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