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.

Biodiversity Spotlight on: The NMNH Invertebrate Zoology Department!

This week a departure from the weekly echinoblogging to spotlight some people behind the biodiversity of marine invertebrates! (although that is a very photogenic Protoreaster lincki on the cover!)

A few weeks ago Ward Appeltans, who was the project manager for the massive World Registry of Marine Species database (here) collected and presented 121 contributors of various marine species, including some plants, protozoans and chromistans, fungi, some chordates and a WHOLE bunch of invertebrates!
The link to the paper is here. I believe it is open access until January 2013.

There are a lot of digests and news articles about this including these:
Natureblog
Discovery News
Phys.org
e!Science News

But of course in a "big picture" treatment, one often lacks some detail so I thought I would spotlight a department with which I was most familiar:  Invertebrate Zoology at the National Museum of Natural History!

Eight out of the 121 contributors of the paper (that's about 6%) are residents/associates/employees of  the Invertebrate Zoology Dept. at the National Museum of Natural History!!(part of the Smithsonian Institution)

Top: Jon Norenburg (worms), Dennis Opresko (antipatharians aka black corals), Stephen Cairns (scleractinians and gorgonians)

Middle: Rafael Lemaitre (anomuran crabs), Kristian Fauchald (polychaetes)

Lower: T. Chad Walter (copepods), Marilyn Schotte (isopods)

Bottom: Me (starfish)

6 % may not seem like a lot, but it is the largest contribution of the 95 different organizations which participated.  Only the Dept. of Marine Zoology at the Naturalis Biodiversity Center in the Netherlands had the 2nd highest number of contributors (n=7)

A look at the number of records modified per taxonomic editor below. Several of the largest contributors are persons from the NMNH!

This graph from the WoRMS statistics page

Among the names and numbers!

Chris Mah with 6,060

Marilyn Schotte with 14, 384

Chad Walter with 27, 508

and Kristian Fauchald with a whopping 36, 480 records!!

Here's which Marine Invertebrate Databases and/or taxa they oversee..

Kristian Fauchald (lead editor: Geoff Read): World Polychaeta Database and Twitter: @WPolyDB

Chad Walter (with Geoff Boxshall): World of Copepod Database! 

Marilyn Schotte: World List of Marine, Freshwater and Terrestrial Isopod Crustaceans

Jon Norenburg: WoRMS- the Nemertea (ribbon worms)

Dennis Opresko: WoRMS-the Antipatharia (black corals)

Steve Ciarns: WoRMS-the Scleractinia (hard corals)

Rafael LeMaitre: WoRMS-the Paguroidea (hermit crabs)

Chris Mah:  World Asteroidea Database (starfishes and sea stars)

Some Neat Factoids about the NMNH Invertebrate Zoology Dept.

• The Collection includes a representative of every recognized animal phylum, including the two most recently recognized-the Loricifera and the Cycliophora! 
• You can always check the holdings by going to the online catalog here! 
• The dept. has over ONE MILLION cataloged specimens in its database! 
• IZ oversees one of, if not the largest collection of Antarctic invertebrates in North America. Here is the USARP page!
• IZ currently hosts 10 active on-staff research zoologists whose interests range from deep-sea cucumbers, freshwater mollusks, midwater polychaete worms, to barcoding and understanding tropical biodiversity.
• Go Check out the IZ Twitter page:  @InvertebratesDC

The Natural History Museum & How You Describe a New Species!

First..my apologies for the delay in new posts!..my laptop died last week and much needed to be done to remedy the situation...

This week, some "behind the scenes" action about the process of discovering a new species!!!

So, everyone hears about this. New species are discovered daily. Journals are filled with them and statistics repeat how many are found per year. But really, what happens?
What are the dynamics?

So, how does this whole "describing the world's biodiversity" thing work, exactly??
and WHY are Natural History Museums SO important to the process???

First, some background on the Natural History Museum can be found here.(short version: Natural History Museums house many, many specimens...)

Let us now proceed....

1. Exploring the Collection. So, every museum I've ever been to has what's called "the backlog". This is an area (or areas) set aside in the museum collection where all of the incompletely identified material is kept.
Specimens arrive from many different places: expeditions, ecological assessment surveys, vouchers for scientific studies, the list goes on. These speciemens are sorted, processed, labelled, housed in archival materials, and ultimately shelved and stored. (Go see this post to get a flavor of how this works)
BUT most museums don't always have the resources to completely identify and process all of the specimens they've collected.

Big museums often receive specimens from all over the world. The Smithsonian has stuff from everywhere in the world. Paris, Cal Academy in San Francisco..every primary natural history museum has material collected from all over the world.

All these big international expeditions you hear about? Like this one and this one? If specimens are collected, they end up in a big museum.

Most museums don't consider a specimen "done" until its been identified to species (or subspecies) and, so they go into a special holding area to await a time when a knowledgeable person can go through it. The wait for such a person can literally be YEARS.

I've seen some museums that still have unidentified or unprocessed material from the Research Steamer USFC Albatross from the early 20th Century!! and people can STILL find new species in "old stuff" like that as well...
This lag in finding experts to help "shrink the backlog" can be for many reasons, none of which are mutually exclusive.

• The animal group is big and you find lots of them (e.g., worms or shrimps)
• The specialists for the group are far and few between (The number of starfish people in the world can be counted on one hand)
• A specific animal group is hard to identify and/or requires special methods to ID (e.g., taking histological sections)
• A small collection of that specific group that one doesn't normally associate with being at a particular museum (e.g., recent starfish at a museum in Utah)

So, when a specialist DOES reach this collection?? Its a win-win.

The museum folk are usually happy to tie up this HUGE "loose end" and get the collection put away, cataloged and available to the scientific community.

The expert/researcher gets to spend a big chunk of time going through a bunch of specimens with the possibility of discoveries!!! Older, previous collections may often come from surprising or unusual places: deep-sea, distant seas, localities that are now gone or difficult to access for political or other reasons.

While travelling to these places-I have spent up to a MONTH just going through 'backlog' collections.

So, you find something you haven't been able to identify as a known species-what next???

2. The Study/Comparison Process. Next thing that happens? You need to make sure you got something new!! and not just something known.

THIS is where the specimens in a Natural History museum come in handy-because you have an instant reference for comparing known versus unknown specimens. (and also why its very important that when the aforementioned experts DO identify something that they do it correctly!)
And of course, where you don't have specimens, you often need to fall back on the scientific literature for comparative descriptions of other similar or dissimilar species.

This can often be very tricky because the animal in question may be VERY close to something that is known and specimens are the best way to compare features.
During this process, its often common to actually discover MORE new species. Mainly because when you learn the taxonomic 'concept' of the known species (i.e., what the original author used to distinguish his/her species) you get a good notion of what a separate and new species would be like.

3. Description & Analysis. The next step is to compare and describe your potentially new species relative to what's already known.

In the historical and classical taxonomic style, this usually just involved an identification guide called a key or some other kind of table describing your species using relevant body characteristics (e.g., # of spines on each species, shape of granules on each species, shape of body on each species)

This usually involves describing the new species in highly specialized terminology outlining the specific features, especially as they pertain to similarities across ALL of the known species.

So, if all of the species you look at have a big glassy knob, then you look at how that glassy knob varies (if it does at all) across all of the species you're trying to compare it against.
Its often common practice to describe new species in the context of a phylogenetic analysis. And that usually involves further processing different characters (whether from morphological features or DNA) from the subject animals into a computer and analysing those results in order to get a tree that supports evolutionary relationships.

(note snazzy new laptop!)

So, in addition to your new species-you have a good comparative/evolutionary context!

What happens next? Write it up and publish it! But that's another story!! (soon!)

The Natural History Museum: An Overview

Today, I thought it would be interesting to talk about how natural history museums and natural history collections are important to biology, and to the "big picture" in general..

A lot of people who are reading this are probably already quite familiar with all of this-but I discover in one way or another that every day is filled with an educated person who knows NOTHING about what I or so many others do at work.

What is a natural history collection??A natural history collection is a massive storage "warehouse" of sorts, that includes almost exclusively natural history type specimens. Historically, they have included minerals, gems, anthropological artifacts, shells, insects, plants, pelts of mammals, birds, and preserved specimens of a myriad of other animals.

The amassed aggregations of these artifacts led to people who began to study and describe them. Often for the first time. It is for this reason that a great deal of taxonomy and systematics is done at museums.

It is important to note that the collection data (i.e., where it was collected, when, by who) is crucial towards the value of these artifacts. Without them..all you have, at best, is a pretty display specimen.

When new species are described there are rules in the International Commissions for Zoological and Botanical Nomenclature which mandate that some kind of voucher specimen must be deposited for long-term storage. Specimens can be dried, preserved in some sort of fluid (ethanol, formalin, etc.) or sometimes even as a slide or a video (although this is not very common).


This is done for many pragmatic reasons, the least of which, is so that someone else can clearly see the concept for that animal on an actual specimen. In other words...what does "big spine" or "cruciform lip" mean???

There might be a picture..but ultimately seeing the original specimen..known as the "type series" and other subsequent representatives give future generations a tangible idea (and sometimes even the intentions) of the original author.

Where do natural history collections come from??
A lot of natural history museums have their roots in either a federal, state, or some local government natural resources survey (or surveys) or sometimes the massive collection of a private collector.

Pictured above is the the United States Fisheries Commission vessel Albatross which was reputedly one of the first vessels ever built for marine research. USFC Albatross surveyed throughout the Atlantic and the Pacific, ranging from the Caribbean to Alaska, Hawaii and Japan.

During the tour of the Albatross, she collected thousands of specimens of animals, plants, and etc. from around the world. These were part of the first natural resource and biodiversity assessment performed for the United States.

Can you imagine a Washington or California coast where we didn't know ANYTHING about the animals that live there? (note that there are now about 2 dozen field guides for this area alone!

They did.
Specimens from the Albatross were among the first to collect and return those specimens to the scientists of the day for description and our understanding.

Today, modern biodiversity expeditions and similar natural resource studies continue to provide the main fodder for museum collections. Everything from SCUBA trips to fisheries studies to submersible dives amass materials which are studied and eventually deposited in a natural history museum.

How do you tell what specimens were used for an environmental assessment?
Go check out the museum vouchers.

How can you be sure that all of the specimen identifications for that phylogeny of the Fang-toothed Astropectinidae were correctly identified?

Go check out the museum vouchers.

Where do you go to make sure that you identified all of the rare cookie-monster jaws from your recent expedition to the Mongolian mountains?

Go check out the museum specimens. (or the types in this case...)
What are the dynamics at a Natural History Museum??
The modern natural history museum acts as a library/storage vault of valuable biological vouchers. There's a couple of things that makes places like this pretty cool:

* Specimen treasure awaits!!
 Generally speaking most scientific expeditions bring back hundreds to thousands of specimens with MANY different taxa. Often, the initial exploratory "cut" of an expedition may not identify or sort all of the specimens collected. Because of this, specimens, often rare or even NEW SPECIES will often sit for decades before someone identifies it. That someone could be YOU.

*Historical Wonder.Most natural history museums contains specimens anywhere from hundreds to MILLIONS of specimens, sometimes collected over the course of hundreds of years. Specimens at the Museum nationale d'Historie naturalle in Paris, France for example, have specimens studied by Lamarck, d'Orbigny from the 19th century and thereabouts.

Between specimens I've seen at the California Academy of Sciences, the Smithsonian, and the MNHN in Paris..I've held specimen tags written by Ed Ricketts, Lamarck, Darwin, d'Orbigny Walter K. Fisher, Austin H. Clark, the crown prince of Japan, and any number of other prominent biological luminaries.

*Museum people+environments=funky, cool science place.These specimens attract museum-oriented research visitors, making museums a great networking source. You can practically have mini-scientific conferences during a good visit. At the right time, at the right museum I've been around when 3 or 4 of the world's experts have just been coming through town and stopped into say hello.

Like universities, natural history museums are academic environments but with the added dynamic of the exhibitry, adult education classes, school group tours, etc, etc. There isn't as regular an input of students, but you get many different types of people in and around the facility.

Often times, museums are places where cutting edge innovation (e.g., DNA barcode extraction) meets classical 19th century conceptuals (e.g., taxonomic codes). You may or may not get critical mass..but you can get a lot of smart, creative, and unusual individuals around in a unique setting.

How do they keep track of all those specimens and how is that important?

(this is not an actual museum database)

With computers and electronic databases!!  

So, of course, one needs to be able to keep track and retrieve a needle in a haystack (so to speak). Museums can have millions of specimens and they would be lost without some way of retrieving them.
But this has been taken one step further and the data from these databases has found use for all sorts of things!  Museums have been around for a long time and often think about recording long-term changes.

They can record changes of baseline faunas over hundreds of years. What did San Francisco Bay look like when the Albatross first surveyed versus what it looks like now? All interesting challenges for these database assessments.

Even an assessment of an expedition of specimens from a particular place can be compared over time to assess how many species live there and where. And where they are no longer...

Some of the original specimens even contain enough DNA for studies of animal specimens that are 10s to 100s of years old!!