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Public version of the LepNet 2014 proposal

Via Neil Cobb, a public version of the LepNet proposal (October, 2014). Complete title: “Collaborative Research: Digitization TCN: Lepidoptera of North America Network: Documenting Diversity in the Largest Clade of Herbivores”.

PDF available here.

Weekly reading: SISRS – Site Identification from Short Read Sequences

This week’s discussion will focus on a novel method to identify and separate signal from noise for Next-Generation sequencing datasets – SISRS.

Schwartz, R.S., K. Harkins, A.C. Stone & R.A. Cartwright. 2014. A composite genome approach to identify phylogenetically informative data from Next-Generation Sequencing.

Course announcement: Sonoran Desert Field Botany, Spring 2015

PLB498-598-2015An announcement for the combined PLB 498/598 Sonoran Desert Field Botany course, offered in the Spring 2015 Semester by Elizabeth Makings (Vascular Plant Herbarium) at the Alameda space.

Download the course flyer with additional information.

Course announcement: Plant Diversity and Evolution, Spring 2015

PLB300-ImageAn announcement for the PLB 300 Plant Diversity and Evolution course, offered in the Spring 2015 Semester by Drs. Kathleen Pigg (Fossil Plant Collection) and Walter Fertig (Herbarium) at the Alameda space.

Download the course flyer with additional information.

BIGCB Workshop at UC Berkeley: Tackling the Taxon Concept Problem

November 7-9, 2014. Coolest workshop theme, like, ever. Organized by Brent Mishler and Staci Markos of the UC Berkeley Jepson Herbarium.

Understanding Taxon Ranges in Space and Time: Tackling the Taxon Concept Problem

A Workshop Sponsored by the Berkeley Initiative in Global Change Biology

Friday, November 7, 2014, 1002 VLSB, open to all who are interested.

1:00 pm: Brent Mishler  –  Introduction to the themes and goals of this workshop.

1:10 pm: Edward Gilbert  –  Ideas for incorporating taxonomic concepts into Symbiota.

1:40 pm: Robert Guralnick  –  Map of Life and the challenge of heterogeneous names data for determining species ranges.

2:10 pm: Gaurav Vaidya  –  Tracking taxonomic changes: how, where and why, with examples from the Avibase database of taxon concepts. Link & PDF

2:40 pm: Coffee Break.

3:00 pm: Robert Peet  –  Taxon concepts as essential infrastructure for large-scale data integration: lessons from VegBank, SEEK and BIEN. PDF

3:30 pm: Nico Franz  –  Tracking taxonomic change across classifications and phylogenies. PDF

4:00 pm: Alan Weakley  –  Applying concept maps to 7100 vascular plants of the Southeastern United States, and some thoughts on ‘atomic concepts’ and their utility at the specimen level.  PDF

4:30 pm: Nico Cellinese  –  Thoughts on the right approach to query trees based on phyloreferences (ontologized phylogenetic definitions).

Additional Workshop Notes

  • Communicated by Robert Peet  –  Taxonomic concept infrastructure-related entities requiring identifiers. PDF

Weekly reading: Intermittent evolution and robustness of phylogenetic models

Models of evolution used in phylogenetic reconstruction make specific assumptions which (in their entirety, and globally applied) are ultimately wrong. They are also approximately right. What does this even mean? This week’s reading gets us into the notion of robustness of phylogenetic models to violations of their inherent assumptions. An important piece of the “which method should I use?” puzzle. Let’s see if we can identify other pieces too.

Nguyen, M.A.T., T. Gesell & A. von Haeseler. 2012. ImOSM: Intermittent evolution and robustness of phylogenetic methods. Molecular Biology and Evolution 29: 663-673. Available on-line here.

Weekly reading: Bayesian analysis outperforms parsimony for morphological data

We had a lively Weekly Discussion of Kumar et al. 2012, and are staying with the general theme (hereby undemocratically coined) of “new insights in statistical phylogenetics/phylogenomics”. Models, biases, assumptions, data. Thus, for next week:

Wright, A.M. & D.M. Hillis. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLoS ONE 9(10): e109210. Available on-line here.

Weekly reading: Kumar et al. on Statistics and Truth in Phylogenomics

It seems as though we are moving on in the Weekly Discussion series from NextGen (a.k.a. massively parallel) sequencing methods to (possibly more entertaining) “what it all means” themes. Last week Lemmon et al. 2012 was appreciated as one of the most promising NextGen approaches for systematics; however we concluded that while the presentation was very impressive, the crustacean use case chosen to illustrate the method’s unique resolution strengths was not challenging enough.

Hence, up this week: statistics and truth. It is not statistics or truth, though if it were then I would prefer the latter.

Kumar, S., A.J. Filipski, F.U. Battistuzzi, S.L. Kosakovsky Pond & K. Tamura. 2012. Statistics and truth in phylogenomics. Molecular Biology and Evolution 29: 457-472. Available on-line here.