Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes )

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

(2017) Jacob A. Esselstyn et al.   Genome Biology and Evolution

PhyloNetworks: A Package for Phylogenetic Networks

(2017) Claudia Solís-Lemus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic evidence of gene flow during reinforcement in Texas Phlox

(2017) Federico Roda et al.   MOLECULAR ECOLOGY

Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium )

(2017) Oscar M. Vargas et al.   NEW PHYTOLOGIST

What, if anything, are hybrids: enduring truths and challenges associated with population structure and gene flow

(2016) Zachariah Gompert et al.   Evolutionary Applications

Powerful methods for detecting introgressed regions from population genomic data

(2016) Benjamin K. Rosenzweig et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

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

Hybridization and hybrid speciation under global change

(2016) Mario Vallejo-Marín et al.   NEW PHYTOLOGIST

Hybridization in Plants: Old Ideas, New Techniques

(2016) Benjamin E. Goulet et al.   PLANT PHYSIOLOGY

Inconsistency of Species Tree Methods under Gene Flow

(2016) Claudia Solís-Lemus et al.   SYSTEMATIC BIOLOGY

Distinct Processes Drive Diversification in Different Clades of Gesneriaceae

(2016) Eric H. Roalson et al.   SYSTEMATIC BIOLOGY

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

(2016) B. M. vonHoldt et al.   Science Advances

Postzygotic barriers isolate sympatric species of Cyrtandra (Gesneriaceae) in Hawaiian montane forest understories

(2015) Melissa A. Johnson et al.   AMERICAN JOURNAL OF BOTANY

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

(2015) Ruth Davidson et al.   BMC GENOMICS

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

(2015) Jed Chou et al.   BMC GENOMICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Increased divergence in floral morphology strongly reduces gene flow in sympatric sexually deceptive orchids with the same pollinator

(2015) Julia Gögler et al.   EVOLUTIONARY ECOLOGY

hybridcheck: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data

(2015) Ben J. Ward et al.   Molecular Ecology Resources

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

PREDICTABILITY AND IRREVERSIBILITY OF GENETIC CHANGES ASSOCIATED WITH FLOWER COLOR EVOLUTION INPENSTEMON BARBATUS

(2013) Carolyn A. Wessinger et al.   EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)

(2013) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species

(2012) Alexander N. Schmidt-Lebuhn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Testing for Ancient Admixture between Closely Related Populations

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Bayesian inference of ancient human demography from individual genome sequences

(2011) Ilan Gronau et al.   NATURE GENETICS

Hybrid floral scent novelty drives pollinator shift in sexually deceptive orchids

(2010) Nicolas J Vereecken et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary breakdown of pollination specialization in a Caribbean plant radiation

(2010) Silvana Martén-Rodríguez et al.   NEW PHYTOLOGIST

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

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

Evaluation of pollination syndromes in Antillean Gesneriaceae: evidence for bat, hummingbird and generalized flowers

(2009) Silvana Martén-Rodríguez et al.   JOURNAL OF ECOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Pollinator convergence and the nature of species' boundaries in sympatric Sardinian Ophrys (Orchidaceae)

(2008) P. Cortis et al.   ANNALS OF BOTANY

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Untangling Gloxinieae (Gesneriaceae). II. Reconstructing Biogeographic Patterns and Estimating Divergence Times Among New World Continental and Island Lineages

(2008) Eric H. Roalson et al.   SYSTEMATIC BOTANY