<div dir="ltr"><br><br><div class="gmail_quote"><div dir="ltr">---------- Forwarded message ---------<br>From: <span dir="ltr"><<a href="mailto:evoldir@evol.biology.mcmaster.ca">evoldir@evol.biology.mcmaster.ca</a>></span><br>Date: Tue, Dec 4, 2018 at 11:53 PM<br>Subject: Workshop: 2019 BODEGA APPLIED PHYLOGENETIC WORKSHOP<br>To: <<a href="mailto:mbarlow@ucmerced.edu">mbarlow@ucmerced.edu</a>><br></div><br><br><br>
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[LAST CALL: APPLICATIONS DUE FRIDAY]<br>
UC Davis WORKSHOP IN APPLIED PHYLOGENETICS<br>
at Bodega Marine Laboratory, Bodega Bay, California<br>
<br>
May 25-June 2, 2019<br>
<br>
Sponsored by the University of California, Davis and Bodega Marine Laboratory<br>
<br>
website: <a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a> <<a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a>><br>
<br>
Introduction<br>
Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at all levels of organization ranging from molecules to ecological communities. The estimation of phylogenetic trees is now a formalized statistical problem with general agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to novel problems outside systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.<br>
<br>
This Spring, for the eighteenth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The 8-day course is an intensive exploration of problems to which modern phylogenetic approaches are being applied and the most current statistical tools and methods that are used to solve those problems. We cover a wide range of topics in comparative statistical phylogenetics. The course starts with recent advances in phylogenetic inference, and then focuses on methods for making inferences from phylogenies.<br>
<br>
The course will be held at the Bodega Marine Laboratory on the beautiful Northern California coast, which has on-site housing. The course format will involve equal parts of lecture and hands-on software training with an emphasis on performing analyses using RevBayes: <a href="http://revbayes.github.io" rel="noreferrer" target="_blank">http://revbayes.github.io</a> <<a href="http://revbayes.github.io/" rel="noreferrer" target="_blank">http://revbayes.github.io/</a>>, with instruction in other inference software (MrBayes, BEAST, etc.) based on student interest. One afternoon during the week will be left free for field trips to local natural areas.<br>
<br>
Topics Covered<br>
* Estimating, evaluating and interpreting phylogenetic trees<br>
* Recent advances in Bayesian inference of phylogeny<br>
* Model specification: model selection, adequacy and uncertainty<br>
* Diagnosing MCMC performance<br>
* Divergence-time estimation: relaxed clocks, fossil calibration<br>
* Species-tree estimation and species delimitation<br>
* Character evolution: discrete- and continuous-trait evolution<br>
* Lineage diversification: detecting rate shifts, testing key-innovation hypotheses<br>
<br>
Instructor Team<br>
* Cecile Ane (UW, Madison)<br>
* Sebastian Hohna (LMU, Munich)<br>
* John Huelsenbeck (UC, Berkeley)<br>
* Michael Landis (Washington University) <br>
* Mike May (UC, Berkeley) <br>
* Brian Moore (UC, Davis)<br>
* Bruce Rannala (UC, Davis) <br>
* Bob Thomson (U Hawaii, Manoa) <br>
* Peter Wainwright (UC, Davis) <br>
<br>
Prerequisites<br>
Available housing limits course enrollment to ~30 students. Preference is given to doctoral candidates who are in the early to middle stages of their thesis research, and who have completed sufficient prerequisites (through previous coursework or research experience) to provide some familiarity with phylogenetic methods. Unfortunately, because of limits on class size, postdocs and faculty are generally discouraged from applying.<br>
<br>
Admission and Fees<br>
Students will be admitted based on academic qualifications and appropriateness of research interests. The course fee is $850. This includes room and board at BML for duration of the course (arriving on Saturday, May 25; departing on Sunday, June 2) and return transportation from Davis to the Bodega Marine Labs.<br>
<br>
Application Information<br>
Applications are due by Friday, December 7, 2018. Please fill out our application form and send your CV and one letter of recommendation from your major advisor. Applications should be sent via email as PDFs to <a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a> <mailto:<a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a>>. Students will be notified via e-mail by December 14, 2018 of acceptance. Visit the Bodega website for additional information: <a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a> <<a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a>>.<br>
<br>
Send all application materials to:<br>
<br>
Jiansi Gao<br>
Department of Evolution and Ecology<br>
5343 Storer Hall<br>
University of California Davis<br>
Davis, CA<br>
95616<br>
email: <a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a> <mailto:<a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a>><br>
<br>
<br>
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<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class=""><div class="">[LAST CALL: APPLICATIONS DUE FRIDAY]</div><div class="">UC Davis WORKSHOP IN APPLIED PHYLOGENETICS</div><div class="">at Bodega Marine Laboratory, Bodega Bay, California</div><div class=""><br class=""></div><div class="">May 25-June 2, 2019</div><div class=""><br class=""></div><div class="">Sponsored by the University of California, Davis and Bodega Marine Laboratory</div><div class=""><br class=""></div><div class="">website: <a href="<a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a>" class=""><a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a></a></div><div class=""><br class=""></div><<br>
div class="">Introduction</div><div class="">Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at all levels of organization ranging from molecules to ecological communities. The estimation of phylogenetic trees is now a formalized statistical problem with general agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to novel problems outside systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely.</div><div class=""><br class=""></div><div class="">This Spring, for the eighteenth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The 8-day cours<br>
e is an intensive exploration of problems to which modern phylogenetic approaches are being applied and the most current statistical tools and methods that are used to solve those problems. We cover a wide range of topics in comparative statistical phylogenetics. The course starts with recent advances in phylogenetic inference, and then focuses on methods for making inferences from phylogenies.</div><div class=""><br class=""></div><div class="">The course will be held at the Bodega Marine Laboratory on the beautiful Northern California coast, which has on-site housing. The course format will involve equal parts of lecture and hands-on software training with an emphasis on performing analyses using RevBayes: <a href="<a href="http://revbayes.github.io" rel="noreferrer" target="_blank">http://revbayes.github.io</a>" class=""><a href="http://revbayes.github.io" rel="noreferrer" target="_blank">http://revbayes.github.io</a></a>, with instruction in other inference software (MrBayes, BEAST, etc.) based on student interest. One afternoon during the week will be left free for field trips to local natural areas.</div><div cl<br>
ass=""><br class=""></div><div class="">Topics Covered</div><div class="">* Estimating, evaluating and interpreting phylogenetic trees</div><div class="">* Recent advances in Bayesian inference of phylogeny</div><div class="">* Model specification: model selection, adequacy and uncertainty</div><div class="">* Diagnosing MCMC performance</div><div class="">* Divergence-time estimation: relaxed clocks, fossil calibration</div><div class="">* Species-tree estimation and species delimitation</div><div class="">* Character evolution: discrete- and continuous-trait evolution</div><div class="">* Lineage diversification: detecting rate shifts, testing key-innovation hypotheses</div><div class=""><br class=""></div<br>
><div class="">Instructor Team</div><div class="">* Cecile Ane (UW, Madison)</div><div class="">* Sebastian Hohna (LMU, Munich)</div><div class="">* John Huelsenbeck (UC, Berkeley)</div><div class="">* Michael Landis (Washington University) </div><div class="">* Mike May (UC, Berkeley) </div><div class="">* Brian Moore (UC, Davis)</div><div class="">* Bruce Rannala (UC, Davis) </div><div class="">* Bob Thomson (U Hawaii, Manoa) </div><div class="">* Peter Wainwright (UC, Davis) </div><div class=""><br class=""></div><div class="">Prerequisites</div><div class="">Available housing limits course enrollment to ~30 students. Preference is given to doctor<br>
al candidates who are in the early to middle stages of their thesis research, and who have completed sufficient prerequisites (through previous coursework or research experience) to provide some familiarity with phylogenetic methods. Unfortunately, because of limits on class size, postdocs and faculty are generally discouraged from applying.</div><div class=""><br class=""></div><div class="">Admission and Fees</div><div class="">Students will be admitted based on academic qualifications and appropriateness of research interests. The course fee is $850. This includes room and board at BML for duration of the course (arriving on Saturday, May 25; departing on Sunday, June 2) and return transportation from Davis to the Bodega Marine Labs.</div><div class=""><br class=""></div><div class=""><div class="">Application Information</div><div class="">Applications are due by Friday, December 7, 2018. Please fill out our application form and send your CV and one letter of recommendat<br>
ion from your major advisor. Applications should be sent via email as PDFs to <a href="mailto:<a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a>" class=""><a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a></a>. Students will be notified via e-mail by December 14, 2018 of acceptance. Visit the Bodega website for additional information: <a href="<a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a>" class=""><a href="http://treethinkers.org/" rel="noreferrer" target="_blank">http://treethinkers.org/</a></a>.</div><div class=""><br class=""></div></div><div class="">Send all application materials to:</div><div class=""><br class=""></div><div class="">Jiansi Gao</div><div class="">Department of Evolution and Ecology</div><div class="">5343 Storer Hall</div><div class="">University of California Davis</div><div class="">Davis, CA</div><div class="">95616</div><div class="">email: <a href="mailto:<a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a>" class=""><a href="mailto:jsigao@gmail.com" target="_blank">jsigao@gmail.com</a></a></div><div class=""><br class=""></div></div></div></body></html><br>
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</div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">Miriam Barlow</div><div dir="ltr">Founding Faculty and Professor<div>Chair, Quantitative and Systems Biology</div><div>University of California, Merced</div><div><br></div><div>209.228.4174</div><div><a href="mailto:miriam.barlow@gmail.com" target="_blank">miriam.barlow@gmail.com</a></div><div><br></div></div></div></div></div></div></div></div>