Supplementary Materials for - Science

Originally published 11 April 2013; corrected 15 April 2013

www.sciencemag.org/content/340/6129/1233062/suppl/DC1

Supplementary Materials for Dental Morphology and the Phylogenetic “Place” of Australopithecus sediba Joel D. Irish, Debbie Guatelli-Steinberg, Scott S. Legge, Darryl J. de Ruiter, Lee R. Berger *Corresponding author. E-mail: [email protected] Published 11 April 2013 in Science 340, 1233062 (2013) DOI: 10.1126/science.1233062 This PDF file includes: Materials and Methods Supplementary Text Figs. S1 and S2 Table S1 Full References

Correction: An updated Fig. S2 was submitted by the author and appears in this revision.

Materials and Methods Arizona State University Dental Anthropology System (ASUDAS) attributes The primary purpose of the ASUDAS is to standardize the scoring of key morphological features of the permanent dentition (19); in addition, these specific traits: A) can be recorded despite moderate attrition or are unaffected by it (i.e., root form and number), B) are easily identifiable, C) yield excellent intra- and inter-observer replicability, D) have high heritability (18, 32-34) where h2 can reach 0.8-0.9 (18, 35), to serve as a reliable proxy for DNA and other genetic markers (18, 36, 37), E) exhibit low or no sexual dimorphism (19, 24, 35, 38), F) represent all tooth classes [or as suggested by some researchers -- morphogenetic fields (39, 40)], G) are, as “minor” or “secondary” features of the dentition, relatively little affected by selection (18), and H) though polymorphic have, as seen in the fossil record, “shown that (whatever their adaptive value) they evolve very slowly” (18, p. 13); therefore, the conservative nature of their evolution makes them ideal for biodistance analyses (33), at least relative to other, more variable skeletal characters. Moreover, of direct concern here, all ASUDAS traits have been formally assessed for pairwise correlation in many studies over the past 20 years (18, 19, 24); minimal rs and tau-b values indicate little or no character redundancy to bias cladistic analyses (15, 16, 41). The latter is especially important regarding molar traits, given the recently described connection between accessory cusp formation and primary inter-cusp spacing and crown size (20, 42). Use of ASUDAS traits to study modern and fossil specimens Several ASUDAS traits have been used to define fossils since the early 20th Century (43), but the original intent of the ASUDAS was to assess modern variation. As such, not all expression is fully represented in early hominins (21, 32, 44). That said, 29 of 36 traits used by J.D.I. to study recent humans (22, 45, 46) are definable (21). Of these, 22 can be recorded in the partial Au. sediba dentitions; they have also been used to compare fossil hominins (21, 22, 24-26, 32, 47, 48) and Pan and Gorilla (45, 48). Before that, Wood [e.g., (46)] used Dahlberg plaques, the direct ASUDAS “ancestor,” to describe early hominins. ASUDAS traits, evolution, and homoplasy The dentition is essential to survival in animals that rely on their teeth to obtain and process food (18). Thus, “primary” features relating to the dentition as a unit are undoubtedly subject to natural selection, including: tooth number, size, different tooth classes, and inter- and intra-class specializations (e.g., toothcombs in some gumivores, carnassials in certain carnivores, etc.) (18, 39, 40, 49). Selection may have acted upon some minor or secondary ASUDAS variants as well, particularly given the time scale involved in hominin evolution (18, 50). Such traits have been suggested to include shoveling, which provides extra strength (51-52), Carabelli’s (53-54) and other accessory cusps (55), which increase crown mass, and, likely, additional primary cusps that increased the chewing surface area of already-large posterior teeth in Paranthropus. However, the potential functional benefits of these traits have not been clearly demonstrated to be adaptive; their levels of expression are largely, at least since the Pleistocene, population-specific – even in groups exposed to similar environments and diets for similar durations (18). Moreover, many traits are ostensibly 1

