The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods

Mana Dembo, Davorka Radovčić, Heather M. Garvin, Myra F. Laird, Lauren Schroeder, Jill E. Scott, Juliet Brophy, Rebecca R. Ackermann, Chares M. Musiba, Darryl J. de Ruiter, Arne Ø. Mooers, Mark Collard

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Abstract

Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka (thousands of years ago). This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed.
Original languageEnglish
Pages (from-to)17-26
Number of pages10
JournalJournal of Human Evolution
Volume97
Early online date12 Jun 2016
DOIs
Publication statusPublished - Aug 2016

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Bayesian analysis
Homo
phylogenetics
phylogeny
fossil
Bayesian theory
methodology
fossils
method
South Africa
analysis

Keywords

  • Dinaledi hominins
  • Bayesian phylogenetic analysis
  • Morphological clock
  • Genus Homo

Cite this

Dembo, M., Radovčić, D., Garvin, H. M., Laird, M. F., Schroeder, L., Scott, J. E., ... Collard, M. (2016). The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods. Journal of Human Evolution, 97, 17-26. https://doi.org/10.1016/j.jhevol.2016.04.008

The evolutionary relationships and age of Homo naledi : an assessment using dated Bayesian phylogenetic methods. / Dembo, Mana; Radovčić, Davorka; Garvin, Heather M.; Laird, Myra F.; Schroeder, Lauren ; Scott, Jill E.; Brophy, Juliet; Ackermann, Rebecca R.; Musiba, Chares M.; de Ruiter, Darryl J.; Mooers, Arne Ø.; Collard, Mark.

In: Journal of Human Evolution, Vol. 97, 08.2016, p. 17-26.

Research output: Contribution to journalArticle

Dembo, M, Radovčić, D, Garvin, HM, Laird, MF, Schroeder, L, Scott, JE, Brophy, J, Ackermann, RR, Musiba, CM, de Ruiter, DJ, Mooers, AØ & Collard, M 2016, 'The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods', Journal of Human Evolution, vol. 97, pp. 17-26. https://doi.org/10.1016/j.jhevol.2016.04.008
Dembo, Mana ; Radovčić, Davorka ; Garvin, Heather M. ; Laird, Myra F. ; Schroeder, Lauren ; Scott, Jill E. ; Brophy, Juliet ; Ackermann, Rebecca R. ; Musiba, Chares M. ; de Ruiter, Darryl J. ; Mooers, Arne Ø. ; Collard, Mark. / The evolutionary relationships and age of Homo naledi : an assessment using dated Bayesian phylogenetic methods. In: Journal of Human Evolution. 2016 ; Vol. 97. pp. 17-26.
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title = "The evolutionary relationships and age of Homo naledi: an assessment using dated Bayesian phylogenetic methods",
abstract = "Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka (thousands of years ago). This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed.",
keywords = "Dinaledi hominins, Bayesian phylogenetic analysis, Morphological clock, Genus Homo",
author = "Mana Dembo and Davorka Radovčić and Garvin, {Heather M.} and Laird, {Myra F.} and Lauren Schroeder and Scott, {Jill E.} and Juliet Brophy and Ackermann, {Rebecca R.} and Musiba, {Chares M.} and {de Ruiter}, {Darryl J.} and Mooers, {Arne {\O}.} and Mark Collard",
note = "Acknowledgements We wish to express our gratitude to the National Geographic Society and the National Research Foundation of South Africa for funding the discovery, recovery, and analysis of the H. naledi material. The study reported here was also made possible by grants from the Social Sciences and Humanities Research Council of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, the Canada Research Chairs Program, Simon Fraser University, the DST/NRF Centre of Excellence in Palaeosciences (COE-Pal), as well as by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, a Young Scientist Development Grant from the Paleontological Scientific Trust (PAST), a Baldwin Fellowship from the L.S.B. Leakey Foundation, and a Seed Grant and a Cornerstone Faculty Fellowship from the Texas A&M University College of Liberal Arts. We would like to thank the South African Heritage Resource Agency for the permits necessary to work on the Rising Star site; the Jacobs family for granting access; Wilma Lawrence, Bonita De Klerk, Merrill Van der Walt, and Justin Mukanku for their assistance during all phases of the project; Lucas Delezene for valuable discussion on the dental characters of H. naledi. We would also like to thank Peter Schmid for the preparation of the Dinaledi fossil material; Yoel Rak for explaining in detail some of the characters used in previous studies; William Kimbel for drawing our attention to the possibility that there might be a problem with Dembo et al.’s (2015) codes for the two characters related to the articular eminence; Will Stein for helpful discussion about the Bayesian analyses; Mike Lee for his comments on this manuscript; John Hawks for his support in organizing the Rising Star workshop; and the associate editor and three anonymous reviewers for their valuable comments. We are grateful to S. Potze and the Ditsong Museum, B. Billings and the School of Anatomical Sciences at the University of the Witwatersrand, and B. Zipfel and the Evolutionary Studies Institute at the University of the Witwatersrand for providing access to the specimens in their care; the University of the Witwatersrand, the Evolutionary Studies Institute, and the South African National Centre of Excellence in PalaeoSciences for hosting a number of the authors while studying the material; and the Western Canada Research Grid for providing access to the high-performance computing facilities for the Bayesian analyses. Last but definitely not least, we thank the head of the Rising Star project, Lee Berger, for his leadership and support, and for encouraging us to pursue the study reported here.",
year = "2016",
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T1 - The evolutionary relationships and age of Homo naledi

T2 - an assessment using dated Bayesian phylogenetic methods

AU - Dembo, Mana

AU - Radovčić, Davorka

AU - Garvin, Heather M.

