We recognized recently that our approach to generating semantic phenotype data (e.g., see Balhoff et al. 2013 and Mikó et al. 2014) needed better documentation. Alas, here is the first draft of our manual, available through figshare:
Mikó I, Yoder MJ, Balhoff JP, Deans AR (2015): Generating semantic phenotypes. figshare. DOI: 10.6084/m9.figshare.1314904
We wrote it using Overleaf, which, I have to say, is pretty awesome.
Overleaf in action.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, et al. (2015) Finding Our Way through Phenotypes. PLoS Biology 13(1): e1002033. doi: 10.1371/journal.pbio.1002033
Abstract.—Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today’s data barriers and facilitate analytical reproducibility.
Mikó I, Copeland RS, Balhoff JP, Yoder MJ, Deans AR (2014) Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania). PLoS ONE 9(5): e94056. doi:10.1371/journal.pone.0094056
Be sure to check out our origami supplemental figure (.tif) Can you make it work? And here’s some press!
CLSM volume rendered image showing the ventral region of the head of Evania sp., medial view, distal to the bottom, DOI: 10.6084/m9.figshare.956282
Our latest morphological analysis is out! Check it out at the Journal of Hymenoptera Research:
Popovici O, Mikó I, Seltmann KC, Deans AR (2014) The maxillo-labial complex in Sparasion (Platygastroidea: Platygastridae). Journal of Hymenoptera Research 37: 77–111 DOI: 10.3897/jhr.37.5206
Check it out! Our latest open access paper is out:
Mikó I, Masner L, Johannes E, Yoder MJ, Deans AR (2013) Male terminalia of Ceraphronoidea: morphological diversity in an otherwise monotonous taxon. Insect Systematics & Evolution 44 (3–4), 261–347. DOI: 10.1163/1876312X-04402002 (or try this link)
Confocal Laser Scanning Micrographs, SEM, and brightfield images were used to illustrate ceraphronoid characters.
This was an invited contribution, part of a special issue on male genitalia. These anatomical structures are not especially informative for phylogenetic estimation in most Hymenoptera, but in Ceraphronoidea male genitalia offer dozens of characters. István (primarily) and the rest of us spent more than four years acquiring these data, imaging the phenotypes, and refining the characters. The resulting dataset is perhaps the most robust morphological data matrix in the history of phylogenetics. Seriously, it’s a benchmark for future publications, at least from our lab group. All data are available in figshare.
István (left) and Kyle discuss ovipositor morphology, while searching for small Hymenoptera in State College. Photo by Andy Deans (CC BY 2.0).
I’m a bit late with this announcement, but Kyle Burks has joined the lab this fall. Welcome! Kyle comes to us from UC San Diego, where he worked on bees and glands in the Nieh lab. We’ll provide updates as his project develops, but we’re focused on the systematics and comparative morphology of Ichneumonoidea.
You may have run into it already, but we have a new blog for the Frost Entomological Museum. It’ll probably be a bit more active shortly (and certainly more active than our lab blog). Anyway, we just posted an advert for FOUR Frost Museum biodiversity interns, which is pretty exciting. We’re also about to start posting regularly on our progress to digitize the Beatty Odonata collection. Very exciting things happening with respect to those specimens! You can check out the first phase here: spreadsheet of verbatim collecting events, Beatty Mexico expeditions (1957–1959, 1962).
Image of Salto de Eyipantla, from a postcard collected by the Beattys during one of their expeditions to Mexico. Odonata were collected here in 1959 by them.
We also have a couple more papers that have been accepted, which are probably worth discussing in more detail. I’ll wait for the ‘online early’ version, though. One was described as a “tour de force”, which, I have to admit, feels pretty good.