Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships

Proceedings of the Royal Society B: Biological Sciences

Volumn 282, Issue 1812, 2015, Pages

  Dembo, Mana ^a   Matzke, Nicholas J ^b   Mooers, Arne Ø ^a   Collard, Mark ^a,c  

^a SIMON FRASER UNIVERSITY   (Canada)

^b UNIVERSITY OF TENNESSEE   (United States)

^c UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Bayesian morphological analysis; Human origins; Phylogeny

Indexed keywords

BAYESIAN ANALYSIS; DATA SET; FOSSIL RECORD; HOMINID; HUMAN EVOLUTION; MORPHOLOGY; PALEOBIOLOGY; PHYLOGENETICS; PHYLOGENY; STATISTICAL ANALYSIS; TAXONOMY; BASELINE SURVEY; HYPOTHESIS TESTING; UNCERTAINTY ANALYSIS;

EAST NUSA TENGGARA; FLORES [LESSER SUNDA ISLANDS]; LESSER SUNDA ISLANDS; SUNDA ISLES;

AUSTRALOPITHECUS;

ANATOMY AND HISTOLOGY; ANIMAL; BAYES THEOREM; CLASSIFICATION; EVOLUTION; FOSSIL; GEORGIA; HOMINID; INDONESIA; PHYLOGENY; SOUTH AFRICA;

ANIMALS; BAYES THEOREM; BIOLOGICAL EVOLUTION; FOSSILS; GEORGIA; HOMINIDAE; INDONESIA; PHYLOGENY; SOUTH AFRICA;

EID: 84937899678     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2015.0943     Document Type: Article

References (71)

1. Huxley TH. 1863 Evidence as to man’s place in nature. New York, NY: D. Appleton and company.
2. Ruvolo M. 1997 Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets. Mol. Biol. Evol. 14, 248–265. (doi:10.1093/oxfordjournals.molbev.a025761)
3. Gibbs S, Collard M, Wood BA. 2000 Soft-tissue characters in higher primate phylogenetics. Proc. Natl Acad. Sci. USA 97, 11 130–11 132. (doi:10.1073/pnas.190252697)
4. Strait D, Grine FE, Fleagle JG. 2015 Analyzing hominin phylogeny: cladistic approach. In Handbook of paleoanthropology (eds W Henke, I Tattersall), 2nd edn. pp. 1989–2014. New York, NY: Springer Reference.
5. Kimbel WH, Rak Y, Johanson DC. 2004 Taxonomic and phylogenetic status of Australopithecus afarensis. In The skull of Australopithecus afarensis (eds WH Kimbel, Y Rak, DC Johanson), pp. 215–220. New York, NY: Oxford University Press.
6. Martinón-Torres M, Bermúdez de Castro JM, Gomez- Robles A, Arsuaga JL, Carbonell E, Lordkipanidze D, Manzi G, Margvelashvili A. 2007 Dental evidence on the hominin dispersals during the Pleistocene. Proc. Natl Acad. Sci. USA 104, 13 279–13 282. (doi:10.1073/pnas.0706152104)
7. Strait DS, Grine FE. 2004 Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa. J. Hum. Evol. 47, 399–452. (doi:10.1016/j.jhevol.2004.08.008)
8. Zeitoun V. 2009 The human canopy: Homo erectus, Homo soloensis, Homo pekinensis and Homo floresiensis. Oxford, UK: J. and E. Hedges.
9. Kluge AG. 1989 A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7–25. (doi:10.2307/2992432)
10. Argue D, Morwood MJ, Sutikna T, Jatmiko, Saptomo W. 2009 Homo floresiensis: a cladistic analysis. J. Hum. Evol. 57, 623–639. (doi:10.1016/j.jhevol.2009.05.002)
11. Berger LR, de Ruiter DJ, Churchill SE, Schmid P, Carlson KJ, Dirks PHGM, Kibii JM. 2010 Australopithecus sediba: a new species of Homo-like australopith from South Africa. Science 328, 195–204. (doi:10.1126/science.1184944)
12. Cameron DW, Groves CP. 2004 Bones, stones and molecules: out of Africa and human origins. San Diego, CA: Elsevier.
13. Cameron D, Patnaik R, Sahni A. 2004 The phylogenetic significance of the Middle Pleistocene Narmada hominin cranium from central India. Int. J. Osteoarchaeol. 14, 419–447. (doi:10.1002/oa.725)
14. Chang ML. 2005 Neandertal origins, Middle Pleistocene systematics, and tests of current taxonomic and phylogenetic hypotheses. PhD dissertation, University of Pennsylvania, Philadelphia, PA, USA.
15. Gilbert WH. 2008 Homo erectus cranial anatomy. In Homo erectus: Pleistocene evidence from the Middle Awash, Ethiopia (eds WH Gilbert, B Asfaw), pp. 265–311. Berkeley, CA: University of California Press.
16. Irish JD, Guatelli-Steinberg D, Legge SS, de Ruiter DJ, Berger LR. 2013 Dental morphology and the phylogenetic ‘place’ of Australopithecus sediba. Science 340, 1233062. (doi:10.1126/science.1233062)
17. Lordkipanidze D, Ponce de León MS, Margvelashvili A, Rak Y, Rightmire GP, Vekua A, Zollikofer CPE. 2013 A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo. Science 342, 326–331. (doi:10.1126/science.1238484)
18. Mounier A, Marchal F, Condemi S. 2009 Is Homo heidelbergensis a distinct species? New insight on the Mauer mandible. J. Hum. Evol. 56, 219–246. (doi:10.1016/j.jhevol.2008.12.006)
19. Nylander J, Ronquist F, Huelsenbeck J, Nieves-Aldrey J. 2004 Bayesian phylogenetic analysis of combined data. Syst. Biol. 53, 47–67. (doi:10.1080/10635150490264699)
20. Pyron RA. 2011 Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60, 466–481. (doi:10.1093/sysbio/syr047)
21. Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP. 2012 A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera. Syst. Biol. 61, 973–999. (doi:10.1093/sysbio/sys058)
22. Bergsten J, Nilsson AN, Ronquist F. 2013 Bayesian tests of topology hypotheses with an example from diving beetles. Syst. Biol. 62, 660–673. (doi:10.1093/sysbio/syt029)
23. Lee MSY, Cau A, Naish D, Dyke GJ. 2014 Morphological clocks in palaeontology, and a mid-Cretaceous origin of crown Aves. Syst. Biol. 63, 442–449. (doi:10.1093/sysbio/syt110)
24. Kass RE, Raftery AE. 1995 Bayes Factors. J. Am. Stat. Assoc. 90, 773–795. (doi:10.1080/01621459.1995.10476572)
