Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

Testing the SI × SC rule: Pollen-pistil interactions in interspecific crosses between members of the tomato clade (Solanum section Lycopersicon , Solanaceae)

(2015) You Soon Baek et al.   AMERICAN JOURNAL OF BOTANY

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Process and pattern in cichlid radiations - inferences for understanding unusually high rates of evolutionary diversification

(2015) Ole Seehausen   NEW PHYTOLOGIST

Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives

(2015) Gregory J. Baute et al.   NEW PHYTOLOGIST

Confluence, synnovation, and depauperons in plant diversification

(2015) Michael J. Donoghue et al.   NEW PHYTOLOGIST

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

(2015) James B. Pease et al.   SYSTEMATIC BIOLOGY

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Plant carotenoids: genomics meets multi-gene engineering

(2014) Giovanni Giuliano   CURRENT OPINION IN PLANT BIOLOGY

Clumped isotope evidence for diachronous surface cooling of the Altiplano and pulsed surface uplift of the Central Andes

(2014) Carmala N. Garzione et al.   EARTH AND PLANETARY SCIENCE LETTERS

Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

(2014) Joanne A. Labate et al.   GENOME

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanumsect.Lycopersicon)

(2014) S. L. Vosters et al.   MOLECULAR ECOLOGY

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

Gibbon genome and the fast karyotype evolution of small apes

(2014) Lucia Carbone et al.   NATURE

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation with gene flow in equids despite extensive chromosomal plasticity

(2014) Hákon Jónsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Fluorescence In Situ Hybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome

(2014) Lindsay A. Shearer et al.   G3-Genes Genomes Genetics

Diversity-Dependence, Ecological Speciation, and the Role of Competition in Macroevolution

(2013) Daniel L. Rabosky   Annual Review of Ecology Evolution and Systematics

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES

(2013) Rongfeng Cui et al.   EVOLUTION

Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies

(2013) Simon H. Martin et al.   GENOME RESEARCH

Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation

(2013) Philip W. Hedrick   MOLECULAR ECOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Dissection of Tomato Lycopene Biosynthesis through Virus-Induced Gene Silencing

(2013) E. Fantini et al.   PLANT PHYSIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

Ecological opportunity and sexual selection together predict adaptive radiation

(2012) Catherine E. Wagner et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Chromosome evolution in Solanum traced by cross-species BAC-FISH

(2012) Dóra Szinay et al.   NEW PHYTOLOGIST

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

(2012) Sung-Chur Sim et al.   PLoS One

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species

(2012) Jiaxin Xu et al.   THEORETICAL AND APPLIED GENETICS

A “Forward Genomics” Approach Links Genotype to Phenotype using Independent Phenotypic Losses among Related Species

(2012) Michael Hiller et al.   Cell Reports

Genome-Wide Association Mapping in Tomato ( Solanum lycopersicum ) Is Possible Using Genome Admixture of Solanum lycopersicum var. cerasiforme

(2012) Nicolas Ranc et al.   G3-Genes Genomes Genetics

Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life

(2012) Daniel L. Rabosky et al.   PLOS BIOLOGY

Compatibility and incompatibility in S-RNase-based systems

(2011) Bruce McClure et al.   ANNALS OF BOTANY

Testing for Ancient Admixture between Closely Related Populations

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

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Chromosomal rearrangements between tomato and Solanum chilense hamper mapping and breeding of the TYLCV resistance gene Ty-1

(2011) Maarten G. Verlaan et al.   PLANT JOURNAL

Ecological and geographic modes of species divergence in wild tomatoes

(2010) Takuya Nakazato et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic Insights on Adaptive Radiation

(2010) Richard E. Glor   Annual Review of Ecology Evolution and Systematics

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Structural Differences in Chromosomes Distinguish Species in the Tomato Clade

(2010) L.K. Anderson et al.   CYTOGENETIC AND GENOME RESEARCH

Andean uplift, ocean cooling and Atacama hyperaridity: A climate modeling perspective

(2010) René D. Garreaud et al.   EARTH AND PLANETARY SCIENCE LETTERS

Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus

(2010) Kenneth D. Whitney et al.   NEW PHYTOLOGIST

Resource polyphenism increases species richness: a test of the hypothesis

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

Equilibrium speciation dynamics in a model adaptive radiation of island lizards

(2010) D. L. Rabosky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid Incompatibility "Snowballs" Between Solanum Species

(2010) L. C. Moyle et al.   SCIENCE

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

(2010) C. Hoorn et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Thinking in continua: beyond the “adaptive radiation” metaphor

(2009) Mark E. Olson et al.   BIOESSAYS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

(2009) Flor Rodriguez et al.   BMC EVOLUTIONARY BIOLOGY

Sequence diversity in three tomato species: SNPs, markers, and molecular evolution

(2009) José M Jiménez-Gómez et al.   BMC PLANT BIOLOGY

Adaptive Radiation: Contrasting Theory with Data

(2009) S. Gavrilets et al.   SCIENCE

Biogeographic diversification inNolana(Solanaceae), a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America

(2009) Michael O. DILLON et al.   Journal of Systematics and Evolution

Direction and timing of uplift propagation in the Peruvian Andes deduced from molecular phylogenetics of highland biotaxa

(2008) Damien Picard et al.   EARTH AND PLANETARY SCIENCE LETTERS

ECOLOGICAL AND EVOLUTIONARY GENOMICS IN THE WILD TOMATOES (SOLANUM SECT. LYCOPERSICON)

(2008) Leonie C. Moyle   EVOLUTION

Loss of Self‐Incompatibility and Its Evolutionary Consequences

(2008) Boris Igic et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Rise of the Andes

(2008) C. N. Garzione et al.   SCIENCE

Adaptive evolution in invasive species

(2008) Peter J. Prentis et al.   TRENDS IN PLANT SCIENCE