Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

Multiple colonizations, hybridization and uneven diversification in Cyrtandra (Gesneriaceae) lineages on Hawai'i Island

(2019) Melissa A. Johnson et al.   JOURNAL OF BIOGEOGRAPHY

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

(2018) Wade R. Roberts et al.   AMERICAN JOURNAL OF BOTANY

HyDe: A Python Package for Genome-Scale Hybridization Detection

(2018) Paul D Blischak et al.   SYSTEMATIC BIOLOGY

Origins of the Hawaiian flora: Phylogenies and biogeography reveal patterns of long‐distance dispersal

(2018) Jonathan P. Price et al.   Journal of Systematics and Evolution

PhyloNetworks: A Package for Phylogenetic Networks

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

A molecular phylogeny of the Pacific clade of Cyrtandra (Gesneriaceae) reveals a Fijian origin, recent diversification, and the importance of founder events

(2017) Melissa A. Johnson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genomic perspective on hybridization and speciation

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

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

(2016) Andreanna J. Welch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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

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

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

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

(2015) Jed Chou et al.   BMC GENOMICS

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

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

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The resurrection genome ofBoea hygrometrica: A blueprint for survival of dehydration

(2015) Lihong Xiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Protocol for Targeted Enrichment of Intron-Containing Sequence Markers for Recent Radiations: A Phylogenomic Example from Heuchera (Saxifragaceae)

(2015) Ryan A. Folk et al.   Applications in Plant Sciences

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

Biogeographic insights on PacificCoprosma(Rubiaceae) indicate two colonizations to the Hawaiian Islands

(2014) Jason T. Cantley et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Incipient radiation within the dominant Hawaiian tree Metrosideros polymorpha

(2014) E A Stacy et al.   HEREDITY

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

Comparative transcriptome resources of elevenPrimulinaspecies, a group of ‘stone plants’ from a biodiversity hot spot

(2014) Bin Ai et al.   Molecular Ecology Resources

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Potential use of low-copy nuclear genes in DNA barcoding: a comparison with plastid genes in two Hawaiian plant radiations

(2013) Yohan Pillon et al.   BMC EVOLUTIONARY BIOLOGY

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa

(2013) Tilottama Roy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene discordance in phylogenomics of recent plant radiations, an example from Hawaiian Cyrtandra (Gesneriaceae)

(2013) Yohan Pillon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Evolution and Biogeographic Origins of the Endemic Hawaiian Genusn Hesperomannia (Asteraceae)

(2013) Clifford W. Morden et al.   PACIFIC SCIENCE

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

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

A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid Genomes

(2013) Gregory W. Stull et al.   Applications in Plant Sciences

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Area and the rapid radiation of Hawaiian Bidens (Asteraceae)

(2012) Matthew L. Knope et al.   JOURNAL OF BIOGEOGRAPHY

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

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

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

Testing for Ancient Admixture between Closely Related Populations

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

Estimating the species tree for Hawaiian Schiedea (Caryophyllaceae) from multiple loci in the presence of reticulate evolution

(2011) Ann Willyard et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Hawaiian angiosperm radiations of North American origin

(2010) B. G. Baldwin et al.   ANNALS OF BOTANY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Ecological opportunity and the origin of adaptive radiations

(2010) J. B. YODER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

Patterns of diversification and ancestral range reconstruction in the southeast Asian–Pacific angiosperm lineage Cyrtandra (Gesneriaceae)

(2009) John R. Clark et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

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

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

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation

(2008) J. Mallet   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Progressive island colonization and ancient origin of Hawaiian Metrosideros (Myrtaceae)

(2008) D. M Percy et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origin, adaptive radiation and diversification of the Hawaiian lobeliads (Asterales: Campanulaceae)

(2008) T. J Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages

(2008) John R. Clark et al.   SYSTEMATIC BIOLOGY

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

(2008) Elizabeth A. Friar et al.   SYSTEMATIC BOTANY