Insect Biodiversity and Evolution revolution

Last fall I gave a talk at the ESA annual meeting (see blog post about it) about re-envisioning our course on insect biodiversity and evolution (currently called, weirdly enough, Insect Biodiversity and Evolution (ENT432)). We’re in week five of the “revolution”, and it’s time to start being a bit more public about our efforts. That was, after all, the whole point of the talk I gave at ESA.

Redesigning a course is a complex undertaking, especially when we’re building on eight years of teaching history and bits and pieces of content from various colleagues. Hence we chose to start more or less from scratch, breaking the course down into modules that could be worked on in parallel:

  1.  Introduction – mostly logistics but also addresses the following questions: What are arthropods? What is systematics and why is it relevant?
  2. Arthropod morphology – lays the groundwork for understanding adaptations, evolution, and diagnosis
  3. Systematics and Evolution – basics of evolution (natural selection, adaptation, Hox genes), history of classification and phylogenetics (Aristotle to Hennig and beyond); puts our knowledge into context
  4. Early arthropods, fossils, terrestrialization – fossilization processes, important arthropod fossils, adaptations to the challenges of terrestrial environments; where did arthropods come from?
  5. Outgroups – covers non-insect arthropods and the likely sister to Arthropoda, Onychophora [see drafts of slideshow and handout]
  6. Non-pterygote hexapods – this and the rest are self-explanatory
  7. Palaeoptera
  8. Polyneoptera
  9. Acercaria
  10. Hymenoptera
  11. Neuropterida
  12. Coleoptera, Strepsiptera
  13. Antliophora
  14. Amphiesmenoptera
  15. Natural history collections (could/should be done as one of the first modules)

Additionally, we’ve identified a set of cool stories, bro (20+ min, could involve a paper and discussion) that are highly relevant and important for students training to become professional entomologists to know:

  • origin of wings
  • holometabolous development
  • leaf mining/herbivory strategies
  • galls/galling
  • mimicry/aposematism
  • sound production – percussion (Plecoptera), stridulation (Hemiptera: Heteroptera, Coleoptera, Lepidoptera, others), tymbals (Cicadamorpha), forced air (Blattodea)
  • sexual selection
  • fighting/weapons – or include in sexual selection? 
  • sociality – haplodiploidy, other conditions that contribute to rise of eusociality
  • nest architecture
  • myrmecophily – tie in with nest architecture?
  • symbioses – seems too diverse for one long discussion, maybe better as series of short vignettes (one on Blattabacterium, one on polydnaviruses, another on yeasts in hemipterans, etc.)
  • aquatic adaptations (breathing, swimming) – lentic, lotic, boundary layer, plastron breathing, air straps, hydrofuge hairs, semiaquatic, surface skimming
  • silk – which glands produce it, chemical composition, uses

And short vignettes (5–10 min, not much discussion maybe):

  • camouflage
  • pheromones
  • migration
  • wing coupling
  • cryophily
  • relicts
  • sucking mouth
  • xylophagy
  • resilin, jumping
  • tympana
  • mating position
  • foveation
  • parasitoidism
  • parasitism
  • predation

That could/should be peppered throughout the modules and revisited in multiple modules as necessary.

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“Outgroups” handout, in development at Overleaf

We’re still getting organized about how to engage colleagues and share emerging content. At the moment we use Google Slides for the lecture slideshows (slide example) and Overleaf for handouts (above; see also handout example). Our rules are: (1) maximize note-taking potential where possible, i.e., minimize text and use images to stimulate discussion, (2) use CC BY or CC0 images where possible (avoid copyrighted images unless we have permission that we can document and/or we are using them in the spirit of fair use), (3) document all content, including image source(s), content source(s), and dates of retrieval, (4) develop content in a way that maximizes safe re-use.

Any thoughts? What have we missed? Expect more frequent engagement (hopefully weekly) as this project unfolds! We’ll tag ’em, so that they can be browsed conveniently: InsectSystematics.

Emerging semantics to link phenotype and environment – our latest open access publication

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Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. (2015) Emerging semantics to link phenotype and environment. PeerJ 3:e1470. DOI: 10.7717/peerj.1470

Abstract.—Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.

Redescription of Conostigmus albovarius Dodd, 1915 … – our latest open access publication

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Trietsch C, Deans AR, Mikó I (2015) Redescription of Conostigmus albovarius Dodd, 1915 (Hymenoptera, Megaspilidae), a metallic ceraphronoid, with the first description of males. Journal of Hymenoptera Research 46: 137-150. doi: 10.3897/JHR.46.5534

Abstract.— Conostigmus albovarius Dodd, 1915 (Hymenoptera: Megaspilidae) is a species previously known by a single female holotype. Here, we provide a redescription of this peculiar ceraphronoid based on several female specimens and describe the male of the species for the first time. Intraspecifically-variable morphological traits such as female antenna color pattern are documented and discussed. A phenotype bank of morphological characters is provided for use in future megaspilid taxonomic treatments. We also provide phenotypic data in a semantic form to allow for ease of data integration and accessibility, making taxonomic data more accessible to future systematic efforts.

Our 2015 ECN/ESA talks

I gotta say that I am really proud of the talks my lab gave at this year’s Entomological Collections Network and Entomological Society of America meetings. You can find the slides below:

Emily Sandall et al. (2015) Digitization of the Beatty Odonata Collection at the Frost Entomological Museum (PSUC): the terrain of ecological niche modeling. ECN annual meeting 2015. DOI: 10.6084/m9.figshare.1602235 (Sandall et al. program link)

Kyle Burks (2015) Revision of Dendrocerus (Hymenoptera, Megaspilidae): Deciphering an esoteric taxon through an integrative approach. ESA annual meeting 2015. DOI: 10.6084/m9.figshare.1603028

Carolyn Trietsch (2015) Conostigmus spp. (Hymenoptera: Megaspilidae) of the Holarctic. ESA annual meeting 2015. DOI: 10.6084/m9.figshare.1609733

István Mikó and Andrew R. Deans (2015) Insect integument: The link between insect taxonomy and evolutionary developmental biology. ESA annual meeting 2015. DOI: 10.6084/m9.figshare.1606223

I also gave my own talk, in which I summarized our experiences with a recent morphology course we offered: Know your insect (ENT 530):

Andrew R. Deans and István Mikó (2015) Know your insects! New approaches to teaching insect morphology and systematics. ESA annual meeting 2015. DOI: 10.6084/m9.figshare.1609692

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It could’ve (should’ve?) been one of the worst talk experiences I have ever had—crackly voice, blistering headache, sore throat, cough of death—except that I was overwhelmed by the massive interest people seemed to have in the topic. The room was completely filled, with every square centimeter of floor space covered by entomologists and a huge overflow out into the hallway. I couldn’t believe it! And, to top it off, there was a massive line afterwards to talk to me about morphology course ideas.

Based on these interactions, as well as some incredible talks by my colleagues (I’m looking at you, Brian Wiegmann), I’m now more motivated than ever to pursue some of the ideas we have for training the next generation of entomologists in core entomological knowledge. Watch this space for a deeper explanation, updates about collaboratively-developed educational materials, and news of an upcoming morphology workshop for graduate students.

Thank you all for making ECN and ESA such vibrant, accepting, and exciting communities!

Our latest preprint: Phenotypes in insect biodiversity research

Our latest preprint is now available!

Mikó, I and AR Deans (2015) Phenotypes in insect biodiversity research. Available through bioRxiv, DOI: 10.1101/032425

This is a first (rough!) draft of a book chapter that will accompany several other articles about insect biodiversity research. In it we try to describe some advances in the field of phenotype data representation and how they are infiltrating biodiversity research. We’d love your feedback.

Also, I love bioRxiv, but I admit that it didn’t seem to be the right outlet for what amounts to a review paper. They ask you to classify your manuscript as New Results, which is “an advance in a field” [I guess this is us?], Confirmatory Results, which means “findings largely replicate and confirm previously published work”, or Contradictory Results, which “replicate[s] experimental approaches used in previously published work but results contradict and/or do not support it”. This slight confusion will not stop me from using bioRxiv, however, which is an awesome resource.

#MustReads in entomology

[Note: This post was originally published on the Frost Curators’ blog.]

I’ve been working on my course (ENT 432) syllabus for what seems like forever, though it’s only been eight years. In the latest iteration I’ve tried to incorporate required reading from the primary literature—mostly empirical studies, rather than reviews—for each lecture. This exercise was mush more difficult than I anticipated!

My class is usually made up of incoming grad students and late stage undergrads, 99% of whom have no systematics background. I don’t want to require highly technical papers about phylogenetics and classification, or at least I don’t want that to be the emphasis of our conversation. I wanted to find papers that discuss key innovations, evolutionary trends and processes, and/or that tell compelling (and contemporary if possible) research stories. Two examples:

  • When we reach Hemiptera we could talk about so many aspects of their biology—adaptations for sedentary lifestyle, sucking pump and mouthpart morphology, phylogeny and classification (Homoptera vs. Hemiptera)—that it gets difficult to choose just one paper. For now I am going with sound production: Wessel et al. (2014).
  • For Diptera, it’s a no-brainer. Students should read Wiegmann et al.’s (2011) Episodic radiations in the fly tree of life. Sure it’s technical in its methods, but it also tells an interesting story about how Diptera have been so successful, describes natural history trends we see across the phylogeny, and discusses how robust the current classification is.

Perhaps you can see already the challenges in choosing #MustReads for entomology. Insecta is SO diverse and SO fascinating that numerous cool papers will invariably get left out. When we hit Dictyoptera what do we read about? Bioinspired robots? The evolution of eusociality? Bat detection? What papers do you feel are #MustReads for a course on insect biodiversity and evolution? Here is my first draft of a list: ENT 432 syllabus (2015). I would love some feedback!

scales on a butterfly wing, some flat, some hair-like

We will start discussing and examining Lepidoptera in late November. Scales are certainly a contributing factor to Lepidoptera’s diversity, and their patterns are important for determining species. Is their a great read about lep scales? Or should we focus our discussion on host plat relationships, chemical defense, moth avoidance, proboscis morphology …? Photo by Johan J.Ingles-Le Nobel (CC BY-NC-ND 2.0). Click for original.

Our latest preprint: Generating semantic phenotypes

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.

screenshot showing how Overleaf.com appears

Overleaf in action.