seems to accompany the various funding issues which accompany universities which have shifted their emphasis away from programs focusing on general knowledge.

Many reasons have been offered for this decline but ultimately I think the best I can do to support future generations and my other colleagues is to continue my outreach and shed a light on the challenges faced and why supporting taxonomists is worthwhile!

At this point, someone will bring up privatization or "Why don't you charge people for what you do?" And yes. Its crossed my mind..but that's a discussion for another post..

Five Surprising Points about Discovering New Species & Taxonomy

Austin H. Clark, first curator of echinoderms at the Smithsonian's NMNH. Also, butterfly enthusiast.

This week, a post about my broader field.. TAXONOMY, evolution and the discovery of new species!

Many of you may or may not realize that, although I am widely studied in echinoderms, my *actual* research focuses on starfish, specifically the diversity of starfish, including the description of new species and how they "fit" into the evolutionary classification of the echinoderms and all other animals.  I've written a bit about the description of new species before (many years ago now) here.  here and here.

Taxonomy is often one of the first things you learn about biology. How do you classify the organism? Plant? Animal?  Phylum? Class? Family? Genus?  Species?
                                               
There are scientists (and citizen scientists) whose entire expertise is devoted to studying a singular group of plants, animals, or "other" (protists, fungi, etc.) just as mine is devoted to studying sea stars.

These scientists, such as myself, discover which species are new, which are known and place them within a broad "family tree" of relationships. It is the ongoing effort of these scientists to document potentially important new species for a variety of reasons. Some have important medical uses, others are economically important.. while others are ecologically important.

Some, such as the recent and mysterious genus Dendrogramma may have broad evolutionary relevance to our understanding of life on Earth.  Or at the very least, might just be some odd, evolutionary novelty which has peaked everyone's curiosity.

New species are exciting! and hold the promise of new knowledge. A new predator?? A living member of an extinct group?? Or perhaps a new species with an unusual adaptation??

This whole process of discovering new species has changed over the years. So, here are some recent discussions/dynamics/opportunities that I find worth mentioning and that might be surprising.

A caveat: the points below are skewed towards what I have experienced and how the broad patterns have relevance to what I've done. So, yeah, plants, fungus and protists are a bit different but much of the essential dynamic remains the same. And yes.. there's undoubtedly some stuff I've left out.

5. There are a LOT of new species left to be found, but are there enough scientists to describe them? (Data from Costello et al. 2013. Science 339: 413-416) and Tancoigne & Dubois 2013. Cladistics 29: 567-570

In 2002, a one month survey of the seabed in New Caledonia found 127,652 specimens and 2,738 species of mollusks. 80% of them were new to science!  

MANY new species await discovery and description. But do we have enough scientists who can do so?? Are we losing that expertise? Is there not enough taxonomy being done to document organisms before extinction overtakes them?? This is part of what is called the "Taxonomic Impediment",i.e. the number of species/taxa described is limited (and possibly declining) relative to their need.  

One interesting contradictory result in answer to this question in the the two recent papers above, is that both of those papers allege that there are MORE taxonomists (people who describe new species and etc.) and MORE papers about new species being published now than there have been in the past.

But then, WHY is there still a perception that there STILL aren't enough taxonomists? And is that expertise decreasing?

Tancoigne & Dubois have argued that essentially, even though there are MORE people working, the problem is BIGGER. And so, we haven't really upped our game so much as we have just "kept up" rather than made a real dent in the problem. Taxonomic inertia rather than momentum.

Remember that there is an urgency to describe the world's biodiversity before it goes extinct. This is the so-called "6th Extinction" or "Holocene Extinction." You can go here to see more about it. 

The question is complex.. but I can tell you that from my experience, I am currently considered one of the only regularly publishing, broadly trained starfish taxonomists/systematists. There are a couple of regional specialists and maybe 3 starfish paleontologists but very few people work on the broad biodiversity of starfishes.  (as I did here in Japan early this year..)
                                
I have a backlog of easily a dozen or more species currently "cued up" in my "immediate projects" list. With many, MANY more waiting my attention. Remember that trip I took to the North Pacific with MBARI?  Almost ALL of the species I found were new! Who knows how many more new species await discovery with more workers in the wings?? So I guess that boils down to the question "Is that enough?" 

There are easily whole phyla of animals for whom there may be all of one or two specialists in the world. Based on what I've read the estimates for undiscovered marine biodiversity, especially for invertebrates is pretty high.  And I can definitely tell you that the number of staff or faculty jobs for invertebrate zoologist/taxonomists is pretty small.

So, yeah.. we're gonna need more taxonomists! But also jobs!

4. Most new species are "found" in museum collections rather than immediately on expeditions.

So, you know how I'm always taking these big trips to Paris, here and here. and Japan? This is because I'm visiting museums which have extensive holdings of deep-sea Indo-Pacific starfishes.

While its certainly true that I go into the field to collect starfishes in remote and exotic places (e.g., Antarctica-see below)

The truth is that many of the new species I've described are found from rooting around through buckets and which looks more like this.

Every time I go back to say, the collections in Paris I can reliably depend on finding several new species.

A paper by Fontaine, Perrard and Bouchet (2012) report on time between museum storage & publication (more on that below) but they review one important point: Most specimens accumulate in museums following collection. Its often a misconception that new species are automatically recognized in the field and whisked away to be instantly described.... (although yes, it does happen..it depends..)

They are often stored in a museum, where they are sorted, preserved and shelved until a scientist can work on them.

How long does that take between museum storage to publication??

3. It takes on average about 21 years for a species to be described from "shelf" to publication

This is something I can verify: A new species can take a LONG time to reach publication. Note this new genus and species from Antarctica I described in 2011. Collection date?? 14 March, 1966!! This was collected 4 years before I was born!! Ha.

The Fontaine et al. paper further sampled researchers from a variety of fields and found that for a variety of disciplines, it took on average about two decades for a new species to be described following collection and museum storage.

There are a LOT of considerations of course.. Some specimens undergo years of study. DNA is extracted. Comparisons are made. Histology is performed. It depends on what kind of work is done.
Some fields have lost their only workers for literally a decade. There was easily a gap for about 10 to 15 years, when there was no one who was "the starfish  expert"until I came along.

2. Taxonomy from Images: Flickr & More!
So, image proliferation on the Internet has started to make a HUGE impact on natural history and taxonomy.

There is now a massive proliferation of images of habitats, organisms, and etc. via MANY different crowd sourced  (e.g., Flickr or Youtube) or other conveniently available resources. For example: screengrabs/twitter pics of the live stream Okeanos Explorer deep-sea feed!

From crowd-sourced photo hosts?  There was THIS famous story on the news in 2012 about an entomologist who discovered a new species of insect on the crowd-sourced photo bank Flickr! 

I've actually spoken to several of my colleagues about whether images they've seen on Flickr or Facebook could be new species and indeed, it is surprising HOW many there are! And why not? People who post their pictures travel all around the world or are in very distant settings. Some with great camera set ups and a good eye. There's a HUGE potential for data mining here with a nearly infinite number of pictures (many are never labelled).

Some might argue that usefulness of pictures remain limited, since no specimen is available for positive identification or vouchering in a museum. But who knows what kind of behavior? or habitat is spied by these videos?

For the deep-sea species.. even seeing the life mode and color is a HUGE step in knowledge over what scientists in the 20th Century, who often worked with a dead, dried specimen. 

1. New Specimens via... Ebay?? 
Back in 2006, Dr. Simon Coppard, a sea urchin taxonomist recovered specimens of a new species of sea urchin, Coelopleurus exquisitus from the online auction website, Ebay! 

This sounds kind of ...unusual, the truth is that scientists and natural historians have been buying exotic shells and items from vendors of "exotic goods" since the 1800s. Many species described from this time period were based on specimens obtained from "Far East" purchases. The Internet auction house puts a 21st Century spin on 19th Century practice.

Fortunately, this species was described in good order and with apparently little hassle (and I can only hope- good locality data!)

I have heard of subsequent "finds" via Ebay and as remarkable as it sounds, there are unusual and rarely encountered animals which sometimes come up for sale as "dried curios" or "seashells" or what have you.  Fossils also.

Relying on vendors isn't a good option relative to a formal expedition or even just a professional scientist collecting on his/her own. MANY issues can be at play. Permits are common place and some specimens may have been illegally collected. Some organisms, such as coral are protected by international regulations. Obtained specimens could be poorly preserved or have incomplete or downright incorrect locality data (i.e., where they were found). But sometimes, it can be another way to discover new biodiversity. Strange but there it is.

The Colorful Challenge of Identifying Fromia monilis, an Indo-Pacific species complex!

From Wikipedia! 

Identifying animals is tricky business.

The other day, I was helping some folks out with an identification of a starfish they had photographed diving, but I stopped short of giving them the full species. "Why?" they asked. "Isn't this just the the XXX?" (they quoted the most common and easily identified species).

"Well.  Its complicated."

Hard to explain these things in a a few lines on Facebook or on Twitter so I thought I would take an example of how complicated the whole taxonomy and identification process is, using a widely photographed example, a starfish called Fromia monilis.

F. monilis occurs widely throughout the Indo-Pacific. It goes by many common names, Necklace star, Tiled star, Candycane star, Peppermint star, etc.  Scientists don't use those names because they're so inconsistently used and often because its a contrived name in a field guide, created as a convenience for readers.

This species is often seen in the wild and is a common species in the aquarium trade. You can see it in shallow-reefs from Okinawa to New Caledonia, in the Philippines, Indonesia, etc. and over to the edge of the Indian Ocean.

Bottom line: This species is distributed over a VAST area. Because it does, the range of variation (discussed below) is likely to be greater.

F. monilis is a bright red and white species with a distinctive color pattern. The plates on its body surface (i.e., the many circles and shapes you see on the body) are also pretty diagnostic. Most of these starfish are about 2-3 inches (about 5-6 cm) in diameter. So far so good.

Here is what I would say is the most commonly encountered and "typical" form of this species.

From Wikipedia. Here

But bear in mind, that often times, as biologists (such as myself) who specialize in describing and identifying these species, what we often end up working with is a specimen like this...

The dry specimen isn't as impressive as the real, living color one of course, but specimens like this are extremely useful for understanding the species definitions, evolution and ultimately, the taxonomy of these animals.

Some of these specimens have been in museums for, literally hundreds of years and remain essential to our understanding of how these species are defined.

Many of these species get distinguished by fine character differences on these specimens. Some might vary by plate pattern arrangements, or by the number of spines present on the underside, or the particular shape of granules present on the surface.  Its often difficult to synch up these characteristics (i.e. the species definitions) with qualities of the animal when it was alive.

BUT, because of dry specimens above, we can usually look at a specimen like this crazy thing below and tell that it is STILL Fromia monilis.

                 

Why?

Specimens in museums, accumulate over time and can be very abundant, giving us an idea of the natural VARIATION of a species. Size. Body forms. Aberrant shapes. etc.

So, you know how, some people have blond vs. brown hair? Or how some people can roll their tongue or perhaps more exceptionally,some folks have an extra toe or finger? Well, this kind of variation is present in all species and can make understanding classification and understanding evolutionary relationships...interesting.

For a species that we have virtually no understanding of, any character variation (without seeing its presence in the population) might be used to distinguish a separate species. Without an understanding of this kind of variation (or having population genetics data of course), someone who has never seen a human being before could separate me from Morgan Freeman as a different species. 

In the case of the above specimen of Fromia monilis, having seen MANY other specimens of this species, and understanding (we think?) the variation at play,  we know that most known individuals have 5 arms that don't bifurcate. The bifurcation is perhaps due to an attack or some damage during the animal's life time. The extra rays are just an unusual trait, perhaps equivalent to a person with an extra finger. 

Color in the individual above is also consistent. Red disk with red armtips. White in between. Okay. What could be more unusual than the 7 rayed crazy thing above??

Enter the 21st Century (and late 20th Century) and the era of Flickr and digital cameras ALL OVER THE WORLD!

So remember how the "typical" Fromia monilis had that particular color pattern??

What happens when you don't have the red color on the armtips?? Could this be a juvenile? (no size indicator on this pic unfortunately)?  This specimen is from Indonesia. Could these vary by region?
The one above (w/the red disk) is from Borneo.

Is this the same species? But simply with a different color pattern?? Or a different species??  Some species of starfish are thought to vary by color based on their food, does this one as well??  How important is the color as a feature in identification?

The same questions here. Color patterns vary even more drastically. No red on the disk, but there IS red on the armtips! The patterns are a little different?  Is this variation? Size? Or a new species? This one is from Lembeh Strait (Indonesia). 

This one from Papua New Guinea. Same color pattern as above. 

Here is a Fromia sp from Thailand. Color and plate patterns are different. Is this a new species?? Or the same species (F. monilis) showing the starfish equivalent to having lactose intolerance? Or blond hair?

Here is another closely related species, Fromia nodosa which occurs primarily in the Indian Ocean. This species is primarily distinguished based on the larger and more prominent round plates running down the radius of each arm. But it looks familiar, doesn't it??

This individual is from the Maldives (tropical Southern Indian Ocean). It shows the same pattern as F.monilis above and the distinguishing characteristic is kind of variable itself. In other words, it doesn't always hold up.  Does that mean it should just be consolidated into F. monilis??

Here's another indivdiual of Fromia nodosa, also from the Maldives. On both of these individuals, we also see the marginal plates as larger and uneven in one but NOT the other?? 

This one is from Thailand... Mayyybe?  its F. nodosa?? And what's going on with the dark armtips???

This strange thing is from the Philippines. It adheres to the definition of Fromia nodosa (big radial plates, etc.) but its a different color (or at least I assume this is not some photo artefact)!!

And then to make it even MORE confusing.. we have these things from the Red Sea and adjacent areas...

I initially thought this was Fromia monilis but in fact, they might actually be a separate, already established , but this species might actually be a species in a poorly known genus called Paraferdina. Further examination of specimens and research is needed to figure out which one is which... This specimen is from the Red Sea.

This one is from Egypt. The color pattern is familiar but the plate patterns on the arms?? Very different and yet, similar... F. nodosa? F. monilis? Paraferdina???

..and so on...

This is mainly to demonstrate the limits of how the colors and patterns get complicated quite quickly.

And yes, at some point, someone may work this out.. Lots of diving and subsequent DNA lab time. Plus looking over photos and museum visits! Woo!

But this also explains why scientists, such as myself,  are often more reluctant to give you a full species name for a picture when its sent for identification without a specimen. Are these one species? MANY species? Which ones correspond to pre-existing species?

Falling back on the one, most common name can often disguise the truly rich diversity in these wide-ranging, closely related species which are only now, just becoming understood. I argued that this was also the case with the "Bobbit worm" (Eunice aphroditois)

So, yes. Knowing more doesn't necessarily give you all the answers, but it does give you some pretty exciting questions!