Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies

(2015) Hayley C. Lanier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

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

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

Two New Species, Heuchera soltisii and H. inconstans, with Further Taxonomic Notes for the Western Group of Heuchera Section Heuchera (Saxifragaceae)

(2015) Ryan A. Folk et al.   SYSTEMATIC BOTANY

“Sky islands” in the eastern U.S.A.? — Strong phylogenetic structure in the Heuchera parviflora group (Saxifragaceae)

(2015) Ryan A. Folk et al.   TAXON

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

Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci

(2014) R. A. Folk et al.   AMERICAN JOURNAL OF BOTANY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Divergence with gene flow within the recent chipmunk radiation (Tamias)

(2014) J Sullivan et al.   HEREDITY

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Interspecific introgressive origin of genomic diversity in the house mouse

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

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Revision of Heuchera Section Rhodoheuchera Subsections Hemsleyanae and Rosendahliae Subsectio Nova (Saxifragaceae)

(2014) Ryan A. Folk et al.   SYSTEMATIC BOTANY

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

(2014) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

Microsatellite Primers for the Gynodioecious Grassland Perennial Saxifraga granulata (Saxifragaceae)

(2014) Sascha van der Meer et al.   Applications in Plant Sciences

Polyploidization in Heuchera cylindrica (Saxifragaceae) did not result in a shift in climatic requirements

(2013) William Godsoe et al.   AMERICAN JOURNAL OF BOTANY

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

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

Gene tree rooting methods give distributions that mimic the coalescent process

(2013) Yuan Tian et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

Concatenation versus coalescence versus "concatalescence"

(2013) J. Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity

(2013) S. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Phylogenetics and Taxonomy of the Genus Boechera and Related Genera (Brassicaceae: Boechereae)

(2013) Patrick J. Alexander et al.   SYSTEMATIC BOTANY

Origin of land plants using the multispecies coalescent model

(2013) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

Heuchera lakelae (Saxifragaceae), a new species from the Sierra La Marta and Sierra Coahuilón, Coahuila and Nuevo León, Mexico

(2013) RYAN FOLK   Phytotaxa

Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia

(2012) Anahí Espíndola et al.   ECOLOGY LETTERS

Genome sequencing reveals complex speciation in the Drosophila simulans clade

(2012) D. Garrigan et al.   GENOME RESEARCH

Random roots and lineage sorting

(2012) Jeffrey A. Rosenfeld et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

Phylogeny and Biogeography of the Carnivorous Plant Family Sarraceniaceae

(2012) Aaron M. Ellison et al.   PLoS One

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

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

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

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

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

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

Tanglegrams for rooted phylogenetic trees and networks

(2011) C. Scornavacca et al.   BIOINFORMATICS

Fast and accurate methods for phylogenomic analyses

(2011) Jimmy Yang et al.   BMC BIOINFORMATICS

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

(2011) David Gerard et al.   BMC EVOLUTIONARY BIOLOGY

Entangling Ancient Allotetraploidization in Asian Mitella: An Integrated Approach for Multilocus Combinations

(2011) Y. Okuyama et al.   MOLECULAR BIOLOGY AND EVOLUTION

JML: testing hybridization from species trees

(2011) SIMON JOLY   Molecular Ecology Resources

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

The Potential Role of Androgenesis in Cytoplasmic–Nuclear Phylogenetic Discordance

(2010) Shannon M. Hedtke et al.   SYSTEMATIC BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

The Role of Hybridization in Plant Speciation

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

(2009) Michael S. Barker et al.   Genome Biology and Evolution

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Mitochondrial DNA of Vitis vinifera and the Issue of Rampant Horizontal Gene Transfer

(2008) V. V. Goremykin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel floral adaptations to pollination by fungus gnats within the genus Mitella (Saxifragaceae)

(2008) Yudai Okuyama et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION