upcoming pubs and other observations
It's been an eventful semester here in the Insect Museum, as evidenced by the lack of any recent posts (seems weird that a dearth of activity actually signals an abundance of activity, but I promise it's true!). Here's an update about some of the manuscripts we've been crankin' on these last couple months:
28 of the species in the blue–white–black mimicry ring of pyrgine and hesperiine ACG Hesperiidae, with the first 11 (reading text-wise) being species of male "Astraptes fulgerator." DNA barcodes helped sort out this tricky group of taxa (see Hebert et al. 2004). Will they help us with Evaniidae as well?
- One of us (me) contributed to a review (Janzen et al. 2009 - it's open access!) of how DNA "barcoding" - that is, using a ~650 nt fragment of the mitochondrial cytochrome c oxidase subunit I gene to help understand species limits and diagnose taxa - is proving to be a critical part of the taxonomic process (see image below) for some groups. One of my recent grants (DEB-0842289) will incorporates a large-scale test of DNA barcoding in Evaniidae, including an exploration of alternative markers. We're still looking for a student if you know anyone who's interested!
- István Mikó and I also had a manuscript accepted recently, where we use three ontologies from the OBO Foundry, in combination with our Hymenoptera Anatomy Ontology (HAO), to describe a whacky (that is, a very cool looking) new genus and species of Ceraphronidae. I'll definitely make time to explore this topic further - ontologies in biodiversity and evolutionary biology - but I need to catch my breath first. We secured funding recently (DBI-0850223) to develop the HAO and some tools to exploit existing ontologies, but it might be another month or two before the team's settled in and the posts start rolling.
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I read close to 300 articles (2005-2009) last month as part of a review of Bayesian approaches and their impact(s) on insect phylogenetics. More details on that manuscript later, but two attributes of my literature perusal are worth mentioning here (since they weren't part of the MS in review):
- Entomologists are terrible at citing software. PAUP* is the most fequently used package for estimating phylogenies, at least in my sample, and it was referred to by FIFTY-THREE (53) different names - e.g., 4.0b10 of paup*, PAUP, PAUP 4.0 b, PAUP 4.0 b10, paup 4.0b10*, paup 4*b10, PAUP* version 4.0b10, paup*4 version beta 10, PAUP4.0b10, Paup* b10 - and variably cited as Swofford 1998, Swofford 1999, Swofford 2000, Swofford 2001, Swofford 2002, or Swofford 2003. Ummmm...riiiiight. Perhaps I am too nitpicky (we get the gist of what they used, right?), but there is a "how to cite" section of the PAUP* website.
- Less than 50% of this published research is repeatable - and I am being generous with that estimate and strict with my definition of "repeatable." Sure the sequences are invariably deposited in GenBank, and the morphological characters and scorings were always added as a table in the appendix or as a supplement. But where are the DNA alignments? Most datasets include rR(D)NA genes/fragments, whose alignments were "manually tweaked" and the "hypervariable regions were excluded." Other datasets had nuclear protein encoding genes with intron issues. Too many of these authors did not explicitly avail their alignments. Repeatability is a fundamental tenet of science, and yet these examples of science are not repeatable. Also, where are the command blocks? Too many papers were not explicit in how they implemented their models, how they determined their burn-in, how many generations they ran their analyses for, or they excluded critical details about other analysis variables. Some authors even claimed to implement models of sequence evolution in MrBayes that are impossible.
28 of the species in the blue–white–black mimicry ring of pyrgine and hesperiine ACG Hesperiidae, with the first 11 (reading text-wise) being species of male "Astraptes fulgerator." DNA barcodes helped sort out this tricky group of taxa (see Hebert et al. 2004). Will they help us with Evaniidae as well?
