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Weekly reading: Mikó et al. 2012. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

Our next reading is a response to a 2011 article (that paper available here) interpreting the “prothoracic helmet” of treehoppers as serially homologous with wings. Mikó et al. showcase some modern techniques for visualizing morphology, such as confocal laser scanning microscopy (CLSM) and micro-computed tomography (μ-CT) to provide an alternate interpretation, and discuss the importance of having well-defined morphological concepts for interpreting complex morphological structures.

Mikó et al. 2012 is available online here.

Software Carpentry Workshop report

During the weekend of Feb 21 & 22, Joe Hunter, an undergraduate research student, and I attended a Software Carpentry workshop at University of Arizona hosted by the iPlant Collaborative. The workshop was intended to teach scientists to analyze and manage data (beyond just using Excel and storing data in a laptop). Read more

Weekly reading: Nikolov et al. on arthropod cuticle design principles

Hi everyone! For this week’s discussion, we will be reading a paper by Nikolov et al. (found here) discussing the mechanical properties of lobster cuticle as described using a set of nested, hierarchical equations. There are two papers that discuss this topic, of which, this is the less-technical. The other paper can be found here, and has some neat figures outlining the structure of the cuticle. Come ready to discuss how this model might be connected to and incorporated within an anatomy ontology, and how this might (or not) be useful in a phylogenetic context. There a few terms/concepts I really recommend looking up on Wikipedia before reading the paper, simply because they get used frequently (they are easy):

1.) Isotropic vs. Anisotropic

2.) Stress & Strain

3.) Young’s Modulus of Elasticity

4.) Poisson’s Ratio

Enjoy!

http://onlinelibrary.wiley.com/doi/10.1002/adma.200902019/epdf

Announcing the Sixth Annual Lepidoptera Course, 16–25 August, 2015

Held at the Southwestern Research Station (SWRS) in the Chiricahua Mountains in SE Arizona (a 2.5 hour drive from Tucson), the focus of the Lep Course 2015 (August 16-25, 2015) is to train graduate students, postdocs, faculty, state and federal employees, and citizen-scientists in the classification and identification of adult Lepidoptera and their larvae. Topics to be covered include the biology and systematics of major families of Lepidoptera, an introduction to adult and larval morphology with a focus on taxonomically important traits, extensive field work that concentrates on  both collecting and photographing adults and larvae, collecting and curatorial techniques, genitalic dissection, larval classification, use (and abuse) of DNA barcoding, and general topics in Lepidoptera systematics, ecology, and evolution.

With its extensive series of Sky Island mountain ranges, SE Arizona has the highest Lepidoptera diversity in the United States. With low desert scrub, oak and mixed oak-pine woodland, lush riparian, juniper, Douglas fir, and mountain meadow habitats – all within a 40 minute drive from the station – the SWRS is an ideal location from which to sample this diversity of both habitats and species.

If you want to interact with other Lepidoptera enthusiasts, see a spectacular Dysschema, identify the Organ of vom Rath, sort through trap samples with hundreds of species, learn about diversity of Lepidoptera, and enjoy the vistas of the SE Arizona, then this course will provide a unique experience.

Partial list of invited instructors (subject to change):

  • Richard Brown (Mississippi Entomological Museum)
  • Jennifer Bundy (RD4AG)
  • Chris Grinter (Illinois Natural History Survey)
  • Don Harvey (Smithsonian Institution)
  • Sangmi Lee (Arizona State University Hasbrouck Insect Collection)
  • Chris Schmidt (Canadian National Collection)
  • Bruce Walsh (University of Arizona)

For more information, see http://research.amnh.org/swrs/education/lepidoptera-course or www.lepcourse.org or contact Bruce Walsh at jbwalsh@u.arizona.edu. You can also see photos and comments from students in the 2011 course at their facebook site, “2011 Lep Course, SWRS SEAZ”.

What might we (systematists) want out of phenotype ontologies

Quick note ahead of the main entry: New paper by István Mikó et al. 2015. Generating semantic phenotypes. Worth a careful read.

The innovative paper by Ramírez & Michalik (2014) made for (another) lively discussion last week. The paper is rich with ideas and densely presented, which motivated an attempt by us to enumerate the sequence of data production and analytical steps. Another interesting question is to what extent (and why!) the authors’ approach moves away from the prevalent multi-taxon phenotype ontology approach. For instance, statements like the following (page 642) depart from the prevalent OBO language:

“As the Spider Ontology arose to manage the morphological concepts used in phylogenetic datasets, it is natural that it incorporated much of the pre-processed homology correspondences on its structure and definitions, to make room for the variety of form and function that the same organ may have in different organisms. In this way, the ontology accommodates the vast majority of homology statements currently accepted in spider systematics.”

Read more