Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Earth history and the passerine superradiation

(2019) Carl H. Oliveros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting Amazonian, Cerrado, and Atlantic forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins ( Neopelma / Tyranneutes , Aves: Pipridae)

(2018) João Marcos Guimarães Capurucho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny and systematics of Chiroxiphia and Antilophia manakins (Aves, Pipridae)

(2018) Sofia Marques Silva et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae)

(2018) Cleyssian Dias et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Optimal rates for phylogenetic inference and experimental design in the era of genome-scale datasets

(2018) Alex Dornburg et al.   SYSTEMATIC BIOLOGY

Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird

(2017) Alfredo O. Barrera-Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Why Concatenation Fails Near the Anomaly Zone

(2017) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

(2017) Sushma Reddy et al.   SYSTEMATIC BIOLOGY

A new species of manakin (Aves: Pipridae; Machaeropterus) from Peru with a taxonomic reassessment of the Striped Manakin (M. regulus) complex 

(2017) DANIEL F. LANE et al.   ZOOTAXA

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

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

PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

(2016) Alex Dornburg et al.   BMC EVOLUTIONARY BIOLOGY

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

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY 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

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

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

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

(2015) Jed Chou 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

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

(2015) Peter A. Hosner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

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

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

(2015) Meng-Yun Chen et al.   SYSTEMATIC BIOLOGY

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman 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

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia)

(2014) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

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

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

Molecular phylogeny of the manakins (Aves: Passeriformes: Pipridae), with a new classification and the description of a new genus

(2013) Jan I. Ohlson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

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

Phylogeny and classification of the New World suboscines (Aves, Passeriformes)

(2013) JAN I. OHLSON et al.   ZOOTAXA

Next-generation phylogenetics takes root

(2012) John E. McCormack et al.   MOLECULAR ECOLOGY

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phylogenetic Analysis of the Evolution of Display Behavior in the Neotropical Manakins (Aves: Pipridae)

(2010) Richard O. Prum   ETHOLOGY

A molecular phylogenetic hypothesis for the manakins (Aves: Pipridae)

(2010) Bailey D. McKay et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Phylogeny and phylogenetic classification of the tyrant flycatchers, cotingas, manakins, and their allies (Aves: Tyrannides)

(2009) Jose G. Tello et al.   CLADISTICS

Ecological niches and their evolution among Neotropical manakins (Aves: Pipridae)

(2009) Marina Anciães et al.   JOURNAL OF AVIAN BIOLOGY

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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

Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes)

(2008) Jan Ohlson et al.   ZOOLOGICA SCRIPTA