Wednesday, September 17, 2014

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 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.

Tuesday, September 9, 2014

(More than!) Five Cool Things We Could See if the Okeanos Went Back to Indonesia

So, over the weekend, the livestream of Okeanos Explorer briefly mentioned and entertained the idea that they might head back to Indonesia for a revisitation of their inaugural expedition from 2010! (The INDEX-SATAL Mission). (I think someone mentioned the ambassador was on ship?)

That expedition was, of course, 4 years ago and the program had just begun. Updates were not as forthcoming. But an opportunity to RETURN to Indonesia? With the benefit of hindsight, experience and further preparation?? That would be awesome!

That area is known as home to probably one of the MOST diverse marine faunas of anywhere in the world.  And although there's a lot known from shallow and deep habitats, the deep sea areas (below 200 m) in the Indonesian area will likely make all the stuff R/V Okeanos Explorer and E/V Nautilus have been observing in the Atlantic look like a goldfish bowl by comparison! 

A LOT of the species in this area are likely undescribed. A veritable gold mine of biodiversity to be studied! Some of these taxa have no Atlantic members. (It would be even better if these were enhanced by collections of course!)

Here's some highlights that I would love to see again!  

1. The Sea Cucumbers
I don't think I've seen ALL the pics but the ones I have were brilliant. This red elasiopod would be something I think everyone should see again... 
Okeanos from expl2168

The oddball swimming sea cucumber with the big lobe: the appropriately named Psychropotes
From Okeanos expl5494
and this gorgeous swimming Enypniastes? Or something similar to it.. But wow! Transparent body! You can literally SEE the sediment filled intestine THROUGH the body wall!
from Okeanos expl5475
2. The Hydrothermal Vents
When people talk about hydrothermal vents, there's 2 or 3 places that register as the most iconic spots.. the Mid-Atlantic and the East Pacific Rise.  There's others but one vent site that no one really talks about much?  The ones surveyed by Okeanos in Indonesia! 

These are the hydrothermal vents found on the undersea volcano Kawio Barat (West Kawio) 
from Okeanos expl2184
Amazingly gorgeous spires created by hydrothermal activity. 0.5 to 1 meter tall active and inactive spires on the summit of the Kawio Barat submarine volcano. Spires observed at 1849 meters depth. 
From Okeanos expl2188
Further venting through some of these chimneys gives us these amazing structures covered by barnacles! 
from Okeanos expl 2195
What's that? you want to see those barnacles more close up? here ya' go...
fr. Okeanos expl 2196

3. The Insane Stalked Crinoid Diversity
One of the very interesting animals noted in the expedition pictures notes was the incredible diversity of stalked crinoids which were observed.. I've only shown two of them below..but the gallery shows many different types of stalked crinoids.. to say nothing of the feather stars (aka unstalked crinoids)

This red one, as identified by Dr. Marc Eleaume in Paris is likely Proisocrinus ruberrimus 
From Okeanos expl5403
 And an likely unidentified member of the Hyocrinidae...                                     

4. Bizarre and wonderous Deep Sea Sponges (Hexactinellid or Glass Sponges? I think)
A wonderous cladorhizid carnivorous sponge from about 1000 m! 
from Okeanos expl5560
A bizarre sponge with unusual body morphology
from Okeanos expl 5599
5. And the underappreciated Slit Shell Snails (Pleurotamariidae)! 
I'm honestly not sure how many people recognized a majority of the animals observed on the 2010 dive but some of the shots from the NOAA Photo Library showed some awesome images of that most treasured of marine snails: The Slit Shelled Snail (family Pleurotamariidae).       

These snails have always held a certain appeal to shell collectors. The shells are known from the fossil record and have a distinct slotted opening near the shell's opening. They are one of the largest marine snails observed in deep-sea settings..
from Okeanos expl5650
 The images place the slit-shell moving into this gorgeous field of corals..                                  
From Okeanos expl 5648
Some of these snails are predators on echinoderms, such as sea stars and possibly serpent stars (ophiuroids). So, conceivably this one is about to feed...
From Okeanos expl5646
PLUS! those Hermit Crabs with shells replaced by sea 
fr. Okeanos 5671
fr. Okeanos 5672
ONE More GREAT thing?? In situ observations of WOOD FALL COMMUNITIES!  These are some of the weirdest, rarest of deep-sea habitats as written by Craig McClain at Deep-sea news as he's documented here and here.  What are they? Deep-sea communities based entirely on wood from the surface that have fallen to the deeps!!

Some of these species are known ONLY from wood substrates!

But how often do you get to see an established wood fall community??  Here's what looks like those wood-eating urchins I wrote about a few years ago...
Okeanos expl 5968
and here's a close up of some more urchins and polychaetes
from Okeanos expl 5972

and yeah, there was a LOT more...

So, Okeanos Decision Committee?? LET'S GO BACK TO INDONESIA!!! 

Wednesday, September 3, 2014

AWESOME vintage 1841 Forbes Echinoderm Plates via the Internet Archive Book Gallery & the Biodiversity Heritage Library!

This week's post is a bit late but trust me, you will LOVE THIS. Thanks to a new round of scanned images on Flickr via the Internet Book Archive  (from the Internet Archive) and from the Biodiversity Heritage Library a host of EPIC  images from the classic 1841 A history of British star-fishes, and other animals of the class Echinodermata by the famous naturalist Edward Forbes.

Brittle stars ARE THE DEVIL'S SERVANTS! (this one NEEDS to be turned into an animated GIF!)

When Sea Cucumbers fought Poseidon FOR THE WORLD! BE THANKFUL TO THEM!

Starfish! Always between the Devil and a hard place!


Even in 1841, Echinoderms were ever subjects by Women in Science!

Field Work was an arduous task in those days!

Young Men & Women Studying the Sea Urchin in Ye Olden Times! Note the humor! "urchin" in Latin meant hedgehog! And in olde English meant "unkept little child" And what's that next to it??? (thanks to Emily for her tip!)

And finally.. for David Shiffman at @WhySharksMatter MERMAIDS fighting over the Star-Fishe! 

Wednesday, August 27, 2014

Giant Deep Sea Amoebas! Meet the Xenophyophores!!

So, following up with all of the NOAA deep-sea Okeanos Explorer stuff, I've found that I am just FASCINATED by these things called Xenophyophores!! The name means "Bearer of foreign bodies".

But what are they? To put it they simply, they are giant, deep-sea amoebas that live in large, sediment "houses" called "tests" (similar to the way that echinoderm skeletons are also known as tests).

Footnote on the classificaiton: a quick survey of the various Protist classifications tells me that even calling these organisms "amoebas" is probably incorrect. But the nuances of this dynamic are for another day..

This one group, the Xenophyophorea live in the deep-sea.. DEEP in the deep-sea! Xenophyophores were observed as deep as10 KM (over 6 miles!) in the deepest of marine trenches (the Mariana) and occur in almost ALL of the world's oceans (except the Arctic).

They are considered among the world's largest living SINGLE CELLED organisms.

Xenophyophores create these large tests which they inhabit. The tests come in a variety of forms. There are 42 known species in 13 genera. As I understand it, xenophyophores are considered as a subgroup within the Foraminifera (these are amoeba-like unicellular organisms with tests).

Here's a variety of xenophyophore tests spied by the Okeanos Explorer below..but other patterns include big leafy structures and more network-like arrays of tubes. They vary quite a bit...
                              From the NOAA Photo Library here.                            
From the NOAA Photo Library here
From the Gulf of Mexico, NOAA photo library
Here's some fun facts!  Several different sources including the "Paleoecology and ecology of Xenophyophores" by Lisa Levin and others cited below...

1. How Big Are They?? So, here's the thing. I've read plenty of accounts that jump to the conclusion "These are the MONSTER AMOEBAS!!!" But what a lot of these accounts seem to forget is that the large sizes considered by a lot of popular accounts are the TESTS (i.e., the skeletons).

To be sure, these structures can be pretty big (for something made by amoebas!) The example below is apparently about 25 cm (almost a foot!) across!

Most of the accounts I've read sort of assume (and I suppose this is reasonable) that the animal inhabits ALL of the test all the time, or perhaps with pseudopods or tentacles extended throughout? Frankly, none of the accounts I read could clarify how much of the test, the actual organism inhabits.

However, One estimate (here) indicates that the test volume might be as little as < 1% "protoplasm" (which if I understand the terminology includes cytoplasm, etc.).. so, the actual organisms are probably not as monstrous as some folks would think. I would imagine its quite difficult to measure an amoeba for something like this.

2. What Do They Eat?
  So, when you think of big deep-sea amoebas, perhaps automatically we think "oh WOW! Wouldn't it be NEAT if they actually could eat ANIMALS?" Just like in the movies??  And in truth, there ARE marine amoebas which probably devour animals ... but to date, very little evidence is available on the full range of what xenophyophores actually eat. and the truth is sadly not likely to be as romantic as some would think...
One paper by Laureillard, Mejanelle and Sibuet from 2004 studied the xenophyophore Syringammina corbicula and utilized a study of various lipids and amino acids to look at their nutrition. Their study showed that bacteria were present in great abundance!

Xenophyophores have strings of mucus which are deployed along the test which build up feces and sediment called stercomes. It was suggested that a flora of these bacteria were present in abundance on these mucous threads. Perhaps being farmed and being utilized as a source of food.

Their mucous threads also are constantly pulling and trapping particles from the surrounding area, presumably in part to provide further nutrition.

Here is an Scanning Electron Microscope Image of a stercome showing up close details of what's on them...

So, there seems to be a heavy dependence on poop and other "marine snow" that falls down to the bottom.. as well as bacterial/microbial growth. But very little is known about feeding in xenophyophores, so who knows what else they do??

3. What are those structures (tests) made of? 
Tests on xenophyophores are made up of a patchwork of different bits. Sediment, but also the shells of other marine organisms such as radiolarians, other foraminiferans, and so on...

The test is the outer "crunchy" later... Within the test are a series of tubes called granellare, through which the animal's cytoplasm and etc. flow through...

These tests are actually an important part of xenophyophores ecological role, as they provide habitats and such.....

4. Ecology!
Probably the most interesting thing that I've picked up about Xenophyophores?? Is how potentially important they are to deep-sea ecosystems. Xenos are VERY abundant in the deep-sea, sometimes reaching up to 2000 per 100 square meters!

Lisa Levin published this neat paper in 1991 about their roles in deep-sea communities.  Basically it turns out that where xenos are found, there are "hotspots" of animal diversity!

The pic below shows two big xenophyophore tests with brittle stars on them...
Why might a cluster of xenophyophore tests represent a "hotspot" of animal diversity?? They apparently present both food AND habitats for a plethora of deep-sea animals!

Examples of how animals use these tests?
  • Habitats for worms, copepods, crustaceans, ophiuroids, and even snail embryos!
  • Peanut worms that live IN "dead" tests
  • Eggs from various animals (worms or snails) on xenophyophore tests.
  • Suspension feeding colonial animals called bryozoans sometimes are found "intergrown" on tests
  • Some xenophyophores found ON sea urchins.
  • Some amphipod crustaceans are thought to prey on the xenophyophores
  • Plus other MORE! Possibly/probably associated with the bacteria growing on the surface?? 
5. Mystery fossils: Xenophyophores??
So, one of the aforementioned articles by Levin on Xenophyophore paleoecology makes the case that tests and other modern examples of sediment structures by these organisms can explain various trace fossils, and other mysterious fossil structures.

Perhaps one of the best known is that of the fossil ichnogenus (like an organism name but for a trace fossil) Paleodictyon!

Paleodictyon was famously studied by oceanographer Peter Rona who made it an obsession of his career. It has covered by many other natural history blogs such as this and this. 

Basically.. a trace fossil which looks like this.
This is seen throughout the deep-sea in many places. The above image from the Gulf of Mexico but its been seen throughout the deep-sea, sometimes as deep as 3700 meters!!

Its also been seen in the fossil record.. dating back to the Paleozoic...  The parallel and similar appearance has led to much debate over whether the same type of organism has created these patterns in the sediment.. namely, did a xenophyophore or something similar create them?? 
And anyway, there's a LOT more on them in this regard and there seem to be more questions than answers.... A neat group of critters! (can I use that for amoebas?) 

Wednesday, August 20, 2014

Golden Tickets in the NOAA Photo Library! Rarely seen Pelagic Sea Cucumber!

From NOAA Photo Library here. 
HOLY CARP!! So, as you know, I've been going through and finding some GREAT stuff in the NOAA Photo Library (see this post from a few days ago) but every once in awhile you find one that is especially... striking!

