Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)

A phylogenomic rodent tree reveals the repeated evolution of masseter architectures

(2019) Mark T. Swanson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Unraveling Deep Branches of the Sigmodontinae Tree (Rodentia: Cricetidae) in Eastern South America

(2018) Pablo R. Gonçalves et al.   JOURNAL OF MAMMALIAN EVOLUTION

How many species of mammals are there?

(2018) Connor J Burgin et al.   JOURNAL OF MAMMALOGY

Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements

(2018) Princess S. Gilbert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

When did anoles diverge? An analysis of multiple dating strategies

(2018) Cristian Román-Palacios et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

(2018) Stephen A. Smith et al.   PLoS One

The Role of Geography in Adaptive Radiation

(2018) John J. Schenk et al.   AMERICAN NATURALIST

Tracing the diversification history of a Neogene rodent invasion into South America

(2018) Renan Maestri et al.   ECOGRAPHY

Impacts Of Inference Method And Dataset Filtering On Phylogenomic Resolution In A Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)

(2018) Bryan S McLean et al.   SYSTEMATIC BIOLOGY

Rodent systematics in an age of discovery: recent advances and prospects

(2018) Guillermo D’Elía et al.   JOURNAL OF MAMMALOGY

The ecology of a continental evolutionary radiation: Is the radiation of sigmodontine rodents adaptive?

(2017) Renan Maestri et al.   EVOLUTION

Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

(2017) Jacob A. Esselstyn et al.   Genome Biology and Evolution

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

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

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

(2015) Brant C. Faircloth   BIOINFORMATICS

The influence of ecological and geographical context in the radiation of Neotropical sigmodontine rodents

(2015) Andrés Parada et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary affinities of the ‘Lost World’ mouse suggest a late Pliocene connection between the Guiana and Brazilian shields

(2015) Yuri L. R. Leite et al.   JOURNAL OF BIOGEOGRAPHY

Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents

(2015) Yuri Kimura et al.   Scientific Reports

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Assignment of Calibration Information to Deeper Phylogenetic Nodes is More Effective in Obtaining Precise and Accurate Divergence Time Estimates

(2014) Beatriz Mello et al.   Evolutionary Bioinformatics

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of calibration and clock-model choice on molecular estimates of divergence times

(2014) Sebastián Duchêne et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

In the Wake of Invasion: Tracing the Historical Biogeography of the South American Cricetid Radiation (Rodentia, Sigmodontinae)

(2014) Rafael N. Leite et al.   PLoS One

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Sigmodontine rodents diversified in South America prior to the complete rise of the Panamanian Isthmus

(2013) Júlio F. Vilela et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY 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

Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents

(2013) John J. Schenk et al.   SYSTEMATIC BIOLOGY

A phylogenetic appraisal of Sigmodontinae (Rodentia, Cricetidae) with emphasis on phyllotine genera: systematics and biogeography

(2013) Jorge Salazar-Bravo et al.   ZOOLOGICA SCRIPTA

A glimpse on the pattern of rodent diversification: a phylogenetic approach

(2012) Pierre-Henri Fabre et al.   BMC EVOLUTIONARY BIOLOGY

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

(2012) Andrés Parada et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini

(2009) Stephan Koblmüller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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