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Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open accessAbstract
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 27,843
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts199 · Cited by 20,027
APE: analyses of phylogenetics and evolution in R language
Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 11,335
Creating the CIPRES Science Gateway for inference of large phylogenetic trees
Miller, M. A., Pfeiffer, W., & Schwartz, T. (2010) · 2010 Gateway Computing Environments Workshop (GCE) · doi:10.1109/gce.2010.5676129 · Cited by 11,228
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 10,063
Lanfear, R., Calcott, B., Ho, S. Y. W., & Guindon, S. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss020 · Cited by 5,732
Mammal Species of the World: A Taxonomic and Geographic Reference
Schmid, R., Wilson, D. E., & Reeder, D. M. (1993) · Taxon · doi:10.2307/1223169 · Cited by 5,386
Species diversity in space and time
(1996) · Choice Reviews Online · doi:10.5860/choice.33-2720 · Cited by 4,573
Defaunation in the Anthropocene
Dirzo, R., Young, H. S., Galetti, M., Ceballos, G., Isaac, N. J. B., & Collen, B. (2014) · Science · doi:10.1126/science.1251817 · Cited by 4,474
The global diversity of birds in space and time
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012) · Nature · doi:10.1038/nature11631 · Cited by 3,934
Self-citationSpecies Diversity in Space and Time
Rosenzweig, M. L. (1995) · doi:10.1017/cbo9780511623387 · Cited by 3,690
The biodiversity of species and their rates of extinction, distribution, and protection
Pimm, S. L., Jenkins, C. N., Abell, R., Brooks, T. M., Gittleman, J. L., Joppa, L. N., Raven, P. H., Roberts, C. M., & Sexton, J. O. (2014) · Science · doi:10.1126/science.1246752 · Cited by 3,542
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1195 · Cited by 3,261
Ceballos, G., Ehrlich, P. R., & Dirzo, R. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1704949114 · Cited by 2,663
Cellular Scaling Rules for the Brains of Marsupials: Not as “Primitive” as Expected
Dos Santos, S. E., Porfirio, J., da Cunha, F. B., Manger, P. R., Tavares, W., Pessoa, L., Raghanti, M. A., Sherwood, C. C., & Herculano-Houzel, S. (2017) · Brain, Behavior and Evolution · doi:10.1159/000452856 · Cited by 2,642
A phylogenomic study of birds reveals their evolutionary history
Hackett, S. J., Kimball, R. T., Reddy, S., Bowie, R. C. K., Braun, E. L., Braun, M. J., Chojnowski, J. L., Cox, W. A., Han, K.-L., Harshman, J., et al. (2008) · Science · doi:10.1126/science.1157704 · Cited by 2,125
The delayed rise of present-day mammals
Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2007) · Nature · doi:10.1038/nature05634 · Cited by 2,082
THE MAJOR FEATURES OF EVOLUTION
Olson, E. C. (1954) · Evolution · doi:10.1111/j.1558-5646.1954.tb00114.x · Cited by 2,026
Wilman, H., Belmaker, J., Simpson, J., de la Rosa, C., Rivadeneira, M. M., & Jetz, W. (2014) · Ecology · doi:10.1890/13-1917.1 · Cited by 1,994
Self-citation(2005) · Applying Evolutionary Archaeology · doi:10.1007/0-306-47468-9_7 · Cited by 1,644
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
Pyron, R., Burbrink, F. T., & Wiens, J. J. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-93 · Cited by 1,641
Mitochondrial DNA sequences of primates: tempo and mode of evolution
Brown, W. M., Prager, E. M., Wang, A., & Wilson, A. C. (1982) · Journal of Molecular Evolution · doi:10.1007/bf01734101 · Cited by 1,554
Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification
Meredith, R. W., Janečka, J. E., Gatesy, J., Ryder, O. A., Fisher, C. A., Teeling, E. C., Goodbla, A., Eizirik, E., Simão, T. L. L., Stadler, T., et al. (2011) · Science · doi:10.1126/science.1211028 · Cited by 1,464
Federhen, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1178 · Cited by 1,436 · cited 28×
“NCBI, National Center for Biotechnology Information.”
BackgroundMethodInfluentialMoving in the Anthropocene: Global reductions in terrestrial mammalian movements
Tucker, M. A., Böhning-Gaese, K., Fagan, W. F., Fryxell, J. M., Van Moorter, B., Alberts, S. C., Ali, A. H., Allen, A. M., Attias, N., Avgar, T., et al. (2018) · Science · doi:10.1126/science.aam9712 · Cited by 1,281
The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals
O'Leary, M. A., Bloch, J. I., Flynn, J. J., Gaudin, T. J., Giallombardo, A., Giannini, N. P., Goldberg, S. L., Kraatz, B. P., Luo, Z.-X., Meng, J., et al. (2013) · Science · doi:10.1126/science.1229237 · Cited by 1,196
How many species of mammals are there?
Burgin, C. J., Colella, J. P., Kahn, P. L., & Upham, N. S. (2018) · Journal of Mammalogy · doi:10.1093/jmammal/gyx147 · Cited by 1,168
Self-citationComputational Molecular Evolution
Yang, Z. (2006) · doi:10.1093/acprof:oso/9780198567028.001.0001 · Cited by 1,148
Mammals on the EDGE: Conservation Priorities Based on Threat and Phylogeny
Isaac, N. J. B., Turvey, S. T., Collen, B., Waterman, C., & Baillie, J. E. M. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000296 · Cited by 1,109
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
Rabosky, D. L. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089543 · Cited by 1,090
Tree of Life Reveals Clock-Like Speciation and Diversification
Hedges, S. B., Marin, J., Suleski, M., Paymer, M., & Kumar, S. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv037 · Cited by 972
A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera
Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D. L., & Rasnitsyn, A. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys058 · Cited by 930
Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times
Ho, S. Y. W., & Phillips, M. J. (2009) · Systematic Biology · doi:10.1093/sysbio/syp035 · Cited by 887
The fossilized birth-death process for coherent calibration of divergence-time estimates
Heath, T. A., Huelsenbeck, J. P., & Stadler, T. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319091111 · Cited by 834
Potential Applications and Pitfalls of Bayesian Inference of Phylogeny
Huelsenbeck, J. P., Larget, B., Miller, R. E., & Ronquist, F. (2002) · Systematic Biology · doi:10.1080/10635150290102366 · Cited by 812
Best Practices for Justifying Fossil Calibrations
Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, T. D., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. G., Ksepka, D. T., et al. (2012) · Systematic Biology · doi:10.1093/sysbio/syr107 · Cited by 780
Missing Data, Incomplete Taxa, and Phylogenetic Accuracy
Wiens, J. J. (2003) · Systematic Biology · doi:10.1080/10635150390218330 · Cited by 691
Jetz, W., & Pyron, R. A. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0515-5 · Cited by 607
Self-citationGlobal priorities for an effective information basis of biodiversity distributions
Meyer, C., Kreft, H., Guralnick, R., & Jetz, W. (2015) · Nature Communications · doi:10.1038/ncomms9221 · Cited by 595
Self-citationRabosky, D. L. (2010) · Evolution · doi:10.1111/j.1558-5646.2009.00926.x · Cited by 589
Fritz, S. A., Bininda‐Emonds, O. R. P., & Purvis, A. (2009) · Ecology Letters · doi:10.1111/j.1461-0248.2009.01307.x · Cited by 585
A general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546
A Jurassic eutherian mammal and divergence of marsupials and placentals
Luo, Z.-X., Yuan, C.-X., Meng, Q.-J., & Ji, Q. (2011) · Nature · doi:10.1038/nature10291 · Cited by 541
Transformation and diversification in early mammal evolution
Luo, Z.-X. (2007) · Nature · doi:10.1038/nature06277 · Cited by 540
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., & Yang, Z. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2012.0683 · Cited by 526
Extant timetrees are consistent with a myriad of diversification histories
Louca, S., & Pennell, M. W. (2020) · Nature · doi:10.1038/s41586-020-2176-1 · Cited by 502
Estimating diversification rates from phylogenetic information
Ricklefs, R. E. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.06.013 · Cited by 501
Fully-sampled phylogenies of squamates reveal evolutionary patterns in threat status
Tonini, J. F. R., Beard, K. H., Ferreira, R. B., Jetz, W., & Pyron, R. A. (2016) · Biological Conservation · doi:10.1016/j.biocon.2016.03.039 · Cited by 486
Self-citationTracking virus outbreaks in the twenty-first century
Grubaugh, N. D., Ladner, J. T., Lemey, P., Pybus, O. G., Rambaut, A., Holmes, E. C., & Andersen, K. G. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0296-2 · Cited by 485
Nyakatura, K., & Bininda-Emonds, O. R. (2012) · BMC Biology · doi:10.1186/1741-7007-10-12 · Cited by 474
The earliest known eutherian mammal
Ji, Q., Luo, Z.-X., Yuan, C.-X., Wible, J. R., Zhang, J.-P., & Georgi, J. A. (2002) · Nature · doi:10.1038/416816a · Cited by 461
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
Wiens, J. J., & Morrill, M. C. (2011) · Systematic Biology · doi:10.1093/sysbio/syr025 · Cited by 452
Groves, C. (2011) · Johns Hopkins University Press eBooks · doi:10.56021/9781421400938 · Cited by 446
Inferring Evolutionary Process from Phylogenetic Tree Shape
Mooers, A. O., & Heard, S. B. (1997) · The Quarterly Review of Biology · doi:10.1086/419657 · Cited by 440
Mammalian phylogeny reveals recent diversification rate shifts
Stadler, T. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016876108 · Cited by 430
Phylogenetic supertrees: Assembling the trees of life
Sanderson, M. J., Purvis, A., & Henze, C. (1998) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(97)01242-1 · Cited by 429
Incorporating Evolutionary Measures into Conservation Prioritization
REDDING, D. W., & MOOERS, A. Ø. (2006) · Conservation Biology · doi:10.1111/j.1523-1739.2006.00555.x · Cited by 421
Total-Evidence Dating under the Fossilized Birth–Death Process
Zhang, C., Stadler, T., Klopfstein, S., Heath, T. A., & Ronquist, F. (2016) · Systematic Biology · doi:10.1093/sysbio/syv080 · Cited by 419
The supermatrix approach to systematics
DEQUEIROZ, A., & GATESY, J. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2006.10.002 · Cited by 417
Lemmon, A. R., Brown, J. M., Stanger-Hall, K., & Lemmon, E. M. (2009) · Systematic Biology · doi:10.1093/sysbio/syp017 · Cited by 415
Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue, P. C. J., & Benton, M. J. (2007) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2007.05.005 · Cited by 413
Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia
Pyron, R. A. (2011) · Systematic Biology · doi:10.1093/sysbio/syr047 · Cited by 413
Diversity dynamics: molecular phylogenies need the fossil record
Quental, T. B., & Marshall, C. R. (2010) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2010.05.002 · Cited by 403
Reconciling molecular phylogenies with the fossil record
Morlon, H., Parsons, T. L., & Plotkin, J. B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102543108 · Cited by 381
Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates
Steppan, S. J., & Schenk, J. J. (2017) · PLOS ONE · doi:10.1371/journal.pone.0183070 · Cited by 368
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
Roure, B., Baurain, D., & Philippe, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss208 · Cited by 365
Accommodating Phylogenetic Uncertainty in Evolutionary Studies
Huelsenbeck, J. P., Rannala, B., & Masly, J. P. (2000) · Science · doi:10.1126/science.288.5475.2349 · Cited by 351
Global elevational diversity and diversification of birds
Quintero, I., & Jetz, W. (2018) · Nature · doi:10.1038/nature25794 · Cited by 344
Self-citationBayesian molecular clock dating of species divergences in the genomics era
dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.8 · Cited by 339
Heterotachy and long-branch attraction in phylogenetics
Philippe, H., Zhou, Y., Brinkmann, H., Rodrigue, N., & Delsuc, F. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-50 · Cited by 339
Speciation dynamics during the global radiation of extant bats: BAT SPECIATION DYNAMICS
Shi, J. J., & Rabosky, D. L. (2015) · Evolution · doi:10.1111/evo.12681 · Cited by 338
Bayesian inference of character evolution
RONQUIST, F. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.07.002 · Cited by 335
Speciation gradients and the distribution of biodiversity
Schluter, D., & Pennell, M. W. (2017) · Nature · doi:10.1038/nature22897 · Cited by 333
Global priorities for conservation across multiple dimensions of mammalian diversity
Brum, F. T., Graham, C. H., Costa, G. C., Hedges, S. B., Penone, C., Radeloff, V. C., Rondinini, C., Loyola, R., & Davidson, A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706461114 · Cited by 329
Bininda-Emonds, O. R. P. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.03.015 · Cited by 319
Graur, D., Hide, W. A., & Li, W.-H. (1991) · Nature · doi:10.1038/351649a0 · Cited by 313
Constraints on the timescale of animal evolutionary history
Benton, M., Donoghue, P., Vinther, J., Asher, R., Friedman, M., & Near, T. (2015) · Palaeontologia Electronica · doi:10.26879/424 · Cited by 284
The Fossil Record of North American Mammals: Evidence for a Paleocene Evolutionary Radiation
Alroy, J. (1999) · Systematic Biology · doi:10.1080/106351599260472 · Cited by 280
Mammal madness: is the mammal tree of life not yet resolved?
Foley, N. M., Springer, M. S., & Teeling, E. C. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0140 · Cited by 264
Tempo of trophic evolution and its impact on mammalian diversification
Price, S. A., Hopkins, S. S. B., Smith, K. K., & Roth, V. L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1117133109 · Cited by 259
The (Super)Tree of Life: Procedures, Problems, and Prospects
Bininda-Emonds, O. R. P., Gittleman, J. L., & Steel, M. A. (2002) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.33.010802.150511 · Cited by 259
Finarelli, J. A., & Flynn, J. J. (2006) · Systematic Biology · doi:10.1080/10635150500541698 · Cited by 254
Smith, S. A., Beaulieu, J. M., & Donoghue, M. J. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-37 · Cited by 254
Tree thinking: an introduction to phylogenetic biology
(2013) · Choice Reviews Online · doi:10.5860/choice.50-4979 · Cited by 243
Hosner, P. A., Faircloth, B. C., Glenn, T. C., Braun, E. L., & Kimball, R. T. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msv347 · Cited by 240
A simple polytomy resolver for dated phylogenies
Kuhn, T. S., Mooers, A. Ø., & Thomas, G. H. (2011) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00103.x · Cited by 237
The phylogenomics of evolving virus virulence
Geoghegan, J. L., & Holmes, E. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0055-5 · Cited by 232
Zachos, F. E., Apollonio, M., Bärmann, E. V., Festa-Bianchet, M., Göhlich, U., Habel, J. C., Haring, E., Kruckenhauser, L., Lovari, S., McDevitt, A. D., et al. (2013) · Mammalian Biology · doi:10.1016/j.mambio.2012.07.083 · Cited by 229
Spaulding, M., O'Leary, M. A., & Gatesy, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007062 · Cited by 226
Climate, Critters, and Cetaceans: Cenozoic Drivers of the Evolution of Modern Whales
Marx, F. G., & Uhen, M. D. (2010) · Science · doi:10.1126/science.1185581 · Cited by 221
A biologist’s guide to Bayesian phylogenetic analysis
Nascimento, F. F., Reis, M. D., & Yang, Z. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0280-x · Cited by 212
Barker, F. K., Burns, K. J., Klicka, J., Lanyon, S. M., & Lovette, I. J. (2015) · The Auk · doi:10.1642/auk-14-110.1 · Cited by 209
Mammal diversity will take millions of years to recover from the current biodiversity crisis
Davis, M., Faurby, S., & Svenning, J.-C. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804906115 · Cited by 201
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O’Reilly, J. E., King, B. L., O’Connell, M. J., Asher, R. J., Warnow, T., et al. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evv261 · Cited by 199
Bat Systematics in the Light of Unconstrained Analyses of a Comprehensive Molecular Supermatrix
Amador, L. I., Moyers Arévalo, R. L., Almeida, F. C., Catalano, S. A., & Giannini, N. P. (2018) · Journal of Mammalian Evolution · doi:10.1007/s10914-016-9363-8 · Cited by 198
Body Size Evolution in Mammals: Complexity in Tempo and Mode
Cooper, N., & Purvis, A. (2010) · The American Naturalist · doi:10.1086/652466 · Cited by 197
ADAPTIVE ZONES AND THE ORDERS OF MAMMALS
Van Valen, L. (1971) · Evolution · doi:10.1111/j.1558-5646.1971.tb01898.x · Cited by 183
Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates?
Title, P. O., & Rabosky, D. L. (2019) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13153 · Cited by 182
Dispersal limitation promotes the diversification of the mammalian gut microbiota
Moeller, A. H., Suzuki, T. A., Lin, D., Lacey, E. A., Wasser, S. K., & Nachman, M. W. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1700122114 · Cited by 174
SCALE AND HIERARCHY IN MACROEVOLUTION
JABLONSKI, D. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2006.00615.x · Cited by 172
Romiguier, J., Ranwez, V., Delsuc, F., Galtier, N., & Douzery, E. J. P. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst116 · Cited by 170
Phylogenetic trees and the future of mammalian biodiversity
Davies, T. J., Fritz, S. A., Grenyer, R., Orme, C. D. L., Bielby, J., Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., Gittleman, J. L., Mace, G. M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801917105 · Cited by 167
Wiens, J. J., & Tiu, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042925 · Cited by 167
Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity
Foley, N. M., Hughes, G. M., Huang, Z., Clarke, M., Jebb, D., Whelan, C. V., Petit, E. J., Touzalin, F., Farcy, O., Jones, G., et al. (2018) · Science Advances · doi:10.1126/sciadv.aao0926 · Cited by 166
The phylogenetic roots of human lethal violence
Gómez, J. M., Verdú, M., González-Megías, A., & Méndez, M. (2016) · Nature · doi:10.1038/nature19758 · Cited by 164
Belmaker, J., & Jetz, W. (2015) · Ecology Letters · doi:10.1111/ele.12438 · Cited by 162
Self-citationRabosky, D. L. (2015) · Evolution · doi:10.1111/evo.12817 · Cited by 162
A Jurassic mammaliaform and the earliest mammalian evolutionary adaptations
Zhou, C., Wu, S., Martin, T., & Luo, Z. (2013) · Nature · doi:10.1038/nature12429 · Cited by 160
Rodent systematics in an age of discovery: recent advances and prospects
D’Elía, G., Fabre, P., & Lessa, E. P. (2018) · Journal of Mammalogy · doi:10.1093/jmammal/gyy179 · Cited by 157
Rodent Evolution: Back to the Root
Churakov, G., Sadasivuni, M. K., Rosenbloom, K. R., Huchon, D., Brosius, J., & Schmitz, J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq019 · Cited by 155
Inferences from tip‐calibrated phylogenies: a review and a practical guide
Rieux, A., & Balloux, F. (2016) · Molecular Ecology · doi:10.1111/mec.13586 · Cited by 155
Phylogenomics with incomplete taxon coverage: the limits to inference
Sanderson, M. J., McMahon, M. M., & Steel, M. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-155 · Cited by 153
A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales
Bajpai, S., & Gingerich, P. D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.26.15464 · Cited by 152
Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
Liu, L., Zhang, J., Rheindt, F. E., Lei, F., Qu, Y., Wang, Y., Zhang, Y., Sullivan, C., Nie, W., Wang, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1616744114 · Cited by 150
Investing in evolutionary history: implementing a phylogenetic approach for mammal conservation
Collen, B., Turvey, S. T., Waterman, C., Meredith, H. M. R., Kuhn, T. S., BAILLIE, J. E. M., & Isaac, N. J. B. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0109 · Cited by 139
Faurby, S., & Svenning, J. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.11.001 · Cited by 138
Quantitative Analysis of the Timing of the Origin and Diversification of Extant Placental Orders
Archibald, J. D., & Deutschman, D. H. (2001) · Journal of Mammalian Evolution · doi:10.1023/a:1011317930838 · Cited by 137
Esselstyn, J. A., Oliveros, C. H., Swanson, M. T., & Faircloth, B. C. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx168 · Cited by 135
Self-citationOsborn, H. F. (1902) · The American Naturalist · doi:10.1086/278137 · Cited by 129
A new arboreal haramiyid shows the diversity of crown mammals in the Jurassic period
Zheng, X., Bi, S., Wang, X., & Meng, J. (2013) · Nature · doi:10.1038/nature12353 · Cited by 128
Closing the gap between rocks and clocks using total-evidence dating
Ronquist, F., Lartillot, N., & Phillips, M. J. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0136 · Cited by 128
Incomplete Lineage Sorting in Mammalian Phylogenomics
Scornavacca, C., & Galtier, N. (2016) · Systematic Biology · doi:10.1093/sysbio/syw082 · Cited by 127
Erratum: The delayed rise of present-day mammals
Bininda‐Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2008) · Nature · doi:10.1038/nature07347 · Cited by 127
Simpson, G. G. (1951) · Cited by 126
Unraveling the evolution of uniquely human cognition
MacLean, E. L. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521270113 · Cited by 126
O'Leary, M. A., & Gatesy, J. (2008) · Cladistics · doi:10.1111/j.1096-0031.2007.00187.x · Cited by 118
The non-uniformity of fossil preservation
Holland, S. M. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0130 · Cited by 118
Hierarchy in adaptive radiation: A case study using the Carnivora (Mammalia)
Slater, G. J., & Friscia, A. R. (2019) · Evolution · doi:10.1111/evo.13689 · Cited by 118
Jansa, S. A., Goodman, S. M., & Tucker, P. K. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00267.x · Cited by 117
Cladistic analysis of molecular and morphological data
Mishler, B. D. (1994) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330940111 · Cited by 114
Luo, Z., Gatesy, S. M., Jenkins, F. A., Amaral, W. W., & Shubin, N. H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1519387112 · Cited by 114
Pyron, R. A., & Burbrink, F. T. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.09.007 · Cited by 109
Extinction can be estimated from moderately sized molecular phylogenies
Beaulieu, J. M., & O’Meara, B. C. (2015) · Evolution · doi:10.1111/evo.12614 · Cited by 104
Jansa, S. A. (1999) · Cladistics · doi:10.1006/clad.1999.0106 · Cited by 103
Lartillot, N., & Delsuc, F. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01558.x · Cited by 101
PASTIS : an R package to facilitate phylogenetic assembly with soft taxonomic inferences
Thomas, G. H., Hartmann, K., Jetz, W., Joy, J. B., Mimoto, A., & Mooers, A. Ø. (2013) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12117 · Cited by 99
Self-citationNeither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals
dos Reis, M., Donoghue, P. C. J., & Yang, Z. (2014) · Biology Letters · doi:10.1098/rsbl.2013.1003 · Cited by 96
Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation
Pagel, M. D., & Lutzoni, F. M. (2007) · Springer eBooks · doi:10.1007/3-540-45692-9_8 · Cited by 94
Time best explains global variation in species richness of amphibians, birds and mammals
Marin, J., & Hedges, S. B. (2016) · Journal of Biogeography · doi:10.1111/jbi.12709 · Cited by 94
Rapacciuolo, G., Graham, C. H., Marin, J., Behm, J. E., Costa, G. C., Hedges, S. B., Helmus, M. R., Radeloff, V. C., Young, B. E., & Brooks, T. M. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0744-7 · Cited by 88
Lartillot, N. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss239 · Cited by 86
Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana
Huttenlocker, A. K., Grossnickle, D. M., Kirkland, J. I., Schultz, J. A., & Luo, Z. (2018) · Nature · doi:10.1038/s41586-018-0126-y · Cited by 86
Evolution of terrestrial birds in three continents: biogeography and parallel radiations
Ericson, P. G. P. (2011) · Journal of Biogeography · doi:10.1111/j.1365-2699.2011.02650.x · Cited by 83
Relating Traits to Diversification: A Simple Test
Freckleton, R. P., Phillimore, A. B., & Pagel, M. D. (2008) · The American Naturalist · doi:10.1086/588076 · Cited by 81
Tooth Loss Precedes the Origin of Baleen in Whales
Peredo, C. M., Pyenson, N. D., Marshall, C. D., & Uhen, M. D. (2018) · Current Biology · doi:10.1016/j.cub.2018.10.047 · Cited by 81
Springer, M. S., Signore, A. V., Paijmans, J. L. A., Vélez‐Juarbe, J., Domning, D. P., Bauer, C. E., He, K., Crerar, L. D., Campos, P. F., Murphy, W. J., et al. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.05.022 · Cited by 75
Technical Comment on “The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals”
Springer, M. S., Meredith, R. W., Teeling, E. C., & Murphy, W. J. (2013) · Science · doi:10.1126/science.1238025 · Cited by 75
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Swanson, M. T., Oliveros, C. H., & Esselstyn, J. A. (2019) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.0672 · Cited by 75
Self-citationSpecies 2000 & ITIS Catalogue of Life: 2013 Annual Checklist [DVD]
Roskov, Y., Kunze, T., Paglinawan, L. E., Orrell, T. M., Nicolson, D. T., Culham, A., Bailly, N., Kirk, P. M., Bourgoin, T., Baillargeon, G., et al. (2013) · Cited by 72
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Phillips, M. J. (2015) · Systematic Biology · doi:10.1093/sysbio/syv115 · Cited by 72
The shape of mammalian phylogeny: patterns, processes and scales
Purvis, A., Fritz, S. A., Rodríguez, J., Harvey, P., & Grenyer, R. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0025 · Cited by 67
O’Leary, M. A., & Uhen, M. D. (1999) · Paleobiology · doi:10.1017/s0094837300020376 · Cited by 67
A likelihood look at the supermatrix–supertree controversy
Ren, F., Tanaka, H., & Yang, Z. (2008) · Gene · doi:10.1016/j.gene.2008.04.002 · Cited by 63
Phylogenetically informed spatial planning is required to conserve the mammalian tree of life
Rosauer, D. F., Pollock, L. J., Linke, S., & Jetz, W. (2017) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2017.0627 · Cited by 61
Self-citationQuantifying the completeness of the bat fossil record
Brown, E. E., Cashmore, D. D., Simmons, N. B., & Butler, R. J. (2019) · Palaeontology · doi:10.1111/pala.12426 · Cited by 61
Nakagawa, S., & de Villemereuil, P. (2018) · Systematic Biology · doi:10.1093/sysbio/syy089 · Cited by 59
Towards a Global Names Architecture: The future of indexing scientific names
Pyle, R. L. (2016) · ZooKeys · doi:10.3897/zookeys.550.10009 · Cited by 58
Multiple morphological clocks and total-evidence tip-dating in mammals
Lee, M. S. Y. (2016) · Biology Letters · doi:10.1098/rsbl.2016.0033 · Cited by 58
Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats
Teeling, E. C., Jones, G., & Rossiter, S. J. (2016) · Springer handbook of auditory research · doi:10.1007/978-1-4939-3527-7_2 · Cited by 56
Congruence, fossils and the evolutionary tree of rodents and lagomorphs
Asher, R. J., Smith, M. R., Rankin, A., & Emry, R. J. (2019) · Royal Society Open Science · doi:10.1098/rsos.190387 · Cited by 56
Bayesian placement of fossils on phylogenies using quantitative morphometric data
Parins‐Fukuchi, C. (2018) · Evolution · doi:10.1111/evo.13516 · Cited by 52
Gatesy, J., & Springer, M. S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715318114 · Cited by 51
Penone, C., Weinstein, B. G., Graham, C. H., Brooks, T. M., Rondinini, C., Hedges, S. B., Davidson, A. D., & Costa, G. C. (2016) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.1028 · Cited by 50
Springer, M. S., Emerling, C. A., Meredith, R. W., Janečka, J. E., Eizirik, E., & Murphy, W. J. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.017 · Cited by 49
Bias and Sensitivity in the Placement of Fossil Taxa Resulting from Interpretations of Missing Data
Sansom, R. S. (2014) · Systematic Biology · doi:10.1093/sysbio/syu093 · Cited by 48
Primate Taxonomy: Inflation or Real?
