An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus )

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

(2018) David S. Gernandt et al.   AMERICAN JOURNAL OF BOTANY

New prospects in the detection and comparative analysis of hybridization in the tree of life

(2018) Ryan A. Folk et al.   AMERICAN JOURNAL OF BOTANY

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

(2018) Diego F. Morales-Briones et al.   NEW PHYTOLOGIST

The on-again, off-again relationship between mitochondrial genomes and species boundaries

(2017) Daniel B. Sloan et al.   MOLECULAR ECOLOGY

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

(2017) Nicolás García et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide genotyping-by-sequencing data provide a high-resolution view of wild Helianthus diversity, genetic structure, and interspecies gene flow

(2016) Gregory J. Baute et al.   AMERICAN JOURNAL OF BOTANY

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

(2016) K Harrisson et al.   HEREDITY

Revisiting a classic case of introgression: hybridization and gene flow in Californian sunflowers

(2016) Gregory L. Owens et al.   MOLECULAR ECOLOGY

Species tree estimation of diploid Helianthus (Asteraceae) using target enrichment

(2015) J. D. Stephens et al.   AMERICAN JOURNAL OF BOTANY

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance

(2015) Hernán E. Morales et al.   MOLECULAR ECOLOGY

Automation and Evaluation of the SOWH Test with SOWHAT

(2015) Samuel H. Church et al.   SYSTEMATIC BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

(2014) José Melo-Ferreira et al.   Genome Biology and Evolution

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequential adaptive introgression of the mitochondrial genome inDrosophila yakubaandDrosophila santomea

(2014) Ana Llopart et al.   MOLECULAR ECOLOGY

On the adaptive value of cytoplasmic genomes in plants

(2014) Dan G. Bock et al.   MOLECULAR ECOLOGY

Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars,Populus balsamiferaandP. trichocarpa(Salicaceae)

(2014) Daisie I. Huang et al.   NEW PHYTOLOGIST

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

(2014) Susan F. Bailey et al.   Nature Communications

Cytonuclear Genomic Interactions and Hybrid Breakdown

(2013) Ronald S. Burton et al.   Annual Review of Ecology Evolution and Systematics

Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (SaxifragasectionPorphyrionsubsectionOppositifoliae)

(2013) Manuela Winkler et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

Local Adaptation along Smooth Ecological Gradients Causes Phylogeographic Breaks and Phenotypic Clustering

(2012) Darren E. Irwin   AMERICAN NATURALIST

Adaptive evolution of the rbcL gene in Brassicaceae

(2012) Lei Liu et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

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 biogeography of mitochondrial and nuclear discordance in animals

(2012) DAVID P. L. TOEWS et al.   MOLECULAR ECOLOGY

Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)

(2012) Michael L. Moody et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

RECONCILING EXTREMELY STRONG BARRIERS WITH HIGH LEVELS OF GENE EXCHANGE IN ANNUAL SUNFLOWERS

(2011) Julianno B.M. Sambatti et al.   EVOLUTION

JML: testing hybridization from species trees

(2011) SIMON JOLY   Molecular Ecology Resources

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

(2009) Satoko Iida et al.   PLoS One

Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers

(2008) Julianno B. M. Sambatti et al.   ECOLOGY LETTERS

Effective population size and tests of neutrality at cytoplasmic genes in Arabidopsis

(2008) STEPHEN I. WRIGHT et al.   Genetics Research

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION