A species-level timeline of mammal evolution integrating phylogenomic data

[1]  W. Murphy,et al.  Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. , 2020, Annual review of animal biosciences.

[2]  Simon Portegies Zwart,et al.  The ecological impact of high-performance computing in astrophysics , 2020, Nature Astronomy.

[3]  S. Magallón,et al.  The delayed and geographically heterogeneous diversification of flowering plant families , 2020, Nature Ecology & Evolution.

[4]  Matthew W. Pennell,et al.  Extant timetrees are consistent with a myriad of diversification histories , 2020, Nature.

[5]  Mark N. Puttick,et al.  MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees , 2019, Bioinform..

[6]  W. Jetz,et al.  Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation , 2019, PLoS biology.

[7]  A. Siepel Challenges in funding and developing genomic software: roots and remedies , 2019, Genome Biology.

[8]  M. Suchard,et al.  Posterior summarisation in Bayesian phylogenetics using Tracer , 2022 .

[9]  Juan Carlos Castilla-Rubio,et al.  Earth BioGenome Project: Sequencing life for the future of life , 2018, Proceedings of the National Academy of Sciences.

[10]  John Gatesy,et al.  On the importance of homology in the age of phylogenomics , 2018 .

[11]  Ziheng Yang,et al.  Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case , 2017, bioRxiv.

[12]  P. Williams,et al.  Ctenophore relationships and their placement as the sister group to all other animals , 2017, Nature Ecology & Evolution.

[13]  Yu Wang,et al.  Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary , 2017, Proceedings of the National Academy of Sciences.

[14]  Philip C J Donoghue,et al.  The evolution of methods for establishing evolutionary timescales , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[15]  M. Phillips Geomolecular Dating and the Origin of Placental Mammals. , 2016, Systematic biology.

[16]  Raymond J. Moran,et al.  The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference , 2016, Genome biology and evolution.

[17]  Ziheng Yang,et al.  Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales , 2015, Current Biology.

[18]  J. Vinther,et al.  Constraints on the timescale of animal evolutionary history , 2015 .

[19]  P. Donoghue,et al.  Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors , 2015, Proceedings of the Royal Society B: Biological Sciences.

[20]  Md. Shamsuzzoha Bayzid,et al.  Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.

[21]  Thomas K. F. Wong,et al.  Phylogenomics resolves the timing and pattern of insect evolution , 2014, Science.

[22]  M. Suchard,et al.  The early spread and epidemic ignition of HIV-1 in human populations , 2014, Science.

[23]  M. Meyer,et al.  Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. , 2014, Molecular biology and evolution.

[24]  Ziheng Yang,et al.  The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci , 2014, Systematic biology.

[25]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[26]  Ziheng Yang,et al.  Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals , 2014, Biology Letters.

[27]  Ari Löytynoja,et al.  Phylogeny-aware alignment with PRANK. , 2014, Methods in molecular biology.

[28]  Sean R. Eddy,et al.  nhmmer: DNA homology search with profile HMMs , 2013, Bioinform..

[29]  Andrea L. Cirranello,et al.  The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals , 2013, Science.

[30]  Ziheng Yang,et al.  The unbearable uncertainty of Bayesian divergence time estimation , 2012 .

[31]  Masami Hasegawa,et al.  Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny , 2012, Proceedings of the Royal Society B: Biological Sciences.

[32]  Albert J. Vilella,et al.  Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm , 2012, Bioinform..

[33]  Christopher,et al.  Best Practices for Justifying Fossil Calibrations , 2011, Systematic biology.

[34]  Tianqi Zhu,et al.  Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. , 2012, Molecular biology and evolution.

[35]  Sudhir Kumar,et al.  Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. , 2011, Molecular biology and evolution.

[36]  Syed Haider,et al.  Ensembl BioMarts: a hub for data retrieval across taxonomic space , 2011, Database J. Biol. Databases Curation.

[37]  Ziheng Yang,et al.  Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. , 2011, Molecular biology and evolution.

[38]  Ming-Hui Chen,et al.  Improving marginal likelihood estimation for Bayesian phylogenetic model selection. , 2011, Systematic biology.

[39]  Philip C J Donoghue,et al.  The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. , 2010, Systematic biology.

[40]  Shigenori Maruyama,et al.  Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals , 2009, Proceedings of the National Academy of Sciences.

[41]  Zhe‐Xi Luo,et al.  Transformation and diversification in early mammal evolution , 2007, Nature.

[42]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[43]  Ziheng Yang,et al.  Inferring speciation times under an episodic molecular clock. , 2007, Systematic biology.

[44]  Kate E. Jones,et al.  The delayed rise of present-day mammals , 1990, Nature.

[45]  C. Janis,et al.  Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia , 2006, Journal of Mammalian Evolution.

[46]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[47]  M. Plummer,et al.  CODA: convergence diagnosis and output analysis for MCMC , 2006 .

[48]  Ziheng Yang,et al.  Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. , 2006, Molecular biology and evolution.

[49]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[50]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[51]  M. Stanhope,et al.  Molecules consolidate the placental mammal tree. , 2004, Trends in ecology & evolution.

[52]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[53]  D. Deutschman,et al.  Quantitative Analysis of the Timing of the Origin and Diversification of Extant Placental Orders , 2001, Journal of Mammalian Evolution.

[54]  Ziheng Yang Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[55]  H. Kishino,et al.  Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. , 2003, Genes & genetic systems.

[56]  S. O’Brien,et al.  Placental mammal diversification and the Cretaceous–Tertiary boundary , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[57]  M. Benton,et al.  Early origins of modern birds and mammals: molecules vs. morphology. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[58]  J. Alroy The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. , 1999, Systematic biology.

[59]  H. Kishino,et al.  Estimating the rate of evolution of the rate of molecular evolution. , 1998, Molecular biology and evolution.

[60]  A. Cooper,et al.  Evolutionary explosions and the phylogenetic fuse. , 1998, Trends in ecology & evolution.

[61]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[62]  Joseph P. Romano,et al.  The stationary bootstrap , 1994 .

[63]  H. Kishino,et al.  A New Molecular Clock of Mitochondrial DNA and the Evolution of Hominoids , 1984 .