Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

Evolutionary analysis of the female-specific avian W chromosome

(2015) Linnéa Smeds et al.   Nature Communications

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Bayesian Inference of Local Trees Along Chromosomes by the Sequential Markov Coalescent

(2014) Chaozhi Zheng et al.   JOURNAL OF MOLECULAR EVOLUTION

ABC inference of multi-population divergence with admixture from unphased population genomic data

(2014) John D. Robinson et al.   MOLECULAR ECOLOGY

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

(2014) Tami E. Cruickshank et al.   MOLECULAR ECOLOGY

Estimation of linkage disequilibrium and interspecific gene flow inFicedulaflycatchers by a newly developed 50k single-nucleotide polymorphism array

(2014) Takeshi Kawakami et al.   Molecular Ecology Resources

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Inferring the demographic history of European Ficedula flycatcher populations

(2013) Niclas Backström et al.   BMC EVOLUTIONARY BIOLOGY

MORE ACCURATE PHYLOGENIES INFERRED FROM LOW-RECOMBINATION REGIONS IN THE PRESENCE OF INCOMPLETE LINEAGE SORTING

(2013) James B. Pease et al.   EVOLUTION

Sampling strategies for species trees: The effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal

(2013) Ammon Corl et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

(2013) Krystyna Nadachowska-Brzyska et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The Effects of Deleterious Mutations on Evolution at Linked Sites

(2012) Brian Charlesworth   GENETICS

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

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

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

The genomics of speciation-with-gene-flow

(2012) Jeffrey L. Feder et al.   TRENDS IN GENETICS

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

Increased divergence but reduced variation on the Z chromosome relative to autosomes inFicedulaflycatchers: differential introgression or the faster-Z effect?

(2012) Silje Hogner et al.   Ecology and Evolution

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Quantifying the Variation in the Effective Population Size Within a Genome

(2011) Toni I. Gossmann et al.   GENETICS

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

A HIGH-DENSITY SCAN OF THE Z CHROMOSOME IN FICEDULA FLYCATCHERS REVEALS CANDIDATE LOCI FOR DIVERSIFYING SELECTION

(2010) Niclas Backström et al.   EVOLUTION

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

(2010) A. McKenna et al.   GENOME RESEARCH

Ecology and genetics of speciation inFicedulaflycatchers

(2010) GLENN-PETER SAETRE et al.   MOLECULAR ECOLOGY

Speciation in Ficedula flycatchers

(2010) A. Qvarnstrom et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

POSTZYGOTIC ISOLATION OVER MULTIPLE GENERATIONS OF HYBRID DESCENDENTS IN A NATURAL HYBRID ZONE: HOW WELL DO SINGLE-GENERATION ESTIMATES REFLECT REPRODUCTIVE ISOLATION?

(2009) Chris Wiley et al.   EVOLUTION

Bayesian Computation and Model Selection Without Likelihoods

(2009) C. Leuenberger et al.   GENETICS

Efficient Approximate Bayesian Computation Coupled With Markov Chain Monte Carlo Without Likelihood

(2009) Daniel Wegmann et al.   GENETICS

Bayesian Inference of Species Trees from Multilocus Data

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

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE

(2008) Michael P. Cummings et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

The genetic mosaic suggests a new role for hitchhiking in ecological speciation

(2008) SARA VIA et al.   MOLECULAR ECOLOGY

Natural and sexual selection against hybrid flycatchers

(2008) N. Svedin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers

(2003) Glenn-Peter Saetre et al.   MOLECULAR ECOLOGY