AU - Laird, Myra F.

AU - Schroeder, Lauren

AU - Scott, Jill E.

AU - Brophy, Juliet

AU - Ackermann, Rebecca R.

AU - Musiba, Chares M.

AU - de Ruiter, Darryl J.

AU - Mooers, Arne Ø.

AU - Collard, Mark

N1 - Acknowledgements We wish to express our gratitude to the National Geographic Society and the National Research Foundation of South Africa for funding the discovery, recovery, and analysis of the H. naledi material. The study reported here was also made possible by grants from the Social Sciences and Humanities Research Council of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, the Canada Research Chairs Program, Simon Fraser University, the DST/NRF Centre of Excellence in Palaeosciences (COE-Pal), as well as by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, a Young Scientist Development Grant from the Paleontological Scientific Trust (PAST), a Baldwin Fellowship from the L.S.B. Leakey Foundation, and a Seed Grant and a Cornerstone Faculty Fellowship from the Texas A&M University College of Liberal Arts. We would like to thank the South African Heritage Resource Agency for the permits necessary to work on the Rising Star site; the Jacobs family for granting access; Wilma Lawrence, Bonita De Klerk, Merrill Van der Walt, and Justin Mukanku for their assistance during all phases of the project; Lucas Delezene for valuable discussion on the dental characters of H. naledi. We would also like to thank Peter Schmid for the preparation of the Dinaledi fossil material; Yoel Rak for explaining in detail some of the characters used in previous studies; William Kimbel for drawing our attention to the possibility that there might be a problem with Dembo et al.’s (2015) codes for the two characters related to the articular eminence; Will Stein for helpful discussion about the Bayesian analyses; Mike Lee for his comments on this manuscript; John Hawks for his support in organizing the Rising Star workshop; and the associate editor and three anonymous reviewers for their valuable comments. We are grateful to S. Potze and the Ditsong Museum, B. Billings and the School of Anatomical Sciences at the University of the Witwatersrand, and B. Zipfel and the Evolutionary Studies Institute at the University of the Witwatersrand for providing access to the specimens in their care; the University of the Witwatersrand, the Evolutionary Studies Institute, and the South African National Centre of Excellence in PalaeoSciences for hosting a number of the authors while studying the material; and the Western Canada Research Grid for providing access to the high-performance computing facilities for the Bayesian analyses. Last but definitely not least, we thank the head of the Rising Star project, Lee Berger, for his leadership and support, and for encouraging us to pursue the study reported here.

PY - 2016/8

Y1 - 2016/8

N2 - Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka (thousands of years ago). This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed.

AB - Homo naledi is a recently discovered species of fossil hominin from South Africa. A considerable amount is already known about H. naledi but some important questions remain unanswered. Here we report a study that addressed two of them: “Where does H. naledi fit in the hominin evolutionary tree?” and “How old is it?” We used a large supermatrix of craniodental characters for both early and late hominin species and Bayesian phylogenetic techniques to carry out three analyses. First, we performed a dated Bayesian analysis to generate estimates of the evolutionary relationships of fossil hominins including H. naledi. Then we employed Bayes factor tests to compare the strength of support for hypotheses about the relationships of H. naledi suggested by the best-estimate trees. Lastly, we carried out a resampling analysis to assess the accuracy of the age estimate for H. naledi yielded by the dated Bayesian analysis. The analyses strongly supported the hypothesis that H. naledi forms a clade with the other Homo species and Australopithecus sediba. The analyses were more ambiguous regarding the position of H. naledi within the (Homo, Au. sediba) clade. A number of hypotheses were rejected, but several others were not. Based on the available craniodental data, Homo antecessor, Asian Homo erectus, Homo habilis, Homo floresiensis, Homo sapiens, and Au. sediba could all be the sister taxon of H. naledi. According to the dated Bayesian analysis, the most likely age for H. naledi is 912 ka (thousands of years ago). This age estimate was supported by the resampling analysis. Our findings have a number of implications. Most notably, they support the assignment of the new specimens to Homo, cast doubt on the claim that H. naledi is simply a variant of H. erectus, and suggest H. naledi is younger than has been previously proposed.

KW - Dinaledi hominins

KW - Bayesian phylogenetic analysis

KW - Morphological clock

KW - Genus Homo

U2 - 10.1016/j.jhevol.2016.04.008

DO - 10.1016/j.jhevol.2016.04.008

M3 - Article

VL - 97

SP - 17

EP - 26

JO - Journal of Human Evolution

JF - Journal of Human Evolution

SN - 0047-2484

ER -