Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards

(2016) Jesse L. Grismer et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of the island archipelago frog genus Sanguirana : Another endemic Philippine radiation that diversified ‘Out-of-Palawan’

(2016) Rafe M. Brown et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spatiotemporal Diversification of the True Frogs (GenusRana): A Historical Framework for a Widely Studied Group of Model Organisms

(2016) Zhi-Yong Yuan et al.   SYSTEMATIC BIOLOGY

Tectonic collision and uplift of Wallacea triggered the global songbird radiation

(2016) Robert G. Moyle et al.   Nature Communications

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Phylogeny of frogs from the genus Physalaemus (Anura, Leptodactylidae) inferred from mitochondrial and nuclear gene sequences

(2015) Luciana B. Lourenço et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

(2015) Princess S. Gilbert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Systematics and biogeography of the Hylarana frog (Anura: Ranidae) radiation across tropical Australasia, Southeast Asia, and Africa

(2015) Lauren A. Oliver et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae)

(2015) Tao Thien Nguyen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenomic analysis of turtles

(2015) Nicholas G. Crawford et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

(2015) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders

(2015) Xing-Xing Shen et al.   SYSTEMATIC BIOLOGY

Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

(2015) Rafe M. Brown et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

Ultraconserved Elements Sequencing as a Low-Cost Source of Complete Mitochondrial Genomes and Microsatellite Markers in Non-Model Amniotes

(2015) Fábio Raposo do Amaral et al.   PLoS One

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

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The complete mitochondrial genome ofMicrohyla pulchra(Amphidia, Anura, Microhylidae)

(2014) Xiaoyou Wu et al.   Mitochondrial DNA

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

(2014) Brant C. Faircloth et al.   Molecular Ecology Resources

The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

(2014) K. Sun et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Bayesian Long Branch Attraction Bias and Corrections

(2014) Edward Susko   SYSTEMATIC BIOLOGY

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

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

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

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

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

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

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

Evolutionary Processes of Diversification in a Model Island Archipelago

(2013) Rafe M. Brown et al.   Annual Review of Ecology Evolution and Systematics

AN ADAPTIVE RADIATION OF FROGS IN A SOUTHEAST ASIAN ISLAND ARCHIPELAGO

(2013) David C. Blackburn et al.   EVOLUTION

The palaeogeography of Sundaland and Wallacea since the Late Jurassic

(2013) Robert Hall   JOURNAL OF LIMNOLOGY

Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs

(2013) Peng Zhang 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

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Origin of land plants using the multispecies coalescent model

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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

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

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Low Diversity in the Mitogenome of Sperm Whales Revealed by Next-Generation Sequencing

(2012) Alana Alexander et al.   Genome Biology and Evolution

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model

(2012) Patrick Kück et al.   PLoS One

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Adaptive Radiation and Ecological Opportunity in Sulawesi and Philippine Fanged Frog (Limnonectes) Communities

(2011) Mohammad I. Setiadi et al.   AMERICAN NATURALIST

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

(2011) V. C. Mason et al.   GENOME RESEARCH

Short Reads, Circular Genome: Skimming SOLiD Sequence to Construct the Bighorn Sheep Mitochondrial Genome

(2011) Joshua M. Miller et al.   JOURNAL OF HEREDITY

Testing for Ancient Admixture between Closely Related Populations

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

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

(2011) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nuclear–mitochondrial discordance and gene flow in a recent radiation of toads

(2011) Brian E. Fontenot et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Phylogenetic Insights on Adaptive Radiation

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

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

(2010) A. McKenna et al.   GENOME RESEARCH

Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks

(2010) Simon Y. W. Ho et al.   Mitochondrial DNA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Frequent mitochondrial gene introgression among high elevation Tibetan megophryid frogs revealed by conflicting gene genealogies

(2009) WEI CHEN et al.   MOLECULAR ECOLOGY

Vast underestimation of Madagascar's biodiversity evidenced by an integrative amphibian inventory

(2009) D. R. Vieites et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tectonic setting of a composite terrane: A review of the Philippine island arc system

(2008) Graciano P. Yumul et al.   GEOSCIENCES JOURNAL

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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

Complete mitochondrial genomes of three neobatrachian anurans: A case study of divergence time estimation using different data and calibration settings

(2007) Takeshi Igawa et al.   GENE