I'm still alive

OK... I've been really bad about keeping up with this blog. Here's some relevant updates with respect to my academic life. Here they are in no particular order.

1) I have a new paper in Integrative and Comparative Biology with Nathan Whelan and Ken Halanych: Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians

2) I have a new paper in PNAS with Nathan Whelan, Leonid Moroz, and Ken Halanych: Error, signal, and the placement of Ctenophora sister to all other animals

3) I'm very excited to announce that I signed an offer letter from The University of Alabama! I'll be joining the University of Alabama Department of Biological Sciences and the Alabama Museum of Natural History in January as an assistant professor and assistant curator of invertebrates.

4) I attended the New Generation of Polar Researchers Symposium (http://disccrs.org/ngpr) and it was an amazing experience!

Panulirus interruptus seen during a night snorkel off Catalina Island

New paper on scaly foot gastropod sclerites

How the mollusc got its scales: convergent evolution of the molluscan scleritome

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.