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New course – Spring 2015: Current topics in systematics

Short announcement – we will continue our now formally offered Weekly Discussion sessions during the Spring 2015 Semester, in the format of a 1-credit “Current Topics in Systematics” seminar/course with a double billing as either BIO 494 (undergraduate level) or EVO 598 (graduate level). Wednesdays, 12:00 – 1:00 pm, seminar room pending. Ontologies and reasoning are part of the envisioned themes to explore. Hoping for good turnout and discussions. ASU’s Course Catalogue is available on-line here.

Weekly reading: RADICAL – Random Addition Concatenation Analysis

An interesting paper and powerful tool that cuts empirically through the longstanding and somewhat dispiriting total evidence ‘versus’ partitions discussion thread in our field.

Narechania, A., R.H. Baker, R. Sit, S.O. Kolokotronis, R. DeSalle & P.J. Planet. 2012. Random Addition Concatenation Analysis: A novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biology and Evolution 4(1): 30-43. Available on-line here.

EntSoc14 Twitter pride and joy


ECN 2014 and ESA 2014 in Portland have come and gone. Great meeting, and dare I say a new sense of togetherness via social media that can improve science communication, science itself.

ESA 2014 presentation – Aligning insect phylogenies: Perelleschus and other cases

Slides are up for the Euler/X Perelleschus (+) presentation at Entomology 2014.

Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases from taxonbytes

Presentations and posters at ECN and ESA 2014

Our lab has had an eventful joint ECN/ESA 2014 meeting and presentation/poster schedule of activities. Most presentations are now posted. Great meetings – even won recognition for our Twitter contributions.

ECN 2014

Symposium – Harvesting the fruits of our labor: Utilizing collections databases to advance 21st century entomology.

1. Neil Cobb, Katja Seltmann & Nico Franz. 2014. The current state of arthropod biodiversity data: Addressing impacts of global change. Presentation.

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Graduate research opportunity – insect diversity in Mormon cricket ecosystems

Graduate Student Opportunity – M.Sc. in Biology

Franz Lab and Hasbrouck Insect Collection, School of Life Science, Arizona State University

Our lab (http://taxonbytes.org/) has an opening for a funded M.Sc. research project involving biodiversity surveys and information products related to rangeland grasshoppers and Mormon cricket pests and associated non-target organisms from the grasshopper and Mormon cricket ecosystem. The project will be co-advised by research entomologists of the USDA Center for Plant Health Science and Technology in Phoenix, Arizona, under the leadership of Dr. Larry Jech. A central research objective is to characterize the effects of a new insecticide, chlorantraniliprole, on diverse non-target arthropods in rangeland ecosystems in 17 western states, with emphasis on orthopteran groups.

The selected candidate will be broadly trained in insect biodiversity science, informatics, and applied entomology. Interested candidates are strongly encouraged to contact Dr. Nico Franz (e-mail: nico.franz@asu.edu) to learn more about this opportunity. Applications to the M.Sc. in Biology program should be submitted on-line at: https://sols.asu.edu/graduate/ biology-masters-and-phd- programs.

The application submission deadline is December 15, 2014.

Knowledge Representation in Systematic Biology – Edited book proposal seeking comments, contributions

I have an opportunity to edit a new book in the series “Species and Systematics” (originally UC Press; now CRC Press). The draft outline is below, but is subject to change and expansion as deemed appropriate.

I am looking for suggestions, and for potential contributors (naturally, while reserving standard/common sense rights to kindly accept or decline). The book will to collect a number of strong, diverse chapters on various projects and directions in this still very young field. Lead authors of chapters will coordinate with co-authors as preferred. I also intend to give authors much freedom to do and say things they maybe could not express using different publication outlets (while keeping things fair and high-minded).

Another key issue is (of course) – who may have time and motivation to contribute an original and impactful chapter in the coming six months? Either way, I am open to suggestions, contact me on- or off-line.

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Taxonomic concept identification, reconciliation, and the Open Tree of Life – Part 1

“Part 1” – allowing for subsequent parts (e.g., for the blue/non-blue use case; now added at end of post). The relevant OpenTree background discussion is here:

https://github.com/OpenTreeOfLife/muriqui/issues/15

There as several interesting and generally closely overlapping issues and views here. I will pick just (or mainly) the one introduced by Jonathan Rees (November 02, 2014).

“Here’s another example I’m struggling with: there are currently a couple of species in OTT that are misclassified as crustaceans instead of molluscs. When we fix this problem, there will be an incompatible ‘change’ in the membership of Arthropoda. Does this mean that the new group should get a new identifier? – after all its identity in some sense has changed. If so, annotations and OTU mappings linked to the old id have no home in the tree. It doesn’t get a new id with the current taxonomy generator, which assumes that names are tied uniquely to taxon concepts (with some exceptions), but with a more principled system where groups are defined by membership or phylogenetic hypotheses, it might. This would have an impact on OTU mappings and annotation carryover. I don’t have a good answer to this one, but am working on ways to anchor the semantics of ids.”
 

I am attempting to reproduce this under varying scenarios in the Euler/X toolkit. Starting simple, then expanding. I have created an initial scenario with two phylogenetic perspectives of the Ecdysozoa (molting animals) sec. ott1 (= OpenTree Topology at time =1; the later version) versus Ecdysozoa sec. ott0 (OTT at time = 0; the earlier version. Initially, an alignment with complete taxonomic congruence.

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