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Environmental drivers of megafauna and hominin extinction in Southeast Asia


Southeast Asia has emerged as an important region for understanding hominin and mammalian migrations and extinctions. High-profile discoveries have shown that Southeast Asia has been home to at least five members of the genus Homo1,2,3. Considerable turnover in Pleistocene megafauna has previously been linked with these hominins or with climate change4, although the region is often left out of discussions of megafauna extinctions. In the traditional hominin evolutionary core of Africa, attempts to establish the environmental context of hominin evolution and its association with faunal changes have long been informed by stable isotope methodologies5,6. However, such studies have largely been neglected in Southeast Asia. Here we present a large-scale dataset of stable isotope data for Southeast Asian mammals that spans the Quaternary period. Our results demonstrate that the forests of the Early Pleistocene had given way to savannahs by the Middle Pleistocene, which led to the spread of grazers and extinction of browsers—although geochronological limitations mean that not all samples can be resolved to glacial or interglacial periods. Savannahs retreated by the Late Pleistocene and had completely disappeared by the Holocene epoch, when they were replaced by highly stratified closed-canopy rainforest. This resulted in the ascendency of rainforest-adapted species as well as Homo sapiens—which has a unique adaptive plasticity among hominins—at the expense of savannah and woodland specialists, including Homo erectus. At present, megafauna are restricted to rainforests and are severely threatened by anthropogenic deforestation.

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Fig. 1: Map of the Indochinese and Sundaic subregions.
Fig. 2: Distribution of δ13C values across geological subepochs and epochs.

Data availability

All accession numbers, and data generated and used during this study, are included in the Article and its Supplementary Information.


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We thank E. Hoeger, R. Voss, L. Kok Peng, A. van Heteren, J. Cuisin, V. Nicolas, G. Véron, J. Lesur and C. Lefèvre for allowing access to specimens under their care, N. Boivin and the Max Planck Society for support and J. Ilgner, M. Lucas, E. Perruchini and S. Marzo for their assistance with analysis of the samples. The map in Fig. 1 was provided by CartoGIS Services, ANU College of Asia and the Pacific, The Australian National University; we thank S. Potter and K. Pelling for providing the map. This research was supported by an Australian Research Council Future Fellowship to J.L. (FT160100450). P.R. was funded by the Max Planck Society and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 850709).

Author information




J.L. conceived this research and conducted the statistical analyses. P.R. performed the stable isotope analyses. Both authors contributed equally to study design, data acquisition, interpretation of data and the writing of the final manuscript.

Corresponding authors

Correspondence to Julien Louys or Patrick Roberts.

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Peer review information Nature thanks Thure Cerling and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data figures and tables

Extended Data Fig. 1 Distribution of δ13C values across the Quaternary.

Distribution is shown with a jitter plot and corresponding kernel density for Indochina (blue) and Sundaland (red). Kernel densities are exaggerated vertically, such that the peaks for both provinces are equal. Shaded boxes represent the division between δ13C values associated with forests (left) and grasslands (right).

Extended Data Fig. 2 Temporal trends of δ13C and δ18O values under different geochronological scenarios.

a, δ13C values assuming minimum age for each site. b, δ18O values assuming minimum age for each site. c, δ13C values assuming median age for each site. d, δ18O values assuming median age for each site. e, δ13C values assuming maximum age for each site. f, δ18O values assuming maximum age for each site. Each panel is shown relative to the Lisiecki Raymo benthic oxygen-isotope stack. The 95% confidence interval for each curve was based on 999 random replicates using resampling of residuals.

Extended Data Fig. 3 Distribution of δ13C values for browsers across fossil sites through Southeast Asia.

Indochina, dark green; Sundaland, light green. Horizontal line represents the −29‰ zone that indicates the beginning of subcanopy and closed-canopy environments. The long lower whiskers in the box and whisker plot, which indicate a very negatively skewed distribution, are most closely associated with highly stratified forests. The boxes show the median and the lower (25%) and upper (75%) quartiles; the whiskers encompass the minimum and maximum values. Independent sample sizes: Juyuandong, n = 4; Longudong, n = 26; Mohui, n = 5; Sanhe, n = 25; Semedo, n = 6; Sangiran, n = 4; Upper Pubu, n = 4; Khok Sung, n = 5; Pha Bong, n = 15; Tham Wiman Nakin, n = 10; Baxian, n = 32; Boh Damban, n = 18; Nam Lot, n = 39; Quzai, n = 32; Sibrambang, n = 6; Wajak, n = 4; Cipeundeuy, n = 2; Indochina, n = 74; and Sundaland, n = 158.

Extended Data Fig. 4 Changes in mean δ13C and δ18O values for mammals classified at the ordinal level.

Continuities (non-significant differences in mean) of δ13C values within orders between epochs are illustrated with arrows at the top of each plot. Continuities between orders in a single epoch are illustrated with circles bounding similar δ13C means. Variation within orders and epochs is indicated at 1 s.d.

Extended Data Table 1 Sites included in the analyses with corresponding sources for the isotope data
Extended Data Table 2 Univariate statistics for each geological subepoch and biogeographical province
Extended Data Table 3 Univariate statistics for each geological subepoch and trophic group
Extended Data Table 4 Count data for Early and Middle Pleistocene herbivores and omnivores
Extended Data Table 5 Age ranges for fossil sites and the time bins to which they were allocated for each age modelling scenario
Extended Data Table 6 Stable isotope values for different orders of mammals across different geological subepochs and epochs of the Quaternary

Supplementary information

Supplementary Table

This excel spreadsheet lists all the isotope data considered in the manuscript, including all published data, raw original data, and fractionation adjustments. Worksheet 1 lists the combined dataset. Worksheet 2 list data from Zoologische Staatssammlung München (ZSM), Germany; Worksheet 3 the Lee Kong Chian Natural History Museum (LKCNHM); Worksheet 4 the Muséum National d’Histoire Naturelle (MNHN), Paris, France; and Worksheet 5 the American Museum of Natural History (AMNH), New York, United States of America.

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Louys, J., Roberts, P. Environmental drivers of megafauna and hominin extinction in Southeast Asia. Nature 586, 402–406 (2020).

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