Likelihood-based inference of population history from low-coveragede novogenome assemblies

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Understanding the origin of species with genome-scale data: modelling gene flow

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Genetic hitchhiking in spatially extended populations

(2013) N.H. Barton et al.   THEORETICAL POPULATION BIOLOGY

Inferring Demographic History from a Spectrum of Shared Haplotype Lengths

(2013) Kelley Harris et al.   PLoS Genetics

Reconstructing Community Assembly in Time and Space Reveals Enemy Escape in a Western Palearctic Insect Community

(2012) Graham N. Stone et al.   CURRENT BIOLOGY

Large-scale longitudinal gradients of genetic diversity: a meta-analysis across six phyla in the Mediterranean basin

(2012) Cyrille Conord et al.   Ecology and Evolution

Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture

(2012) John E. Pool et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

RADSeq: next-generation population genetics

(2011) J. W. Davey et al.   Briefings in Functional Genomics

A General Method for Calculating Likelihoods Under the Coalescent Process

(2011) K. Lohse et al.   GENETICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Controlling for non-independence in comparative analysis of patterns across populations within species

(2011) G. N. Stone et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Community impacts of anthropogenic disturbance: natural enemies exploit multiple routes in pursuit of invading herbivore hosts

(2010) James A Nicholls et al.   BMC EVOLUTIONARY BIOLOGY

A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY

(2010) Nicholas H. Barton et al.   EVOLUTION

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Large-Scale mtDNA Screening Reveals a Surprising Matrilineal Complexity in East Asia and Its Implications to the Peopling of the Region

(2010) Q.-P. Kong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Concordant phylogeography and cryptic speciation in two Western Palaearctic oak gall parasitoid species complexes

(2010) JAMES A. NICHOLLS et al.   MOLECULAR ECOLOGY

Recombination and Its Impact on the Genome of the Haplodiploid Parasitoid Wasp Nasonia

(2010) Oliver Niehuis et al.   PLoS One

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Estimating Divergence Parameters With Small Samples From a Large Number of Loci

(2009) Y. Wang et al.   GENETICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Isolation with Migration Models for More Than Two Populations

(2009) Jody Hey   MOLECULAR BIOLOGY AND EVOLUTION

An information-theoretical approach to phylogeography

(2009) BRYAN C. CARSTENS et al.   MOLECULAR ECOLOGY

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Africa goes Europe: The complete phylogeography of the marbled white butterfly species complex Melanargia galathea/M. lachesis (Lepidoptera: Satyridae)

(2008) J HABEL et al.   ORGANISMS DIVERSITY & EVOLUTION

Demographic History of European Populations of Arabidopsis thaliana

(2008) Olivier François et al.   PLoS Genetics

Phylogeographical variation of chloroplast DNA in holm oak (Quercus ilex L.)

(2003) R. Lumaret et al.   MOLECULAR ECOLOGY