|
Programme for Task Force meeting 29th
April 2004 in Leiden 13.30 General announcements
-
finalise program for forthcoming meetings, courses etc.
-
technical/lab matters, protocols
-
website update
-
finalise NHN protocol for DNA sampling from herbarium
material
-
TF MSPB more flesh on the bones of the NHN research plan.
Call for more details for individual research projects.
14.00 Introductory presentation by Hugh
Cross.
14.30 Peter Hovenkamp will give a demonstration on
the possibilities of the new analysis program TNT (Goloboff, Farris & Nixon,
2004).
15.30 Freek Bakker will give a short presentation on
Bayessian analysis and possibilities for parallel computing. Two papers relevant
to this and to the journal club discussion:
-
Feng, Bell, Rose, and Waddell. 2002. Parallel algorithms for
Bayesian phylogenetic inference. J. Parallel Distrib. Comput. 63: 707–718. (download
the PDF file)
-
Rannala. 2002. Identifiability of Parameters in MCMC
Bayesian Inference of Phylogeny. Syst. Biol. 51:754–760. (download
the PDF file)
15.45 Journal Club: chair-person will be
Barbara who will initiate the discussion on the following paper:
-
Johan A. A. Nylander, Fredrik Ronquist, John P. Huelsenbeck, José Luis
Nieves-Aldrey 2004. Bayesian Phylogenetic Analysis of Combined Data. Syst.
Biol. 53(1):47-67. (download the PDF file)
Programme
for Task Force meeting 15th July 2004 in Wageningen
13.30 General announcements
14.30 Presentation by Johan Mols:
Geographic speciation in Annonaceae
15.00 Presentation by Floris Breman: Mitochondrial
DNA sequence evolution & plant phylogenetics
15.30 Journal Club. Discussion on the following paper:
-
Webb, C.O., Ackerley, D.D., McPeek, M.A. and Donoghue, M.J.
2002. Phylogenies and community ecology. Annual Review of Ecology and
Systematics 33:475-505. (availabe
as PDF file)
After Journal Club there will be a dinner in a restaurant
in Wageningen.
Programme
for Task Force meeting 4th November 2004 in
Leiden
Please note that the meeting will take place in room B113!!
13.30 General announcements.
14.00 Bastiaantje Vriesendorp will give a brief summary of the Upsala Meeting
she attended earlier this year.
14.15 Demonstration of r8s and use of Multidivtime update.
-
R8s is a program for estimating absolute rates
of molecular evolution and divergence times on a phylogenetic tree. The
Bayes dating method (Thorne et al. 1998) uses a probabilistic model to
describe the change in evolutionary rate over time and uses the Markov chain
Monte Carlo (MCMC) procedure to derive the posterior distribution of rates
and times.
-
You can find the r8s manual at Mike Sandersons website
http://ginger.ucdavis.edu/sandlab/SOFTWARE/software.htm
-
Also check some of Mike Sandersons literature related to
this software and the approaches taken:
Sanderson, M. J. 2003. r8s; inferring absolute rates of
evolution and divergence times in the absence of a molecular clock.
Bioinformatics 19:301-302 [download
PDF].
Sanderson, M. J. 2002. Estimating absolute rates of
molecular evolution and divergence times: a penalized likelihood approach.
Mol. Biol. Evol. 19:101-109 [download
PDF].
Sanderson, M. J. 1997. A nonparametric approach to
estimating divergence times in the absence of rate constancy. Mol. Biol.
Evol., 14:1218-1231 [download PDF].
Thorne, J.L., H. Kishino and I.S. Painter. 1998. Estimating
the rate of evolution of the rate of molecular evolution. Molecular Biology
and Evolution 15:1647-1657 [download
PDF].
Coffee and tea break!!!
15.15 Journal Club: DNA Barcoding
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004)
Identification of birds through DNA barcodes. PLoS Biol 2: e312 [download
PDF].
Moritz C, Cicero C (2004) DNA barcoding: Promise and
pitfalls. PLoS Biol 2(10): e354 [download
PDF].
Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM 2004.
Response to commentary by Moritz and Cicero on Identification of birds
through DNA barcodes. PLoS 2(10): e312 [download
PDF].
Drinks & snacks!!
|