Bayesian Analysis Using a Simple Likelihood Model Outperforms Parsimony for Estimation of Phylogeny from Discrete Morphological Data

Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

(2014) David W. Bapst   PALEOBIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa

(2013) David W. Bapst   Methods in Ecology and Evolution

INTEGRATING FOSSILS WITH MOLECULAR PHYLOGENIES IMPROVES INFERENCE OF TRAIT EVOLUTION

(2012) Graham J. Slater et al.   EVOLUTION

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals Ancient Vicariance Patterns in the Palpimanoid Spiders

(2012) Hannah Marie Wood et al.   SYSTEMATIC BIOLOGY

Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates

(2011) P. J. Wagner   Biology Letters

Likelihood reinstates Archaeopteryx as a primitive bird

(2011) M. S. Y. Lee et al.   Biology Letters

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa

(2010) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Estimating trees from filtered data: Identifiability of models for morphological phylogenetics

(2009) Elizabeth S. Allman et al.   JOURNAL OF THEORETICAL BIOLOGY

Morphological and molecular evidence for phylogeny and classification of South American pitvipers, generaBothrops,Bothriopsis, andBothrocophias(Serpentes: Viperidae)

(2009) ALLYSON M. FENWICK et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Mosaicism, Modules, and the Evolution of Birds: Results from a Bayesian Approach to the Study of Morphological Evolution Using Discrete Character Data

(2008) Julia A. Clarke et al.   SYSTEMATIC BIOLOGY