Fast Bayesian inference of phylogenies from multiple continuous characters
暂无分享,去创建一个
[1] F. Ronquist,et al. Closing the gap between rocks and clocks using total-evidence dating , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.
[2] Leandro C. S. Assis,et al. Individuals, kinds, phylogeny and taxonomy , 2011, Cladistics : the international journal of the Willi Hennig Society.
[3] P. Palmqvist,et al. A three-dimensional analysis of the morphological evolution and locomotor behaviour of the carnivoran hind limb , 2014, BMC Evolutionary Biology.
[4] Luke J. Harmon,et al. Geiger V2.0: an Expanded Suite of Methods for Fitting Macroevolutionary Models to Phylogenetic Trees , 2014, Bioinform..
[5] T. Stadler. Sampling-through-time in birth-death trees. , 2010, Journal of theoretical biology.
[6] David Penny,et al. Evolutionary biology: Relativity for molecular clocks , 2005, Nature.
[7] Daniel L. Ayres,et al. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.
[8] Csaba Pal,et al. Differential impact of simultaneous migration on coevolving hosts and parasites , 2007, BMC Evolutionary Biology.
[9] L. Garamszegi,et al. Effects of sample size and intraspecific variation in phylogenetic comparative studies: a meta‐analytic review , 2010, Biological reviews of the Cambridge Philosophical Society.
[10] D. Adams,et al. A METHOD FOR ASSESSING PHYLOGENETIC LEAST SQUARES MODELS FOR SHAPE AND OTHER HIGH‐DIMENSIONAL MULTIVARIATE DATA , 2014, Evolution; international journal of organic evolution.
[11] Emmanuel F. A. Toussaint,et al. Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths , 2019, Proceedings of the National Academy of Sciences.
[12] P. Joyce,et al. A NOVEL COMPARATIVE METHOD FOR IDENTIFYING SHIFTS IN THE RATE OF CHARACTER EVOLUTION ON TREES , 2011, Evolution; international journal of organic evolution.
[13] Ming-Hui Chen,et al. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. , 2011, Systematic biology.
[14] Mark N. Puttick,et al. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data , 2016, Biology Letters.
[15] Michael S. Y. Lee,et al. Morphological Phylogenetics in the Genomic Age , 2015, Current Biology.
[16] James H. Degnan,et al. GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS , 2005, Evolution; international journal of organic evolution.
[17] F. Rohlf,et al. Extensions of the Procrustes Method for the Optimal Superimposition of Landmarks , 1990 .
[18] Laura Kubatko,et al. Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. , 2014, Journal of theoretical biology.
[19] Alexei J. Drummond,et al. Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation , 2011, Systematic biology.
[20] J. Stachowicz,et al. Trait vs. phylogenetic diversity as predictors of competition and community composition in herbivorous marine amphipods. , 2013, Ecology letters.
[21] P. Gunz,et al. A brief review of shape, form, and allometry in geometric morphometrics, with applications to human facial morphology , 2013 .
[22] Alan Turner,et al. The Big Cats and Their Fossil Relatives: An Illustrated Guide to Their Evolution and Natural History , 1997 .
[23] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[24] J. Welch,et al. Molecular dates for the "cambrian explosion": the influence of prior assumptions. , 2005, Systematic biology.
[25] M. O'Leary,et al. Parsimony Analysis of Total Evidence from Extinct and Extant Taxa and the Cetacean-Artiodactyl Question (Mammalia, Ungulata)☆ , 1999 .
[26] Hong-Wei Xue,et al. Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling , 2016, Nature Communications.
[27] T. F. Hansen,et al. TRANSLATING BETWEEN MICROEVOLUTIONARY PROCESS AND MACROEVOLUTIONARY PATTERNS: THE CORRELATION STRUCTURE OF INTERSPECIFIC DATA , 1996, Evolution; international journal of organic evolution.
[28] P. David,et al. Diversity spurs diversification in ecological communities , 2017, Nature Communications.
[29] Andreas R. Pfenning,et al. Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.
[30] H. Ellegren,et al. The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds , 2015, PLoS biology.
[31] A. Turner,et al. FIRST KNOWN COMPLETE SKULLS OF THE SCIMITAR-TOOTHED CAT MACHAIRODUS APHANISTUS (FELIDAE, CARNIVORA) FROM THE SPANISH LATE MIOCENE SITE OF BATALLONES-1 , 2004 .
[32] Andrew P. Martin,et al. Body size, metabolic rate, generation time, and the molecular clock. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[33] D. Muzny,et al. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability , 2019, bioRxiv.
[34] Xing Xu,et al. Pennaraptoran Theropod Dinosaurs Past Progress and New Frontiers , 2020, Bulletin of the American Museum of Natural History.
[35] Matthew W. Hahn,et al. Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time. , 2016, Molecular biology and evolution.
[36] C. Parins-Fukuchi. Bayesian placement of fossils on phylogenies using quantitative morphometric data , 2018, Evolution; international journal of organic evolution.
[37] Xiaoming Wang,et al. Phylogenetic Systematics of the North American Fossil Caninae (Carnivora: Canidae) , 2009 .
[38] R. Kümmerli,et al. Quorum sensing triggers the stochastic escape of individual cells from Pseudomonas putida biofilms , 2015, Nature Communications.
[39] M. Newton. Approximate Bayesian-inference With the Weighted Likelihood Bootstrap , 1994 .
[40] Sebastián Duchêne,et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis , 2019, PLoS computational biology.
[41] D. Silvestro,et al. Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors , 2018, Systematic biology.
[42] Matthew W. Hahn,et al. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation , 2016, PLoS biology.
[43] J. Skilling. Nested sampling for general Bayesian computation , 2006 .
[44] K. Strimmer,et al. Statistical Applications in Genetics and Molecular Biology A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics , 2011 .
[45] H. Morlon,et al. Accelerated body size evolution during cold climatic periods in the Cenozoic , 2017, Proceedings of the National Academy of Sciences.
[46] A. Lister. The role of behaviour in adaptive morphological evolution of African proboscideans , 2013, Nature.
[47] J. Gower. Generalized procrustes analysis , 1975 .
[48] Md. Shamsuzzoha Bayzid,et al. Whole-genome analyses resolve early branches in the tree of life of modern birds , 2014, Science.
[49] F. K. Mendes,et al. A multi‐platform package for the analysis of intra‐ and interspecific trait evolution , 2020, Methods in Ecology and Evolution.
[50] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.
[51] H. Poinar,et al. Ancient DNA: Do It Right or Not at All , 2000, Science.
[52] Chao Zhang,et al. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees , 2018, BMC Bioinformatics.
[53] M. Donoghue,et al. Rates of Molecular Evolution Are Linked to Life History in Flowering Plants , 2008, Science.
[54] Michael J. Landis,et al. Pulsed evolution shaped modern vertebrate body sizes , 2017, Proceedings of the National Academy of Sciences.
[55] R. Bleiweiss. Slow rate of molecular evolution in high-elevation hummingbirds. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[56] A. Goswami,et al. The macroevolutionary consequences of phenotypic integration: from development to deep time , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.
[57] H. Kishino,et al. Estimation of Divergence Times from Molecular Sequence Data , 2005 .
[58] S. O’Brien,et al. Phylogeny and evolution of cats (Felidae) , 2010 .
[59] T. F. Hansen. STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION , 1997, Evolution; international journal of organic evolution.
[60] M. Pagel,et al. Speciation as an active force in promoting genetic evolution. , 2010, Trends in ecology & evolution.
[61] Ming-Hui Chen,et al. Choosing among Partition Models in Bayesian Phylogenetics , 2010, Molecular biology and evolution.
[62] Liam J. Revell,et al. phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .
[63] E. Hook,et al. Paternal age. , 1983, Human genetics.
[64] M. O'Leary. Parsimony Analysis of Total Evidence from Extinct and Extant Taxa and the Cetacean‐Artiodactyl Question (Mammalia, Ungulata) , 1999, Cladistics : the international journal of the Willi Hennig Society.
[65] W. Wheeler,et al. Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology , 2007, Cladistics : the international journal of the Willi Hennig Society.
[66] A. Brower. Comment on "Molecular Phylogenies Link Rates of Evolution and Speciation" (II) , 2004, Science.
[67] S. Wright,et al. An Analysis of Variability in Number of Digits in an Inbred Strain of Guinea Pigs. , 1934, Genetics.
[68] Mark Pagel,et al. Molecular Phylogenies Link Rates of Evolution and Speciation , 2003, Science.
[69] D. Adams,et al. Multivariate Phylogenetic Comparative Methods: Evaluations, Comparisons, and Recommendations , 2018, Systematic biology.
[70] D. Labie,et al. Molecular Evolution , 1991, Nature.
[71] D. Adams,et al. Are rates of species diversification correlated with rates of morphological evolution? , 2009, Proceedings of the Royal Society B: Biological Sciences.
[72] Tanja Stadler,et al. Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration , 2014, PLoS Comput. Biol..
[73] Joseph Felsenstein,et al. Using the quantitative genetic threshold model for inferences between and within species , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.
[74] Leonard J. Gray,et al. Three Dimensional Analysis , 2008 .
[75] P. D. Polly,et al. A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates , 2019, Evolution; international journal of organic evolution.
[76] A Bayesian Approach for Inferring the Impact of a Discrete Character on Rates of Continuous-Character Evolution in the Presence of Background-Rate Variation , 2019, Systematic biology.
[77] P. Goloboff,et al. Continuous characters analyzed as such , 2006, Cladistics : the international journal of the Willi Hennig Society.
[78] Seraina Klopfstein,et al. A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera , 2012, Systematic biology.
[79] L. Gillman,et al. The road from Santa Rosalia: A faster tempo of evolution in tropical climates , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[80] J. Cheverud. Genetics and analysis of quantitative traits , 1999 .
[81] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[82] Matthew W. Hahn,et al. Why Concatenation Fails Near the Anomaly Zone , 2018, Systematic biology.
[83] L. Pauling,et al. Molecules as documents of evolutionary history. , 1965, Journal of theoretical biology.
[84] Ziheng Yang,et al. Computational Molecular Evolution , 2006 .
[85] C. Parins-Fukuchi. Use of Continuous Traits Can Improve Morphological Phylogenetics , 2017, bioRxiv.
[86] J. Felsenstein,et al. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.
[87] M. Lynch,et al. Genetics and Analysis of Quantitative Traits , 1996 .
[88] Christopher,et al. Best Practices for Justifying Fossil Calibrations , 2011, Systematic Biology.
[89] Seth Kaufman,et al. MorphoBank: phylophenomics in the “cloud” , 2011, Cladistics : the international journal of the Willi Hennig Society.
[90] A. King,et al. Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution , 2004, The American Naturalist.
[91] RICHARD H. Thomas,et al. Problems of reproducibility – does geologically ancient DNA survive in amber–preserved insects? , 1997, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[92] Bryan Kolaczkowski,et al. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous , 2004, Nature.
[93] T. Garland,et al. Within-species variation and measurement error in phylogenetic comparative methods. , 2007, Systematic biology.
[94] Michael S. Barker,et al. A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys. , 2013, American journal of botany.
[95] David L. Swofford,et al. Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics , 1997, Journal of Mammalian Evolution.
[96] Simon Whelan,et al. Statistical Methods in Molecular Evolution , 2005 .
[97] A. Ozga,et al. Dire wolves were the last of an ancient New World canid lineage , 2021, Nature.
[98] A. Meyer,et al. Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. , 2000, The Journal of experimental zoology.
[99] Carnivore Behavior, Ecology, and Evolution , 1989 .
[100] T. F. Hansen,et al. Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. , 2012, Systematic biology.
[101] J. Felsenstein,et al. EVOLUTIONARY TREES FROM GENE FREQUENCIES AND QUANTITATIVE CHARACTERS: FINDING MAXIMUM LIKELIHOOD ESTIMATES , 1981, Evolution; international journal of organic evolution.
[102] J. Huelsenbeck,et al. The fossilized birth–death process for coherent calibration of divergence-time estimates , 2013, Proceedings of the National Academy of Sciences.
[103] D. Robinson,et al. Comparison of phylogenetic trees , 1981 .
[104] S. Ho,et al. Elevated substitution rates estimated from ancient DNA sequences , 2007, Biology Letters.
[105] A. Kluge. A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes) , 1989 .
[106] Matthew W. Pennell,et al. Rethinking phylogenetic comparative methods. , 2018, Systematic biology.
[107] H. Philippe,et al. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. , 2004, Molecular biology and evolution.
[108] Seán G. Brady,et al. The history of early bee diversification based on five genes plus morphology , 2006, Proceedings of the National Academy of Sciences.
[109] Sebastián Duchêne,et al. Molecular‐clock methods for estimating evolutionary rates and timescales , 2014, Molecular ecology.
[110] Alex Wong,et al. Evolution of protein-coding genes in Drosophila. , 2008, Trends in genetics : TIG.
[111] Gonzalo Giribet,et al. Arthropod phylogeny based on eight molecular loci and morphology , 2001, Nature.
[112] H. Morlon,et al. Assessing the causes of diversification slowdowns: temperature-dependent and diversity-dependent models receive equivalent support. , 2019, Ecology letters.
[113] N. Solounias,et al. The Hyaenidae: Taxonomy, Systematics and Evolution , 1991 .
[114] H. Philippe,et al. Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough , 2011, PLoS biology.
[115] R. Lanfear,et al. Watching the clock: studying variation in rates of molecular evolution between species. , 2010, Trends in ecology & evolution.
[116] Ziheng Yang,et al. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. , 2003, Genetics.
[117] Ziheng Yang,et al. Exploring uncertainty in the calibration of the molecular clock , 2012, Biology Letters.
[118] J. L. Gittleman,et al. EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA , 2010, Evolution; international journal of organic evolution.
[119] David Mandzuk,et al. Exploring Uncertainty , 2018, Navigating Uncertainty.
[120] Michael J. Sanderson,et al. TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD , 2006, Evolution; international journal of organic evolution.
[121] J. Schraiber,et al. A multispecies coalescent model for quantitative traits , 2018, eLife.
[122] P. Lewis. A likelihood approach to estimating phylogeny from discrete morphological character data. , 2001, Systematic biology.
[123] Tanja Stadler,et al. Dating phylogenies with sequentially sampled tips. , 2013, Systematic biology.
[124] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[125] W. Wheeler,et al. Phylogenetic relationships within the Cimicomorpha (Hemiptera: Heteroptera): a total‐evidence analysis , 2009 .
[126] M. Bendall,et al. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). , 2014, Systematic biology.
[127] C. Witt,et al. Comment on "Molecular Phylogenies Link Rates of Evolution and Speciation" (I) , 2004, Science.
[128] Mark N. Puttick,et al. Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al. , 2018 .
[129] Alexei J Drummond,et al. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. , 2005, Molecular biology and evolution.
[130] W. Wheeler,et al. PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE) , 2006 .
[131] S. Blomberg,et al. Beyond Brownian Motion and the Ornstein-Uhlenbeck Process: Stochastic Diffusion Models for the Evolution of Quantitative Characters , 2020, The American Naturalist.
[132] A. Goswami,et al. The evolution of orbit orientation and encephalization in the Carnivora (Mammalia) , 2009, Journal of anatomy.
[133] L. Werdelin. Carnivoran ecomorphology: a phylogenetic perspective , 1996 .
[134] F. Ayala,et al. This paper was presented at a colloquium entitled ‘ ‘ Genetics and the Origin of Species , ’ ’ organized , 1997 .
[135] Tanja Stadler,et al. Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts. , 2019, Theoretical population biology.
[136] Eric W Goolsby,et al. Likelihood-Based Parameter Estimation for High-Dimensional Phylogenetic Comparative Models: Overcoming the Limitations of "Distance-Based" Methods. , 2016, Systematic biology.
[137] G. Merceron,et al. mvmorph: an r package for fitting multivariate evolutionary models to morphometric data , 2015 .
[138] J. Leeuw,et al. More on Multidimensional Scaling and Unfolding in R: smacof Version 2 , 2022, J. Stat. Softw..
[139] L. O.,et al. A Likelihood Approach to Estimating Phylogeny from Discrete Morphological Character Data , 2002 .
[140] S. Ho,et al. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. , 2009, Systematic biology.
[141] H. Morlon,et al. Uncovering Higher‐Taxon Diversification Dynamics from Clade Age and Species‐Richness Data , 2016, Systematic biology.
[142] Robert P. Freckleton,et al. Fast likelihood calculations for comparative analyses , 2012 .
[143] H. Ross,et al. Latitude, elevation and the tempo of molecular evolution in mammals , 2009, Proceedings of the Royal Society B: Biological Sciences.
[144] D. Soltis,et al. Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets. , 2007, Systematic biology.
[145] Anjali Goswami,et al. Bayesian Estimation of Species Divergence Times Using Correlated Quantitative Characters , 2018, bioRxiv.
[146] L. Harmon,et al. A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data , 2014, bioRxiv.
[147] T. Stadler,et al. Parallel Likelihood Calculation for Phylogenetic Comparative Models: the SPLITT C++ Library , 2018, bioRxiv.
[148] Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales. , 2021, Systematic biology.
[149] Daniel S. Caetano,et al. ratematrix: An R package for studying evolutionary integration among several traits on phylogenetic trees , 2017 .
[150] E. Hagelberg,et al. Ancient DNA: the first three decades , 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.
[151] D. Silvestro,et al. Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach. , 2016, Systematic biology.
[152] Luke J. Harmon,et al. A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data , 2014 .
[153] Claudia R. Solís-Lemus,et al. Phylogenetic comparative methods on phylogenetic networks with reticulations , 2017, bioRxiv.
[154] H. Morlon. Phylogenetic approaches for studying diversification. , 2014, Ecology letters.
[155] E. Rayfield,et al. A virtual world of paleontology. , 2014, Trends in ecology & evolution.
[156] J. A. Fuentes,et al. A phylogenetic test of the Red Queen Hypothesis: Outcrossing and parasitism in the Nematode phylum , 2015, Evolution; international journal of organic evolution.
[157] Matthew W. Hahn,et al. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression , 2020, bioRxiv.
[158] H. Philippe,et al. Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.
[159] D. Field,et al. Genomic Signature of an Avian Lilliput Effect across the K‐Pg Extinction , 2018, Systematic biology.
[160] J. Felsenstein. Phylogenies and the Comparative Method , 1985, The American Naturalist.
[161] Simon Whelan,et al. Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable. , 2020, Systematic biology.
[162] R. Bouckaert,et al. Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling , 2017, Systematic biology.
[163] A. Pyron,et al. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. , 2011, Systematic biology.
[164] Matthew W. Hahn,et al. Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression , 2020, PLoS biology.
[165] G. Slater. Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution , 2015, Proceedings of the National Academy of Sciences.
[166] Andrew Rambaut,et al. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies , 2000, Bioinform..
[167] Tanja Stadler,et al. Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins , 2015, Systematic biology.
[168] P. Goloboff,et al. Morphological Data Sets Fit a Common Mechanism Much More Poorly than DNA Sequences and Call Into Question the Mkv Model , 2018, Systematic biology.
[169] A. Rodrigo,et al. Measurably evolving populations , 2003 .
[170] N. M. Koch,et al. A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data. , 2020, Systematic biology.
[171] François Balloux,et al. Inferences from tip‐calibrated phylogenies: a review and a practical guide , 2016, Molecular ecology.
[172] P. Christiansen. Phylogeny of the sabertoothed felids (Carnivora: Felidae: Machairodontinae) , 2013, Cladistics : the international journal of the Willi Hennig Society.
[173] Emmanuel Paradis,et al. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..
[174] L. Bromham. Why do species vary in their rate of molecular evolution? , 2009, Biology Letters.
[175] T. Quental,et al. Arboreality constrains morphological evolution but not species diversification in vipers , 2017, Proceedings of the Royal Society B: Biological Sciences.
[176] A. Cooper,et al. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence , 2018, Systematic biology.
[177] Luke J. Harmon,et al. GEIGER: investigating evolutionary radiations , 2008, Bioinform..
[178] E. Goldberg,et al. TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION , 2012, Evolution; international journal of organic evolution.
[179] J. Huelsenbeck,et al. Bayesian phylogenetic analysis of combined data. , 2004, Systematic biology.
[180] Michael J. Landis,et al. RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language , 2016, Systematic biology.
[181] Matthew W. Hahn,et al. Irrational exuberance for resolved species trees , 2016, Evolution; international journal of organic evolution.
[182] E. Seiffert. A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence , 2007, BMC Evolutionary Biology.
[183] C. Griswold,et al. Total evidence analysis of the phylogenetic relationships of Lycosoidea spiders (Araneae, Entelegynae) , 2015, Invertebrate Systematics.
[184] Pierre Alquier,et al. Approximate Bayesian Inference , 2020, Entropy.