Ancient and recent introgression shape the evolutionary history of pollinator adaptation and speciation in a model monkeyflower radiation (Mimulus section Erythranthe)

A Combinatorial View on Speciation and Adaptive Radiation

(2019) David A. Marques et al.   TRENDS IN ECOLOGY & EVOLUTION

A Three-Sample Test for Introgression

(2019) Matthew W Hahn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

Selfing Can Facilitate Transitions between Pollination Syndromes

(2018) Carolyn A. Wessinger et al.   AMERICAN NATURALIST

When Two Rights Make a Wrong: The Evolutionary Genetics of Plant Hybrid Incompatibilities

(2018) Lila Fishman et al.   Annual Review of Plant Biology

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids

(2018) Joana Isabel Meier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demographic compensation does not rescue populations at a trailing range edge

(2018) Seema Nayan Sheth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

(2018) Matthew R. Jones et al.   SCIENCE

Monkeyflowers (Mimulus ): new model for plant developmental genetics and evo-devo

(2018) Yao-Wu Yuan   NEW PHYTOLOGIST

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

(2017) Henrique V. Figueiró et al.   Science Advances

A genomic perspective on hybridization and speciation

(2016) Bret A. Payseur et al.   MOLECULAR ECOLOGY

Genomic and functional approaches reveal a case of adaptive introgression fromPopulus balsamifera(balsam poplar) inP. trichocarpa(black cottonwood)

(2016) Adriana Suarez-Gonzalez et al.   MOLECULAR ECOLOGY

Population structure and local selection yield high genomic variation inMimulus guttatus

(2016) Joshua R. Puzey et al.   MOLECULAR ECOLOGY

Competition between anthocyanin and flavonol biosynthesis produces spatial pattern variation of floral pigments betweenMimulusspecies

(2016) Yao-Wu Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

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

The genomics of organismal diversification illuminated by adaptive radiations

(2015) Daniel Berner et al.   TRENDS IN GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Pollinator-mediated competition influences selection for flower-color displacement in sympatric monkeyflowers

(2014) Dena L. Grossenbacher et al.   AMERICAN JOURNAL OF BOTANY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

Chromosomal rearrangements directly cause underdominant F1pollen sterility inMimulus lewisii-Mimulus cardinalishybrids

(2014) Angela Stathos et al.   EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

The genetic architecture of traits associated with the evolution of self-pollination inMimulus

(2014) Lila Fishman et al.   NEW PHYTOLOGIST

Floral volatile alleles can contribute to pollinator-mediated reproductive isolation in monkeyflowers (Mimulus)

(2014) Kelsey J. R. P. Byers et al.   PLANT JOURNAL

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Speciation and Introgression between Mimulus nasutus and Mimulus guttatus

(2014) Yaniv Brandvain et al.   PLoS Genetics

CHROMOSOMAL REARRANGEMENTS AND THE GENETICS OF REPRODUCTIVE BARRIERS INMIMULUS(MONKEY FLOWERS)

(2013) Lila Fishman et al.   EVOLUTION

Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator-Mediated Reproductive Isolation Between Sister Species ofMimulus

(2013) Yao-Wu Yuan et al.   GENETICS

The Color Genes of Speciation in Plants

(2013) Daniel Ortiz-Barrientos   GENETICS

Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations

(2013) D. L. Mahler et al.   SCIENCE

Lessons from flower colour evolution on targets of selection

(2012) Carolyn A. Wessinger et al.   JOURNAL OF EXPERIMENTAL BOTANY

The biogeography of mitochondrial and nuclear discordance in animals

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

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

(2012) Kanchon K. Dasmahapatra et al.   NATURE

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

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

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Testing for Ancient Admixture between Closely Related Populations

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

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic Insights on Adaptive Radiation

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive Radiation: Contrasting Theory with Data

(2009) S. Gavrilets et al.   SCIENCE

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Explaining Evolutionary Shifts between Bee and Hummingbird Pollination: Convergence, Divergence, and Directionality

(2008) James D. Thomson et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES