Phylogeny of terraranan frogs based on 2,665 loci and impacts of missing data on phylogenomic analyses

A new terraranan genus from the Brazilian Atlantic Forest with comments on the systematics of Brachycephaloidea (Amphibia: Anura)

(2021) Ana Paula Motta et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

(2020) Paul M Hime et al.   SYSTEMATIC BIOLOGY

Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?

(2020) Daniel M Portik et al.   SYSTEMATIC BIOLOGY

Causes and analytical impacts of missing data in RADseq phylogenetics: Insights from an African frog (Afrixalus )

(2019) Marco Crotti et al.   ZOOLOGICA SCRIPTA

Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

(2019) Marcio R. Pie et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic support for evolutionary relationships of New World direct-developing frogs (Anura: Terraranae)

(2018) Matthew P. Heinicke et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci

(2018) Jeffrey W. Streicher et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The interplay of past diversification and evolutionary isolation with present imperilment across the amphibian tree of life

(2018) Walter Jetz et al.   Nature Ecology & Evolution

Molecular insights into the phylogenetic placement of the poorly known genus Niceforonia Goin & Cochran, 1963 (Anura: Brachycephaloidea)

(2018) ANDRÉS R. ACOSTA-GALVIS et al.   ZOOTAXA

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

(2017) Yan-Jie Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Alana M. Alexander et al.   EVOLUTION

An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

(2016) Daniel M. Portik et al.   Molecular Ecology Resources

Phylogenomic analyses reveal novel relationships among snake families

(2016) Jeffrey W. Streicher et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

(2016) Kelly A. Meiklejohn et al.   SYSTEMATIC BIOLOGY

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

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

A phylogenomic analysis of turtles

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

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

(2015) Jeffrey W. Streicher et al.   SYSTEMATIC BIOLOGY

Assessing the efficiency of multiple sequence alignment programs

(2014) Fabiano Sviatopolk-Mirsky Pais et al.   Algorithms for Molecular Biology

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

Using historical biogeography to test for community saturation

(2014) Nelsy Rocío Pinto-Sánchez et al.   ECOLOGY LETTERS

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Biogeographic Analysis Reveals Ancient Continental Vicariance and Recent Oceanic Dispersal in Amphibians

(2014) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria

(2014) JOSÉ M. PADIAL et al.   ZOOTAXA

New Morphological Synapomorphies for the New World Direct-Developing Frogs (Amphibia: Anura: Terrarana)

(2013) Carlos Taboada et al.   HERPETOLOGICA

STRAW: Species TRee Analysis Web server

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

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

PHYLOGENETIC ANALYSES REVEAL UNEXPECTED PATTERNS IN THE EVOLUTION OF REPRODUCTIVE MODES IN FROGS

(2012) Ivan Gomez-Mestre et al.   EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

Correlates of species richness in the largest Neotropical amphibian radiation

(2011) A. GONZALEZ-VOYER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

The Great American Biotic Interchange in frogs: Multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae)

(2011) Nelsy Rocío Pinto-Sánchez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY