Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia

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

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

(2016) Mark P. Simmons 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

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

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

(2015) Siavash Mirarab et al.   BIOINFORMATICS

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

(2015) Jed Chou et al.   BMC GENOMICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

The Impact of Missing Data on Species Tree Estimation

(2015) Zhenxiang Xi et al.   MOLECULAR BIOLOGY 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

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

(2015) Richard O. Prum et al.   NATURE

Spectral shifts of mammalian ultraviolet-sensitive pigments (short wavelength-sensitive opsin 1) are associated with eye length and photic niche evolution

(2015) Christopher A. Emerling et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Evolutionary conservation in genes underlying human psychiatric disorders

(2014) Lisa M. Ogawa et al.   Frontiers in Human Neuroscience

Papahu taitapu, gen. et sp. nov., an early Miocene stem odontocete (Cetacea) from New Zealand

(2014) Gabriel Aguirre-Fernández et al.   JOURNAL OF VERTEBRATE PALEONTOLOGY

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

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY 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

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

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

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

Evolution of hantaviruses: Co-speciation with reservoir hosts for more than 100MYR

(2014) Alexander Plyusnin et al.   VIRUS RESEARCH

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

(2013) Georgia Tsagkogeorga et al.   CURRENT BIOLOGY

Making the Impossible Possible: Rooting the Tree of Placental Mammals

(2013) E. C. Teeling et al.   MOLECULAR BIOLOGY AND EVOLUTION

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying localized biases in large datasets: A case study using the avian tree of life

(2013) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

STRAW: Species TRee Analysis Web server

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

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

(2013) Vikas Kumar et al.   PLoS One

Concatenation versus coalescence versus "concatalescence"

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

Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity

(2013) S. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

Origin of land plants using the multispecies coalescent model

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

Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary

(2013) Graham J. Slater   Methods in Ecology and Evolution

Retrophylogenomics Place Tarsiers on the Evolutionary Branch of Anthropoids

(2013) Gerrit Hartig et al.   Scientific Reports

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

(2012) Katrin Nyakatura et al.   BMC BIOLOGY

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Random roots and lineage sorting

(2012) Jeffrey A. Rosenfeld et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenetic blueprint for a modern whale

(2012) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

(2012) Mark S. Springer et al.   PLoS One

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

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

(2011) Jonathan H Geisler et al.   BMC EVOLUTIONARY BIOLOGY

Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes

(2011) Alexandre Hassanin et al.   COMPTES RENDUS BIOLOGIES

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

Genomic data reject the hypothesis of a prosimian primate clade

(2011) Natalie M. Jameson et al.   JOURNAL OF HUMAN EVOLUTION

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

(2011) Ted M. Townsend et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals

(2011) Björn M. Hallström et al.   PLoS One

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

The Oldest and Youngest Records of Afrosoricid Placentals from the Fayum Depression of Northern Egypt

(2010) Erik R. Seiffert   ACTA PALAEONTOLOGICA POLONICA

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences

(2010) Eduardo Eizirik et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

(2010) Huateng Huang et al.   SYSTEMATIC BIOLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Phylogeny and conservation priorities of afrotherian mammals (Afrotheria, Mammalia)

(2010) Matjaž Kuntner et al.   ZOOLOGICA SCRIPTA

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny of the Ferungulata (Mammalia: Laurasiatheria) as determined from phylogenomic data

(2009) Zhuo-cheng Hou et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

(2009) Michael R. McGowen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora

(2009) Ingi Agnarsson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

(2009) H. Nishihara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Radiation of Extant Cetaceans Driven by Restructuring of the Oceans

(2009) Mette E. Steeman et al.   SYSTEMATIC BIOLOGY

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

(2008) Pablo A. Goloboff et al.   CLADISTICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets

(2008) Arjun B. Prasad et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY