56(3) June 2007

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Data sets and supplementary material for articles this issue can be downloaded here. Files are (typically) in NEXUS, Word, or HTML formats. Note that the authors may also have deposited their data in GenBank and TreeBASE, or have additional data on their own web sites.

Fossils, Molecules, Divergence Times, and the Origin of Lissamphibians
David Marjanovic Michel Laurin
Methods and sources used to compile the main phylogeny
Supertree based on the tree by Frost et al. (2006).
Comparison between the estimated minimal age of various taxa under our supertree and under the phylogeny of Frost et al. (2006).
Estimated date of appearance of selected taxa in the supertree
Estimated date of appearance of selected taxa under various random resolutions of the polytomies in the supertree.
Biological nomenclature
Model parameters
Quartets used for quartet-dating
Quartet dates
r8s dates
Pathd8 dates

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies
Naiara Rodr�­guez-Ezpeleta, Henner Brinkmann, B�©atrice Roure, Nicolas Lartillot, B. Franz Lang, Herv�© Philippe
Supplementary figures

Phylogeny of Extant and Fossil Juglandaceae Inferred from the Integration of Molecular and Morphological Data Sets
Paul S. Manos, Pamela S. Soltis, Douglas E. Soltis, Steven R. Manchester, Sang-Hun Oh, Charles D. Bell, David L. Dilcher, Donald E. Stone

Inferring Speciation Times under an Episodic Molecular Clock
Bruce Rannala, Ziheng Yang
Primate data
Primate trees
Johnson 2006 data
Johnson 2006 trees

The Utility of Amplified Fragment Length Polymorphisms in Phylogenetics: A Comparison of Homology within and between Genomes
David M. Althoff; Matthew A. Gitzendanner; Kari A. Segrave
AFLP script instructions

Species Trees from Gene Trees: Reconstructing Bayesian Posterior Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions
Liang Liu; Dennis K. Pearl
Finch data
Macaque data

Correcting the Problem of False Incongruence Due to Noise Imbalance in the Incongruence Length Difference (ILD) Test
Donald L. J. Quicke; Owen R. Jones; Daniella R. Epstein
Demonstrate linearisation with different sized trees
Parse PAUP output files and plotting for replacement noise
Generate Nexus files for addition noise
Generate Nexus files for replacement noise
Parse PAUP output files and plotting for addition noise

Evidence for Time Dependency of Molecular Rate Estimates
Simon Y. W. Ho; Beth Shapiro; Matthew J. Phillips; Alan Cooper; Alexei J. Drummond
Amakihi data
Amerindian data
Crane data
Neandertal dates
Neandertal no dates
Subirds 1
Subirds 2
Subirds 3

Taxonomy in a Changing World: Seeking Solutions for a Science in Crisis
Ingi Agnarsson; Matjaz Kuntner
Comments offered by the 1995 and 1997 cohort peetsters in the survey