Wednesday, May 13, 2015

The Adventures of Jenna and Mandy: Mission Impossible?

Our mission, should we choose to accept it, will be to find the worm Chaetopterus pergamentaceus from its type locality of "Antilles."  Armed with that informative location description (thanks, Cuvier), Jenna's keen sense of worm-dar, and Google Earth, we gladly accepted the mission and headed off to Puerto Rico for 10 days of intensive worm hunting!

This is probably covered elsewhere in the blog, but the type locality is the place where the original describer of the species found the specimen upon which he/she based the description.  Ideally that specimen was kept and deposited in a museum to be designated as the holotype of that species, the exemplar to which other animals can be compared.  Sometimes, especially in older descriptions, a drawing is all that remains of the holotype,  And in some cases "Antilles" is all you get for a type locality.  Greater?  Lesser?  Netherlands?  Puerto Rico it is!

So we got off the plane, and we started snorkeling in a diverse array of habitats.

Sand bottom?  Check!
Mud bottom?  Check!
Seagrass bottom?  Check!
Mangroves?  Check!
Sheltered area?  Check!
Areas with some wave action?  Check!
Populated areas?  Check!
More remote areas?  Check!   
Chaetopterus pergamentaceus?...((crickets))

We checked here:


We checked here:


We began to get discouraged.


With only a few days left to find them, Jenna expanded her Google Earth explorations to other parts of the island.  One bay in particular set her worm-dar to pinging.  It had an ideal orientation to the current, the right amount of protection from the waves, and, to add an element of danger to the expedition, it was also in a part of the island where cars on the beach often get their windows smashed in if valuables are visible.  Turns out the bottom is also composed of an appetizing mix of silty mud and garbage.  Bonus!


And then, as we were contemplating the vista before us, Jenna made a discovery:


The telltale paired ends of the worms' u-shaped tube.  They were everywhere.  And thanks to the gross goopy-ness of the bottom, they were pretty easy to dig out.

Back at the marine lab on the other side of the island the worms were lovingly dissected from their tubes, photographed, subsampled, and preserved for science and posterity.


A big thanks to Mariel Cruz, Nick Hammerman, and Nikolaos Schizas at the University of Mayagüez, Isla Magueyes Marine Lab.  Without their invaluable assistance our worm mission would have turned out to be truly impossible.

Mission Accomplished!





:) Mandy



Friday, March 27, 2015

Frantic February gives way to March Madness

So February was crazy.  Even by our usual standards of busy-ness, everything was just a little bit more hectic in February.

There was a lot of background busyness in the form of job seminars.  Most weeks, sometimes twice a week, the whole museum shlepped over to Powell Hall (the public face of the FLMNH) to hear candidates for our two new faculty positions present their research.  The talks were interesting, and the receptions afterwards were catered.  That's an all-around win.

Some of the recent new hires have already arrived (or will be arriving soon).  And although it might seem impossible to get blood from a stone, the museum needed to find space to put them.  So we're all playing musical offices, and one of the offices getting shuffled is Fred's.  We spent several weeks moving Fred out of his office and moving most of our freshwater mollusks out to a nice, new, storage facility.  I say "we," and we all chipped in, but most of the work was done by John, George, and a large team of professional movers.  The area with stacks of shelves that you might have seen in earlier blog posts now looks like this.


 We got everything set up and cleaned off just in time to host the 6th annual FUM meeting that we last hosted 4 years ago.  John spent a lot of time making the meeting website, organizing talks, booking meeting space, organizing a reception, arranging for meals, testing computers, making a program, all in addition to preparing his own talk.  I was unable to attend this year, but by all accounts it was a great success.  One day I'll get enough new slug data to present at FUM again...or maybe enough time will pass that no one will realize I'm giving the exact same talk.

Thanks to Carole Marshall for this photo
 Why host one giant meeting per month when you can host two?..is something that we have never wondered.  And yet in spite of that, February also saw us hosting a marine biodiversity workshop for high school science teachers at Whitney Lab in Marineland, FL.  Nearly 25 teachers from all over the state came to learn about our techniques for documenting biodiversity and how they can be applied in the classroom.  It was the first of three such workshops that we will be hosting.  Patrick did most of the organizational legwork for this one, with Gustav, Tania, François, and John all pitching in at game time.  Maria Sgambati from Seahorse Key and Lisa Lundgren from the UF Education school were also on hand to lend their expertise.

Two big meetings and I missed them both.  What kind of slacker gets away with that?  The kind that is stuck with much of the paperwork and purchasing for the event.

Also on the docket for February, John and I began working with Warren in preparation for migrating our database from Microsoft Access to Specify.  Several ranges have already made the move, so the Specify team in Kansas is no stranger to the myriad ways in which various ranges store, organize, and name their data.  For example, "field number" to IZ is the number assigned in the field which links a particular specimen with it's photograph and DNA sample.  It also links the specimen to a station number with location information in the notes that we take for the trip.  To other ranges, "field number" equates with our "station number."  And what kind of data should you include in the "station number" or location information?  Is depth specific to the specimen or to the location?  What about habitat?  Or collector?  These are all important decisions and are just the tip of the iceberg.  Specify is a very different beast from our familiar Access template, and the process of familiarization has just begun.

Access on the left, Specify on the right

We also had several visitors in February, including Matt Leray and Nancy Knowlton.  Did I mention way back in 2013 that François went to the Line Islands with a team from the Smithsonian?  It was with Matt and Nancy.  It was long ago, and those specimens are largely on the shelves, cataloged, photos matched, DNA cataloged into the cryofreezer.  Turns out there were a few boxes of unsorted bulk lots in the back.  So, how much could it be?  We already have 916 lots cataloged and shelved.  Maybe there are a few stragglers...


There were a lot of stragglers.  This doesn't even begin to demonstrate the magnitude of the stragglers.  Several thousand lots were created from sorting existing mixed lots of tiny specimens, mostly crabs and shrimp.  Somebody has got to subsample these and put them into plates for sequencing at the Smithsonian.  This looks like a job for Team Plating Party!..of which I am the only remaining member.  But it was a team effort after all.  Matt, Elizabeth, Tania, and I all did several hours worth of plating.

So is March shaping up to be a little more mild?  Well, the job talks are over, and we have no meetings to host (that I know of), but we have already had several visitors and have several more on the way. Specify-readiness training is ongoing, we received a shipment of 10 drums of ethanol, and we have been working with customs through a shipping company to try and arrange for delivery of specimens that Gustav collected last year in French Guiana with folks from the Paris Museum.  Seems like we're just getting ramped up.  What's a good assonant word for hectic that I can pair with April....

:) Mandy

Tuesday, December 16, 2014

Hey everyone,

I'm spending time at the Smithsonian National Museum of Natural History these days, and wrote a short blog post about another recent leg of the Red Sea Biodiversity Project over at the No Bones blog - why don't you go and check it out here?

Wormly,
Jenna

Friday, October 3, 2014

Goldilocks and the three crab size classes: New paper out this week on coral guard-crabs

Remember Seabird? He was a Ph. D. student in the lab, and is now Dr. Seabird McKeon at the Smithsonian Marine Station in Ft. Pierce, Florida. A paper we co-authored on Trapezia defense against coral predators came out this week in PeerJ, and even made the front page. It's open access, so you can read it for yourself right here. These plucky little crabs defend their coral hosts against different species of corallivores, including the snail Drupella cornus, the cushion sea star Culcita novaeguineae, and the fearsome Acanthaster planci, or Crown-of-Thorns sea star (COTS if you're in the know).

Photo © David Liitschwager
The response of the four species of Trapezia we tested against these predators varied by the size of the crab species. Little Trapezia serenei and Trapezia punctimanus defended their hosts effectively against Drupella cornus (the little snail predator), but couldn't do much about the big predators. Medium sized Trapezia serenei and Trapezia bidentata could fend off Culcita novaeguineae, but didn't bother with the snail threat. And the biggest crabs, Trapezia flavopunctata, had a striking effect on their host survival in a natural experiment in Moorea, French Polynesia during an outbreak of Crown-of-Thorns sea stars.

Terrifying: Acanthaster chowing down on Pocillopora
There's also been a bit of buzz about the article on some news sites, so if popular articles are more your cup of tea, here's a few features of the article, featuring the gorgeous photography of Trapezia by David Liitschwager:

Science News
Smithsonian Magazine
Science World Report
Phys.org

Worm wishes,
Jenna

Sunday, May 25, 2014

Not bad atoll...

The 2014 Marine Biodiversity Workshop on Magoodhoo Island, Maldives

Photo: Francesca Benzoni
This is a busy summer of fieldwork for the IZ crew: Gustav just returned from an expedition in the Philippines, Nat is off wrestling portunids in Palau and Guam, and I spent the past two weeks participating in a great workshop organized by Drs. Francesca Benzoni and Paolo Galli of the University of Milan, Bicocca.

Many invertebrate researchers from universities and museums in the Netherlands, Japan, Saudi Arabia, Italy, and the US gathered on Magoodhoo Island to document the biodiversity of the Maldives, as well as contribute lectures and practical courses to a wonderful group of Master's students.

Photo: Luis Gutierrez

The students got a taste of our team's field and curation techniques through collecting their own specimens from the local lagoon, replete with seagrass beds, a lovely fringing reef, and all the sand a sea cucumber could eat. Here are some of the students hard at work hunting for creatures in dead coral rubble and sorting the catch:


The students took to our processing techniques immediately, and documented, photographed, DNA subsampled, relaxed and preserved the specimens provided by the sorting teams like champions!


After the biodiversity sampling lecture and practical, the students filed back into the classroom for a lecture on marine annelid biology, which are my favorite group of spineless creatures. They got a thorough indoctrination lesson on the wonderful world of worm biology.

In exchange for the wonderful opportunity to interact with these very bright and eager students, the visiting researchers also sampled the local reefs during daily excursions on the dhoni, a traditional wooden Maldivian boat outfitted these days with SCUBA tank racks, diesel engines and sound systems.

Photos: Francesca Benzoni
These excursions provided us with new specimens of crustaceans, echinoderms, molluscs, and of course, annelids, for the Florida Museum Marine Invertebrate collection. I will resist the extreme temptation to show off some of the beautiful chaetopterid polychaete worms, in favor of this incredibly adorable leopard-print Indian Ocean endemic nudibranch, Chromodoris gleniei:


Stay tuned for a post on the upcoming expedition to Kavieng, Papua New Guinea!

Worm wishes,
Jenna

Monday, February 24, 2014

Team Unionid

Taxonomy is a wily beast.  As François discussed in his previous post, keeping up with who is called what can be a complex issue.  Species can be synonomized with other species, moved to other genera, split from their current species into a new species (or new genus), and back again and so forth.  This can make things somewhat complicated for museum collections, especially when we receive collections that have been collected throughout history.  We get specimens that have the ID that was correct when they were collected 50 years ago, but what is the current correct name? What is the name in our database?  Is it one of those two or one of the many steps in between?  There are a (very) few groups that have current taxonomy listings on line, but we deal with so many groups from so many phyla.  It usually takes an expert, who is familiar with the current literature of their particular group to clear things up. Fortunately for us, we know an expert for one of our largest groups, the Unionidae family of freshwater mussels, and he's recruited others.

Jim Williams, Matthew Rowe, and Jordan Holcomb have been combing through countless brown shells and getting our taxonomy in order. 


To give you an idea of what "countless" means...


Yeah, you could totally count that, but multiply it by...


That's still doable, might take a while, but...

Nearly that entire aisle is Unionids, and there are even a few cabinets worth in the previous aisle.  Let's not forget the wet collection.  Below is less than half of it.


Even though they are all caught up on the current taxonomy of this group, it still isn't always as straightforward as changing all specimens of one name to another.  Here is an excerpt of an email I got from Jordan outlining the specimen labels they needed updated and printed for the Lampsilis teres/floridensis group:



We will need everything from Florida listed as Lampsilis teres to be changed to Lampsilis floridensis.  All records from Georgia except those from Walker, Chattooga, Gordon, Floyd, Bartow, Whitfield, Murray, Gilmer, Catoosa and Polk counties listed as Lampsilis teres need to be changed to Lampsilis floridensis.  Finally, all Lampsilis teres holdings in Alabama from Butler, Barbour, Chambers, Conecuh, Covington, Crenshaw, Coffee, Escambia, Dale, Geneva, Henry, Houston, Lee, Pike, and Russell counties should be changed to Lampsilis floridensis. 


And this doesn't even account for the L. teres floridensis that we had cataloged from Iowa and Arkansas, or the L. teres teres specimens that needed to become L. teres.  So it's complicated, and we are really grateful that they are willing to spend all this time and effort helping to get our collection up to date.  We're also grateful for the bribes they bring us to keep the updated labels flowing.


Unionids are a challenging group to work with, but the challenges that they present to us pale in comparison to the challenges with which humanity has presented them.  Many species are critically endangered and some are suspected to now be extinct.  As a freshwater group, they rely on many of the same waterways that we utilize for drinking water, power, recreation, and many other uses.  Pollution and habitat loss have wreaked havoc on this group that is very sensitive to changes to their ecosystem.  If you want to know more about Unionids, check out Jim's book on the Alabama mussels, and keep your eyes peeled for his next one.

:) Mandy

Thursday, February 6, 2014

Invertebrate Zoology is Nice(ville)

This past weekend we were visited by a group of high school students from Niceville, FL.  They have come to visit us every year for the past several years to get a taste of what we do, and to incorporate some of our techniques into their own projects and fieldwork.

They divided into three groups.  The first group explored the collection for a broad overview of the kind of biodiversity we have in our collection.  Of course Bathynomus giganteus, a giant isopod, was a hit.


Who could resist a face like this?

Photo from Wikipedia Commons
We had several exercises for them down in the collection.  Jenna worked with a group of students trying to sort brittle stars.  There is a group that has been historically identified as a single species, however genetics and the discerning eye of Tania (a visiting researcher) can find significant differences between several groups within the species.  We challenged the high school students to do the same, armed with Tania's genetic tree and a microscope


The students also braved the world of tunicates with Ronaldo who is visiting from Brazil.  He showed them some nice clear diagrams with taxinomically significant features highlighted.  They then looked through the microscope at a prepared specimen to see how tiny and easily confused these features really are.

Then they tried their hand at some microscope work of their own and prepared some sea cucumber ossicle slides with guidance from Starmer John and myself.  He even brought in the big fancy microscope from our office for the occasion, to demonstrate how ossicles show up under polarized light.


The second station was upstairs in the lab with Nat and Jennifer.  After explaining the PCR process and how we use it in our lab, the students all gloved up and prepared solutions for PCRing.  Since running the actual PCR is a process that takes several hours in the thermal cycler, Nat and Jennifer ran some pre-loaded gels so they could see the bands of DNA fragments of various lengths.


After their stint in the DNA lab, the students headed downstairs to work with François on aligning and cleaning DNA sequences using Geneious.  After we send our PCR products out for sequencing, the results we get back still need some hands-on attention before they are ready for prime-time, so the students got a taste of that.  François has undoubtedly spend many an hour in front of the computer with color-coded nucleotides dancing before his eyes. 




We had a great experience with the group and it's always fun to share our love of what we do, especially with potential future scientists.  In fact, you can never be too young to be engaged in invertebrate zoology...


...even if what that means for now is that you're drawing some octopus and crabs in with your flowers.

Friday, January 31, 2014

At last Mookie has a sea cucumber species named after him, let me introduce you to Phyrella mookiei

In 2010, during the sea cucumber taxonomy workshop we organized in Guam, we collected what we thought was a new sea cucumber species of the order Dendrochirotida. At least, we knew it was interesting as this order was known to have only two species in Guam, and this clearly was neither.

Back to the museum, we started to examine the specimen more closely to assign it to the appropriate genus. It soon became apparent that this species belonged to the genus called Phyrella (family Phyllophoridae). To determine if it was a new species, we first went through all species that are currently in this genus, and our species did not match any of the 4 species assigned to Phyrella. At this stage, it looked like describing this new species would have been a quick and easy side project. It was not. The paper is pretty large (40 pages), and took a long time to put together. So, what happened?

The species description turned into the revision of the Phyrella. We realized that two genera were synonym of Phyrella (Thyonidiella and Semperiella); one species that was assigned to Phyrella did not belong there (we transfered it to the genus Euthyonidiella); and that other species might actually belong to Phyrella. Making these decisions involved spending a lot of time reading through old taxonomic descriptions (most of them in German), and also examining specimens from many places (Australia, Japan, the Philippines, Panama) and type specimens that are housed in the natural history museums of Paris, Geneva, Washington D.C., Copenhagen and Perth.

If you are not acquainted with the inner workings of taxonomy you might be wondering what a "revision" is, and why we "transfer" species between genera or "synonymize" them. Taxonomy strives to create groups that reflect the evolutionary history of the species they include. In other words, the classification of a species should give you a rough idea of its position on the tree of life. In the past, the only way to estimate how species are related to each others was to find morphological characters that are shared among them. Sea cucumbers don't have many morphological characters that can be used to make these groupings. In addition, over the history of sea cucumber taxonomy, different authors had divergent opinions on which characters to use. Another problem is that many species were described based only on a few specimens so previous authors didn't appreciate the variation in these characters within a species. These factors led to a confused taxonomy with many genera that do not group related species together. A taxonomic revision fixes that, and with our paper, we clean up a little corner of the giant mess that is currently the Dendrochirotid taxonomy.

An important advantage that we now have compared to past sea cucumber workers is that we can use DNA to infer how species are related to each others. It gives us an independent line of evidence we can use to clarify the morphological characters that define genera. Our study is the first to use DNA to guide a taxonomic revision in Dendrochirotida. We learned that there is a lot more morphological variation in Dendrochirotida than was previously appreciated. For instance, before our study, all Phyrella were thought to have 20 tentacles. However, after painstakingly counting the tentacles of many specimens, it is clear that this number is variable, even within a species.

And what about the new species? Its name is Phyrella mookiei, the etymology of the paper says:
Named after Mookie, the dog of our collection assistant Ms. Mandy Bemis, because the "woolly" appearance and color of this species is similar to the soft coat of wheaten terriers, the breed to which Mookie belongs.
The timing couldn't be better as tomorrow is Mookie's birthday. Here are some pictures of Phyrella mookiei and Mookie so that you can decide for yourself of the resemblance. You can download the full article here. It's open access so feel free to distribute widely and re-use the content as you please.

Monday, September 23, 2013

Summer Activities

So what have we been doing all summer.  Well...lots of things!


Gustav was gone most of the summer teaching a class up at Friday Harbor Lab in Washington (state).  Here he is teaching the same class from a few years ago.

Should I mention that it was an intensive invertebrate zoology class, or is that obvious from his disguise as Nephrops norvegicus with Cycliophora?

We also got several shipments from the field including specimens from the Tuamotus, Red Sea, and Singapore expeditions that various of us were on recently.  You know what those shipments look like as they have been featured on this blog before. They are beloved by both airline personnel and USPS workers alike due to both their contraband appearance and intoxicating aroma.



Speaking of contraband appearance, check these out!  Any guesses as to what we have here?

If you said, "whale bones!?!" then you'd be right.  If you said "*yawn* whale bones?" then you'd also be technically right, but we could do with a little more enthusiasm.  We in invertebrate zoology don't usually get too fired up about bones, but every once in a while those vertebrate divisions come across some cool specimens of their own.

Like this specimen that was found in a tank full of sharks.

I'm sure that Rob couldn't believe his luck when he found this squid fraternizing with his sharks out at the large specimen storage facility.  I know it's hard to tell from this picture, but the squid is actually in pretty good shape and even in his contracted/preserved state is maybe about 5 feet long with tentacles extended.  His label was also in surprisingly good shape and this Ommastrephes bartrami is now an official member of our collection.

Our collection has actually been getting a lot of new members lately.

Lots of people have spent lots of hours going though our backlog of donated collections and rehousing them and cataloging them into our collection.  No sooner is the range table cleared off then...
...boom!  Another trip to the offsite storage facility yields a fresh bounty of (mostly) molluscs to be accessioned.

All this accessioning is thirsty work.

For the specimens I mean.  Another gagillion samples, another ethanol order.  Randy (from fishes), Adania, John and I met the truck to help unload the ten or so 55-gallon drums that we had collectively ordered.

And the collection isn't the only thing growing.  Our lab has been growing too, due to several long-term visitors including Andréa, in the photo below, who is visiting us for a year to study didemnids, a type of colonial tunicate.

If you've ever seen a rock in the ocean that was encrusted with a brightly colored substance...well, it might have been a sponge...or an alga...but it also might have been a didemnid tunicate!  In addition to Andréa, Ronaldo is also visiting us for a year.  He is studying solitary tunicates.  But lest you think we are neglecting the other phyla, Tania was here most of the summer, and she plowed through the lion's share of our brittle star collection, IDing things left and right...we're hoping we haven't seen the last of her.  Plus, Jenna is back!

But now she and Gustav have headed back to the Red Sea with a few other familiar faces to do some boat-based sampling in the Gulf of Aqaba.  I think François and Nat are going on some adventures as well.  I'm sure they'll all have some interesting photos and stories to share.

:) Mandy