Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

The Effect of Gene Flow on Coalescent-based Species-Tree Inference

(2018) Colby Long et al.   SYSTEMATIC BIOLOGY

Phylogeny and Evolution of the Neotropical Radiation of Lachemilla (Rosaceae): Uncovering a History of Reticulate Evolution and Implications for Infrageneric Classification

(2018) Diego F. Morales-Briones et al.   SYSTEMATIC BOTANY

Bayesian inference of phylogenetic networks from bi-allelic genetic markers

(2018) Jiafan Zhu et al.   PLoS Computational Biology

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a MediterraneanCampanula(Campanulaceae) clade

(2017) Andrew A. Crowl et al.   EVOLUTION

PhyloNetworks: A Package for Phylogenetic Networks

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

Bayesian Inference of Species Networks from Multilocus Sequence Data

(2017) Chi Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

(2017) Nicolás García 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

Against all odds: reconstructing the evolutionary history of Scrophularia (Scrophulariaceae) despite high levels of incongruence and reticulate evolution

(2017) Agnes Scheunert et al.   ORGANISMS DIVERSITY & EVOLUTION

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

(2017) Dario Copetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

(2017) Dingqiao Wen et al.   SYSTEMATIC BIOLOGY

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

(2017) Dahiana Arcila et al.   Nature Ecology & Evolution

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

(2016) Hussein A. Hejase et al.   BMC BIOINFORMATICS

In the light of deep coalescence: revisiting trees within networks

(2016) Jiafan Zhu et al.   BMC BIOINFORMATICS

A performance study of the impact of recombination on species tree analysis

(2016) Zhiwei Wang et al.   BMC GENOMICS

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data

(2016) George P. Tiley et al.   Genome Biology and Evolution

Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics

(2016) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

(2016) Dingqiao Wen et al.   MOLECULAR ECOLOGY

A genomic perspective on hybridization and speciation

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

Untangling the phylogeny of Leandra s.str. (Melastomataceae, Miconieae)

(2016) Marcelo Reginato et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing

(2016) Carl J. Rothfels et al.   NEW PHYTOLOGIST

Inconsistency of Species Tree Methods under Gene Flow

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

Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)

(2016) R. Alexander Pyron et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

(2016) Dingqiao Wen et al.   PLoS Genetics

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Low-Coverage, Whole-Genome Sequencing of Artocarpus camansi (Moraceae) for Phylogenetic Marker Development and Gene Discovery

(2016) Elliot M. Gardner et al.   Applications in Plant Sciences

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

(2016) Chodon Sass et al.   PeerJ

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

(2016) Simon Uribe-Convers et al.   PLoS One

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 analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

(2015) Karolina Heyduk et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting

(2015) Kamil Konowalik et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

(2015) A.L. Mugrabi de Kuppler et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Re-evaluating the phylogeny of allopolyploid Gossypium L.

(2015) Corrinne E. Grover 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

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

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

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

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

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Concatenation versus coalescence versus "concatalescence"

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

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

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria

(2012) José Luis Blanco-Pastor et al.   PLoS One

Is Recombination a Problem for Species-Tree Analyses?

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes

(2011) Noah Reid et al.   SYSTEMATIC BIOLOGY

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Patterns of hybridization in plants

(2010) Kenneth D. Whitney et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification

(2009) Magnus Lundberg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reticulation, Data Combination, and Inferring Evolutionary History: An Example from Danthonioideae (Poaceae)

(2009) Michael D. Pirie et al.   SYSTEMATIC BIOLOGY

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

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Speciation in fungi

(2008) Tatiana Giraud et al.   FUNGAL GENETICS AND BIOLOGY

Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification

(2008) B. Gehrke et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Introduction. Extent, processes and evolutionary impact of interspecific hybridization in animals

(2008) K. Schwenk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Reticulate History of Medicago (Fabaceae)

(2008) Iván J. Maureira-Butler et al.   SYSTEMATIC BIOLOGY