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. 2021 Aug;596(7873):543-547.
doi: 10.1038/s41586-021-03823-6. Epub 2021 Aug 25.

Genome of a middle Holocene hunter-gatherer from Wallacea

Selina Carlhoff #  1   2 , Akin Duli #  3 , Kathrin Nägele  1   2 , Muhammad Nur  3 , Laurits Skov  2 , Iwan Sumantri  3 , Adhi Agus Oktaviana  4   5 , Budianto Hakim  6 , Basran Burhan  7 , Fardi Ali Syahdar  8 , David P McGahan  7 , David Bulbeck  9 , Yinika L Perston  7 , Kim Newman  7 , Andi Muhammad Saiful  6 , Marlon Ririmasse  4 , Stephen Chia  10 , Hasanuddin  6 , Dwia Aries Tina Pulubuhu  11 , Suryatman  6 , Supriadi  3 , Choongwon Jeong  12 , Benjamin M Peter  2 , Kay Prüfer  1   2 , Adam Powell  2 , Johannes Krause  13   14 , Cosimo Posth  15   16   17 , Adam Brumm  18
Affiliations

Genome of a middle Holocene hunter-gatherer from Wallacea

Selina Carlhoff et al. Nature. 2021 Aug.

Abstract

Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Study site location.
a, Sulawesi and Wallacea. The red rectangle indicates the region shown in b. b, Leang Panninge. The dotted line indicates Toalean site distribution.
Fig. 2
Fig. 2. The Leang Panninge genome within the regional genetic context.
a, PCA calculated on present-day individuals from eastern Eurasia and Near Oceania, projecting key ancient individuals from the region,–. b, Shared genetic drift of present-day groups with the Leang Panninge individual, as calculated using f3 (Mbuti; Leang Panninge, X) mapped at the geographical position of the tested group. WGA, whole genome amplification. c, The amount of introgressed Denisovan sequence in fragments longer than 0.05 cM in present-day (Simons Genome Diversity Project) individuals and longer than 0.2 cM in ancient individuals (measured with admixfrog). Each bar represents the posterior mean estimate from a single genome and the whiskers indicate 2 s.d. (estimated from 200 samples from the posterior decoding).
Fig. 3
Fig. 3. Admixture signals detected in the Leang Panninge genome.
a, Admixture proportions modelling Leang Panninge as a combination of Papuan and Tianyuan or Onge groups as estimated by qpAdm using Mbuti, Denisovan, Kostenki 14 (ref. ) and ancient Asian individuals, as rotating reference groups (Supplementary Table 26). The error bars denote standard errors as calculated with block jacknife in the qpAdm software. b, c, Admixture graphs placing Leang Panninge on the branch with the present-day Near Oceanian clade and showing the admixture with a deep Asian-related ancestry in TreeMix (b) (Extended Data Fig. 10, Supplementary Fig. 6) and qpGraph (c) (worst z-score of −2.194; Supplementary Figs. 7–11),–,. In b, ‘1’ and ‘2’ refer to the order in which the TreeMix software added ‘migration events’ (indicated by the arrows) to the graph. When plotting qpGraph results (c), the dotted arrows indicate admixture edges.
Extended Data Fig. 1
Extended Data Fig. 1. Toalean artefact types and excavations at Leang Panninge.
a, b, Typical middle-to-late Holocene artefact types from Toalean assemblages in South Sulawesi; pressure-flaked stone ‘Maros points’ (both artefacts are from Leang Pajae, Maros) (a) and backed microliths (top: Leang Pajae; bottom: Leang Bulu Bettue, Maros) (b). c, Osseous points (left: from the layer 4 Toalean human burial, Leang Panninge; right: Leang Rakkoe, Maros). d–i, Excavation at Leang Panninge in 2019. Excavation of a trench placed adjacent to the rear wall in the west-facing cave entrance (d, e): viewed from northwest to southeast (note that the name of the cave site is incorrectly transcribed in this locally produced banner) (d); viewed from north to south (e); northwest to southeast (f); detail of the excavation work (g). Excavated trench faces at the end of the 2019 field season, following soil column-sampling (h, i): trench viewed from northeast to southwest, showing the intersection between the western walls of excavation squares S16T6 and S17T6 and southern walls of S17T6 and S17T7 (h); trench viewed from north to south, with the main stratigraphic section facing the viewer showing the northern walls of S16T6 and S16T7 (i). Image credits: Y. Perston (a–c); Leang Panninge research team (d–i).
Extended Data Fig. 2
Extended Data Fig. 2. Site plan, stratigraphy and dating evidence at Leang Panninge.
a–c, Plan views of the cave site showing the locations of previous excavation units and squares S16T6 and S17T6, where the Toalean burial was exposed in 2015. Excavations in the west-facing entrance (which is 10-m high and 28-m wide) yielded dense Toalean archaeological assemblages. Light grey, limestone bedrock; dark grey, speleothem column/pillar; grey with x, stalagmite. Contour levels are in centimetres. Acronyms and initialisms denoting Indonesian archaeological institutions and heritage departments are as follows: BALAR, Balai Arkeologi Sulawesi Selatan; BPCB, Balai Pelestarian Cagar Budaya Makassar; UNHAS, Universitas Hasanuddin. The 2015 trench was extended in 2019, forming squares S16T7 and S17T7. d, Section of the cave mouth. e, Stratigraphy and dating. L1, layer 1; L2, layer 2, and so on. Black dots denote the 3D-plotted positions of stone artefacts, faunal items (bone, teeth and shell), palaeobotanical remains, shells and other findings excavated in 2019. Eight distinct archaeological layers of human occupation are evident: the uppermost cultural stratum, layer 1 (approximately 1.5 kyr cal bp), contains ‘Neolithic’ pottery and Toalean backed microliths; layers 2–4 comprise aceramic Toalean occupation deposits. Maros points pre-date backed microliths and appear in the earliest Toalean level (see also ref. ); layer 5 (approximately 9.4–8.7 kyr cal bp) and underlying strata (layers 6–8) are pre-Toalean. The deepest Toalean horizon, layer 4, a silty clay (7.9–5.1 kyr cal bp), contained the region’s only definite Toalean-associated burial. The burial was revealed in 2015 within the contiguous squares S16T6 and S17T6. In 2019, a 2 × 1 m trench excavated adjacent to these squares exposed undisturbed strata to a depth of 3 m without reaching bedrock (Extended Data Figs. 2, 3). Calibrated AMS 14C ages (95% probability) are shown on the right (Supplementary Information contains details on dating methods). Dated materials comprised samples of wood charcoal (N = 8) and charred Canarium sp. seeds (N = 3). The age inversion in layer 4 suggests a degree of post-depositional mixing that does not affect the inferred burial age. f, Toalean burial from layer 4 (3D image generated using PhotoScan). The individual was interred in a flexed position and covered with large cobbles (denoted 1–5). g, Fragmented cranium. h, i, Maros points recovered with the human remains. An atypical chert Maros point (h) was found just below the cranium. A classic chert Maros point (i) with a hollow base and serrated margins (tip is missing due to breakage) was found approximately 40 mm below the greater sciatic notch. Image credits: Leang Panninge research team (a–g); Y. Perston (h, i).
Extended Data Fig. 3
Extended Data Fig. 3. Stratigraphic section at Leang Panninge.
Data distributions presented in the tables on the left, and calibrated AMS radiocarbon (14C) dates (shown projected onto the stratigraphic profile), are based on the results of the 2019 excavations. Calibrated AMS 14C ages are reported at 95% probability (Supplementary Information contains details on dating methods). The Toalean human skeleton was exposed in 2015 by a Universitas Hasanuddin (UNHAS) team in collaboration with Balar Sulsel and Universiti Sains Malaysia (see Supplementary Information).
Extended Data Fig. 4
Extended Data Fig. 4. Toalean human burial from Leang Panninge.
a, Single adult inhumation. The 17–18-year-old female was buried in a flexed position and partially covered with several large cobbles. b, Detail of the fragment clusters comprising the skull area. The skeleton is fragmentary (Supplementary Table 2), but the skull, although crushed post-mortem, is well represented by the mandible and mandibular dentition, maxilla and maxillary dentition, frontal bone, temporals, right parietal and occipital bone. The cranium was positioned between two large cobbles (denoted 1 and 2). c, Detail of the burial feature; cobble #1 was placed over one of the hands, cobble #4 was positioned over the left foot, and cobble #5 covered the pelvic region. d, Semi-complete pelves and left foot (plantar surface facing up). e, Sediment block containing the cranium, following removal from the archaeological trench and before excavation in the laboratory. Image credits: Leang Panninge research team (a–g).
Extended Data Fig. 5
Extended Data Fig. 5. Toalean stone tool types from the Toalean burial and associated contexts at Leang Panninge.
a, b, Position of the chert Maros point (shown inset in a) found below the right pelvis during excavation of the sediment block containing the semi-complete pelves. The red arrows in a and b indicate the position of the Maros point amidst stone-flaking debris and other cultural artefacts (at the time these photographs were taken, the bones of the pelvic area had already been removed). c, Position of the non-classic chert Maros point (shown inset, original location highlighted by the blue arrow) found below the skull amidst other stone artefacts and cultural remains (human teeth are still visible at the top of the sediment block under excavation). d, Maros point exposed during the excavation. e–h, Examples of Maros points from layer 4, above the level of the Toalean human burial: square S16T6, spit 18 (Find #62) (e); square S16T6, spit 18 (Find #77) (f); square S17T6, spit 18 (Find #54) (g); square S17T6, spit 16 (Find #95) (h). i–k, Examples of Maros points from spits 19 and 20 within squares S16T6 and S17T6, where the Toalean human burial was located. l–p, Examples of Maros points from other excavated squares at Leang Panninge. Image credits: Leang Panninge research team (a–p).
Extended Data Fig. 6
Extended Data Fig. 6. Principal component analyses.
Calculated on present-day groups,,, projecting all ancient genomes,– including either all available SNPs or only damaged DNA fragments after PMD filtering of the single-stranded and double-stranded libraries of the Leang Panninge individual. a, Principal components calculated on individuals from East and southeast Asia where Papuan, Indigenous Australian and Nasioi (from Bougainville) groups are projected. b, Principal components calculated on individuals from East, southeast Asia and Near Oceania.
Extended Data Fig. 7
Extended Data Fig. 7. The position of the Leang Panninge genome within the regional population genetic history.
Tested with f4-statistics, where X denotes the tested group. a, The affinity of East Asian, South Asian, southeast Asian and Oceanian groups to Leang Panninge and Papuan individuals. b, Affinities between present-day Near Oceanian groups and the Leang Panninge genome. c, The affinity of the Leang Panninge genome to the Denisovan genome compared to present-day and ancient individuals from the region,–. d, The affinity of the Leang Panninge genome to ancient genomes from the region,– in comparison to Papuan groups. Data are presented as exact f4-values ± one and three standard errors indicated as dark and light grey lines, respectively; statistics with z-scores above |3| are displayed in green.
Extended Data Fig. 8
Extended Data Fig. 8. Permutation test on the overlap of introgressed Denisovan sequence in the Leang Panninge individual and present-day groups.
After 500 permutations where the Denisovan sequence is distributed randomly across the genome. The dotted vertical line is the observed overlap in the non-permuted data. The empirical p-value indicates how many permutations show more overlap than the observed overlap in the non-permuted data.
Extended Data Fig. 9
Extended Data Fig. 9. Multidimensional scaling plot.
Visualizing the pairwise difference between Leang Panninge and East and southeast Asian and Near Oceanian groups,– as calculated from 1 − f3 (Mbuti; Leang Panninge, X) on the Human Origins dataset.
Extended Data Fig. 10
Extended Data Fig. 10. The genetic relationship of Leang Panninge with other Asia-Pacific groups.
Data for other Asia-Pacific groups from refs. –,,. a–d, Maximum likelihood trees after incrementally adding one migration event (from zero to four) as inferred by TreeMix; corresponding residuals of individual models are presented on the right (Supplementary Fig. 6).
See this image and copyright information in PMC

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