UC Davis<\/p>\n
WORKSHOP IN APPLIED PHYLOGENETICS<\/p>\n
at Bodega Marine Laboratory, Bodega Bay, California<\/p>\n
March 2\u00a1V9, 2013<\/p>\n
Sponsored by the<\/p>\n
University of California, Davis and Bodega Marine Laboratory<\/p>\n
(additional financial support provided by the University of Rochester)<\/p>\n
http:\/\/bodegaphylo.wikispot.org\/Front_Page<\/p>\n
Introduction
\nPhylogenetic methods have revolutionized modern systematics and become
\nindispensable tools in evolution, ecology and comparative biology, playing
\nan increasingly important role in analyses of biological data at levels
\nof organization ranging from molecules to ecological communities. The
\nestimation of phylogenetic trees is now a formalized statistical problem
\nwith general agreement on the central issues and questions. A nearly
\nstandard set of topics is now taught as part of the curriculum at many
\ncolleges and universities. On the other hand, application of phylogenetic
\nmethods to novel problems outside systematics is an area of special
\nexcitement, innovation, and controversy, and perspectives vary widely.<\/p>\n
This Spring, for the fourteenth consecutive year, we will teach a workshop
\nfor graduate students interested in applying phylogenetic methods to
\ndiverse topics in biology. The one-week course is an intensive exploration
\nof problems to which modern phylogenetic approaches are being applied and
\nthe most current statistical tools and approaches that are used to solve
\nthose problems. We cover a range of topics in ecology, phylogenomics,
\nfunctional morphology, macroevolution, speciation, and character
\nevolution. The course starts with recent advances in phylogenetic
\nmethodology, and then focuses on methods and tools that can be brought
\nto bear on these “applied” issues in the context of a given phylogeny.<\/p>\n
The course will be held at the Bodega Marine Laboratory on the Northern
\nCalifornia coast, which has on-site housing. Our newly increased bandwidth
\nand access to computing clusters allows us to utilize computer-intensive
\napproaches even in a one-week course. The course format will involve
\nequal parts of lecture, discussion, and hands-on software training. One
\nafternoon during the week will be left free for field trips to local
\nnatural areas.<\/p>\n
Topics Covered
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Estimating, evaluating and interpreting phylogenetic trees
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Recent advances in Bayesian and Maximum-likelihood estimation
\nof phylogeny
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Estimation of species trees, gene-tree\/species-tree conflicts
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Divergence-time estimation from sequence data: relaxed clocks,
\nfossil calibration
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Analysis of character evolution: maximum likelihood and Bayesian
\napproaches, ancestral-state estimation, rates of trait evolution
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Analysis of morphological form, function of complex
\ncharacter systems
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Inference of diversification rates: detecting rate shifts,
\ntesting key innovation hypotheses
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Model specification issues: model selection, adequacy and
\nuncertainty
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Diagnosing MCMC performance<\/p>\n
Instructors for the 2013 workshop
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Carl Boettiger
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Jeremy Brown
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Jonathan Eisen
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Rich Glor
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Tracy Heath
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Mark Holder
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 John Huelsenbeck
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Luke Mahler
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Brian Moore
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Samantha Price
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Bruce Rannala
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Bob Thomson
\n*\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Peter Wainwright<\/p>\n
Prerequisites
\nAvailable housing limits course enrollment to ~30 students. Preference
\nis given to doctoral candidates who are in the early to middle stages of
\ntheir thesis research, and who have completed sufficient prerequisites
\n(through previous coursework or research experience) to provide some
\nfamiliarity with phylogenetic methods. Unfortunately, because of limits
\non class size, postdocs and faculty are discouraged from applying.<\/p>\n
Admission and Fees
\nStudents will be admitted based on academic qualifications and
\nappropriateness of research interests. The course fee is $650. This
\nincludes room and board at BML for duration of the course (arriving
\nMarch 2, leaving March 9) and transportation from Davis to<\/p>\n
Application Deadline
\nApplications are due by November 16, 2013. Please send a completed
\napplication form and one letter of recommendation from your major
\nadvisor. Applications should be sent via email as PDFs to
\ngbradburd@ucdavis.edu. Students will be notified via e-mail by December
\n1, 2013 of acceptance.<\/p>\n
Application Forms and Information
\nVisit the Bodega website to for additional information and to download
\nan application form: http:\/\/bodegaphylo.wikispot.org\/2013_Workshop<\/p>\n
Send all application materials to:<\/p>\n
Gideon Bradburd
\nDepartment of Evolution and Ecology
\n5343 Storer Hall
\nUniversity of California Davis
\nDavis, CA
\n95616
\nemail: gbradburd@ucdavis.edu<\/p>\n","protected":false},"excerpt":{"rendered":"
UC Davis WORKSHOP IN APPLIED PHYLOGENETICS at Bodega Marine Laboratory, Bodega Bay, California March 2\u00a1V9, 2013 Sponsored by the University of California, Davis and Bodega Marine Laboratory (additional financial support provided by the University of Rochester) http:\/\/bodegaphylo.wikispot.org\/Front_Page Introduction Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing […]<\/p>\n","protected":false},"author":39,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-136","post","type-post","status-publish","format-standard","hentry","category-marine-laboratory"],"_links":{"self":[{"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/posts\/136","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/users\/39"}],"replies":[{"embeddable":true,"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/comments?post=136"}],"version-history":[{"count":0,"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/posts\/136\/revisions"}],"wp:attachment":[{"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/media?parent=136"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/categories?post=136"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/research.bowdoin.edu\/carlon-lab\/wp-json\/wp\/v2\/tags?post=136"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}