Meetings and Journal Club

book1.gif (1495 bytes) Task Force Meetings

NHN Taskforce Molecular Systematics, Phylogeny & Biogeography
Schedule for meetings and Journal Club Information

Program Taskforce meeting Tuesday 3rd of February, NHN Wageningen, starting time 10.30

The Joe Felsenstein news.
New proposals and initiatives. If you would like to a preliminary proposal assessed for feedback by the task force member, please let me know, so documents can be distributed early enough.
Thomas van Gurp (NHN Wageningen) will give a presentation on Epigenetics and Systematics.

An accompanying paper by Bossdorf et al. (2008; Ecol. Lett. 11: 106-115) is entitled Epigenetics for Ecologists. After reading the paper and listening to Thomas you'll know why it's so relevant for systematists too.

More from the DNA barcoding front. Freek Bakker has volunteered to talk us through the latest developments. Robin van Velzen has recently spent some weeks at the Canadian Centre for DNA Barcoding in Guelph, and will present experiences and results. Two papers from the latest issue of Taxon, as well as a recent paper in Syst. Biol., are relevant to this topic, and will be discussed:

Erickson et al. (2008; Taxon 57: 1304-1316), Edwards et al. (2008; Taxon 57: 1317-1327), and Munch et al. (2008; Syst. Biol. 57:750–757).

Two new PhD students, Pulcherie Bissiengou (NHN Wageningen) and Svenja Meinke (NHN Leiden) will present their research projects.
The journal club. As four papers have been dealt with already in connection to topics above, we'll discuss a single paper, dealing with the ever-present challenge of reconstructing species trees from gene trees in the face of incomplete lineage sorting:

Brumfield et al. (2008; Syst. Biol. 57: 719-731).

Program Taskforce meeting Friday 24th of October, NHN Leiden, starting time 10.30

The Joe Felsenstein news.
Thomas Couvreur has volunteered to update us on online analysis services.
Peter van Welzen, holder of the Ornstein special chair in tropical plant biogeography since 1 May 2008, will introduce his plans for the coming time.
Where have we been all summer? Doubtlessly we have been attending conferences and meetings, presenting our results, returning refreshed and inspired. Freek Bakker will bring us up to date with the developments reported at the Annual Meeting of the Society of Molecular Biology and Evolution (SMBE), last June in Barcelona. Lars Chatrou will briefly summarise the highlights of “Climate Change and Systematics”, a meeting organised by the Systematics Association and the Linnean Society, earlier this month in Dublin. Please let me know when you would like to contribute to this item of the programme.
The journal club. Recently several interesting papers in the field of biogeography have been published. The following papers will be discussed:

Nylander et al. 2008. Accounting for Phylogenetic Uncertainty in Biogeography: A Bayesian Approach to Dispersal-Vicariance Analysis of the Thrushes (Aves: Turdus). Syst. Biol. 57: 257-268.
Mansion, et al. 2008. Phylogenetic Analysis Informed by Geological History Supports Multiple, Sequential Invasions of the Mediterranean Basin by the Angiosperm Family Araceae. Syst. Biol. 57: 269-285.
Sanmartín, I., P. van der Mark, F. Ronquist. 2008. Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. J. Biogeogr. 35: 428–449.

Program Taskforce meeting Wednesday 10th of October, NHN Wageningen, starting time 12.30

The Joe Felsenstein news: announcements and alerts on analysis software. A short presentation on DIVA-GIS will be given by Thomas Couvreur.
Virus-induced gene silencing (VIGS), a tool for evo-devo studies on non-model organisms. A short communication by Thomas Couvreur.
Presentation by Kanchana Pruesapan on her PhD project: The molecular phylogeny of Sauropus within tribe Phyllantheae (Phyllanthaceae; Euphorbiaceae sensu lato)
Presentation by Barbara Gravendeel and ensuing discussion on how to write a successful grant proposal
Discussion of two recent papers in Syst. Biol. on methodological challenges related to fossil calibration: Manos et al., 2007, and Rutschmann et al. 2007.

Program Taskforce meeting Friday 16th of February, NHN Wageningen, starting time 10.30

announcement of new research proposals, meetings, courses.
The "Joe Felsenstein news" – notification of new software / analysis tools.
Discussion of Hillis et al. 2005. Analysis and visualization of tree space. Syst. Biol. 54: 471–482.
Mapping of morphological characters under continuous-time Markov models. Following up on Thomas’s presentation of SIMMAP two meetings ago. Thomas Couvreur will present “Traveling through spaces: influence of priors in posterior mapping of discrete morphological characters using empirical data”. Reading: Huelsenbeck et al. 2003. Stochastic Mapping of Morphological Characters. Syst. Biol. 52: 131–158.
Optional item: The last issue of Trends in Ecology and Evolution has the following paper that’s worth reading: Kelchner & Thomas (2007). Model use in phylogenetics: nine key questions.

Program Taskforce meeting Thursday 21 December, NHN Leiden, starting time 10.30

announcement of new research proposals, meetings, courses.
the "Joe Felsenstein news" – notification of new software / analysis tools.
historical biogeography. Two recent papers will be discussed: Biswas & Pawar (J. Biosci. 2006) and Brown et al. (J.Biogeography 2006) This item replaces the Stankiewicz paper.
analysis of AFLP data. Bastienne Vriesendorp and Roy Erkens will present results from their own work. To prepare for this item the paper by Wim Koopman (Syst. Biol., 2005) has been selected.
optional item - a discussion of a recent paper by Yin-Long Qiu, on the deepest divergences in land plants, inferred from phylogenomic evidence (PNAS, October 17 2006)
12.30 Christmas Lunch

Beware that the location had changed from Wageningen to Leiden.

Program Taskforce meeting Thursday 28 September, NHN Utrecht, starting time 12.30

Please note that we’ll convene in a different place in Utrecht than usual: Wentgebouw (first bus stop in ‘De Uithof’), room N406 on the 4^th floor. Looking forward to seeing you next week in Utrecht.

announcement of new research proposals, meetings, courses.
the "Joe Felsenstein news" will be dealt with by Thomas Couvreur. First he’ll give a brief presentation of ‘Are We There Yet’ - a tool for exploring convergence of MCMC chains in Bayesian inference. After that, Thomas will present some of the latest in software for reconstructing ancestral character states. Related to this topic there are also two papers to be discussed: Ronquist (TREE - 2004) and Buschbom & Barker (Syst Biol - 2006).
presentations by PhD students. I thought it’s about time for a revitalisation of one of the objectives of the task force, which is the presentation of results, preferably in an unpolished state, and the subjection to a blend of gentle criticism and compliments. No less than four student presentations (15-20 minutes each) are on the programme, one of them by Steven Janssens, who will be visiting us from the Laboratory of Plant Systematics, KU Leuven – the ‘fourth NHN branch’.
Delia Co – Molecular phylogeny of Entolomataceae, and the use of PHYML
Bastienne Vriesendorp – Recombination, mosaic sequences and their effect on phylogeny estimation accuracy – a simulation approach
Kristo Kulju – Using consensus network techniques to explore datasets
Steven Janssens – Island hopping in Impatiens
historical biogeography. Two recent papers will be discussed: Biswas & Pawar (J. Biosci. 2006) and Stankiewicz et al. (J. Biogeogr. – 2006)

Program Task Force Meeting Thursday 8^th June 2006 – Leiden

Starting time 10.30

Journal club articles:

EVO-DEVO:

Beth A. Krizek and Jennifer C. Fletcher: MOLECULAR MECHANISMS OF FLOWER DEVELOPMENT: AN ARMCHAIR GUIDE

WILLIAM E. FRIEDMAN, RICHARD C. MOORE, AND MICHAEL D. PURUGGANAN: THE EVOLUTION OF PLANT DEVELOPMENT

L. M. ZAHN, J. LEEBENS-MACK, C. W. DEPAMPHILIS, H. MA, AND G. THEISSEN: To B or Not to B a Flower: The Role of DEFICIENS and GLOBOSA Orthologs in the Evolution of the Angiosperms

SUPPERTREES:

Introduction - by Peter Hovenkamp. Click HERE to see the slides.

Amy C. Driskell, Cecile Ane,1.- J. Gordon Burleigh, Michelle M. McMahon, Brian C. O’Meara, Michael J. Sanderson: Prospects for Building the Tree of Life from Large Sequence Databases

Tara L. Fulton, Curtis Strobeck: Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets

Program Task Force Meeting Thursday 13^nd April 2006 – Wageningen

Starting time 10.30 (or possible 11:30, to be announced shortly)

Journal club articles

Rieseberg, L.H. et al. 2006. The nature of plant species. Nature 440:524-526. [PDF]
Ren, F. et al. 2005. An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction. Syst. Biol. 54(5):808–818. [PDF]
Simmons, M.P. & Ochoterena, H. 2000. Gaps as Characters in Sequence-Based Phylogenetic Analyses. Syst. Biol. 49(2):369–381. [PDF]
Muller, K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667–676. [PDF]

Program Task Force Meeting Thursday 22^nd December 2005 – Leiden

10.15 General announcements

Journal Club I: Long branch attraction

Philippe, H. et al. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evolutionary Biology 5:50. [PDF]
Leebens-Mac, J. et al. 2005. Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One’s Way Out of the Felsenstein Zone. Mol. Biol. Evol. 22:1948-1963. [PDF]
Wiens, J.J. 2005. Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction? Syst. Biol. 54:731-742. [PDF]

Journal Club, part 2: DNA Barcoding

Hebert, P.D.N. & Gregory, T.R. 2005. The Promise of DNA Barcoding for Taxonomy. Syst. Biol. 54: 852-859. [PDF]
DeSalle et al. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Phil. Trans. R. Soc. B. (published online) [PDF]

12.30 Christmas Lunch

Program Task Force Meeting Thursday 22^nd September 2005 – Utrecht

13.30 General announcements

Barcode proposal submitted
Appointment of new Task Force Leader

14.00 Discussion on bootstrapping approaches

14.30 Discussion of ALW proposal to be submitted by Ferry Slik. This proposal will be submitted as part of the ALW Geo and Biosphere Program and is entitled ‘Biodiversity measures in Forest Plots in Borneo’.

15.30 Journal Club: Following on from Ferrys proposal discussion the papers for the journal club will be:

Faith, D.P. 2002. Quantifying biodiversity: a phylogenetic perspective. Conservation Biology 16: 248-252. [PDF]
Faith, D.P., C.A.M. Reid and J. Hunter. 2003. Integrating phylogenetic diversity, complementarity and endemism for conservation assessment. Conservation Biology 18: 255-261. [PDF]

Old meetings of year 2005:

Program Task Force Meeting 19th May 2005 - Leiden

Journal Club:

The following papers will be discussed:

FELIX FOREST, VINCENT SAVOLAINEN, MARK W. CHASE, RICHARD LUPIA, ANNE BRUNEAU,and PETER R. CRANE 2005: Teasing Apart Molecular- Versus Fossil-based Error Estimates when Dating Phylogenetic Trees: A Case Study in the Birch Family (Betulaceae). Systematic Botany 30: 118–133. [PDF]
Sean W. Graham, Patrick A. Reeves, Analiese C. E. Burns, and Richard G. Olmstead 2000: MICROSTRUCTURAL CHANGES IN NONCODING CHLOROPLAST DNA: INTERPRETATION, EVOLUTION, AND UTILITY OF INDELS AND INVERSIONS IN BASAL ANGIOSPERM PHYLOGENETIC INFERENCE. Int. J. Plant Sci. 161(6 Suppl.):S83–S96. [PDF]
Scot A. Kelchner · Jonathan F. Wendel 1996: Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 30: 259–262. [PDF]
TAO SANG, DANIEL J. CRAWFORD, AND TOD F. STUESSY 1997: CHLOROPLAST DNA PHYLOGENY, RETICULATE
EVOLUTION, AND BIOGEOGRAPHY OF PAEONIA (PAEONIACEAE). American Journal of Botany 84(9): 1120–1136. [PDF]

Program Task Force Meeting 17^th March 2005 – Wageningen

13.30 General announcements

14.00 Report from the Natural History Museum Consortium for the Barcoding of Life symposium – brief report given by Hugh Cross and followed by a general barcoding discussion. What should the NHN barcoding strategy be? This will include:

Introduction to the EDIT (European Distributed Institute of Taxonomy) proposal. Johan van Valkenburg will briefly talk about this proposal and how DNA barcoding is embedded within it.
Outline of plans to apply for an NWO Groot Investment Subsidy.

The purpose of investment subsidies is to promote a balanced national investment pattern and to encourage the investment policy of research institutes. An initiative is planned by NL-TAF (CBS, NHN, Naturalis, ZMA) to discuss the perspectives for DNA-barcoding and, the focus of Dutch efforts within the global initative. What are the choices and scenarios for such a proposal?

15.30 Journal Club

This meetings journal club will focus on the effects of population size and generation time on rates of molecular evolution. Papers for the discussion are as follows:

Xiang et al. 2004. Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America. Evolution 58: 2175–2184 [download the PDF file]
Chao, L. & D.E. Carr. 1993. The molecular clock and relationship between population size and generation time. Evolution 47: 688-690 [download the PDF file].
Berry, A.J., J.W. Ajiokat & M. Kreitman. 1991. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129: 1111-1117 [download the PDF file].
Extra!! The paper introduced at the meeting by Peter Hovenkamp. Carrie-Ann Whittle & Mark O. Johnston: Broad-Scale Analysis Contradicts the Theory That Generation Time Affects Molecular Evolutionary Rates in Plants. J Mol Evol (2003) 56:223–233 [download the PDF file].

Information about old meetings:

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