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Homo rudolfensis Samples from Olduvai Gorge, East Lake Turkana, and Lake Malawi were included in this study. The East Lake Turkana fossils available prior to 2010 were examined first-hand, while for the Olduvai and Lake Malawi fossils and KNM-ER 60000, 62000, and 62003 we relied on original observations on fossils and casts as well as published reports (Schrenk et al., 1993; Blumenschine et al., 2003; Leakey et al., 2012). We include the following fossils in the hypodigm of H. rudolfensis: KNM-ER 819, KNM-ER 1470, KNM-ER 1482, KNM-ER 1483, KNM-ER 1590, KNM-ER 1801, KNM-ER 1802, KNM-ER 3732, KNM-ER 3891, KNM-ER 60000, KNM-ER 62000, KNM-ER 62003, OH 65, and UR 501. We do recognize that KNM-ER 60000 and KNM-ER 1802 present some conflicting anatomy that some authors have argued precludes them as conspecific specimens (Leakey et al., 2012); by considering both, we aim to be conservative as they encompass more variation within H. rudolfensis., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Australopithecus africanus The samples attributed to Au. africanus from Taung, Sterkfontein and Makapansgat were employed. Original specimens were examined first-hand by the authors., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Paranthropus boisei Samples from the Omo Shungura sequence, East Lake Turkana, Olduvai Gorge and Konso were included in this study. Original specimens from Olduvai Gorge and East Lake Turkana were examined first-hand, while casts and published reports (Tobias, 1967; Suwa et al., 1996, 1997; Do ḿınguez- Rodrigo et al., 2013) were used to study the Omo and Konso materials. Our postcranial considerations of P. boisei are very limited and we did not rely upon the association of KNM-ER 1500 (Grausz et al., 1988) to derive information about the postcranial skeleton of P. boisei. Paranthropus robustus The samples from Kromdraai, Swartkrans, Sterkfontein, Drimolen, Gondolin, and Coopers were included in this study. First-hand observations of original specimens from all localities were used with the exception of Drimolen fossils, which were compared using published reports (Keyser, 2000; Keyser et al., 2000)., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Paranthropus aethiopicus The cranium KNM-WT 17000 was examined first-hand for this study., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Homo erectus Samples from Buia, Chemeron, Daka, Dmanisi, East and West Lake Turkana, Gona, Hexian, Konso, Mojokerto, Olduvai Gorge, Sangiran, Swartkrans, Trinil, and Zhoukoudian were included in this study. South African material is of special interest in this comparison because of the geographic proximity, and because of the difficulty of clearly identifying Homo specimens within the large fossil sample from Swartkrans. In particular, the following specimens from Swartkrans are considered to represent H. erectus: SK 15, SK 18a, SK 27, SK 43, SK 45, SK 68, SK 847, SK 878, SK 2635, SKW 3114, SKX 257/258, SKX 267/ 2671, SKX 268, SKX 269, SKX 334, SKX 339, SKX 610, SKX 1756, SKX 2354, SKX 2355, SKX 2356, and SKX 21204. It has been suggested (Grine et al., 1993, 1996) that SK 847 and Stw 53 might represent the same taxon, and that this taxon is a currently undiagnosed species of Homo in South Africa. However, we agree with Clarke (1977; 2008) that SK 847 can be attributed to H. erectus, and that Stw 53 cannot. Because there is no clear indication that more than one species of Homo is represented in the Swartkrans sample, we consider all this material to belong to H. erectus. We considered ‘ Homo ergaster ’ (and also ‘ Homo aff. erectus ’ from Wood, 1991) to be synonyms of H. erectus for this study; Turkana Basin specimens that are attributed to H. erectus thus include KNM-ER 730, KNM-ER 820, KNM-ER 992, KNM- ER 1808, KNM-ER 3733, KNM-ER 3883, KNM-ER 42700, KNM-WT 15000. Olduvai specimens include OH 9, OH 12 and OH 28. Original fossil materials from Chemeron, Lake Turkana, Swartkrans, Trinil, and Dmanisi were examined first-hand by the authors, while the remainder were based on casts and published reports (Weidenreich, 1943; Wood, 1991; Anton´, 2003; Rightmire et al., 2006; Suwa et al., 2007). A large number of postcranial specimens have been collected from the Turkana Basin and appear consistent with the anatomical range otherwise found in Homo, and inconsistent with known samples of Australopithecus and Paranthropus from elsewhere. These include KNM-ER 1472, KNM-ER 1481, KNM- ER 3228, KNM-ER 737, and others. We may add other fossils from other sites lacking association with craniodental material, such as the partial BOU-VP 12/1 skeleton and even the Gona pelvis. These specimens attributable to Homo but not necessarily to a particular species did inform our understanding of variability within the genus, but for the most part these specimens do not inform our differential diagnosis of H. naledi relative to particular species. For example, the key element of femoral morphology of H. naledi in contrast to other species is the presence of two well-defined mediolaterally running pillars in the femoral neck; the isolated specimens of early Homo do not contradict this apparent autapomorphy. Likewise, no isolated specimens inform us about the humanlike aspects of foot morphology in H. naledi. In these cases, the lack of associations for this evidence actually is less important than the lack of specimens that replicate the distinctive features of the H. naledi morphology., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 27, DOI: 10.7554/eLife.09560

Australopithecus garhi The cranium BOU-VP-12/130 from Bouri was included, with data taken from a published report (Asfaw et al., 1999)., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Australopithecus sediba The partial skeletons MH1 and MH2 from Malapa, South Africa were included in this study, based on examination of the original specimens by the authors., Published as part of Lee R Berger, John Hawks, Darryl J de Ruiter, Steven E Churchill, Peter Schmid, Lucas K Delezene, Tracy L Kivell, Heather M Garvin, Scott A Williams, Jeremy M DeSilva, Matthew M Skinner, Charles M Musiba, Noel Cameron, Trenton W Holliday, William Harcourt-Smith, Rebecca R Ackermann, Markus Bastir, Barry Bogin, Debra Bolter, Juliet Brophy, Zachary D Cofran, Kimberly A Congdon, Andrew S Deane, Mana Dembo, Michelle Drapeau, Marina C Elliott, , Elen M Feuerriegel, Daniel Garcia-Martinez, David J Green, Alia Gurtov, Joel D Irish, Ashley Kruger, Myra F Laird, Damiano Marchi, Marc R Meyer, Shahed Nalla, Enquye W Negash, Caley M Orr, Davorka Radovcic, Lauren Schroeder, Jill E Scott, Zachary Throckmorton, Matthew W Tocheri, Caroline VanSickle, Christopher S Walker, Pianpian Wei & Bernhard Zipfel, 2015, Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa, pp. 1-35 in eLife e 09560 4 on page 26, DOI: 10.7554/eLife.09560

Middle Pleistocene Homo Specimens from the latest Lower Pleistocene and MP of Europe and Africa that cannot be attributed to H. erectus were included in our comparisons. These include fossils that have been attributed to H. heidelbergensis, H. rhodesiensis, ‘archaic H. sapiens ’, or ‘evolved H. erectus ’ by a variety of other authors. Specimens attributed to MP Homo include materials from Eliye Springs, Arago, Atapuerca Sima de los Huesos, Bodo, Broken Hill, Cave of Hearths, Ceprano, Dali, Elandsfontein, Jinniushan, Kapthurin, Mauer, Narmada, Ndutu, Petralona, Reilingen-Schwetzingen, Solo, Steinheim, Swanscombe. This grouping includes the following specimens: KNM-ES 11693, Arago 2, Arago 13, Arago 21, Atapuerca 1, Atapuerca 2, Atapuerca 4, Atapuerca 5, Atapuerca 6, Cave of Hearths, SAM-PQ- EH1, Kabwe, Mauer, Ndutu, Sale´, Petralona, Reilingen-Schwetzingen, Steinheim.