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

Sex-specific clines support incipient speciation in a common European mammal

(2013) A Sutter et al.   HEREDITY

Divergent evolutionary processes associated with colonization of offshore islands

(2013) Natália Martínková et al.   MOLECULAR ECOLOGY

Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis)

(2013) Mathias Beysard et al.   MOLECULAR ECOLOGY

Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron

(2013) Alastair J. Potts et al.   SYSTEMATIC BIOLOGY

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics

(2012) David W. Weisrock et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

Deep mitochondrial introgression and hybridization among ecologically divergent vole species

(2012) Cristiane Bastos-Silveira et al.   MOLECULAR ECOLOGY

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis)

(2011) M. BEYSARD et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis)

(2011) MARTIN C. FISCHER et al.   MOLECULAR ECOLOGY

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Post-glacial partitioning of mitochondrial genetic variation in the field vole

(2011) J. S. Herman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

A new cytochrome b phylogroup of the common vole (Microtus arvalis) endemic to the Balkans and its implications for the evolutionary history of the species

(2010) ELENA V. BUŽAN et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Temporal and spatial variation of dental pattern in the voles, Microtus arvalis, of the Orkney Islands

(2010) Gordon B. Corbet   JOURNAL OF ZOOLOGY

Bayesian statistical treatment of the fluorescence of AFLP bands leads to accurate genetic structure inference

(2010) OSCAR E. GAGGIOTTI   MOLECULAR ECOLOGY

Genomic Scans Support Repetitive Continental Colonization Events during the Rapid Radiation of Voles (Rodentia: Microtus): the Utility of AFLPs versus Mitochondrial and Nuclear Sequence Markers

(2010) Sabine Fink et al.   SYSTEMATIC BIOLOGY

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation

(2010) Jonathan M. Waters et al.   SYSTEMATIC BIOLOGY

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Islands and the evolution of Microtus arvalis (Microtinae)

(2009) R. J. Berry et al.   JOURNAL OF ZOOLOGY

Bayesian Inference of Species Trees from Multilocus Data

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

Transalpine colonisation and partial phylogeographic erosion by dispersal in the common vole (Microtus arvalis)

(2009) SONJA BRAAKER et al.   MOLECULAR ECOLOGY

Phylogenetic Analysis in the Anomaly Zone

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs

(2008) J. E. Horvath et al.   GENOME RESEARCH

New Insight into the Colonization Processes of Common Voles: Inferences from Molecular and Fossil Evidence

(2008) Christelle Tougard et al.   PLoS One

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One