Abstract
The science of metabolic profiling exploits chemical compound byproducts of metabolism called metabolites1 that explain internal biological functions, physiological health and disease, and provide evidence of external influences specific to an organism’s habitat. Here we assess palaeometabolomes from fossilized mammalian hard tissues as a molecular ecological strategy to provide evidence of an ancient organism’s relationship with its environment. From eastern, central and southern African Plio-Pleistocene localities of palaeoanthropological significance, we study six fossils from Olduvai Gorge, Tanzania, one from the Chiwondo Beds, Malawi, and one from Makapansgat, South Africa. We perform endogeneity assessments by analysing palaeometabolomes of palaeosols and the effects of owl digestion on rodent bones to enable prudent ecological inferences. Diagenesis is indicated by metabolites of collagenase-producing bacteria2, whereas the preservation of peptides including those of collagen are identified by proteomics. Endogenous metabolites document biological functions and exogenous metabolites render environmental details including soil characteristics and woody cover, and enable annual minimum and maximum rainfall and temperature reconstructions at Olduvai Gorge, supporting the freshwater woodland and grasslands of Olduvai Gorge Bed I3,4,5, and the dry woodlands and marsh of Olduvai Gorge Upper Bed II6. All sites denote wetter and/or warmer conditions than today. We infer that metabolites preserved in hard tissues derive from an extravasated vasculature serum filtrate that becomes entombed within developing mineralized matrices, and most probably survive palaeontological timeframes in the nanoscopic ‘pool’ of structural-bound water that occurs in hard tissue niches7.
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Data availability
The raw mass spectrometry metabolomics data generated during this study are available at MassIVE (UCSD) (https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp) under the deposition number MSV000097146. Proteomics LC–MS data (proteomics raw mass spectrometry data, peak lists and results) that support the findings of this study are deposited to the ProteomeXchange Consortium via the MassIVE partner repository and can be retrieved with the accession code MSV000097173 and with the dataset identifier PXD061016.
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Acknowledgements
Funding for this project was provided by The Leakey Foundation (grant number Spring202310420) to T.G.B. We thank all institutions, which provided and supported sampling: the CMCK Karonga, Malawi, NMHN Paris, France, and the Senckenberg Research Institute and the Natural History Museum Frankfurt, Germany. We express our gratitude to the Werner Reimers Foundation in Bad Homburg, Germany, which provides the Gustav Heinrich Ralph von Koenigswald collection as a permanent loan for scientific research to the Senckenberg Research Institute and Natural History Museum Frankfurt. Thanks go to the New York University Grossman School of Medicine’s Applied Bioinformatics Laboratories for access to QIAGEN IPA. The Zeiss Gemini 300 FE-SEM used for evaluating bone microanatomy was provided courtesy of the National Institutes of Health S10 Shared Instrumentation Program, grant number 1S10OD026989-01; mass spectrometry instrumentation, National Institutes of Health grant numbers S10 OD023659 and S10 RR027990. We thank P. Ausili and L. Kaleel for assistance with metabolite annotations and data organization. N.R. and M.D.M. are members of the Fonds de Recherche du Québec–Santé (FRQS) Centre for Structural Biology Research at McGill University, and the FRQS Network for Intersectorial Research in Sustainable Oral and Bone Health. M.D.M. is the Canada Research Chair in Biomineralisation, and N.R. is a William Dawson Scholar at McGill University. A.S. is supported by the French government in the framework of the University of Bordeaux’s IdEx ‘Investments for the Future’ programme/GPR ‘Human Past’. This project is an outcome of the 2010 Max Planck Research Award to T.G.B., endowed by the German Federal Ministry of Education and Research to the Max Planck Society and the Alexander von Humboldt Foundation in respect of the Hard Tissue Research Program in Human Paleobiomics.
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Contributions
T.G.B. conceived the study and led the work. C.D., J.K., O.K., F.S. and O.S. prepared and provided fossil samples and extant representatives of African species. G.M.A. and C.D. provided palaeosols. S.Y. and S.B.P. prepared and provided the extant laboratory mouse material, A.S. provided likelihoods of plant resources based on isotopic evidence. B.H. undertook the histology and light and electron microscopy. S.R. produced the fossil bone extracts. T.A.N., C.L.D.J. and H.E.-B. performed the metabolomics and proteomics and their relevant bioinformatics. M.D.M., N.R., D.J.B. and E.I. elaborated the interpretation of the bone ultrastructural metabolite niches. T.G.B. and S.R. annotated the metabolite lists from online databases, and T.G.B. interpreted the metabolic and ecological profiles and wrote the manuscript, with valuable contributions from all co-authors.
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Extended data figures and tables
Extended Data Fig. 1 Polarised light images of specimen M-D. Mus sp. or Dendromus sp., Bed I, Level FLKN1 M3.
a. Birefringent brightness at top and bottom is attributed to heavily crystalised bone domains, while the central curvilinear arc of brightness is attributed to collagen. FW = 1.547 mm; b) Detail of bright bone lamellae and osteocyte lacunae interspersed among them. FW = 0.324 mm.
Extended Data Fig. 2 Polarised light image of specimen Sm. Saccostomus cf. mearnsi, Bed I, Level FLKN1.
a. Birefringent brightness is attributed to collagen. FW = 1.343 mm; b) Detail of bright domains and osteocyte lacunae interspersed among them. FW = 0.324 mm.
Extended Data Fig. 3 Polarised light image of specimen Gg. Gerbilliscus gentryi, Bed I, Level FLKN1 M1.
a. Birefringent brightness is attributed to collagen. FW = 3.922 mm; b) Detail of bright domains and osteocyte lacunae interspersed among them. FW = 0.324 mm.
Extended Data Fig. 4 Polarised light image of specimen Gi. Gerbilliscus sp. indet, Bed I, Level DK.
a. Birefringent brightness is attributed to collagen. FW = 4.506 mm; b) Detail of bright domains and osteocyte lacunae interspersed among them. FW = 0.324 mm.
Extended Data Fig. 5 Polarised light image of specimen Xi. Xerus cf. inauris, Bed I, Level FLKN1 M3.
a. Birefringent brightness is attributed to collagen. FW = 4.434 mm; b) Detail of bright domains and osteocyte lacunae interspersed among them. FW = 0.324 mm.
Extended Data Fig. 6 BSE-SEM image of specimen M-D. Mus sp. or Dendromus sp., Bed I, Level FLKN1 M3.
a. Macroscopic view of the bone fragment. FW = 1.515 mm; b. Detail of bone and osteocyte lacunae and their associated canaliculi. Large cracks are due to diagenesis or preparation. FW = 0.25 mm.
Extended Data Fig. 7 BSE-SEM image of specimen Sm. Saccostomus cf. mearnsi, Bed I, Level FLKN1.
a. Macroscopic view of the bone fragment. FW = 1.329 mm; b. Detail of bone illustrating diagenetically disorganized bony structure but preserving some vascular canals and osteocyte lacunae. FW = 0.25 mm.
Extended Data Fig. 8 BSE-SEM image of specimen Gg. Gerbilliscus gentryi, Bed I, Level FLKN1 M1.
a. Macroscopic view of the bone fragment. FW = 3.726 mm; b. Detail of bone illustrating a vascular canal, mineralization density variation, and osteocyte lacunae and their associated canaliculi. FW = 0.25 mm.
Extended Data Fig. 9 BSE-SEM image of specimen Gi. Gerbilliscus sp. indet, Bed I, Level DK.
a. Macroscopic view of the bone fragment. FW = 4.261 mm; b. Detail of bone illustrating a vascular canal (bottom), mineralization density variation, and osteocyte lacunae and their associated canaliculi. Large cracks are due to diagenesis or preparation. FW = 0.25 mm.
Extended Data Fig. 10 BSE-SEM image of specimen Xi, Xerus cf. inauris, Bed I, Level FLKN1 M3.
a. Macroscopic view of the bone fragment. FW = 4.211 mm; b. Detail of bone illustrating a vascular canal, mineralization density variation, and osteocyte lacunae and their associated canaliculi. FW = 0.25 mm.
Supplementary information
Supplementary Information
Supplementary Figs 1–10.
Reporting Summary
Supplementary Table 1
Detailed list of samples.
Supplementary Table 2
Calcium/phosphate ratios from the study sample.
Supplementary Table 3
UM-HET3 and C57BL-6J mice and diets.
Supplementary Table 4
Olduvai Gorge Mus sp. or Dendromus sp., extant MNHN CD, palaeosols.
Supplementary Table 5
Olduvai Gorge Saccostomus cf. mearnsi, extant MNHN 1991-817, palaeosols.
Supplementary Table 6
Olduvai Gorge Gerbilliscus gentryi, extant MNHN NC, palaeosols.
Supplementary Table 7
Olduvai Gorge Gerbilliscus sp. indet, MNHN NC, palaeosols.
Supplementary Table 8
Olduvai Gorge Xerus cf. inauris, MNHN 2005-575, palaeosols.
Supplementary Table 9
Olduvai Gorge, Kolpochoerus majus, von Koenigswald 1854.
Supplementary Table 10
Chiwondo Beds, Elephas recki shungurensis, EE, palaeosol HCRP-RC-11.
Supplementary Table 11
Makapansgat, Bovidae, EW, palaeosol TF12.
Supplementary Table 12
Site metabolite comparisons.
Supplementary Table 13
OG soil carbonates.
Supplementary Table 14
Statistical tests.
Supplementary Table 15
Fossil Bone Proteomics.
Supplementary Table 16
Summary statistics.
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Bromage, T.G., Denys, C., De Jesus, C.L. et al. Palaeometabolomes yield biological and ecological profiles at early human sites.
Nature (2025). https://doi.org/10.1038/s41586-025-09843-w
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DOI: https://doi.org/10.1038/s41586-025-09843-w
Source: Ecology - nature.com
