Tag Archives: ecology

APRIL WORKSHOP: Phylogenetically correct stats for evolutionary ecologists (RSVP needed)

From CPB Postdoc Luke Mahler:

Dear Davis Ecologists and Evolutionary Biologists,

This Spring Quarter, I’ll be delivering my CPB Postdoctoral Fellowship Workshop, which will be entitled:

“Phylogenetically correct analysis of species data in ecology and evolution”.

This workshop will consist of 3 sessions, to take place over three days:

April 2: 4:10PM-5:30PM (lecture; note this will be the CPB seminar for this week)
April 3: 11:00AM-1:00PM (tutorial 1 – feel free to bring your lunch)
April 4: 1:00PM-3:00PM (tutorial 2)

The format of this workshop will be an introductory lecture followed by two hands-on R tutorials.

In the lecture, which will take place during that week’s CPB seminar slot, my goal is to (1) review why it’s important to account for phylogeny during data analysis, (2) briefly introduce a suite of current methods for doing so, and (3) critically discuss the inherent assumptions and limitations of phylogenetic comparative methods, outlining best practices for conducting basic analyses.

In tutorials, I will lead participants in a series of computer exercises (all in R) designed to provide hands-on experience implementing the most commonly used phylogenetic statistical analyses. In the first tutorial, participants will learn how to prepare and import phylogenetic trees and species data set for analysis, how to visually explore these data, and how to measure phylogenetic signal and select an appropriate model of trait evolution. In the second tutorial, we’ll conduct a number of phylogenetic statistical analyses with a focus on linear models and principal component analysis. We’ll discuss parameter estimation and interpretation under these models, and will cover techniques for assessing sensitivity of results to phylogenetic uncertainty.

The target audience for this workshop are scientists at any stage who are familiar with phylogenetic trees but don’t necessarily have specialized knowledge about how to work with trees when analyzing ecological or other comparative data. No prior experience using R is necessary, although attendees will need to bring their own laptops, and will need to install R in advance of the workshop (it’s free). Attendees do not need to bring data files – we’ll analyze example data sets which I will provide. Faculty, postdocs, and students are all welcome to attend.

If you are interested in attending this workshop, PLEASE CONTACT ME BY EMAILING lmahler@ucdavis.edu. We haven’t decided yet where to hold the workshop – this decision will be based on anticipated attendance. We’ll do our best to secure a room that can accommodate everyone who interested in attending, but can’t guarantee there will be room for you if you don’t let me know in advance.

Thanks, and I hope you can make it.

Best,
Luke Mahler

Center for Population Biology Postdoctoral Fellow
2320 Storer Hall
University of California, Davis
One Shields Avenue
Davis, CA 95616, USA

NCEAS 3-week intensive workshop in ecological analysis and synthesis

Forwarding this email

Hello NCEAS friends,

The National Center for Ecological Analysis and Synthesis (NCEAS) is
pleased to invite applications from early-career researchers for a 3-week
intensive workshop in ecological analysis and synthesis, to take place at
NCEAS in Santa Barbara CA June 19-July 10, 2013.

All travel and living expenses of participants will be covered during the
workshop, thanks to generous support from the Packard Foundation.

Applications are due March 1. For more information and application
instructions, go to:
http://www.nceas.ucsb.edu/news/nceas-summer-institute-2013

From iSEEM project: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities

Quick post.  Another paper is out based on the Gordon and Betty Moore Foundation funded iSEEM project I co-ran with Jessica Green and Katie Pollard.

PLOS Computational Biology: Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.

O’Dwyer JP, Kembel SW, Green JL (2012) Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8(12): e1002832. doi:10.1371/journal.pcbi.1002832.

It has one of my favorite paper figures ever.

Figure 1. The local community and metacommunity framework casts local biodiversity of coexisting species in terms of a sampling process from a larger reference pool, or metacommunity. 

And the paper is definitely worth checking out.

Meta-Omics and Phylogenetics Journal Clubs

If you’re looking to catch up on your reading, come to journal club!

The Meta-omics journal club is run weekly on Tuesdays, from 11-12 in 5202 GBSF (organized by the Facciotti Lab, papers are sent around via an e-mail list).

There is also a bi-weekly Phylogenetics journal club run by the Center for Population Biology, 4-5pm every other Friday in Storer 5343 (The Treehouse). Regardless of journal club, there is always a 5pm Happy Hour at CPB every Friday – although be warned there are always are a substantial number of vertebrate biologists in attendence.

Tom Bruns talk on fungal dispersal at #UCDavis 11/10/11 #ecology #fungi

http://storify.com/phylogenomics/tom-bruns-talk-on-fungal-dispersal-at-uc-davis-11-10-11.js<a href=”http://storify.com/phylogenomics/tom-bruns-talk-on-fungal-dispersal-at-uc-davis-11-10-11″ target=”_blank”>View the story “Tom Bruns talk on fungal dispersal at UC Davis 11/10/11” on Storify</a>]