Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Brown and Polar Bear Y Chromosomes Reveal Extensive Male-Biased Gene Flow within Brother Lineages

(2014) Tobias Bidon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

(2013) Yi-Chiao Chan et al.   BMC EVOLUTIONARY BIOLOGY

Genetic relationships of North American bears (Ursus) inferred from amplified fragment length polymorphisms and mitochondrial DNA sequences

(2013) M.A. Cronin et al.   CANADIAN JOURNAL OF ZOOLOGY

Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

(2013) Heidi E.L. Lischer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Response to Comment on "Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage"

(2013) F. Hailer et al.   SCIENCE

Comment on "Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage"

(2013) S. Nakagome et al.   SCIENCE

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu et al.   SYSTEMATIC BIOLOGY

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion, Multi-kilobase Conversion Tracts, and Rare Inversions

(2013) Pille Hallast et al.   PLoS Genetics

Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution

(2013) James A. Cahill et al.   PLoS Genetics

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cytonuclear discordance among Southeast Asian black rats (Rattus rattuscomplex)

(2012) Marie Pagès et al.   MOLECULAR ECOLOGY

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

(2012) Shancen Zhao et al.   NATURE GENETICS

Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

(2012) Juan Abella et al.   PLoS One

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage

(2012) F. Hailer et al.   SCIENCE

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

Extensive introgressive hybridization within the northern oriole group (GenusIcterus) revealed by three-species isolation with migration analysis

(2012) Frode Jacobsen et al.   Ecology and Evolution

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

(2011) Christian Roos et al.   BMC EVOLUTIONARY BIOLOGY

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

(2011) Ceiridwen J. Edwards et al.   CURRENT BIOLOGY

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

(2011) A. Hobolth et al.   GENOME RESEARCH

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recurrent Introgression of Mitochondrial DNA Among Hares (Lepus spp.) Revealed by Species-Tree Inference and Coalescent Simulations

(2011) J. Melo-Ferreira et al.   SYSTEMATIC BIOLOGY

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

(2010) Ryan C Garrick et al.   BMC EVOLUTIONARY BIOLOGY

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

The Arctic melting pot

(2010) Brendan P. Kelly et al.   NATURE

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

(2009) Johannes Krause et al.   BMC EVOLUTIONARY BIOLOGY

Genetic Variation, Relatedness, and Effective Population Size of Polar Bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

(2009) Matthew A. Cronin et al.   JOURNAL OF HEREDITY

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

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 sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Unequal Rates of Y Chromosome Gene Divergence during Speciation of the Family Ursidae

(2008) Shigeki Nakagome et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals

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

Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

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

Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny

(2007) Marie Pagès et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION