Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

(2015) J. Wang et al.   GENETICS

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

Multilocus analysis of nucleotide variation and speciation in three closely relatedPopulus(Salicaceae) species

(2015) Shuhui Du et al.   MOLECULAR ECOLOGY

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

(2015) Leonardo Campagna et al.   MOLECULAR ECOLOGY

Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data

(2015) Débora Y. C. Brandt et al.   G3-Genes Genomes Genetics

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Populus tremula (European aspen) shows no evidence of sexual dimorphism

(2014) Kathryn M Robinson et al.   BMC PLANT BIOLOGY

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

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

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

(2014) Zhaoshan Wang et al.   PLoS One

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit

(2014) Miguel Carneiro et al.   PLoS Genetics

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

(2013) Line Skotte et al.   GENETICS

Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides)

(2013) Colin M. Callahan et al.   JOURNAL OF BIOGEOGRAPHY

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

(2013) Vitor Sousa et al.   NATURE REVIEWS GENETICS

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Genomic islands of divergence are not affected by geography of speciation in sunflowers

(2013) S. Renaut et al.   Nature Communications

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest treePopulus trichocarpa

(2012) Gancho T. Slavov et al.   NEW PHYTOLOGIST

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Photosynthetic characteristics and growth performance of closely related aspen taxa: On the systematic relatedness of the Eurasian Populus tremula and the North American P. tremuloides

(2011) Annika Müller et al.   FLORA

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Forest tree genomics: growing resources and applications

(2011) David B. Neale et al.   NATURE REVIEWS GENETICS

Genomic divergence during speciation: causes and consequences

(2011) P. Nosil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

(2011) J. L. Strasburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Short-rotation forestry with hybrid aspen (Populus tremulaL.×P. tremuloidesMichx.) in Northern Europe

(2011) Arvo Tullus et al.   SCANDINAVIAN JOURNAL OF FOREST RESEARCH

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

(2010) L. Chikhi et al.   GENETICS

Genomic islandsofspeciation or genomic islandsandspeciation?

(2010) THOMAS L. TURNER et al.   MOLECULAR ECOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Speciation genetics: current status and evolving approaches

(2010) J. B. W. Wolf et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

(2010) Alon Keinan et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Review of the Primer Approximation Multiplex PCR (PAMP) Technique for Detecting Large Scale Cancer Genomic Lesions

(2009) Kedsuda Apichonbancha et al.   Current Bioinformatics

Constructing genomic maps of positive selection in humans: Where do we go from here?

(2009) J. M. Akey   GENOME RESEARCH

Darwinian and demographic forces affecting human protein coding genes

(2009) R. Nielsen et al.   GENOME RESEARCH

Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species

(2009) M A F Noor et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Natural selection in action during speciation

(2009) S. Via   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic linkage mapping in aspen (Populus tremula L. and Populus tremuloides Michx.)

(2009) Birte Pakull et al.   Tree Genetics & Genomes

Genetic diversity in natural populations: a fundamental component of plant–microbe interactions

(2008) Lucie Salvaudon et al.   CURRENT OPINION IN PLANT BIOLOGY

Multilocus Patterns of Nucleotide Polymorphism and the Demographic History of Populus tremula

(2008) P. K. Ingvarsson   GENETICS