Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

Statistical Phylogeography

(2009) L. Lacey Knowles   Annual Review of Ecology Evolution and Systematics

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Multiple nuclear and mitochondrial genes resolve the branching order of a rapid radiation of crested newts (Triturus, Salamandridae)

(2009) G. Espregueira Themudo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Resolving Species Phylogenies of Recent Evolutionary Radiations1

(2008) L. Lacey Knowles et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings

(2008) Matt D. Carling et al.   GENETICS

Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

(2008) A ECKERT et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dealing with incongruence in phylogenomic analyses

(2008) N. Galtier et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)

(2008) Catherine R. Linnen et al.   SYSTEMATIC BIOLOGY

Comparison of Species Tree Methods for Reconstructing the Phylogeny of Bearded Manakins (Aves: Pipridae, Manacus) from Multilocus Sequence Data

(2008) Robb T. Brumfield et al.   SYSTEMATIC BIOLOGY

Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)

(2008) Natalia M. Belfiore et al.   SYSTEMATIC BIOLOGY

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY