A species-level timeline of mammal evolution integrating phylogenomic data (original) (raw)

• Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. Nature 587, 240–245 (2020).
  Article CAS ADS Google Scholar
• Feng, S. et al. Dense sampling of bird diversity increases power of comparative genomics. Nature 587, 252–257 (2020).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Harvey, M. G. et al. The evolution of a tropical biodiversity hotspot. Science 370, 1343–1348 (2020).
  Article CAS PubMed ADS Google Scholar
• dos Reis, M., Donoghue, P. C. J. & Yang, Z. Bayesian molecular clock dating of species divergences in the genomics era. Nat. Rev. Genet. 17, 71–80 (2016).
  Article PubMed Google Scholar
• Meredith, R. W. et al. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. Science 334, 521–524 (2011).
  Article CAS PubMed ADS Google Scholar
• Upham, N. S., Esselstyn, J. A. & Jetz, W. Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLoS Biol. 17, e3000494 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• dos Reis, M. et al. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Biol. Sci. 279, 3491–3500 (2012).
  PubMed PubMed Central Google Scholar
• O’Leary, M. A. et al. The placental mammal ancestor and the post-K-Pg radiation of placentals. Science 339, 662–667 (2013).
  Article PubMed ADS Google Scholar
• dos Reis, M., Donoghue, P. C. & Yang, Z. Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals. Biol. Lett. 10, 20131003 (2014).
  Article PubMed PubMed Central Google Scholar
• Phillips, M. J. Geomolecular dating and the origin of placental mammals. Syst. Biol. 65, 546–557 (2016).
  Article PubMed Google Scholar
• Lewin, H. A. et al. Earth BioGenome Project: sequencing life for the future of life. Proc. Natl Acad. Sci. USA 115, 4325–4333 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Siepel, A. Challenges in funding and developing genomic software: roots and remedies. Genome Biol. 20, 147 (2019).
  Article PubMed PubMed Central Google Scholar
• Faria, N. R. et al. The early spread and epidemic ignition of HIV-1 in human populations. Science 346, 56–61 (2014).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Ramírez-Barahona, S., Sauquet, H. & Magallón, S. The delayed and geographically heterogeneous diversification of flowering plant families. Nat. Ecol. Evol. 4, 1232–1238 (2020).
  Article PubMed Google Scholar
• Whelan, N. V. et al. Ctenophore relationships and their placement as the sister group to all other animals. Nat. Ecol. Evol. 1, 1737–1746 (2017).
  Article PubMed PubMed Central Google Scholar
• Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763–767 (2014).
  Article CAS PubMed ADS Google Scholar
• Jarvis, E. D. et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346, 1320–1331 (2014).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Tao, Q., Tamura, K. & Kumar, S. in The Molecular Evolutionary Clock: Theory and Practice (ed. Ho, S. Y. W.) 197–219 (Springer, 2020).
• Thorne, J. L. & Kishino, H. in Statistical Methods in Molecular Evolution (ed. Nielsen, R.) 235–256 (Springer, 2005).
• Yang, Z. & Rannala, B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23, 212–226 (2006).
  Article CAS PubMed Google Scholar
• Inoue, J., Donoghue, P. C. J. & Yang, Z. The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times. Syst. Biol. 59, 74–89 (2010).
  Article PubMed Google Scholar
• dos Reis, M., Zhu, T. & Yang, Z. The impact of the rate prior on Bayesian estimation of divergence times with multiple Loci. Syst. Biol. 63, 555–565 (2014).
  Article PubMed PubMed Central Google Scholar
• Rannala, B. & Yang, Z. Inferring speciation times under an episodic molecular clock. Syst. Biol. 56, 453–466 (2007).
  Article PubMed Google Scholar
• Springer, M. S., Murphy, W. J., Eizirik, E. & O’Brien, S. J. Placental mammal diversification and the Cretaceous–Tertiary boundary. Proc. Natl Acad. Sci. USA 100, 1056–1061 (2003).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Hasegawa, M., Thorne, J. L. & Kishino, H. Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes Genet. Syst. 78, 267–283 (2003).
  Article CAS PubMed Google Scholar
• Alroy, J. The fossil record of North American mammals: evidence for a Paleocene evolutionary radiation. Syst. Biol. 48, 107–118 (1999).
  Article CAS PubMed Google Scholar
• Benton, M. J. Early origins of modern birds and mammals: Molecules vs. morphology. Bioessays 21, 1043–1051 (1999).
  Article CAS PubMed Google Scholar
• Hunter, J. P. & Janis, C. M. Spiny Norman in the Garden of Eden? Dispersal and early biogeography of Placentalia. J. Mamm. Evol. 13, 89–123 (2006).
  Article Google Scholar
• Luo, Z. X. Transformation and diversification in early mammal evolution. Nature 450, 1011–1019 (2007).
  Article CAS PubMed ADS Google Scholar
• Cooper, A. & Fortey, R. Evolutionary explosions and the phylogenetic fuse. Trends Ecol. Evol. 13, 151–156 (1998).
  Article CAS PubMed Google Scholar
• Archibald, J. D. & Deutschman, D. H. Quantitative analysis of the timing of the origin and diversification of extant placental orders. J. Mamm. Evol. 8, 107–124 (2001).
  Article Google Scholar
• Murphy, W. J., Foley, N. M., Bredemeyer, K. R., Gatesy, J. & Springer, M. S. Phylogenomics and the genetic architecture of the placental mammal radiation. Annu. Rev. Anim. Biosci. 9, 29–53 (2021).
  Article CAS PubMed Google Scholar
• Tarver, J. E. et al. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biol. Evol. 8, 330–344 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, L. et al. Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary. Proc. Natl Acad. Sci. USA 114, E7282–E7290 (2017).
  CAS PubMed PubMed Central Google Scholar
• dos Reis, M. et al. Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case. Syst. Biol. 67, 594–615 (2018).
  Article PubMed PubMed Central Google Scholar
• dos Reis, M. & Yang, Z. The unbearable uncertainty of Bayesian divergence time estimation. J. Syst. Evol. 51, 30–43 (2013).
  Article Google Scholar
• dos Reis, M. & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).
  Article PubMed Google Scholar
• Battistuzzi, F. U., Billing-Ross, P., Paliwal, A. & Kumar, S. Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol. Biol. Evol. 28, 2439–2442 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Donoghue, P. C. J. & Yang, Z. The evolution of methods for establishing evolutionary timescales. Philos. Trans. R. Soc. Lond. B 371, 20160020 (2016).
  Article Google Scholar
• Xie, W., Lewis, P. O., Fan, Y., Kuo, L. & Chen, M.-H. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60, 150–160 (2011).
  Article PubMed Google Scholar
• Thorne, J. L., Kishino, H. & Painter, I. S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647–1657 (1998).
  Article CAS PubMed Google Scholar
• Drummond, A. J., Ho, S. Y. W., Phillips, M. J. & Rambaut, A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, 699–710 (2006).
  Article CAS Google Scholar
• Politis, D. N. & Romano, J. P. The stationary bootstrap. J. Am. Stat. Assoc. 89, 1303–1313 (1994).
  Article MathSciNet MATH Google Scholar
• Nishihara, H., Maruyama, S. & Okada, N. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals. Proc. Natl Acad. Sci. USA 106, 5235–5240 (2009).
  Article CAS PubMed PubMed Central ADS Google Scholar
• Wheeler, T. J. & Eddy, S. R. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487–2489 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Bininda-Emonds, O. R. et al. The delayed rise of present-day mammals. Nature 446, 507–512 (2007).
  Article CAS PubMed ADS Google Scholar
• Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).
  Article CAS PubMed ADS Google Scholar
• Zwart, S. P. The ecological impact of high-performance computing in astrophysics. Nat. Astron. 4, 819–822 (2020).
  Article ADS Google Scholar
• Springer, M. S., Stanhope, M. J., Madsen, O. & de Jong, W. W. Molecules consolidate the placental mammal tree. Trends Ecol. Evol. 19, 430–438 (2004).
  Article PubMed Google Scholar
• Kinsella, R. J. et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database 2011, bar030 (2011).
  Article PubMed PubMed Central Google Scholar
• Löytynoja, A. Phylogeny-aware alignment with PRANK. Methods Mol. Biol. 1079, 155–170 (2014).
  Article PubMed Google Scholar
• Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Springer, M. S. & Gatesy, J. On the importance of homology in the age of phylogenomics. Syst. Biodivers. 16, 210–228 (2018).
  Article Google Scholar
• Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
  Article CAS PubMed Google Scholar
• dos Reis, M. et al. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Curr. Biol. 25, 2939–2950 (2015).
  Article PubMed PubMed Central Google Scholar
• Eddy, S. R. Profile hidden Markov models. Bioinformatics 14, 755–763 (1998).
  Article CAS PubMed Google Scholar
• Löytynoja, A., Vilella, A. J. & Goldman, N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28, 1684–1691 (2012).
  Article PubMed PubMed Central Google Scholar
• Mitchell, K. J. et al. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Mol. Biol. Evol. 31, 2322–2330 (2014).
  Article CAS PubMed Google Scholar
• Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
  Article CAS PubMed Google Scholar
• Hasegawa, M., Kishino, H. & Yano, T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160–174 (1985).
  Article CAS PubMed ADS Google Scholar
• Hasegawa, M., Yano, T.-A. & Kishino, H. A new molecular clock of mitochondrial DNA and the evolution of hominoids. Proc. Japan Acad. B 60, 95–98 (1984).
  Article CAS Google Scholar
• Yang, Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39, 306–314 (1994).
  Article CAS PubMed ADS Google Scholar
• Felsenstein, J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981).
  Article CAS PubMed ADS Google Scholar
• dos Reis, M. & Yang, Z. in Evolutionary Genomics: Statistical and Computational Methods (ed. Anisimova, M.) 309–330 (Springer, 2019).
• Rannala, B., Zhu, T. & Yang, Z. Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference. Mol Biol Evol. 29, 325–335 (2012).
  Article CAS PubMed Google Scholar
• Benton, M. J. et al. Constraints on the timescale of animal evolutionary history. Palaeontol. Electron. 18, 1–106 (2015).
  Google Scholar
• Parham, J. F. et al. Best practices for justifying fossil calibrations. Syst. Biol. 61, 346–359 (2012).
  Article PubMed Google Scholar
• Warnock, R. C. M., Parham, J. F., Joyce, W. G., Lyson, T. R. & Donoghue, P. C. J. Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors. Proc. R. Soc. B 282, 20141013 (2015).
  Article PubMed PubMed Central Google Scholar
• Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Plummer, M., Best, N., Cowles, K. & Vines, K. CODA: convergence diagnosis and output analysis for MCMC. R News 6, 7–11 (2006).
  Google Scholar
• RStan: the R interface to Stan. R package. https://mc-stan.org (Stan Development Team, 2020).
• Puttick, M. N. MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees. Bioinformatics 35, 5321–5322 (2019).
  Article CAS PubMed Google Scholar
• Azzalini, A. The R package ‘sn’: the skew-normal and related distributions such as the skew-t. http://azzalini.stat.unipd.it/SN/ (2019).