neutral (e.g., Y versus X groove) or even disadvantageous (e.g., enamel extensions – that adversely affect gingival attachment), yet are retained. The fact is that, “the role of selection has never been demonstrated for any single [ASUDAS] dental trait” (18, p. 253). Instead, inter-group dental trait variation is thought to result mainly from the chance effects of drift, population structure and, to a lesser extent, mutation (18). The mechanism(s) most responsible for these minor dental variants can, in turn, have an effect on homoplasy. That is, whether through convergence (i.e., trait similarity from different developmental genetic mechanisms or pathways) or parallelism (the same genetic pathways), similar environmental pressures often lead to similar traits in different taxa (see 56). And, whether either type of independent evolution is a result of “adaptively driven homoplasy,” i.e., shared phenotypic adaptations in response to shared life strategies, or “hierarchically determined homoplasy,” i.e., an indirect effect initiated at the level of the genome, the primary causative mechanism is natural selection (56, p. 1032-1033). It thus follows that a minimal role of selection in the appearance and expression of ASUDAS traits should serve to minimize the potential for homoplasy. ASUDAS inter-trait correlation in the present study Very small samples (n = 3-9) precluded determination of correlation in many cases. When Kendall’s tau-b correlation coefficient values were calculated, results support previous findings of low inter-trait correlation. With regard to potentially problematic molar traits, larger inter-trait samples (n = 16-55) allowed more accurate assessment. Values in the maxilla range from tau-b = 0.064 (cusp 5 UM1/Carabelli's UM1) to 0.249 (Carabelli's UM1/ hypocone UM2); those in the mandible are tau-b = 0.032 (cusp 7 LM1/cusp number LM2) to 0.389 (cusp number LM1/ cusp number LM2). Between isomeres, a positive correlation for Carabelli's UM1/protostylid LM1, as might be expected based on recent work (19) occurs; however, it (tau-b = 0.598) is not judged to be high enough in this small comparison (n = 5) to warrant reducing the already low number of traits. Inter-observer concordance in recording ASUDAS traits ASUDAS traits in the teeth of Au. sediba MH1 and MH2 were recorded by J.D.I. Data in the fossil comparative samples were collected in the original specimens by D.G-S. and 11 high resolution casts (see table S1) by J.D.I (21, 22). The two post-Pleistocene H. sapiens samples from sub-Saharan (n=2,309) and North Africa (n=2,262) were recorded by J.D.I. (24-26, 57-59). ASUDAS crown data in the Gorilla gorilla sample (n=44) were recorded by S.S.L. Although specimens were scored by different individuals, inter-observer error should be minimal because the ASUDAS system was used. Any error is minimized further because J.D.I. and D.G-S. jointly reviewed the ASUDAS, and quantified error by scoring the same sample of modern east Africans (n=40) at the American Museum of Natural History (21, 22). A similar comparison was conducted by J.D.I. and S.S.L. at the University of Alaska. No significant differences were revealed, and any deviations were minimal and random.

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Supplementary Text Cladogram statistics and interpretations The consistency index (CI) value of 0.62 falls within the midrange of those in other hominin phylogenetic studies referred to earlier in the text (1, 15-17), among others. The retention index (RI) of 0.48 and rescaled consistency index (RC) of 0.3 are slightly lower. Homoplasy is common in the fossil record (60), but the latter reduction is related in part to standard numeric coding of the ASUDAS characters -- which are mostly quasicontinuous (61). Gap weighting of dichotomized ASUDAS data works well (21), and experimentation (not shown) with the present characters in fewer pooled hominin samples (e.g., aggregating Paranthropus species) yields markedly higher CI, RI, and RC values; however, the Au. sediba sample (n = 2) is too small for this approach.

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Fig. S1.

Fig. S1. Single linkage cluster analysis dendrogram (SPSS 19.0) of eight hominin samples based on 21 ASUDAS trait states from Table 2. LP3 Tome’s root trait was not recorded in the H. erectus sample, so was excluded from the cluster analysis which does not accommodate missing values. Missing data also prompted exclusion of the P. boisei sample. Divergence of the NAF H. sapiens is related to major reduction in morphological complexity (i.e., simplification) relative to fossil hominins and SSA H. sapiens. SSA = sub-Saharan Africans; NAF = North Africans. See text for sample compositions.

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Fig. S2

Right maxillary (on left side of figure) and right mandibular dentition of Au. sediba MH1, showing several of the ASUDAS trait expressions described in the text. *Carabelli’s expression estimated from the appearance at the base of fractured UM1 and interpolation of that on UM2.

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Table S1. Plio-Pleistocene comparative hominin specimens with teeth inspected for the study.1 Australopithecus anamensis KNM-ER 7727 KNM-ER 20420 KNM-ER 20422 KNM-ER 20423 KNM-ER 20427 KNM-ER 20432 A KNM-ER 30200 A KNM-ER 30202 KNM-ER 30731 KNM-ER 30745 KNM-ER 30750 KNM-KP 29287 A KNM-KP 29287 B KNM-LT 329 (cast) Australopithecus afarensis AL 128-23 AL 145-35 AL 176-35 AL 188-1 AL 198 AL 199-1 AL 200-1a AL 200-1b AL 207-13 AL 266 AL 277-1 AL 311-1 AL 315-22 AL 330-5 AL 333-1 AL 333-2 AL 333-82 AL 333-W1a/b AL 333-W57 AL 333-W58 AL 333w-60 AL 333x-2 AL 333x-3 AL 333x-4

AL 333x-20 AL 366-6 AL 400-1a AL 400-1b AL 411-1 AL 413-1 AL 417-1a AL 417-1d AL 438-2 AL 440-1 AL 486-1 AL 539-4e AL 620-1 AL 655-1 AL 763-1 AL 996-1 LH 2 LH 3 (cast) LH 4 (cast) Australopithecus africanus2 MLD 2 MLD 6 MLD 9 MLD 11 MLD 18 MLD 23 MLD 28 MLD 29 MLD 30 MLD 40 MLD 43 STS 1 STS 3 STS 4 STS 8 STS 9 STS 12 STS 17 STS 22 STS 233

STS 243 STS 30 STS 32 STS 40 STS 52 STS 53 STS 55 STS 56 STS 57 STS 61 STS 71 STW 2 STW 6 STW 7 STW 13 (b,f) STW 19b STW 21 STW 23 STW 24 STW 43 STW 44 STW 50 STW 53 STW 56 STW 58 STW 61 STW 71 STW 73 (b–f) STW 75d STW 106 STW 107 STW 109b STW 110 STW 116d STW 123a STW 123b STW 131 (b,c,d) STW 132 STW 143 STW 145 STW 147 STW 148 STW 151 (a,b) 6

STW 179 STW 183 (c,e,h) STW 184 STW 188 STW 192 (a,b) STW 193 (a, b, c, d,e) STW 204 (a,b) STW 212 (a,c,e,f) STW 213 (a–g) STW 234 STW 246 STW 252 (a, c–l ) STW 280c STW 285 (a,b) STW 287 STW 288 STW 291 STW 295 (c,d) STW 305b STW 308 STW 309a STW 319 STW 327 (b–d) STW 351 STW 364 STW 365 STW 369 STW 384e STW 401 STW 402 STW 404 (c,f,g) STW 406 STW 408 STW 412 (a,b) STW 413 STW 420b STW 421 (a,b) STW 422 STW 424 STW 446 STW 447 STW 471 (c,g) STW 475 STW 476 STW 487b STW 491 (b–g )

STW 498 (a–d ) STW 502 STW 513 (c–e) STW 524 STW 529 (b,c) STW 536 STW 537 (d,f,g) STW 558 STW 560 (d,e) STW 566 Taung TM 1511 TM 1512 TM 1523 TM 1527 Homo habilis/ rudolfensis AL 666-1 KNM-ER 1482(cast) KNM-ER 1590 B, C,D,E,F,G KNM-ER 1802 KNM-ER 1805 KNM-ER 1813 KNM-LU 335 OH 7 (cast) OH 13 OH 16 OH 24 OH 39 OH 44 OH 45 OH 62 OH 63 SKW 31144 Homo erectus KNM-BK 67 (cast) KNM-ER 806 B, C KNM-ER 807 KNM-ER 808 C,G KNM-ER 820 KNM-ER 992 A, B KNM-ER 1506 A, B KNM-ER 2597

KNM-WT 15000 OH 12 (cast) OH 22 (cast) SK 154 SKX 2574,5 SKX 2584,5 SKX 2684 SKX 3344 SKX 3394 SKX 6104 Paranthropus robustus KB 5223 SK 1 SK 2 SK 3 SK 5 SK 6 SK 11 SK 13 SK 15 SK 23 SK 24 SK 25 SK 29 SK 30 SK 33 SK 34 SK 37 SK 40 SK 42 SK 44 SK 47 SK 48 SK 49 SK 52 SK 55a SK 57 SK 61 SK 63 SK 656 SK 65a6 SK 676 SK 68 SK 697 SK 72 7

SK 737 SK 81 SK 83 SK 85a8 SK 87 SK 89 SK 938 SK 94 SK 98 SK 104 SK 821 SK 822 SK 823 SK 826a9 SK 829 SK 831 SK 834 SK 837 SK 838a SK 8439 SK 846a9 SK 857 SK 867 SK 1587 SK 1588 SK 3974 SK 3976 SK 14000 SK 14001 SKW 5

SKW 8 SKW 10 SKW 12 SKW 14 SKW 33 SKW 831a SKW 3068 SKW 4767 SKW 4769 SKW 4772 SKX 16210 SKX 24011 SKX 241 SKX 24211 SKX 265 SKX 271 SKX 30810 SKX 31112 SKX 101612 SKX 3300 SKX 3355 SKX 3601 SKX 4446 SKX 5007 SKX 5013 SKX 5023 SKX 6013 SKX 7781 SKX 19031 SKX 19892

SKX 25296 SKX 27524 SKX 28724 TM 1517a TM 1517b TM 1536 TM 1600 TM 1601 Paranthropus boisei KNM-CH 1 (cast) KNM-CH 18 KNM-ER 802 E, F KNM-ER 816 KNM-ER 1171 B, E, F, G, H KNM-ER 1816 KNM-ER 1818 KNM-ER 1820 KNM-ER 3230 KNM-ER 5431 KNM-ER 6080 KNM-ER 6128 KNM-ER 15930 KNM-ER 17760 KNM-ER 25520 OH5 (cast) KNM-WT 17400 Peninj

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KB, SK, SKW, SKX, and TM specimens at Transvaal Museum; KNM, LH, and OH specimens at Kenya National Museum; Original OH5 specimen at the National Museum of Tanzania; MLD, STS, STW, and Taung specimens at University of the Witwatersrand. 2 Following Suwa et al. (62), Sterkfontein Member 5 specimens are included in taxon Au. africanus. 3 STW 23 and STW 24 may be antimeres (D.G-S. personal observation). 4 SKW 3114 through SKX 610 species status has been questioned (27, 63) but, among other reasons, current dental traits are identical to those in Homo habilis/rudolfensis or erectus samples). 5 SKX 257 and SKX 258 are antimeres (64). 6 SK 65/65a/67 from the same individual (65). 7 SK 69 and 73 from the same individual (65). 8 SK 85a and SK 93 from the same individual (65). 9 SK 826a, SK 843, and SK 846a from the same individual (65). 10 SKX 162 and 308 from the same individual (64). 11 SKX 240 and SKX 242 are antimeres (64). 12 SKX 311 and SKX 1016 may be antimeres (64).

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