New paper on hemichordate and echinoderm phylogeny

http://www.cell.com/current-biology/abstract/S0960-9822%2814%2901292-5

New paper on lophotrochozoan TLRs with Ken Halanych

http://www.biolbull.org/content/227/2/201.full

Three new meiofaunal solenogaster species (Mollusca: Aplacophora) from the north-east Pacific

G'day!

Today my first first-author species description paper was published with Christiane Todt! Here, we describe three new species of meiofaunal solenogasters (neomenioids) from virtually right off the dock at Friday Harbor labs. One of them, Macellomenia schanderi, is named after the late Christoffer Schander who was a mentor and dear friend of mine. Thanks for everything, Chris! Another, Macellomenia morseae, is named after M. Patricia Morse who has also been a fantastic mentor to me and is an expert on all things meiofaunal.

One of the most interesting aspects of this paper is the implications for biogeography. The genus Macellomenia was previously only known from the
European Atlantic and Mediterranean Sea. Now we've found two species in the Pacific. The crazy thing is that one of our new Pacific species is pretty clearly more closely related to an Atlantic species with a similar copulatory apparatus than it is to its sympatric cogener. Likewise, Hypomenia is a genus previously only known from the Mediterranean Sea and now we've found a second species in the Pacific!

We've also sequenced transcriptomes for M. schanderi, Hypomenia sanjuanensis, and the other solenogaster previously described from this locality (by Trish Morse) Meiomenia swedmarki for our ongoing aplacophoran phylogenomics project.

Macellomenia schanderi sp. nov. (A) SEM micrograph of entire specimen, oblique ventral view. Position of anterior end (ant) and pedal groove (pg) indicated. Scale bar 200 μm; (B) ventral view of anterior body tip showing the atrium (a), mouth (mo) and the partially everted, ciliated pedal pit (pp). Scale bar 50 μm; (C) SEM micrograph of epidermal sclerites. The small insert shows a pedal scale (ps), the larger image illustrates the morphology of the main sclerite type with broadened base (bs) and flattened, recurved spine (s) covered in minute spinelets. Scale bar 10 μm; (D) SEM micrograph of the partially everted genital cone and pallial cavity opening (pc) with abdominal spines (asp) covered in mucus (muc). Scale bar 50 μm; (E) light micrograph of sclerites. Most of the body sclerites are intact although the acicular portion has been separated from the basal plate from several. There is one pedal scale (ps). Scale bar 50 μm.

Scanning electron micrographs of Macellomenia morseae. (A) Juvenile specimen mounted with ventral surface facing upwards; anterior end (ant) and pedal groove (pg) indicated. Scale bar 200 μm; (B) close-up of pedal groove showing two types of pedal scales, pointed (a) and broad with a notch (b). Scale bar 20 μm; (C) lateral sclerites, some in the centre of the image showing cup-shaped broadened bases Scale bar 25 μm; (D) pedal pit (pp) surrounded by pointed scales (a). Scale bar 25 μm; (E) light micrographs of epidermal sclerites (black background: polarized light filter). Note nail-shaped sclerites (n) and more asymmetri- cally shaped sclerites (asterisk) in lateral (to the left and to the right) and frontal (centre of image) views; both types of pedal sclerites (a, b) are very thin and delicate. Scale bar 50 μm

I'm really excited about this paper and about aplacophoran taxonomy. Hopefully there will be more where this came from soon - I am currently working on some interesting material from the Gulf of Mexico and New Zealand.

The paper can be downloaded here (let me know if you don't have access and want a copy):

http://www.tandfonline.com/doi/full/10.1080/00222933.2014.961987#.VD7tNq1xOPI

Scutopus ventrolineatus mitochondrial genome published

A couple weeks ago the first aplacophoran mitochondrial genome was published by Davide Osca et al.! Way to go Zardoya lab!

Scutopus is considerate enough to have a pretty typical molluscan mitochondrial genome organization and it is not an especially long branch. I was very impressed by the mitochondrial gene trees, which largely agree with the 2011 duelling Nature mollusc phylogenomics papers. When I've tried to make mollusc mt genome trees before they've turned out pretty wacky (but it seems the authors wisely avoided some of the more long-branched taxa). They also conducted analyses including nuclear ribosomal proteins from a diverse sampling of molluscs both with and without the mitochondrial data and found support for Aculifera and Aplacophora (albeit with weak support in some analyses).

Scutopus is actually the second aplacophoran mitochondrial genome that is publicly available. The mitochondrial genome of Chaetoderma nitidulum is also available on NCBI but it was never published.

Link to the paper:
http://www.biomedcentral.com/1471-2148/14/197/

Scutopus ventrolineatus
(photo by Christiane Todt)

2014 Frontiers in Phylogenetics Symposium

Last week I presented a talk entitled "Deep metazoan phylogeny and the utility of taxon-specific ortholog sets" at the Smithsonian Frontiers in Phylogenetics symposium. This year's theme was Genome Scale Phylogenetics: Analyzing the Data. My talk was on my research using custom, taxon-specific core ortholog sets in the program HaMStR as a computationally tractable alternative to more computationally intensive all-versus-all BLAST-based approaches (e.g., OrthoMCL) or similar approaches (e.g., OMA).

Here's a link to a video of the talk for anyone interested in checking it out (Guillermo's introduction for my talk starts around 1:28 in)
http://www.ustream.tv/recorded/52713111

Here's the abstract:
Orthology determination based on a set of pre-defined orthologs is a powerful and computationally tractable approach to identify molecular data suitable for genome-scale phylogenetics. However, genes that are single copy among the taxa used to prepare such a set may have undergone lineage-specific duplications in other clades, suggesting taxon-specific core ortholog sets are advantageous. I will present studies of deep metazoan phylogeny based on custom sets of core orthologs that are specific to the taxon sampling of a given project. By selecting a small but representative subset of around 5-10 taxa with high quality transcriptomes (and ideally at least one taxon with a high quality genome) and using all-versus-all BLAST, OrthoMCL, and our PhyloTreePruner software, HaMStR core ortholog sets that are specific to a group of interest can easily be generated. Importantly, these core ortholog sets tend to contain many more genes than the sets based on broader taxon sampling. Starting from a larger pool of orthologous sequences allows for stricter gene selection criteria, enabling the investigator to exclude genes with e.g., large amounts of missing data, few unambiguously aligned positions, a high rate of evolution, different rates of evolution among taxa, etc.

International Congress on Invertebrate Morphology 3

Last month I attended the International Congress on Invertebrate Morphology in Berlin, Germany. This has quickly become my favorite meeting. A lot of really strong research was presented here and it was really nice to catch up with a lot of old friends. This ICIM had a very strong molluscan showing with a pleasantly surprising majority of the mollusc talks / posters dealing, at least in part, with aculiferans!

Link to the program:
http://www.icim3.org/program.htm

Talks dealing with aculiferans
Evolution and development of photoreceptors in Polyplacophora
Ollie Vöcking

Hox gene expression in polyplacophoran molluscs
Martin Fritsch

It's only a model: seeking an osphradium in more obscure molluscs
Julia Sigwart

Development of the metanephridial and coelomic system in molluscs – more variability than allowed? 
Gerhard Haszprunar

EvoDevo and its bearing on molluscan phylogeny. 
Andi Wanninger

Posters dealing with aculiferans
New insights into molluscan biomineralization through studies of aculiferans
Kevin Kocot

Chitons that live in the dark can see light (Mollusca, Polyplacophora, Lepidopleurida)
Julia Sigwart and Lauren Sumner-Rooney 

A new class of aplacophoran mollusk – or “just” a footless solenogaster?
Christiane Todt  
 
 

Successful Friday Harbor Labs trip

Last week I visited Friday Harbor Labs to collect aplacophorans and chiton's for biomineralization studies. I managed to get about 10 specimens of a soon-to-be described species of Hypomenia and 3 specimens of a new Macellomenia we're working on describing (see pic below).

Macellomenia sp. "schanderi"

The Marine Invertebrate Zoology course shared an unusual mutant Tonicella line at a lacking the normal shell pigment pattern.

Tonicella lineata "blue albino"

Kevin Kocot 2014 Northern Hemisphere Tour

I'm still waiting on official approval from UQ's powers that be, but I will be visiting the U.S. and Germany this July-August.

July 9-15: Auburn (with a trip to NC for friends' wedding)
July 15-21: Friday Harbor Labs
July 21-31: Auburn
August 1-10: Berlin (for the International Conference of Invertebrate Morphology)
August 10-24: Auburn, St. Louis, and Destin, FL (for my sissie's wedding!). Details forthcoming...

My cup overflowith

One challenge I've faced in my project studying aculiferan biomineralization has been getting samples of aplacophorans suitable for RNA-based work. Often times, aplacs can be rare and I really need multiple specimens to have biological replicates for some of the experiments I plan to do. I had hoped to collect Epimenia here in Australia but so far that hasn't panned out. Fortunately, my wonderful collaborator and friend Dr. Christiane Todt was just on a cruise and collected tons of specimens of Stylomenia sulcodoryata and Chaetoderma nitidulum as well as one specimen each of Neomenia carinata and Scutopus ventrolineatus. Now I'm armed with plenty of material for traditional transcriptomes of mantle tissue a well as laser capture microdsisection and CEL-seq and in situ hybridization to look at gene expression in the cells secreting sclerites in these beasts as well as proteomic work looking at the protein component of the sclerites.

Stylomenia sulcodoryata
(source: http://www.artsdatabanken.no/Article/Article/398)

Chaetoderma
(source: http://www.whoi.edu/science/B/aplacophora/defchaetneo.html)

Pleurobrachia bachei (Ctenophora) genome published in Nature this week

No, it's not an aculiferan mollusc but I just had to post about this...

Our paper on the genome of the ctenophore Pleurobrachia bachei was published this week in Nature! I'm really proud to have had a part in this exciting work and I'm eager to see what the future holds for some of the unanswered questions and surprising findings made here and by the Mnemiopsis leidyi genome study.

 

Link to the paper itself at Nature

Link to News & Views write-up by Andy Hejnol

Proofs for Proneomenia custodiens sp. nov.!

Today Christiane Todt and I got our proofs for our upcoming paper (Todt and Kocot in press, Polish Polar Research) describing a new species of Proneomenia I collected during the 2011 IceAGE cruise that broods its babies in its butt!

Here's the abstract:
During August-September 2011, scientists aboard the R/V Meteor sampled marine animals around Iceland for the IceAGE project (Icelandic marine Animals: Genetics and Ecology). The last sample was taken at a site known as “The Rose Garden” off northeastern Iceland and yielded a large number of two species of Proneomenia (Mollusca, Aplacophora, Solenogastres, Cavibelonia, Proneomeniidae). We examined isolated sclerites, radulae, and histological section series for both species. The first, Proneomenia sluiteri Hubrecht, 1880, was originally described from the Barents Sea. This is the first record of this species in Icelandic waters. However, examination of aplacophoran lots collected during the earlier BIOICE campaign revealed additional Icelandic localities from which this species was collected previously. The second represents a new species of Proneomenia, which, unlike other known representatives of the genus, broods juveniles in the mantle cavity. We provide a formal description, proposing the name Proneomenia custodiens n. sp. Interestingly, the sclerites of brooded juveniles are scales like those found in the putatively plesiomorphic order Pholidoskepia rather than hollow needles like those of the adults of this species. Cytochrome c oxidase subunit I (COI) DNA barcode sequences are provided for both species of Proneomenia.

Proneomenia custodiens n. sp. A. Photograph of a brooding specimen in the process of expelling its offspring, presumably a stress response (photo by D. Fiege); scale bar: 0.8 mm. B. Microphotography of one juvenile (photo by M. Błażewicz-Paszkowycz); scale bar: 100 µm. C. Histological cross-section through the mantle cavity (mc) of the holotype brooding juveniles (asterisks); one juvenile is situated in the mantle cavity opening (arrow); scale bar: 500 µm. D. Cross-section of a juvenile from within the mantle cavity of the holotype, showing the cerebral ganglion (cg), pharynx (ph), pedal ciliary pit (cp), and pedal gland of one of the juveniles. The specimen still contains yolk (y) and it is covered in cuticle and surrounded by the folded egg hull; scale bar: 50 µm. 

Shameless self plug

On Thursday, April 10th, I'm giving a talk about work I did on aplacophoran mollusc phylogeny in Ken Halanych's lab. The talk will be at 1 PM in Goddard Building 257 (UQ).

Entonomenia sp. (tricarinata?) from Antarctica

I have data!

My former labmate Joie Cannon and I use the word text as an adjective. As in "This Obelia specimen is totally text." It means that Obelia specimen you are looking at under the microscope looks just like the sketch of it in the textbook. Today I got my first glimpse at my histological sections showing sclerite secretion in Acanthopleura gemmata and Cryptoplax larvaeformis. Sclerite secretion is Acanthopleura gemmata is totally text. Things aren't so clear with Cryptoplax... yet. I also got some amazing micro CT scans of Acanthopleura sclerites back from Jeremy Shaw today.

I can't wait to present some data on chiton biomineralization at the next International Congress of Invertebrate Morphology!

Heron Island debrief

All in all, my time at Heron Island was amazing. That's probably evidenced by the fact that I only actually blogged about twice during the whole time I was there. The biodiversity on the reef was astounding and the meiofauna and communities of animals living on algae were amazing. I spent most of my time snorkeling and flipping over rocks or sitting at the microscope sorting meiofauna or material from "rock washing" or "algae washing." In these samples, I found *one* meiofaunal solenogaster (Meiomenia) that I will send to Katharina Jörger for work she and her student Franzi are doing examining the diversity of meiomeniids. Aside from molluscs, I also found heaps of other interesting animals including Cephalodiscus(!), lots of different species of annelids, benthic chaetognaths, lots of different species of acoels, and a wacky proseriate flatworm with multiple pharynxes (among others).

Cephalodiscus sp. that I found on the red alga Amphiroa. Not an aculiferan, I know, but it is almost certainly a new species and it's pretty darn cute so I had to stick this one in.

I came home with numerous specimens of Cryptoplax larvaeformis as well as some specimens of Acanthopleura gemmata and a couple other interesting but as yet unidentified chitons. I was on the lookout for Schizochiton for Doug Eernisse, Dan Speiser, and Lesley Brooker but unfortunately I didn't find that any. Sorry guys! I was hoping to get the Acanthopleura and maybe the Cryptoplax to spawn but it seems that wasn't in the cards. I'm going to try a few experiments back here to see if I can get them in the mood.

Otherwise, I was on the hunt for aplacophorans. I'm now aware of three sighting of Epimenia (australis?) around Heron but despite flipping over half of the rocks on the island, I left empty handed when it comes to Epimenia. I'm now purusing other avenues to obtain specimens of Epimeina and/or considering other, more reliably accessible species of aplacophorans.

Epimenia (australis?).
Source: http://www.blueanimalbio.com/ruantidongwu/wuban.htm

In the coming weeks, I'm going to be doing tests on various methods to decalcify specimens of chitons for histological sectioning followed by laser-capture microdissection (LMD) in order to extract RNA from specific cell types and study the transcriptomes of cells associated with biomineralization.

First Australian record for Meiomeniidae!

After many hours of searching through the meiofauna, I found *one* specimen of an undescribed species of Meiomenia in a sand sample taken from east of Heron Island. Meiomeniids are tiny, interstitial solenogaster aplacophorans that feed on hydrozoans. They are known from Florida, the Caribbean, Bermuda, the Azores, Norway, Friday Harbor, and now Heron Island. I don't have facilities to take great pictures of meiofauna so instead I'll share Rick Hochberg's video of Meiomenia from Florida (they all look pretty similar anyway).

Otherwise, things are going well here on Heron. I'm fixing samples of Cryptoplax for various gene expression and other experiments and I'm still trying to spawn chitons with limited success... More on that soon.

Found heaps of Cryptoplax!

I was having trouble finding Cryptoplax on the north side of Heron Island. At Bernie's suggestion, I went for a reef walk at low tide on the southern side of the island and pretty easily found about 15 Cryptoplax on the underside of boulders. I brought the animals back to the lab and have since been trying to keep them from escaping from their aquarium.

Cryptoplax larvaeformis

Now I have both Cryptoplax and Acanthopleura and have been trying to convince them to spawn. They didn't cooperate on the full moon (even though it was Valentine's day!) and so far they haven't spawned tonight but I'm keeping a vigil. It's been suggested that thermal stress (both unusually cold and unusually warm) can induce spawning. If they don't spawn in the next couple of days, that'll be my next action.

Experimental aquaria for chiton spawning. If they start to
spawn, males will be isolated to avoid polyspermy and eggs

will be collected in 63 micron sieves, washed, and treated 

with appropriately diluted sperm.

Heron Island

G'day ya'll! I'm writing this post from beautiful Heron Island. I'm here collecting specimens for my postdoctoral research project in Bernie Degnan's Lab at The University of Queensland.

For this project, I'm examining the genes involved in the formation of the calcareous sclerites (sometimes called spicules) in chitons and aplacophorans. Heron is home to several species of chitons and aplacophorans have been seen here at least three times. So far it's been slow going... I've spent several days snorkeling on different parts of the island and seen lots of amazing stuff (beautiful corals, diverse fish, sharks, sea turtles, etc.) but I've only collected one specimen of the species of chiton I'm after: Cryptoplax larvaeformis. It seems that they like to hide during the day and mostly come out at night to feed. They are really good at hiding; I put the one I collected in a tank with a rock and it has completely disappeared (but I know it must be in there somewhere).

Tonight I'm going out for a night snorkel and hopefully it will be more productive!

New paper on the Schwabe organ in lepidopleuridan chitons

Last week a new study published by Sigwart et al. described a hitherto unreported structure in lepidopleuridan chitons called the Schwabe organ. Unlike chitonid chitons, the putatively plesiomorphic lepidopleuridan chitons lack an osphradium (sensory structure associated with the gills of Chitonids). However, in 2008 Enrico Schwabe observed "an elongated pair of patches of brown or purplish pigment stretching posterior from beneath the mouth lappets towards the start of the foot, and extending laterally on either side of the mouth" in Leptochiton algesirensis. The authors describe this structure in beautiful detail using light microscopy, 3D reconstruction, SEM, and TEM. Despite their thorough characterization, the exact function of this sensory structure remains unknown. They also review and compare the literature on chiton nervous systems and other known sensory structures.

Another interesting result of this study is the observation that at least the two species of Leptochiton examined both have a surprisingly large, well-developed brain. This is at odds with the traditional view that chitons have small, simple brains. More comparative studies are needed to determine if assumptions that chitons are "primitive" molluscs misled workers to presume they would have simple nervous systems and overlook this complexity or if there is a substantial difference between lepidopleuridan and chitonid chitons in terms of the size and complexity of the brain.

Leptochiton rugatus - my photo of a somewhat beat-up specimen
collected from Reid Rock near Friday Harbor Laboratories.

University of the Sunshine Coast visit

This weekend I took the train up the the Sunshine Coast to visit Dr. Leslie Brooker. Among other things, Lesley is an expert on chiton radula biomineralization. Aside from giving me innumerable pieces of good advice on my research, Lesley hooked me up with a large body of literature on molluscan biomineralization and pointed me towards some good books on chitons that I need to get my hands on.

Chitons of the World is a really lovely book
illustrating hundreds of chiton species

Lesley and her husband Keith (and pup B.J.) took me to a rocky platform near Beacon Lighthouse. Lesley told me this was a good place to find Acanthopleura gaimardi, a species I'm considering working on, and she wasn't kidding. Nearly every crack in the rock was full of them! We also found several specimens of Onithochiton and one specimen of Callistochiton.

A crevice full of Acanthopleura gaimardi

Callistochiton sp.

Onithochiton sp.

Epimenia - but not the one you think

There comes a time in every scientist's life when he or she has to start thinking about the important things. Not "What questions do I want to ask with my research?" or "What is the utility of my research to mankind?" but "What naming scheme am I going to use to name the computers and equipment in my lab? Animal genera? Star Wars characters?" I was recently faced with this important question.

Meet my snazzy new laptop, Epimenia (animal genera it is). I do a lot of bioinformatics and wanted to have a Linux-based laptop that is powerful enough to handle most of my data processing (but not assembly or phylogenetic analysis) needs. I decided to go with the System76 Kudu Professional. The base model isn't bad but I opted to go with an Intel Core i7-4800MQ Processor (2.7 GHz 6MB L3 Cache - 4 Cores plus hyperthreading) CPU, 16 GB of RAM, a 480 GB solid state mSATA boot drive, and a 1 TB SATA III hybrid hard drive with 8 GB solid state buffer. This thing is fast and so far I'm loving it!

I'm currently using this bad boy/girl (solenogasters are hermaphroditic) to implement the internode certainty and tree certainty indices of Salichos and Rokas 2013, which I plan to include in our upcoming paper on Aplacophoran phylogeny based on transcriptome data. More on that soon!

Acanthopleura gaimaridi

This weekend my roommate Rob, a couple of his friends, and I went on a Road trip up to Noosa National Park. While there we went to Tea Tree Bay beach and Alexandria Bay beach (which turned out to be a clothing-optional beach but that's another story). The rocks at both sites were home to the chiton Acanthopleura gaimardi! This is a close relative to a species I know well from the Florida Keys and is possible I species I will be studying while here.

A genuinely candid photo of me showing Rob Acanthopleura gaimardi
(photo by Anna Csergo).

Acanthopleura gaimardi. This specimen is about 4 cm in length.

Aculifera = Aplacophora + Polyplacophora (chitons)

The Aculifera hypothesis unites the molluscs that possess sclerites by placing Polyplacophora as the sister taxon of Aplacophora. Aculiferans are the sister group to all other living molluscs so this group is important to study in order to understand the evolution of Mollusca as a whole. Molluscs are interesting to researchers because many species are economically important and food, producers of pearls and shells, and as invasive species or biofoulers. Plus they're ace (ace is Australian slang for cool, I'm really not kidding about this cheesy crocodile hunter parody)!


The worm-like aplacophoran molluscs are exclusively marine animals characterized by a narrow or completely reduced foot, a unique dorsoterminal sensory organ, and a small mantle (=pallial) cavity restricted to the posterior-most part of the body. As the name suggests, aplacophorans completely lack a shell. Instead, they are covered in a dense coat of spiny and/or scale-like calcareous sclerites. There are two distinct lineages of aplacophorans: Caudofoveata (also called Chaetodermomorpha) and Solenogastres (also called Neomeniomorpha). Although unfamiliar to even many zoologists, many of the roughly 400 described species of aplacophoran molluscs are important members of many marine benthic communities.

Cavibelonia sp. (Aplacophora, Solenogastres) collected recently during

an expedition in Antarctica. Anterior is to the left.

Polyplacophorans, or chitons are slug-like animals with eight plates covering their backs. These plates overlap somewhat at the front and back margins and articulate with each other to form a flexible dorsal armor. This allows chitons to be flexible, presumably an adaptation for living in the rocky intertidal as many species do. The shell plates are surrounded by mantle tissue bearing sclerites like those found in aplacophorans. Currently around 1,000 species of chitons are described.

Lepidopleurida sp. (Polyplacophora) collected recently during an expedition
in Antarctica. I'm not sure if this is a juvenile or just a really tiny species.
Anterior is to the right.

G'day!

G'day! First thing's first: if you didn't think this was going to be my attempt at a cheesy parody of Steve Irwin's The Crocodile Hunter, you're gravely mistaken. If you read the text of this blog in an American's lousy attempt at a Queensland accent, you'll be adequately in on the joke. For the record, I'm doing this because I think Australians are awesome and I want to be like them, not because I am making fun of them.

Now that that's out of the way, let me begin... My name is Kevin Kocot. I recently finished my Ph.D. at Auburn University in Ken Halanych's lab studying molluscan phylogeny and evolution. I also did a short postdoc in Ken's lab working on basal metazoan phylogenomics, but you're here for the molluscs now aren't ya? Good on ya (see, that's something Australians say). I've just moved to Brisbane Australia to start an NSF International Postdoctoral Fellowship-funded project in Bernie Degnan's lab. I'm going to keep this blog short and sweet and mostly academic but I won't be able to keep some of my observations about life in Australia to myself. So far I'm simply loving it here. Brisbane is a great city. It's big but not as big as I imagined. I arrived on January 4th and it hasn't taken me long to get settled. I'm living in a beautiful apartment right on the Brisbane River directly across from The University of Queensland St. Lucia campus where I'll be working.