This is the "golden ticket" so to speak.. from Charlie & the Chocolate Factory! that moment when Charlie finds that rare golden ticket from millions of chocolate bars! That special ticket to the rare tour of the chocolate factory! From MANY, MANY hours of going through these pictures I've found several GREAT items.
To be sure, there were quite a few "golden tickets" to be found among the thousands of pictures in the NOAA Photo Library (and for professional reasons I haven't shared all of them), but this one made me especially excited!!!   Why??

Because this is probably one of the FIRST public images of the "proper" Swimming sea cucumber Pelagothuria, possibly Pelagothuria natatrix!!  See my post here.  Dr. Dave Pawson at the NMNH confirms its identity. The image was taken from the Galapagos Rift Expedition in 2011. So its been sitting around for several years! 

Translation: A TRUE SWIMMING SEA CUCUMBER and probably the ONLY swimming (i.e. pelagic) echinoderm known!!! 
From NOAA Photo Library here. 
What you're seeing above is the swimming "umbrella" around the mouth, which is facing upwards! The body is the cone -shaped bit below it. 

This species occurs between 570 and 6000 meters in the Atlantic, Pacific and Indian Oceans but is poorly known. 

Previously.. this animal was known only from pictures....
Or from these grainy videos....(from Miller & Pawson)
 I have no doubt that there's scientists (my colleagues) out there who have seen this before and probably have video of this species..but this is the first that is available to share with ANYONE!!

So that's why you guys are getting TWO posts this week!!

Tuesday, August 19, 2014

Because Brisingid Starfish are Fantastic! Stunning Images of Brisingids in the Deep!

This image from NOAA Photo Library. Here. 
Brisingid starfishes were my first professional "love".. I wrote my Masters thesis on them and it was almost 2 years after studying specimens like this...
Before I saw one that was alive!  Now, THAT is dedication for you! 

What are brisingid starfish?? Long story short... Strange deep-sea starfish. They are proper, albeit highly modified sea stars that use their spines, covered with tiny claws which act as velcro to capture tiny prey as food.
This is Novodinia. Photo form NOAA Okeanos Explorer

I was just noticing that there's been a great critical mass of REALLY wonderful pictures of these animals.

For example, here's an amazing close up shot of Novodinia, possibly N. americana from the R/V Okeanos Explorer cruise to the North Atlantic canyons in 2013.  What you're seeing is the disk at the center, surrounded by the many spines covering each of its arms...
This image originally from NOAA Photo Library here. 
shots like these are increasingly common..but trust me when I say that scientists from the mid late 20th Century would have KILLED to have nice high definition picture like this!
Another Pic of Novodinia americana? from 2013. NOAA Photo Library. 
And here was one AMAZING bit of anecdotal observation/biology from the 2013 North Atlantic Okeanos Explorer cruise, this brisingid, unclear which genus, based purely on the pic not only caught a fish but HELD onto it using ONLY its pedicellariae.
Owly Images
Pedicellariae are tiny claw-shaped structures that cover each of those spines..sort of like staples embedded in a sock. These capture various food and prey items.. but mostly it was thought they captured crustaceans. Capturing fish is a bit unusual....

Food caught by the spines and on the surface are then moved down to the underside to the mouth...

Colleague Jackson Chu, provides us with a GREAT pic of the UNDERSIDE of a brisingid, showing the mouth, tube foot grooves and etc.. just what you would expect from any proper sea star...

Here are some stunning panoramic shots of brisingids. Presumably, these occur on places where water currents are favorable for them to capture food...  Both of these are from the North Atlantic via Okeanos Explorer..

These animals feed by holding their arms up into the water and capturing food/prey as it is carried by on the water currents...

This shot was from a spur projecting from the canyon wall in the North Atlantic (Block Canyon) in 2062-2131 m. 

This pic from 2013 Atlantic Canyons Expedition
Here are some great shots from Neptune Canada via Flickr...  A large individual, maybe Brisinga? on a sunken barrel..
some very "at attention" individuals...
Not all species occur on hard bottoms.. Some live on mud and sediment...
This one from the NE Canyons expedition in 2013
And just for a little diversity, From Japan, here is the underside of what I think is Brisingaster or Novodinia... These likely represent an unpublished record of this species in Japan..

Here is what the top side looks like...