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  • Print publication year: 2012
  • Online publication date: November 2012

3 - Rocking clocks and clocking rocks: a critical look at divergence time estimation in mammals

Summary

Introduction

Much has been written about the molecular revolution in phylogenetics and the ongoing conflict between molecules and morphology (Hillis 1987; Patterson 1987; Springer et al. 2004). With reference to therian mammals at least, the supposed conflict has been largely overblown: there is in fact general agreement between the two data sources, something unfortunately overshadowed by a handful of persistent ‘problem children’. The taxonomic content of most mammalian orders and other traditional higher-level taxa originally proposed purely on the basis of morphology has remained unscathed by the application of molecular sequence analysis. Even within these taxa, conflicts between molecular and morphological hypotheses of relationships are comparatively rare and usually relatively minor. For instance, a comparative study within Carnivora (Bininda-Emonds, 2000) revealed that most data sources and methods of analysis pointed at the same general solution, a few admittedly problematic taxa (e.g. Felidae) notwithstanding. In the end, the frequency and nature of disagreements over tree topology is arguably of the same order of magnitude within the separate spheres of molecular and morphological systematics as it is between them (Patterson et al. 1993). In many ways, the situation in mammals parallels that in vertebrates, where a fairly robust tree including gnathostomes, actinopterygians, sarcopterygians, tetrapods, amniotes and diapsids (among many other groups) has been supported by comparative anatomy since the 1800s (Asher and Müller, this volume).

Instead, many of the more celebrated conflicts in mammals tend to represent a lack of information, especially on the morphological side. The evolutionary tree of eutherian mammals presented by Novacek (1992), which exemplified the state-of-the-art morphological opinion at the time, is conspicuous today not for being very wrong (although some clades within it have been overturned by molecular information), but for its lack of resolution. Insectivora was long recognized to be a taxonomic wastebasket for any small brown mammal with sharp teeth that wasn't a rodent and couldn't fly.

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References
Aitchison, J. C.Ali, J. R.Davis, A. M. 2007 When and where did India and Asia collide?Journal of Geophysical Research 112 1
Ali, J. R.Aitchison, J. C. 2008 Gondwana to Asia: plate tectonics, paleogeography and the biological connectivity of the Indian sub-continent from the Middle Jurassic through latest Eocene (166–35 Ma)Earth-Science Reviews 88 145
Ali, J. R.Huber, M. 2010 Mammalian biodiversity on Madagascar controlled by ocean currentsNature 463 653
Ali, J. R.Krause, D. W 2011 Late Cretaceous bioconnections between Indo-Madagascar and Antarctica: refutation of the Gunnerus Ridge causeway hypothesisJournal of Biogeography 38 1855
Alroy, J. 1999 The fossil record of North American mammals: evidence for a Paleocene evolutionary radiationSystematic Biology 48 107
Archibald, J. D.Deutschmann, D. H. 2001 Quantitative analysis of the timing of the origin and diversification of extant placental ordersJournal of Mammalian Evolution 8 107
Archibald, J. D.Zhang, Y.Harper, T.Cifelli, R. L. 2011 , confirmed Cretaceous occurrence of an otherwise Paleocene eutherian (placental?) mammalJournal of Mammalian Evolution 18 153
Aris-Brosou, S.Yang, Z 2002 Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogenySystematic Biology 51 703
Aris-Brosou, S.Yang, Z 2003 Bayesian models of episodic evolution support a late Precambrian explosive diversification of the MetazoaMolecular Biology and Evolution 20 1947
Arnason, U.Adegoke, J. A.Gullberg, A. 2008 Mitogenomic relationships of placental mammals and molecular estimates of their divergencesGene 421 37
Asher, R. J. 1999 A morphological basis for assessing the phylogeny of the ‘Tenrecoidea’ (Mammalia, Lipotyphla)Cladistics 15 231
Asher, R. J. 2001 Cranial anatomy in tenrecid insectivorans: character evolution across competing phylogeniesAmerican Museum Novitates 3352 1
Asher, R. J. 2007 A web-database of mammalian morphology and a reanalysis of placental phylogenyBMC Evolutionary Biology 7
Asher, R. J.Hofreiter, M. 2006 Tenrec phylogeny and the noninvasive extraction of nuclear DNASystematic Biology 55 181
Asher, R. J.Lehmann, T. 2008 Dental eruption in afrotherian mammalsBMC Biology 6
Asher, R. J.Novacek, M. J.Geisler, J. H. 2003 Relationships of endemic African mammals and their fossil relatives based on morphological and molecular evidenceJournal of Mammalian Evolution 10 131
Asher, R. J.Geisler, J. H.Sanchez-Villagra, M. R 2008 Morphology, paleontology, and placental mammal phylogenySystematic Biology 57 311
Averianov, A. O.Skutschas, P. P. 2001 A new genus of eutherian mammal from the Early Cretaceous of Transbaikalia, RussiaActa Palaeontologica Polonica 46 431
Averianov, A. O.Archibald, J. D.Martin, T. 2003 Placental nature of the alleged marsupial from the Cretaceous of MadagascarActa Palaeontologica Polonica 48 149
Beck, R. M. D. 2008
Beck, R. M. D.Godthelp, H.Weisbecker, V.Archer, M.Hand, S. J. 2008 Australia’s oldest marsupial fossils and their biogeographical implicationsPLoS One 3
Benton, M. J.Donoghue, P. C. J. 2007 Paleontological evidence to date the tree of lifeMolecular Biology and Evolution 24 26
Benton, M. J.Donoghue, P. C. J.Asher, R. J. 2009 Calibrating and constraining molecular clocksThe Timetree of LifeHedges, S. B.Kumar, S.Oxford, UKOxford University Press
Bergqvist, L. P.Abrantes, E. A. L.Avilla, L. 2004 The Xenarthra (Mammalia) of São José de Itaboraí Basin (upper Paleocene, Itaboraian), Rio de Janeiro, BrazilGeodiversitas323
Bergsten, J. 2005 A review of long-branch attractionCladistics 21 163
Bininda-Emonds, O. R. P 2000 Factors influencing phylogenetic inference: a case study using the mammalian carnivoresMolecular Phylogenetics and Evolution 16 113
Bininda-Emonds, O. R. P 2007 Fast genes and slow clades: comparative rates of molecular evolution in mammalsEvolutionary Bioinformatics Online 3 59
Bininda-Emonds, O. R. P.Cardillo, M.Jones, K. E. 2007 The delayed rise of present-day mammalsNature 446 507
Bininda-Emonds, O. R. P.Cardillo, M.Jones, K. E. 2008 Corrigendum: The delayed rise of present-day mammalsNature 456
Bloch, J. I.Silcox, M.Boyer, D. M.Sargis, E. J. 2007 New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primatesProceedings of the National Academy of Sciences of the United States of America 104 1159
Boyer, D. M. 2009
Boyer, D. M.Prasad, G. V. R.Krause, D. W. 2010 New postcrania of from the Late Cretaceous of India and their bearing on the evolutionary and biogeographic history of euarchontan mammalsNaturwissenschaften 97 365
Britten, R. J. 1986 Rates of DNA sequence evolution differ between taxonomic groupsScience 231 1393
Britton, T.Anderson, C. L.Jacquet, D.Lundqvist, S.Bremer, K. 2007 Estimating divergence times in large phylogenetic treesSystematic Biology 56 741
Bromham, L.Rambaut, A.Harvey, P. H. 1996 Determinants of rate variation in mammalian DNA sequence evolutionJournal of Molecular Evolution 43 610
Bromham, L.Rambaut, A.Fortey, R.Cooper, A.Penny, D. 1998 Testing the Cambrian explosion hypothesis by using a molecular dating techniqueProceedings of the National Academy of Sciences of the United States of America 95 12 386
Bromham, L.Woolfit, M.Lee, M. S.Rambaut, A. 2002 Testing the relationship between morphological and molecular rates of change along phylogeniesEvolution 56 1921
Brower, A. V. 1994 Rapid morphological radiation and convergence among races of the butterfly inferred from patterns of mitochondrial DNA evolutionProceedings of the National Academy of Sciences of the United States of America 91 6491
Brown, W. M.George, M.Wilson, A. C 1979 Rapid evolution of animal mitochondrial DNAProceedings of the National Academy of Sciences of the United States of America 76 1967
Bryant, H. N. 1989 An evaluation of cladistic and character analyses as hypothetico-deductive procedures, and the consequences for character weightingSystematic Zoology 38 214
Bryant, H. N. 1991 The polarization of character transformations in phylogenetic systematics: role of axiomatic and auxiliary assumptionsSystematic Zoology 40 433
Butler, P. M. 1984 Macroscelidea, Insectivora and Chiroptera from the Miocene of east AfricaPalaeovertebrata 14 117
Cartmill, M. 1981 Hypothesis testing and phylogenetic reconstructionJournal of Zoological Systematics and Evolutionary Research 19 73
Cifelli, R. L. 1999 Tribosphenic mammal from the North American Early CretaceousNature 401 363
Cifelli, R. L.de Muizon, C. 1998 Tooth eruption and replacement pattern in early marsupialsComptes Rendus de l'Académie des Sciences, IIA–Earth and Planetary Science 326 215
Clemens, W. 1986 On Triassic and Jurassic mammalsThe Beginning of the Age of Dinosaurs: Faunal Change across the Triassic-Jurassic BoundaryPadian, K.Cambridge, UKCambridge University Press
Clyde, W. C.Ting, S.Snell, K. E. 2010 New paleomagnetic and stable-isotope results from the Nanxiong Basin, China: implications for the K/T boundary and the timing of Paleocene mammalian turnoverJournal of Geology 118 131
Cooper, A.Fortey, R. 1998 Evolutionary explosions and the phylogenetic fuseTrends in Ecology and Evolution 13 151
Davies, T. J.Savolainen, V. 2006 Neutral theory, phylogenies, and the relationship between phenotypic change and evolutionary ratesEvolution 60 476
de Muizon, C. 1991 La fauna de mamíferos de Tiupampa (Paleoceno Inferior, Formación Santa Lucía), BoliviaFósiles y Facies de BoliviaSuárez-Soruco, R.Santa Cruz, BoliviaRevista Téchnica de Yacimientos Petrolíferos Fiscales Bolivianos
de Muizon, C.Cifelli, R. L. 2000 The ‘condylarths’ (archaic Ungulata, Mammalia) from the early Palaeocene of Tiupampa (Bolivia): implications on the origin of the South American ungulatesGeodiversitas 22 47
de Muizon, C.Cifelli, R. L.Bergqvist, L. P. 1998 Eutherian tarsals from the early Paleocene of BoliviaJournal of Vertebrate Paleontology 18 655
Donoghue, M. J.Doyle, J. A.Gauthier, J.Kluge, A. G.Rowe, T. 1989 The importance of fossils in phylogeny reconstructionAnnual Review of Ecology and Systematics 20 431
Donoghue, P. C. J.Purnell, M. A. 2009 Distinguishing heat from light in debate over controversial fossilsBioEssays 31 178
Douady, C. J.Douzery, E. J. P. 2003 Molecular estimation of eulipotyphlan divergence times and the evolution of ‘Insectivora’Molecular Phylogenetics and Evolution 28 285
Douzery, E. J. P.Delsuc, F.Stanhope, M. J.Huchon, D. 2003 Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrationsJournal of Molecular Evolution 57 S201
Drake, J. W.Charlesworth, B.Charlesworth, D.Crow, J. F. 1998 Rates of spontaneous mutationGenetics 148 1667
Drummond, A. J.Rambaut, A. 2007 BEAST: Bayesian evolutionary analysis by sampling treesBMC Evolutionary Biology 7
Drummond, A. J.Ho, S. Y. W.Phillips, M. J.Rambaut, A. 2006 Relaxed phylogenetics and dating with confidencePLoS Biology 4
Eagles, G. 2007 New angles on South Atlantic openingGeophysical Journal International 168 353
Eagles, G. 2010 The age and origin of the central Scotia SeaGeophysical Journal International 183 587
Evans, S. E.Jones, M. E. H.Krause, D. W. 2008 A giant frog with South American affinities from the Late Cretaceous of MadagascarProceedings of the National Academy of Sciences of the United States of America 105 2951
Flynn, J. J.Parrish, J. M.Rakotosamimanana, B.Simpson, W. F.Wyss, A. R. 1999 A new Middle Jurassic mammal from MadagascarNature 401 57
Foote, M.Hunter, J. P.Janis, C. M.Sepkoski, J. J. 1999 Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammalsScience 283 1310
Gayet, M. 2001 A review of some problems associated with the occurrences of fossil vertebrates in South AmericaJournal of South American Earth Sciences 14 131
Geisler, J. H.Uhen, M. D. 2003 Morphological support for a close relationship between hippos and whalesJournal of Vertebrate Paleontology 23 991
Gelfo, J. N.Goin, F. J.Woodburne, M. O.de Muizon, C. 2009 Biochronological relationships of the earliest South American Paleogene mammalian faunasPalaeontology 52 251
Gheerbrant, E. 2009 Paleocene emergence of elephant relatives and the rapid radiation of African ungulatesProceedings of the National Academy of Sciences of the United States of America 106 10 717
Giallombardo, A.AToL Mammal Morphology Team 2010 Postcanine homologies in MammaliaJournal of Vertebrate Paleontology 30
Gingerich, P. D.Haq, M.Zalmout, I. S.Khan, I. H.Malkani, M. S. 2001 Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from PakistanScience 293 2239
Godthelp, H.Archer, M.Cifelli, R. L.Hand, S. J.Gilkeson, C. F. 1992 Earliest known Australian Tertiary mammal faunaNature 356 514
Godthelp, H.Wroe, S.Archer, M. 1999 A new marsupial from the Early Eocene Tingamarra local fauna of Murgon, southeastern Queensland: a prototypical Australian marsupial?Journal of Mammalian Evolution 6 289
Goswami, A.Prasad, G. V. R.Upchurch, P. 2011
Graur, D.Higgins, D. G. 1994 Molecular evidence for the inclusion of cetaceans within the order ArtiodactylaMolecular Biology and Evolution 11 357
Graur, D.Duret, L.Gouy, M. 1996 Phylogenetic position of the order Lagomorpha (rabbits, hares, and allies)Nature 379 333
Hacking, I. 2001 An Introduction to Probability and Inductive LogicCambridge, UKCambridge University Press
Hennig, W. 1966 Phylogenetic SystematicsUrbana, ILUniversity of Illinois Press
Hershkovitz, P. 1968 The recent mammals of the neotropical regions: a zoogeographic and ecological reivewEvolutions, Mammals, and Southern ContinentsKeast, A.Erk, F. C.Glass, B.Albany, NYState University of New York Press
Hillis, D. M. 1987 Molecular versus morphological approaches to systematicsAnnual Review of Ecology and Systematics 18 23
Ho, S. Y. W. 2007 Calibrating molecular estimates of substitution rates and divergence times in birdsJournal of Avian Biology 38 409
Ho, S. Y. W.Phillips, M. J. 2009 Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence timesSystematic Biology 58 367
Holm, S. 1979 A simple sequentially rejective multiple test procedureScandinavian Journal of Statistics 6 65
Hooker, J. J. 2001 Tarsals of the extinct insectivoran family Nyctitheriidae (Mammalia): evidence for archontan relationshipsZoological Journal of the Linnean Society 132 501
Hug, L. A.Roger, A. J. 2007 The impact of fossils and taxon sampling on ancient molecular dating analysesMolecular Biology and Evolution 24 1889
Inoue, J.Donoghue, P. C. J.Yang, Z. 2010 The impact of the representation of fossil calibrations on Bayesian estimation of species divergence timesSystematic Biology 59 74
Iturralde-Vinent, M. A 2006 Meso-Cenozoic Caribbean paleogeography: implications for the historical biogeography of the regionInternational Geology Review 48 791
Ji, Q.Luo, Z.-X.Yuan, C.-X. 2002 The earliest known eutherian mammalNature 416 816
Kay, R. F.Thewissen, J. G. M.Yoder, A. D. 2001 Cranial anatomy of and the affinities of the PlesiadapiformesAmerican Journal of Physical Anthropology 89 477
Kielan-Jaworowska, Z.Cifelli, R. L.Luo, Z.-X 2004 Mammals from the Age of Dinosaurs: Origins, Evolution, and StructureNew YorkColumbia University Press
Kimura, M. 1983 The Neutral Theory of Molecular EvolutionCambridge, UKCambridge University Press
Kitazoe, Y.Kishino, H.Waddell, P. J. 2007 Robust time estimation reconciles views of the antiquity of placental mammalsPLoS One 2
Krause, D. W. 1986 Competitive exclusion and taxonomic displacement in the fossil record: the case of rodents and multituberculates in North AmericaVertebrates, Phylogeny and Philosophy: A Tribute to George Gaylord SimpsonFlanagan, K. M.Lillegraven, J. ALaramie, WYUniversity of Wyoming
Krause, D. W.Maas, M. C. 1990 The biogeographic origins of late Paleocene– early Eocene mammalian immigrants to the Western Interior of North AmericaDawn of the Age of Mammals in the Northern Part of the Rocky Mountain Interior, North AmericaBrown, T. M.Rose, K. D.Boulder, COGeological Society of America
Kumar, S.Hedges, S. B. 1998 A molecular timescale for vertebrate evolutionNature 392 917
Lanfear, R.Welch, J. J.Bromham, L. 2010 Watching the clock: studying variation in rates of molecular evolution between speciesTrends in Ecology and Evolution 25 495
Lee, M. S.Camens, A. B. 2009 Strong morphological support for the molecular evolutionary tree of placental mammalsJournal of Evolutionary Biology 22 2243
Luckett, W. P.Hong, N. 1998 Phylogenetic relationships between the orders Artiodactyla and Cetacea: a combined assessment of morphological and molecular evidenceJournal of Mammalian Evolution 5 127
Luo, Z. X.Wible, J. R. 2005 A Late Jurassic digging mammal and early mammalian diversificationScience 308 103
Luo, Z.-X.Cifelli, R. L.Kielan-Jaworowska, Z 2001 Dual origin of tribosphenic mammalsNature 409 53
Luo, Z.-X.Crompton, A. W.Sun, A.-L. 2001 A new mammaliaform from the early Jurassic and evolution of mammalian characteristicsScience 292 1535
Luo, Z.-X.Kielan-Jaworowska, Z.Cifelli, R. L 2002 In quest for a phylogeny of Mesozoic mammalsActa Palaeontologica Polonica 47 1
Luo, Z.-X.Ji, Q.Wible, J. R.Yuan, C.-X. 2003 An Early Cretaceous tribosphenic mammal and metatherian evolutionScience 302 1934
Luo, Z.-X.Kielan-Jaworowska, Z.Cifelli, R. L 2004 Evolution of dental replacement in mammalsBulletin of the Carnegie Museum of Natural History 36 159
Luo, Z.-X.Chen, P.Li, G.Chen, M. 2007 A new eutriconodont mammal and evolutionary development in early mammalsNature 446 288
Luo, Z.-X.Ruf, I.Schultz, J. A.Martin, T. 2011 Fossil evidence on evolution of inner ear cochlea in Jurassic mammalsProceedings of the Royal Society B 278 28
Luo, Z.-X.Yuan, C.-X.Meng, Q.-J.Ji, Q. 2011 A Jurassic eutherian mammal and divergence of marsupials and placentalsNature 476 442
MacPhee, R. D. E. 1981 Auditory regions of primates and eutherian insectivores: morphology, ontogeny, and character analysisContributions to Primatology 18 1
MacPhee, R. D. E. 1994 Morphology, adaptations, and relationships of , and a diagnosis of a new order of eutherian mammalsBulletin of the American Museum of Natural History 220 1
MacPhee, R. D. E.Reguero, M. A. 2010 Reinterpretation of a Middle Eocene record of Tardigrada (Pilosa, Xenarthra, Mammalia) from La Meseta Formation, Seymour Island, West AntarcticaAmerican Museum Novitates 3689 1
Marjanović, D.Laurin, M. 2008 Assessing confidence intervals for stratigraphic ranges of higher taxa: the case of LissamphibiaActa Palaeontologica Polonica 53 413
Marshall, L. G.de Muizon, C. 1988 The dawn of the age of mammals in South AmericaNational Geographic Research 4 23
Martin, A. P.Palumbi, S. R. 1993 Body size, metabolic rate, generation time, and the molecular clockProceedings of the National Academy of Sciences of the United States of America 90 4087
Martin, R. D.Soligo, C.Tavaré, S. 2007 Primate origins: implications of a Cretaceous ancestryFolia Primatologica 78 277
Meng, J.Wyss, A. R. 2005 Glires (Lagomorpha, Rodentia)The Rise of Placental Mammals: Origins and Relationships of the Major Extant CladesRose, K. D.Archibald, J. D.Baltimore, MDJohns Hopkins University Press
Misawa, K.Janke, A. 2003 Revisiting the Glires concept – phylogenetic analysis of nuclear sequencesMolecular Phylogenetics and Evolution 28 320
Murphy, W. J.Eizirik, E.Johnson, W. E. 2001 Molecular phylogenetics and the origins of placental mammalsNature 409 614
Near, T. J.Sanderson, M. J. 2004 Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil-based model selectionPhilosophical Transactions of the Royal Society of London B–Biological Sciences 359 1477
Nei, M. 1987 Molecular Evolutionary GeneticsNew YorkColumbia University Press
Novacek, M. J. 1992 Mammalian phylogeny: shaking the treeNature 356 121
Novacek, M. J.AToL Mammal Morphology Team 2008 A team-based approach yields a new matrix of 4,500 morphological characters for mammalian phylogenyJournal of Vertebrate Paleontology 28
Novacek, M. J.Rougier, G. W.Wible, J. R. 1997 Epipubic bones in eutherian mammals from the Late Cretaceous of MongoliaNature 389 483
O'Leary, M. A 2011 MorphoBank: collecting and storing phenomic data for phylogenetic research in the ‘cloudAmerican Journal of Physical Anthropology 144 228
Ohta, T. 1995 Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theoryJournal of Molecular Evolution 40 56
Pascual, R.Ortiz-Jaureguizar, E 1992 Evolutionary pattern of land mamal faunas during the Late Cretaceous and Paleocene in South America: a comparison with the North American patternAnnales Zoologici Fennici 28 245
Pascual, R.Ortiz-Jaureguizar, E 2007 The Gondwanan and South American episodes: two major and unrelated moments in the history of the South American mammalsJournal of Mammalian Evolution 14 75
Patterson, C. 1987 Molecules and Morphology in Evolution: Conflict or Compromise?Cambridge, UKCambridge University Press
Patterson, C.Williams, D. M.Humphries, C. J. 1993 Congruence between molecular and morphological phylogeniesAnnual Review of Ecology and Systematics 24 153
Penny, D.Hasegawa, M.Waddell, P. J.Hendy, M. D. 1999 Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid compositionSystematic Biology 48 76
Phillips, M. J. 2009 Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogenyGene 441 132
Phillips, M. J.Penny, D. 2003 The root of the mammalian tree inferred from whole mitochondrial genomesMolecular Phylogenetics and Evolution 28 171
Phillips, M. J.Delsuc, F.Penny, D. 2004 Genome-scale phylogeny and the detection of systematic biasesMolecular Biology and Evolution 21 1455
Phillips, M. J.Bennett, T. H.Lee, M. S. Y. 2009 Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnasProceedings of the National Academy of Sciences of the United States of America 106 17 089
Polly, P. D. 2001 On morphological clocks and paleophylogeography: towards a timescale for hybrid zonesGenetica 112–113 339
Posada, D.Crandall, K. A. 1998 Modeltest: testing the model of DNA substitutionBioinformatics 14 817
Poux, C.Madsen, O.Glos, J.De Jong, W. W.Vences, M. 2008 Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analysesBMC Evolutionary Biology 8
Prasad, G. V. R.Verma, O.Gheerbrant, E. 2010 First mammal evidence from the Late Cretaceous of India for biotic dispersal between India and Africa at the KT transitionComptes Rendus Palevol 9 63
Purvis, A. 1995 A composite estimate of primate phylogenyPhilosophical Transactions of the Royal Society of London B 348 405
Pyron, R. A. 2010 A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrationsSystematic Biology 59 185
Rannala, B.Yang, Z. 2007 Inferring speciation times under an episodic molecular clockSystematic Biology 56 453
Rauhut, O. W. M.Martin, T.Ortiz-Jaureguizar, E.Puerta, P 2002 A Jurassic mammal from South AmericaNature 416 165
Reisz, R. R.Müller, J. 2004 Molecular timescales and the fossil record: a paleontological perspectiveTrends in Genetics 20 237
Rich, T. H.Vickers-Rich, P.Constantine, A. 1997 A tribosphenic mammal from the Mesozoic of AustraliaScience 278 1438
Rose, K. D. 1996 On the origin of the order ArtiodactylaProceedings of the National Academy of Sciences of the United States of America 93 1705
Rose, K. D.Deleon, V. B.Missiaen, P. 2008 Early Eocene lagomorph (Mammalia) from Western India and the early diversification of LagomorphaProceedings of the Royal Society B 275 1203
Rose, K. D.Rana, R. S.Sahni, A. 2009 Early Eocene primates from Gujarat, IndiaJournal of Human Evolution 56 366
Rougier, G. W.Wible, J. R.Novacek, M. J. 1998 Implications of specimens for early marsupial historyNature 396 459
Rougier, G. W.Martinelli, A. G.Forasiepi, A. M.Novacek, M. J. 2007 New Jurassic mammals from Patagonia, Argentina: a reappraisal of australosphenidan morphology and interrelationshipsAmerican Museum Novitates 3566 1
Rowe, T.Rich, T. H.Vickers-Rich, P.Springer, M. S.Woodburne, M. O 2008 The oldest platypus and its bearing on divergence timing of the platypus and echidna cladesProceedings of the National Academy of Sciences of the United States of America 105 1238
Sánchez-Villagra, M. R.Narita, Y.Kuratani, S 2007 Thoracolumbar vertebral number: the first skeletal synapomorphy for afrotherian mammalsSystematics and Biodiversity 5 1
Sanderson, M. J. 1997 A nonparametric approach to estimating divergence times in the absence of rate constancyMolecular Biology and Evolution 14 1218
Sanderson, M. J. 2002 Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approachMolecular Biology and Evolution 19 101
Sansom, R. S.Gabbott, S. E.Purnell, M. A. 2010 Non-random decay of chordate characters causes bias in fossil interpretationNature 463 797
Sarich, V. M.Wilson, A. C. 1973 Generation time and genomic evolution in primatesScience 179 1144
Schaeffer, B. 1947 Notes on the origin and function of the artiodactyl tarsusAmerican Museum Novitates 1356 1
Seiffert, E. R. 2007 Early evolution and biogeography of lorisiform strepsirrhinesAmerican Journal of Primatology 69 27
Seiffert, E. R. 2007 A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidenceBMC Evolutionary Biology 7
Seiffert, E. R. 2010 The oldest and youngest records of Afrosoricida (Placentalia, Afrotheria) from the Fayum Depression of northern EgyptActa Palaeontologica Polonica 55 599
Seiffert, E. R.Simons, E. L.Attia, Y. 2003 Fossil evidence for an ancient divergence of lorises and galagosNature 422 421
Seiffert, E. R.Simons, E. L.Ryan, T. M.Bown, T. M.Attia, Y. 2007 New remains of Eocene and Oligocene Afrosoricida (Afrotheria) from Egypt, with implications for the origin(s) of afrosoricid zalambdodontyJournal of Vertebrate Paleontology 27 963
Seligmann, H. 2010 Positive correlations between molecular and morphological rates of evolutionJournal of Theoretical Biology 264 799
Shoshani, J.Walter, R. C.Abraha, M. 2006 A proboscidean from the late Oligocene of Eritrea, a ‘missing link’ between early Elephantiformes and Elephantimorpha, and biogeographic implicationsProceedings of the National Academy of Sciences of the United States of America 103 17 296
Smith, T.De Bast, E.Sigé, B. 2010 Euarchontan affinity of Paleocene Afro-European adapisoriculid mammals and their origin in the late Cretaceous Deccan Traps of IndiaNaturwissenschaften 97 417
Spaulding, M.O'Leary, M. A.Gatesy, J 2009 Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolutionPLoS One 4
Springer, M. S. 1997 Molecular clocks and the timing of the placental and marsupial radiations in relation to the Cretaceous-Tertiary boundaryJournal of Mammalian Evolution 4 285
Springer, M. S.Burk-Herrick, A.Meredith, R. 2007 The adequacy of morphology for reconstructing the early history of placental mammalsSystematic Biology 56 673
Springer, M. S.Murphy, W. J.Eizirik, E.O'Brien, S. J. 2003 Placental mammal diversification and the Cretaceous-Tertiary boundaryProceedings of the National Academy of Sciences of the United States of America 100 1056
Springer, M. S.Stanhope, M. J.Madsen, O.de Jong, W. W. 2004 Molecules consolidate the placental mammal treeTrends in Ecology and Evolution 19 430
Stanhope, M. J.Waddell, V. G.Madsen, O. 1998 Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammalsProceedings of the National Academy of Sciences of the United States of America 95 9967
Storch, G. 2008 Skeletal remains of a diminutive primate from the Paleocene of GermanyNaturwissenschaften 95 927
Swofford, D. L. 2002 PAUP*. Phylogenetic analysis using parsimony (*and other methods)Sunderland, MASinauer Associates
Tajima, F. 1993 Simple methods for testing the molecular evolutionary clock hypothesisGenetics 135 599
Tavaré, S.Marshall, C. R.Will, O.Soligo, C.Martin, R. D. 2002 Using the fossil record to estimate the age of the last common ancestor of extant primatesNature 416 726
Teeling, E. C.Springer, M. S.Madsen, O. 2005 A molecular phylogeny for bats illuminates biogeography and the fossil recordScience 307 580
Thewissen, J. G.Williams, E. M.Roe, L. J.Hussain, S. T. 2001 Skeletons of terrestrial cetaceans and the relationship of whales to artiodactylsNature 413 277
Thorne, J. L.Kishino, H. 2002 Divergence time and evolutionary rate estimation with multilocus dataSystematic Biology 51 689
Ting, S.-Y.Meng, J.Qian, L. 2007 , an artiodactyl-like mammal (Ungulata, Mammalia) from the Paleocene, Chijiang Basin, Jiangxi, ChinaVertebrata PalAsiatica 45 278
Vickers, J. 2010 The problem of inductionThe Stanford Encyclopedia of PhilosophyZalta, E. N.Stanford, CAStanford University
Vogt, L.Bartolomaeus, T.Giribet, G. G. 2010 The linguistic problem of morphology: structure versus homology and the standardization of morphological dataCladistics 26 301
Waddell, P. J.Okada, N.Hasegawa, M. 1999 Towards resolving the interordinal relationships of placental mammalsSystematic Biology 48 1
Welch, J. J.Fontanillas, E.Bromham, L. 2005 Molecular dates for the ‘Cambrian Explosion’: the influence of prior assumptionsSystematic Biology 54 672
Whidden, H. P. 2002 Extrinsic snout musculature in Afrotheria and LipotyphlaJournal of Mammalian Evolution 9 161
Whittaker, J. M.Muller, R. D.Leitchenkov, G. 2007 Major Australian-Antarctic plate reorganization at Hawaiian-Emperor bend timeScience 318 3
Wible, J. R.Rougier, G. W.Novacek, M. J. 2005 Anatomical evidence for superordinal/ordinal eutherian taxa in the CretaceousThe Rise of Placental Mammals: Origins and Relationships of the Major Extant CladesRose, K. D.Archibald, J. D.Baltimore, MDJohns Hopkins University Press
Wible, J. R.Rougier, G. W.Novacek, M. J.Asher, R. J. 2007 Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundaryNature 447 1003
Woodburne, M. O.Case, J. A. 1996 Dispersal, vicariance, and the late Cretaceous to early Tertiary land mammal biogeography from South America to AustraliaJournal of Mammalian Evolution 3 121
Woodburne, M. O.Rich, T. H.Springer, M. S. 2003 The evolution of tribospheny and the antiquity of mammalian cladesMolecular Phylogenetics and Evolution 28 360
Yang, Z.Rannala, B. 2006 Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft boundsMolecular Biology and Evolution 23 212
Zuckerkandl, E.Pauling, L. 1962 Molecular disease, evolution, and genetic heterogeneityHorizons in BiochemistryKasha, M.Pullman, B.New YorkAcademic Press
Zuckerkandl, E.Pauling, L. 1965 Evolutionary divergence and convergence in proteinsEvolving Genes and ProteinsBryson, V.Vogel, H. J.New YorkAcademic Press