Groves, C. P. (2014) · Annual Review of Anthropology · doi:10.1146/annurev-anthro-102313-030232 · Cited by 48
Esselstyn, J. A., Maharadatunkamsi, Achmadi, A. S., Siler, C. D., & Evans, B. J. (2013) · Molecular Ecology · doi:10.1111/mec.12450 · Cited by 47
Self-citationThe soft explosive model of placental mammal evolution
Phillips, M. J., & Fruciano, C. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1218-x · Cited by 44
Beck, R. M. D., & Baillie, C. (2018) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2018.1632 · Cited by 42
A comparative study on karyotypic diversification rate in mammals
Martínez, P. A., Jacobina, U. P., Fernandes, R. V., Bessa-Brito, C. D., Penone, C., Amado, T. F., Fonseca, C. R., & Bidau, C. J. (2016) · Heredity · doi:10.1038/hdy.2016.110 · Cited by 38
Davies, T. W., Bell, M. A., Goswami, A., & Halliday, T. J. D. (2017) · Paleobiology · doi:10.1017/pab.2017.20 · Cited by 37
The evolution of capture myopathy in hooved mammals: a model for human stress cardiomyopathy?
Blumstein, D. T., Buckner, J. C., Shah, S., Patel, S., Alfaro, M. E., & Natterson-Horowitz, B. (2015) · Evolution Medicine and Public Health · doi:10.1093/emph/eov015 · Cited by 36
Dating placentalia: Morphological clocks fail to close the molecular fossil gap
Puttick, M. N., Thomas, G. H., & Benton, M. J. (2016) · Evolution · doi:10.1111/evo.12907 · Cited by 36
Liu, L., Zhang, J., Rheindt, F. E., Lei, F., Qu, Y., Wang, Y., Zhang, Y., Sullivan, C., Nie, W., Wang, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715371114 · Cited by 36
The effect of phylogenetic uncertainty and imputation on EDGE Scores
Weedop, K. B., Mooers, A. Ø., Tucker, C. M., & Pearse, W. D. (2019) · Animal Conservation · doi:10.1111/acv.12495 · Cited by 35
Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles
Title, P. O., & Rabosky, D. L. (2016) · Systematic Biology · doi:10.1093/sysbio/syw102 · Cited by 32
Rowe, K. C., Achmadi, A. S., & Esselstyn, J. A. (2014) · Zootaxa · doi:10.11646/zootaxa.3815.4.5 · Cited by 31
Self-citationEnvironmental variation is a major predictor of global trait turnover in mammals
Holt, B. G., Costa, G. C., Penone, C., Lessard, J., Brooks, T. M., Davidson, A. D., Hedges, S. B., Radeloff, V. C., Rahbek, C., Rondinini, C., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.13091 · Cited by 29
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E. Gutiérrez, E., E. Gutiérrez, E., S. T. Garbino, G., & S. T. Garbino, G. (2018) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2018.037 · Cited by 28
Bennett, V., Upchurch, P., Goin, F. J., & Goswami, A. (2018) · Paleobiology · doi:10.1017/pab.2017.34 · Cited by 28
Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations
Phillips, M. (2015) · Palaeontologia Electronica · doi:10.26879/490 · Cited by 24
Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?Preprint
Title, P. O., & Rabosky, D. L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/369124 · Cited by 16
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Pavoine, S., Bonsall, M. B., Davies, T. J., & Masi, S. (2019) · Ecology and Evolution · doi:10.1002/ece3.4630 · Cited by 16
King, B., & Beck, R. M. D. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/533885 · Cited by 10
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Metadata
- Authors
- Upham, N. S., Esselstyn, J. A., & Jetz, W.
- Venue
- PLOS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-12-04
- Volume
- 17
- Issue
- 12
- Pages
- e3000494
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2991998196
- Cited by
- 1,201
- References
- 186
- FWCI
- 76.68
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
