A species-level timeline of mammal evolution integrating phylogenomic data
暂无分享,去创建一个
Asif U. Tamuri | Ziheng Yang | M. dos Reis | P. Donoghue | R. Asher | F. F. Nascimento | Sandra Álvarez-Carretero | Emily Carlisle | Matteo Battini | Emily M. Carlisle | Mario dos Reis
[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 .