Phylogenetics Reading Group

I organize a Phylogenetics Reading Group at Penn which meets weekly on Wednesdays from 12:00 – 1:00PM.

You can request to join the group by adding yourself to the listerv here: Bio-prg

A list of papers read:

July 9th, 2014
Pagel M, A Meade, D Barker. 2004. Bayesian estimation of ancestral character states on phylogenies. Systematic Biology. 53 (5): 673-684

July 2nd, 2014
Charles L Nunn. The Comparative Approach in Evolutionary Anthropology and Biology. University of Chicago Press.
Chapter 3: 52-78

June 25th, 2014
Charles L Nunn. The Comparative Approach in Evolutionary Anthropology and Biology. University of Chicago Press.
Chapters 1 & 2: 1-51

June 18th, 2014
Faria NR, MA Suchard, A Rambaut, DG Streicker, & P Lemey. 2013. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying contraints. Phil Trans R Soc B. 368: 20120196

Steph was collecting ticks for several weeks, PRG was temporarily suspended.

May 7th, 2014
Du Toit N, BJ Van Vuuren, S Matthee, & CA Matthee. 2013. Biogeography and host related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts.
Molecular Ecology. 22 (20): 5185-5204

April 30th, 2014
Lemey P, M Salemi, & AM Vandamme. The Phylogenetic Handbook Second Edition. Chapter 10 Selecting models of evolution. 345-361

April 23rd, 2014
Lemey P, A Rambaut, AJ Drummond, MA Suchard. 2009. Bayesian phylogeography finds its roots. PLoS Computational Biology. DOI: 10.1371/journal.pcbi.1000520

April 16th, 2014
Lemey P, M Salemi, & AM Vandamme. The Phylogenetic Handbook Second Edition. Chapter 19 LaMarc: Estimating population genetic parameters from molecular data. 592-611

April 9th, 2014
Harris RB, MD Carling, IJ Lovette. 2013. The influence of sampling design on species tree inference: A new relationship for the new world chickadees (Aves:Poecile).
Evolution 68-2: 501-513

April 2nd, 2014
Resolving questions brought up during BEAST tutorial discussion (March 19th)

March 26th, 2014
Han E, JS Sinsheimer, & J Novembre. 2013. Characterizing bias in population genetic inferences from low-coverage sequencing data.
Molecular Biology & Evolution. 31(3): 723–735

March 19th, 2014
Lemey P, M Salemi, & A Vandamme. The Phylogenetic Handbook. Ch 18
“Bayesian evolutionary analyses by sampling trees” pp. 564-590

March 12th, 2014
Spring Break – no reading group

March 5th, 2014
J Felsenstein. 2003. Inferring Phylogenies, Ch. 11
“Distance matrix methods” pp. 147-175

Feb 26th, 2014
Nicolaisen LE, MM Desai. 2012. Distortions in genealogies due to purifying selection.
Molecular Biology and Evolution. 29 (11): 3589-3600

Feb 19th, 2014
Philippe Lemey. 2013. Continuous Phylogeography – tutorial in BEAST

Feb 12, 2014
Heled J & AJ Drummond. 2010. Bayesian inference of species trees from multilocus data.
Molecular Biology and Evolution. 27 (3):570-580

Feb 5, 2014
Luo et al. 2010. Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study.
BMC Evolutionary Biology. 10:242
Bergsten et al. 2013. Bayesian tests of topology hypotheses with an example from diving beetles.
Systematic Biology. 62(5): 660-673

Jan 22, 2014
J Felsenstein. 1978. Cases in which parsimony or compatibility methods will be positively misleading.
Sys. Zoology. 27 (4): 401-410
J Felsenstein. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach.
J of Molecular Evolution. 17: 368-376

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