25. Rightmire GP, Lordkipanidze D, Vekua A. 2006 Anatomical descriptions, comparative studies and evolutionary significance of the hominin skulls from Dmanisi, Republic of Georgia. J. Hum. Evol. 50, 115–141. (doi:10.1016/j.jhevol.2005.07.009)
26. Gabunia L et al. 2000 Earliest Pleistocene hominid cranial remains from Dmanisi, Republic of Georgia: taxonomy, geological setting, and age. Science 288, 1019–1025. (doi:10.1126/science.288.5468.1019)
27. Gabounia L, de Lumley MA, Vekua A, Lordkipanidze D, de Lumley H. 2002 De´couverte d’un nouvel hominide´ a` Dmanissi (Transcaucasie, Ge´orgie). C. R. Palevol. 1, 243–253. (doi:10.1016/S1631-0683(02)00032-5)
28. Schwartz JH, Tattersall I, Chi Z. 2014 Comment on ‘A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo‘. Science 344, 360. (doi:10.1126/science.1250056)
29. Martinón-Torres M, Bermúdez de Castro JM, Gómez- Robles A, Margvelashvili A, Prado L, Lordkipanidze D, Vekua A. 2008 Dental remains from Dmanisi (Republic of Georgia): morphological analysis and comparative study. J. Hum. Evol. 55, 249–273. (doi:10.1016/j.jhevol.2007.12.008)
30. Bermúdez de Castro JM, Martinón-Torres M, Sier MJ, Martín-Francés L. 2014 On the variability of the Dmanisi mandibles. PLoS ONE 9, e88212. (doi:10.1371/journal.pone.0088212)
31. Aiello LC. 2015 Homo floresiensis. In Handbook of paleoanthropology (eds W Henke, I Tattersall), 2nd edn, pp. 2281–2297. New York, NY: Springer.
32. Lewis PO. 2001 A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913–925. (doi:10.1080/106351501753462876)
33. Ronquist F et al. 2012 MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61, 539–542. (doi:10.1093/sysbio/sys029)
34. Miller MA, Pfeiffer W, Schwartz T. 2010 Creating the CIPRES science gateway for inference of large phylogenetic trees. In Proc. Gateway Computing Environments Workshop (GCE), pp. 1–8. New York, NY: IEEE. (doi:10.1109/GCE.2010.5676129)
35. Zuckerkandl E, Pauling L. 1962 Molecular disease, evolution, and genetic heterogeneity. In Horizons in biochemistry (eds M Kasha, B Pullman), pp. 189–225. New York, NY: Academic Press.
36. Thorne JL, Kishino H. 2002 Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51, 689–702. (doi:10.1080/10635150290102456)
37. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006 Relaxed phylogenetics and dating with confidence. PLoS Biol. 4, e88. (doi:10.1371/journal.pbio.0040088)
38. Xie W, Lewis PO, Fan Y, Kuo L, Chen MH. 2011 Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol. 60, 150–160. (doi:10.1093/sysbio/syq085)
39. Fan Y, Wu R, Chen MH, Kuo L, Lewis PO. 2011 Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28, 523–532. (doi:10.1093/molbev/msq224)
40. Pickering R, Dirks PHGM, Jinnah Z, de Ruiter DJ, Churchil SE, Herries AIR, Woodhead JD, Hellstrom JC, Berger LR. 2011 Australopithecus sediba at 1.977 Ma and implications for the origins of the genus Homo. Science 333, 1421–1423. (doi:10.1126/science.1203697)
41. Balter M. 2010 Candidate human ancestor from South Africa sparks praise and debate. Science 328, 154–155. (doi:10.1126/science.328.5975.154)
42. Kimbel WH. 2013 Hesitation on hominin history. Nature 497, 573–574. (doi:10.1038/497573a)
43. Collard M, Wood B. 2015 Defining the genus Homo. In Handbook of paleoanthropology (eds W Henke, I Tattersall), 2nd edn, pp. 2107–2144. New York, NY: Springer.
44. Schrenk F, Kullmer O, Bromage T. 2015 The earliest putative Homo fossils. In Handbook of paleoanthropology (eds W Henke, I Tattersall), 2nd edn, pp. 2145–2166. New York, NY: Springer.
45. Villmoare B, Kimbel WH, Seyoum C, Campisano CJ, Dimaggio EN, Rowan J, Braun DR, Arrowsmith JR, Reed KE. 2015 Early Homo at 2.8 Ma from Ledi- Geraru, Afar, Ethiopia. Science 347, 1352–1355. (doi:10.1126/science.aaa1343)
46. Strait DS. 2013 The biogeographic implications of early hominin phylogeny. In The paleobiology of Australopithecus (eds KE Reed, JG Fleagle, RE Leakey), pp. 183–194. New York, NY: Springer.
47. Curnoe D. 2010 A review of early Homo in southern Africa focusing on cranial, mandibular and dental remains, with the description of a new species (Homo gautengensis sp. nov.). Homo 61, 151–177. (doi:10.1016/j.jchb.2010.04.002)
48. Gabunia L, Vekua A. 1995 A Plio-Pleistocene hominid from Dmanisi, East Georgia, Caucasus. Nature 373, 509–512. (doi:10.1038/373509a0)
49. Vekua A et al. 2002 A new skull of early Homo from Dmanisi, Georgia. Science 297, 85–89. (doi:10.1126/science.1072953)
50. Lordkipanidze D et al. 2005 The earliest toothless hominin skull. Nature 434, 717–718. (doi:10.1038/434717b)
51. Lordkipanidze D et al. 2007 Postcranial evidence from early Homo from Dmanisi, Georgia. Nature 449, 305–310. (doi:10.1038/nature06134)
52. Ferring R et al. 2011 Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85– 1.78 Ma. Proc. Natl Acad. Sci. USA 108, 10432–10436. (doi:10.1073/pnas.1106638108)
53. Spoor F. 2013 Small-brained and big-mouthed. Nature 502, 452–453. (doi:10.1038/502452a)
54. Schwartz JH. 2000 Taxonomy of the Dmanisi Crania. Science 289, 55–56. (doi:10.1126/science.289.5476.55b)
55. Skinner MM, Gordon AD, Collard NJ. 2006 Mandibular size and shape variation in the hominins at Dmanisi, Republic of Georgia. J. Hum. Evol. 51, 36–49. (doi:10.1016/j.jhevol.2006.01.006)
56. Zollikofer CPE, Ponce de León MS, Margvelashvili A, Rightmire GP, Lordkipanidze D. 2014 Response to comment on ‘A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo’. Science 344, 360. (doi:10.1126/science.1250081)
57. Brown P, Sutikna T, Morwood MJ, Soejono RP, Jatmiko, Saptomo EW, Due RA. 2004 A new smallbodied hominin from the Late Pleistocene of Flores, Indonesia. Nature 431, 1055–1061. (doi:10.1038/nature02999)
58. Morwood MJ et al. 2004 Archaeology and age of a new hominin from Flores in eastern Indonesia. Nature 431, 1087–1091. (doi:10.1029/2002JA009753)
59. Roberts RG, Westaway KE, Zhao J, Turney CSM, Bird MI, Rink WJ, Fifield LK. 2009 Geochronology of cave deposits at Liang Bua and of adjacent river terraces in the Wae Racang valley, western Flores, Indonesia: a synthesis of age estimates for the type locality of Homo floresiensis. J. Hum. Evol. 57, 484–502. (doi:10.1016/j.jhevol.2009.01.003)
60. Morwood MJ, Jungers WL. 2009 Conclusions: implications of the Liang Bua excavations for hominin evolution and biogeography. J. Hum. Evol. 57, 640–648. (doi:10.1016/j.jhevol.2009.08.003)
61. Kubo D, Kono RT, Kaifu Y. 2013 Brain size of Homo floresiensis and its evolutionary implications. Proc. R. Soc. B 280, 20130338. (doi:10.1098/rspb.2013.0338)
62. Kaifu Y, Baba H, Sutikna T, Morwood MJ, Kubo D, Saptomo EW, Jatmiko, Awe RD, Djubiantono T. 2011 Craniofacial morphology of Homo floresiensis: description, taxonomic affinities, and evolutionary implication. J. Hum. Evol. 61, 644–682. (doi:10.1016/j.jhevol.2011.08.008)
63. Henneberg M, Thorne A. 2004 Flores human may be a pathological Homo sapiens. Before Farming 4, 2–4.
64. Henneberg M, Eckhardt RB, Chavanaves S, Hsu KJ. 2014 Evolved developmental homeostasis disturbed in LB1 from Flores, Indonesia, denotes Down syndrome and not diagnostic traits of the invalid species Homo floresiensis. Proc. Natl Acad. Sci. USA 111, 11 967–11 972. (doi:10.1073/pnas.1407382111)
65. Brown P, Maeda T. 2009 Liang Bua Homo floresiensis mandibles and mandibular teeth: a contribution to the comparative morphology of a new hominin species. J. Hum. Evol. 57, 571–596. (doi:10.1016/j.jhevol.2009.06.002)
66. Hershkovitz I, Kornreich L, Larson Z. 2007 Comparative skeletal features between Homo floresiensis and patients with primary growth hormone insensitivity (Laron syndrome). Am. J. Phys. Anthropol. 132, 535–544. (doi:10.1002/ajpa.20655)
67. Obendorf PJ, Oxnard CE, Kefford BJ. 2008 Are the small human-like fossils found on Flores human endemic cretins? Proc. R. Soc. B 275, 1287–1296. (doi:10.1098/rspb.2007.1488)
68. Dennell R. 2009 The palaeolithic settlement of Asia. New York, NY: Cambridge University Press.
69. Pagel M, Meade A. 2008 Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo. Phil. Trans. R. Soc. B 363, 3955–3964. (doi:10.1098/rstb.2008.0178)
70. Tocheri MW et al. 2007 The primitive wrist of Homo floresiensis and its implications for hominin evolution. Science 317, 1743–1745. (doi:10.1126/science.1147143)
71. Jungers WL, Harcourt-Smith WEH, Wunderlich RE, Tocheri MW, Larson SG, Sutikna T, Due RA, Morwood MJ. 2009 The foot of Homo floresiensis. Nature 459, 81–84. (doi:10.1038/nature07989)