Monday

Today:

  • Application for CPB travel funds.  DONE

  • Faxed receipts from Felsenstein’s visit. DONE

Seminar on Species trees

Coop/Moore Seminar on *BEAST  (Heled & Drummond, 2009) and  BEST (Liu et. al. 2008).

Essential differences: BEST uses Mr. Bayes to compute probabilities over gene trees (over uniform prior).  Then estimates the species tree by importance sampling from this distribution to reflect constraints under a convergence model.  Integrates over effective population sizes rather than estimating (highly uncertain anyway), requires rooting, and a rather fast/loose implementation of ultra-metricizing trees.  In text notes in Mendeley Phylogenetics section.

*BEAST offers a hierarchical approach (simultaneously estimating gene trees and species trees), estimates effective population sizes (with linear rate variation across phylogeny/through time).  Integrates over possible out groups.  Suffers midpoint rooting problems do to rate heterogeneity (whenever two comparably sized clades split by substantial variation in substitution rates, will root between them). Priors to get species tree prior 1) includes birth-death model for tree ->Prior on waiting times of speciation 2) Prior on coalescence times 3) Prior on topologies (uniform over unlabeled histories) Prior on gene trees, all as in BEAST/etc, also reflects the species trees

Warning Signals in an Economic Context

Meeting with Jim and Alan 2:30-4p: (notes to be transcribed)

Misc

  • Algorithms group:

Solved our little puzzle about Bayes factors, corrected the notes. Decided we’ll actually meet sometime Wednesday to do MCMC.

CPB travel funding application

Application requires a list of outreach activities.  Assembling here for my records.

  1. I attend CPB Tuesday seminars regularly. I participated in Fall Monte Carlo with Bruce Rannala on phylogenetic methods, and then voluntarily joined the Winter Monte Carlo with Sharon Strauss on broader impacts and public outreach, as it is a topic I am both interested and involved in.

  2. I helped design and organize the CPB workshop on Hierarchical modeling this January.

  3. I gave an presentation to the first year pop bio students during their orientation (entitled “What I wish I knew three years earlier…”) on computer based research tools for organizing literature, setting up an academic website, and for networking in sciences.

  4. I independentlyorganized a CPB workshop on Data Management, to discuss the implications and opportunities created by new data archiving requirements from NSF and many of our journals. I recruited participation from four editors-in-chief of journals in ecology and evolution, and also the director and assistant director of the California Digital archives to discuss the issues. I arranged that the event would be video-recorded for those that could not attend, which have been viewed 124 times last month.

  5. Throughout this year I have I co-chaired an interdisciplinary group called the Graduate Teaching Community which has been popular among CPB students and other graduate programs as a space to explore and share experiences, methodology, and read literature on studies in effective education strategies.

  6. I also help organize a student group on Open Science, which tries to promote awareness and potential of open access publishing, public data archiving, reproducible research, and tools and opportunities to make large-scale collaborative science possible.

  7. I volunteered as an instructor in the UC Davis Bodega Phylogenetics Workshop.

  8. I served as the student member on the steering committee for the CPB program review.

  9. I served on the student panel interviewing all of the candidates for the Dean of the College of Biological Sciences, and met with the Department of Ecology and Evolution Committee to discuss its recommendation.

References