CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages

(2012) Joseph W Brown et al.   BMC BIOLOGY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Arctic‐Alpine Distributions—Metapopulations on a Continental Scale?

(2009) Christoph Muster et al.   AMERICAN NATURALIST

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Computation vs. cloning: evaluation of two methods for haplotype determination

(2009) RYAN J. HARRIGAN et al.   Molecular Ecology Resources

The causes of mitochondrial DNA gene tree paraphyly in birds

(2009) Bailey D. McKay et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Great American Biotic Interchange in birds

(2009) J. T. Weir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Trees from Highly Incongruent Gene Trees in Rice

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

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

(2009) L. Lacey Knowles   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

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Gene flow and species delimitation

(2009) Rémy J. Petit et al.   TRENDS IN ECOLOGY & EVOLUTION

High mitogenomic evolutionary rates and time dependency

(2009) Sankar Subramanian et al.   TRENDS IN GENETICS

GENETIC DIVERGENCE AND DIFFERENTIATION WITHIN THE WESTERN SCRUB-JAY (APHELOCOMA CALIFORNICA)

(2008) KATHLEEN SEMPLE DELANEY et al.   AUK

Integrating paleoecology and genetics of bird populations in two sky island archipelagos

(2008) John E McCormack et al.   BMC BIOLOGY

HALDANE'S RULE IN AN AVIAN SYSTEM: USING CLINE THEORY AND DIVERGENCE POPULATION GENETICS TO TEST FOR DIFFERENTIAL INTROGRESSION OF MITOCHONDRIAL, AUTOSOMAL, AND SEX-LINKED LOCI ACROSS THEPASSERINABUNTING HYBRID ZONE

(2008) Matthew D. Carling et al.   EVOLUTION

Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina)

(2008) J. E. McCORMACK et al.   MOLECULAR ECOLOGY

Calibrating the avian molecular clock

(2008) J. T. WEIR et al.   MOLECULAR ECOLOGY

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

A well-tested set of primers to amplify regions spread across the avian genome

(2008) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Niche expansion leads to small-scale adaptive divergence along an elevation gradient in a medium-sized passerine bird

(2008) J. E McCormack et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds

(2008) M. Krosby et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

(2008) Dmitry A. Dmitriev et al.   PLoS Computational Biology

Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers

(2003) L. Lacey Knowles   MOLECULAR ECOLOGY