Enamel Proteome shows that Gigantopithecus was an early diverging pongine.

Abstract

Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene¹. Its evolutionary relationships to other great ape species, and their divergence during the Middle and Late Miocene (16-5.3 Mya), remains disputed^2,3. Hypotheses regarding relationships between Gigantopithecus and extinct and extant hominids are difficult to substantiate because of its highly derived dentognathic morphology and the absence of cranial and post-cranial remains^1,3-6. Therefore, proposed hypotheses on the phylogenetic position of Gigantopithecus among hominids have been wide-ranging, but none have received independent molecular validation. We retrieved dental enamel proteome sequences from a 1.9 million years (Mya) old Gigantopithecus blacki molar found in Chuifeng Cave, China^7,8. The thermal age of these protein sequences is approximately five times older than any previously published mammalian proteome or genome. We demonstrate that Gigantopithecus is a sister clade to orangutans (genus Pongo) with a common ancestor about 10-12 Mya, implying that the Gigantopithecus divergence from Pongo is part of the Miocene radiation of great apes. Additionally, we hypothesize that the expression of alpha-2-HS-glycoprotein (AHSG), which has not been observed in enamel proteomes previously, had a role in the biomineralization of the thick enamel crowns that characterize the large molars in the genus^9,10. The survival of an Early Pleistocene dental enamel proteome in the subtropics further expands the scope of palaeoproteomic analysis into geographic areas and time periods previously considered incompatible with genetic preservation.

Gigantopithecus blacki is an extinct, potentially giant hominid species that once inhabited Asia. It was first discovered and identified by von Koenigswald in 1935 when he described an isolated tooth that he found in a Hong Kong drugstore¹¹. The entire Gigantopithecus blacki fossil record, dated between the Early Pleistocene (~2.0 Mya) and the late Middle Pleistocene (~0.3 Mya¹²), includes thousands of teeth and four partial mandibles from subtropical Southeast Asia^1,13,14. All the known Gigantopithecus blacki localities are situated in southern China, stretching from Longgupo Cave, just south of the Yangtze River, to the Xinchong Cave on Hainan Island, and, possibly, into northern Vietnam and Thailand^15,16.

To address the evolutionary relationships between Gigantopithecus and extant hominoids, we performed protein extractions on dentine and enamel samples of a single molar (CF-B-16) found in Chuifeng Cave, China, that is morphologically assigned to Gigantopithecus blacki^7,8. The site is dated using multiple approaches to 1.9±0.2 Mya (Extended Data Figs. 1, 2). Enamel and dentine samples were processed using recently established digestion-free protocols optimized for extremely degraded ancient proteomes¹⁷ (Methods). Enamel demineralization was replicated using two different acids, trifluoroacetic acid (TFA) and hydrochloric acid (HCl).

We identify no endogenous proteins from the dentine, but instead recover an ancient enamel proteome composed of 409 unique peptides matching to six endogenous proteins: amelogenin (AMELX), ameloblastin (AMBN), amelotin (AMTN), enamelin (ENAM), metalloproteinase-20 (MMP20) and alpha-2-HS-glycoprotein (AHSG, also known as FETUA; Extended Data Tab. 2). This observation extends the survival of ancient mammalian proteins to a thermal age, obtained by normalizing the chronological age to a constant temperature of 10°C, to approximately 11.8 Mya@10°C (Extended Data Tab. 1). Such a thermal age is well beyond the thermally oldest DNA (0.25 Mya@10°C, Sima de los Huesos – Spain¹⁸), collagen (0.22 Mya@10°C, Happisburgh – UK¹⁹) and enamel proteome (2.2 Mya@10°C, Dmanisi – Georgia¹⁷) reported to date. The Chuifeng Cave enamel proteome is thus, to the best of our knowledge, the oldest Cenozoic skeletal proteome currently reported (Fig. 1). The survival of a subtropical proteome at approximately 2 Mya suggests that chronologically older specimens from higher latitudes are likely to preserve ancient proteomes as well.

Figure 1. Thermal age of Chuifeng Cave, China, in the subtropics of Southeast Asia (red asterisks).

Chronological and thermal ages of other Cenozoic ancient genomes and proteomes are given for comparison. Inset: geographic location of Chuifeng Cave in the subtropics of Southeast Asia. Base map was generated using public domain data from www.naturalearthdata.com. The red asterisk also encloses the entire known geographic range of Gigantopithecus blacki fossils.

The content of the recovered enamel proteome is consistent with previously reported ancient enamel proteomes^17,20,21, with the addition of several peptides deriving from a single region of AHSG. Peptide matches to these proteins cover a minimum of 43 informative single amino acid polymorphisms (SI Tab. 3). In addition, the retrieved protein regions largely fall within areas previously recovered from an Early Pleistocene Stephanorhinus enamel proteome from Dmanisi¹⁷ (SI Fig. 1). The absence of AMELY-specific peptides suggests that the sampled molar might have belonged to a female Gigantopithecus specimen. The endogenous peptide coverage of 456 amino acids is lower than the previously recovered sequence coverage for a Dmanisi Stephanorhinus specimen (875 amino acids¹⁷; SI Tab. 1). This observation is in agreement with the older thermal age for Chuifeng Cave, compared to Dmanisi¹⁷.

We replicated enamel demineralization using two different acids (TFA and HCl). When comparing the chromatograms of these two extracts, we observe that different peptide populations are released (Extended Data Fig. 3). Due to the partial acidic hydrolysis²², which potentially occurs alongside demineralization, peptide populations with a wider range of acidity (Extended Data Fig. 4a) and hydrophobicity (Extended Data Fig. 4c) are generated using TFA. We observe that the TFA-based demineralization returned 127 more unique non-overlapping peptide sequences compared to the HCl-based demineralization (Extended Data Fig. 4e). The TFA extract, therefore, outperformed the HCl-based extraction, despite a smaller amount of starting material¹⁷. Ultimately, the extended coverage of TFA-based demineralization increases the identification rate of informative single amino acid polymorphisms (SAPs), enhancing the phylogenetic information obtained (Extended Data Fig. 4d). Finally, we observe similar deamidation rates and average peptide lengths in the HCl- and TFA-demineralized samples (Extended Data Fig. 5), which indicate that the two acids release peptide populations modified to the same extend.

The Gigantopithecus enamel proteome is characterized by extensive diagenetic modifications, such as high rates of deamidation (Fig. 2a), and a high degree of degradation, as indicated by relatively short peptide lengths (Fig. 2b), as expected for an ancient proteome preserved in tropical conditions. When quantifying peptide intensities using label-free quantification (LFQ), implemented in MaxQuant²³, we observe that summed and normalized MS1 spectral intensities are higher for shorter peptides compared to longer peptides (Extended Data Fig. 4b). Finally, the peptide lengths of the Chuifeng Cave enamel proteome are shorter than those identified in thermally younger enamel proteomes (Fig. 2b).

Figure 2. Gigantopithecus enamel proteome modifications and degradation.

a, Violin plots of asparagine (N) and glutamine (Q) deamidation for selected proteins (n=1,000 bootstrap replicates of intensity-based peptide deamidation³²). Human dermcidin (DCD) is included as an example of a non-deamidated contaminant. For AMBN, all observed asparagines and glutamines are deamidated. For AMELX, all asparagines are deamidated. For DCD, no observed asparagines and glutamines are deamidated. b, Violin plots of peptide lengths for Gigantopithecus, an Early Pleistocene rhinoceros from Dmanisi, and a Medieval control sample¹⁷. c, Sequence-motif analysis of the over-representation of specific amino acids around the phosphorylated amino acid (position 0; n=14). d, Peptide coverage of AMELX protein isoforms. Matching peptides are indicated by black bars for isoform 1 (n=21) and isoform 3 (n=7). The latter includes an insertion due to alternative splicing between isoform 1, amino acid positions 34 and 35 (coordinates in reference to UniProt Accession number: Q99217-1 [AMELX_HUMAN]). a and b include data on AMELX, AMBN, ENAM, AMTN and MMP20 only. For a and b, boxplots define the range of the data (whiskers extending to 1.5 the interquartile range), 25th and 75th percentiles (boxes), and medians (dots).

Enamel-specific proteins are modified in vivo through protein phosphorylation, alternative splicing of AMELX, and MMP20- and KLK4-mediated proteolysis. Such modifications potentially survive in ancient proteomes. We detected evidence of surviving in vivo post-translational modifications, such as serine phosphorylation in the S-x-E/phS motif, recognised by the secreted kinase FAM20C (Fig. 2c). FAM20C kinase is known to regulate the phosphorylation of extracellular proteins involved in biomineralization²⁴. Finally, we observe two alternative splicing-derived AMELX isoforms (Fig. 2d). These observations are similar to other Early Pleistocene enamel proteomes¹⁷. The Gigantopithecus enamel proteome therefore demonstrates that such in vivo modifications can likewise be recovered from hominid samples across the Pleistocene.

To achieve a protein-based phylogenetic placement of Gigantopithecus, we compared the enamel proteome sequences we retrieved with those of extant apes (Hominoidea). Publicly available whole-genome sequence data were used to predict enamel protein sequences from relevant species^25,26 (SI Tab. 2, SI Figs. 2-12). Our results show that Gigantopithecus represents a sister taxon to all extant orangutans (Pongo sp.) forming a monophyletic group with extant pongines (Fig. 3a; Extended Data Figs. 6, 7). We then attempted to estimate the divergence time between Gigantopithecus and Pongo species using two approaches: (i) a pairwise distance approach and (ii) a Bayesian approach using MrBayes (Methods). While confidence intervals obtained for the divergence estimates of the Pongo-Gigantopithecus split are large, our results indicate that Gigantopithecus diverged from the extant Pongo species in the Middle or Late Miocene (~10 Mya and ~12 Mya using the Bayesian and pairwise distances approaches, respectively; Fig. 3b). This suggests that, despite an exclusively Pleistocene fossil record, Gigantopithecus is a member of an early radiation of pongines, whose diversity peaks during the Middle and Late Miocene (Fig. 3b). Our results thereby resolve the phylogenetic position of Gigantopithecus, but renew the debate on the evolutionary relationships between extant hominids and early hominids present in the fossil record².

Figure 3. Bayesian phylogeny and divergence of Gigantopithecus among extant apes (Hominoidea).

a, Time-calibrated Bayesian phylogeny of Gigantopithecus. Circled nodes were fixed for topology (see Methods). Grey error bars represent the 95% highest posterior density (HPD) intervals for the divergence estimates. b, Distribution of probable and possible extinct pongines known from the fossil record, including Gigantopithecus (black bars). Grey bars represent the 95% HPD interval obtained from the Bayesian approach, and the 95% confidence interval obtained from the pairwise-distance based approach, of the Gigantopithecus-Pongo divergence.

The presence of AHSG in the Gigantopithecus proteome is intriguing, as this protein is not commonly observed in (modern) hominid enamel proteomes. All retrieved peptides derive from a single, highly conserved region that is bordered by disulfide cysteine bonds on either side (Extended Data Fig. 8). AHSG is highly glycosylated in vivo, but we observed no glycosylation during our bioinformatics analysis. The observed sequence contains regularly spaced aspartic acid residues that provide a suitable motif for binding to basic calcium phosphate lattices²⁷. The notion that this specific peptide sequence is involved in biomineral binding is supported by the observation that this region is: (i) presented on the external surface of AHSG²⁸, (ii) that such surfaces have been demonstrated to bind biominerals in other systems as well²⁹, and (iii) that this type of binding enhances peptide preservation²⁹. AHSG acts as a key component of bone and dentine mineralization processes through the inhibition of extrafibrillar mineralization of collagen type I helices³⁰ and has previously been hypothesized to have a role in amelogenesis⁹. In our extracts, there are no endogenous plasma proteins present, such as serum albumin, or other common dentine proteins, such as collagen type I. We also do not identify any AHSG peptides in our dentine sample. We therefore exclude the possibility that the AHSG peptides derive from dentine. Gigantopithecus is known to have relatively long enamel formation times and thick enamel compared to several extant and extinct hominids, including its phylogenetically closest relatives^10,31. We therefore hypothesize that Gigantopithecus has recruited AHSG as an additional molecular component to favour enamel biomineralization during prolonged amelogenesis, ultimately playing a role comparable to the one it has in bone and dentine mineralization⁹.

With our study, we are able to reveal the long-debated phylogenetic position of Gigantopithecus as an early diverging pongine. We demonstrate the ability to retrieve ancient enamel proteomes from Early Pleistocene samples preserved in subtropical conditions, well beyond the current limitations of biomolecular research in hominid and hominin evolution. In addition, the survival of an Early Pleistocene Gigantopithecus enamel proteome allows us to assess the presence of multiple forms of in vivo modifications. Finally, we demonstrate that palaeoproteomic analysis allowed revealing a hitherto unknown biological component of extinct hominid tooth formation. This finding suggests that the palaeoproteomic analysis of hominid enamel has great potential to provide a molecular perspective on human and great ape evolution.

METHODS

0. CHUIFENG CAVE

The Chuifeng Cave (23°34′27″N, 107°00′ 22″E) is one of the most representative sites for the Early Pleistocene Gigantopithecus blacki fauna⁸. The site is located in the Bubing Basin in the north-western part of the Guangxi Zhuang Autonomous Region, south China (Extended Data Fig. 1). The cave is 19 m in length, 0.5–2 m in width and 1.5–5 m in height, penetrating the limestone from southeast to northwest at a height of ~ 77 m above the local valley floor. A fossiliferous sandy-clay with a few limestone breccias fills most part of the cave, with an average depth of 1.3 m (Extended Data Fig. 2). Four excavation areas (A, B, C, and D) were excavated down to limestone bedrock in 10 cm intervals. Twenty-four large mammalian species, including 92 Gigantopithecus blacki teeth, were unearthed from the cave⁸. The Chuifeng Cave mammalian fauna is characterized by the occurrence of typical Early Pleistocene species, such as Hystrix magna, Sinomastodon sp., Stegodon preorientalis, Ailuropoda microta, Pachycrocuta licenti, Tapirus sanyuanensis, and Sus peii⁸. This mammalian fauna is comparable with other Gigantopithecus-containing faunas of the Early Pleistocene in southern China, such as Baikong³³, Longgupo³⁴, and Liucheng³⁵. The mammalian fauna composition is consistent with the age results (~ 1.9 Mya) of combined ESR/U-series dating and sediment paleomagnetic studies³⁶. In the present study, we collected one well-preserved Gigantopithecus blacki tooth (excavation number CF-B-16) for palaeoproteomic analysis. This tooth was excavated from area B at a depth of 90 cm from the sediment surface and, based on its stratigraphic position, is dated to ~ 1.9 Mya. No other samples were tested prior to CF-B-16, and no specific selection was made as to which Gigantopithecus tooth would be analysed.

1. THERMAL AGE

Thermal age was calculated to allow comparison with previously published ancient genomes, ancient proteomes, and collagen peptide mass fingerprinting studies, from other temporal and geographic localities. Temperature estimates for the hominin occupation of Dmanisi based on herpetological fauna suggest a temperature about 3.1 °C above current mean annual temperature, while the sea surface temperature record used ²⁹ predicts a negative ΔT at the time of hominin occupation. Given this discrepancy and the widely different temperature estimates for the last glacial maximum (LGM) in the Caucasus, we conservatively use a scale factor of 0, correlating with a ΔT of approximately -0.2 °C, and a current mean annual temperature of 11.2 °C. Our thermal age prediction for Dmanisi (2.2 Myr@10 °C) should therefore be seen as conservative. Thermal age for Chuifeng Cave was calculated with a general lapse rate between mean annual temperature (MAT) and altitude of 5.0 °C/km, a scale factor of 0.7, and a ΔT at LGM of -3 °C. Again, actual ΔT at LGM might have been more pronounced, leading to a conservative estimate of thermal age for Chuifeng Cave as well. MAT was estimated based on the ten closest weather stations listed in publicly accessible World Meteorological Organization (WMO) data (Extended Data Table. 21). Thermal age calculations are, among other factors, altitude dependent, but only five out of these ten weather stations have altitude directly associated with them. We therefore estimated the altitude of the other five weather stations through an online resource (https://www.advancedconverter.com/map-tools/find-altitude-bycoordinates). The correlation between WMO altitude and estimated altitude was R = 0.99, providing sufficient validity to our estimated altitudes. The MATs for all weather stations were then averaged to obtain an approximate MAT for Chuifeng Cave. Next, thermal age was calculated for chronological ages of 1.7 Myr, 1.9 Myr and 2.1 Myr, giving estimates of the minimum (9.2 Myr@10 °C), maximum (15.0 Myr@10 °C), and mean (11.8 Myr@10 °C) thermal ages associated with the Chuifeng Cave fauna within a 95% confidence interval (Fig. 1). The Chuifeng Cave proteome is thereby substantially older than the oldest collagen peptide mass fingerprint (Ellesmere Island, 0.003 Myr@10 °C), oldest mammalian genome (Thistle Creek, 0.03 Myr@10 °C), oldest hominin genome (Sima de los Huesos, 0.25 Myr@10 °C), and oldest enamel proteome (Dmanisi, 2.2 Myr@10 °C) published to date²⁹. Full thermal age calculations can be found in Supplementary Information File 3.

2. PROTEIN EXTRACTION

Ancient protein extractions took place in facilities at the Natural History Museum of Denmark dedicated to extracting ancient DNA and ancient proteins. These laboratories include clean rooms fitted with filtered ventilation and positive air pressure³⁷. A negative extraction blank was processed alongside the ancient extractions, with the additional inclusion of injection blanks during MS/MS analysis to monitor potential protein contamination during all stages of analysis.

Two enamel (185 and 118 mg, respectively) and one dentine (192 mg) samples were removed from the same molar (CF-B-16), using a sterilized drill, and crushed to a rough powder. One enamel and the dentine sample were demineralized in 1.2 M HCl at 3°C for 24 hours, while the other enamel sample was demineralized at the same temperature and duration using 10% TFA. Subsequently, solubilized protein residues were cleaned, concentrated and immobilized on C18 Stage-Tips using previously published methods¹⁷. No other samples from Chuifeng Cave were analysed prior to or during the analysis of CF-B-16.

3. LC-MS/MS ANALYSIS

The extracts were analyzed by nanoflow liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) using a 15 cm capillary column (75 μm inner diameter, packed with 1.9 μm C18 beads (Reprosil-AQ Pur, Dr. Maisch)) on an EASY-nLC™ 1200 system (Proxeon, Odense, Denmark) connected to a Q-Exactive HF-X mass spectrometer (Thermo Scientific, Bremen, Germany). The nLC gradient and MS parameters followed a previously published Q-Exactive HF-X method³². System wash blanks were performed before and after every sample to hinder cross-contamination.

4. DATABASE CONSTRUCTION

We constructed a protein sequence database for Hominoidea proteins known to be present in enamel proteomes (SI Tab. 2), to which we added the homologous sequences from one Cercopithecoid (Macaca mulatta) as an outgroup for phylogenetic analysis. As few protein sequences are publicly available for Pongo pygmaeus, we predicted those sequences from publicly available genomic sequence data using the known gene coordinates of Pongo abelii homologous. Similarly, we generated de novo AMELY sequences for Pongo abelii and Pongo pygmaeus as well. Finally, we added common laboratory contaminants to allow spectra from such proteins to be confidently identified (file taken from the supplements of Hendy et al.³⁷).

Ancestral Sequence Reconstruction

Previous research indicates that cross-species proteomic effects, observed during spectral identification, significantly reduce the identification of phylogenetically informative amino acid positions at large evolutionary distances³⁸. We reasoned that this was likely to occur in the case of Gigantopithecus proteins³⁹, and therefore reconstructed the ancestral protein sequences of enamel-specific proteins. Ancestral Sequence Recontruction (ASR) was conducted across the entire Hominoidea phylogeny using PhyloBot⁴⁰. Input sequences were constrained phylogenetically to (Macaca,(Nomascus,((Pongo abelii, Pongo pygmaeus),Gorilla,(Homo,((Pan paniscus, Pan troglodytes)))))). We added those sequences to the reference protein database to account for them in the database search of PEAKS and MaxQuant.

Isoform variation

After obtaining complete protein sequences for all extant hominids, we added isoforms not present in UniProt or Genbank for the proteins AMELX, AMELY, AMBN, AMTN, KLK4, and TUFT1, including the reconstructed ASR sequences of these proteins, to the database. We assumed that the isoforms for these non-human hominids would result from identically placed alternative splicing across species and ancestral nodes (as also supported by all UniProt isoforms present for the studied proteins). Thus, we copied these alternative splicing sites onto the available reference sequences to create the missing isoforms. Database sequence names for these proteins were appended with “_ManIso2” or “_ManIso3”.

5. PROTEOMIC DATA ANALYSIS

Raw mass spectrometry data was searched per sample type (enamel, dentine, extraction blank and injection blanks) against a sequence database containing all common enamel proteins for all extant hominids (see above). We used PEAKS⁴¹ (v. 7.5) and MaxQuant²³ (v. 1.6.2.6) software. The de novo and error-tolerant implementations of PEAKS, and the dependent peptide algorithm implemented in MaxQuant, were used to generate possible, additional, single-amino acid polymorphism (SAP) variation in enamel protein sequences. Such novel SAPs could represent unique amino acid substitutions on the Gigantopithecus lineage, which are not relevant to its phylogenetic placement but are relevant on dating the Pongo–Gigantopithecus divergence. Next, these potential sequence variants were added to a newly constructed sequence database and verified in separate searches in PEAKS and MaxQuant. We defined as variable modifications methionine oxidation, proline hydroxylation, glutamine and asparagine deamidation, pyro-glutamic acid from glutamic acid, pyro-glutamic acid from glutamine, and phosphorylation (STY). No fixed modifications were selected. We did not use an enzymatic protease during sample preparation, therefore the digestion mode was set to “unspecific”. For PEAKS, peptide spectrum matches were only accepted with an FDR ≤ 1.0%, and precursor mass tolerance was set to 10 ppm and fragment mass tolerance to 0.05 Da. For MaxQuant, peptide spectrum matches (PSM) and protein FDR were set at ≤ 1.0%, with a minimum Andromeda scores of 40 for all peptides. Protein matches were accepted with a minimum of two unique peptide sequences in at least one of the MaxQuant or PEAKS searches, including the removal of non-specific peptides after BLASTp searches of peptides matching to non-enamel proteins against UniProt and GenBank databases. Proteins that are retained after applying these criteria are listed in Extended Data Table 2. Examples of annotated MS/MS spectra after MaxQuant analysis can be found in Supplementary Figures S3 to S12.

Assessment of protein damage and degradation followed protocols explained elsewhere^17,32,42 and included rates of deamidation and a comparison of observed peptide lengths. Peptide hydrophobicity was calculated using the R package “Peptides”, with the scale set to “KyteDoolittle”.

6. PHYLOGENETIC and DIVERGENCE ANALYSIS

Comparative reference dataset

We assembled a reference dataset with five protein sequences retrieved from the ancient sample (AMBN, AMELX, AMTN, ENAM and MMP20) and relevant extant species (SI Tab. 2). Protein sequences for human (Homo sapiens), common chimpanzee (Pan troglodytes), bonobo (Pan paniscus), Sumatran orangutan (Pongo abelii), Western gorilla (Gorilla gorilla), rhesus macaque (Macaca mulatta), and the white-cheeked gibbon (Nomascus leucogenys), were obtained from the UniProt database. Additionally, we expanded our dataset with protein sequences from publicly available whole-genome sequence data from present-day great apes, (in total 27 orangutans, 42 gorillas, 11 bonobos and 61 chimpanzees^25,26,43), as well as 19 human individuals from the Simons Genome Diversity Project⁴⁴. See the Supplementary Information for the human sample numbers taken from the SGDP dataset.

Reconstruction of protein sequences from whole-genome sequencing data

DNA sequence reads for reference samples used were mapped to human genome (version hg19) using BWA-MEM v0.7.5a-r405 (http://bio-bwa.sourceforge.net/bwa.shtml) with default parameters. PCR and optical duplicates were identified and removed using PICARD v1.91 (https://sourceforge.net/projects/picard/files/picard-tools/1.91/). Single nucleotide polymorphisms were called on the read alignments using the GATK UnifiedGenotyper: (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_genotyper_UnifiedGenotyper.php).

To reconstruct the protein sequences from the genotype calls, we first created a consensus sequence for each of the five genes of interest and for each sample. Indels were not considered and a random allele was chosen at heterozygous positions. Next, we removed the intron sequences from each gene using the annotation of the reference human genome (hg19) available in the ENSEMBL database. For each of the in silico spliced genes, we performed a tblastn search⁴⁵ using the human reference protein as the query. Finally, we obtained the translated protein sequences from the resulting alignments.

Assessing the phylogenetic position of Gigantopithecus blacki

We compared the Gigantopithecus blacki protein sequences with the corresponding homologous of the species in the reference panel. For each gene, we built two multiple sequence alignments using mafft⁴⁶. The first incorporated all samples in the reference panel (n=164). The second incorporated only a single sample per species (SI Tab. 3). To account for isobaric amino acids (leucines=L and isoleucines=I), which cannot be distinguished in the ancient protein data, we changed all I to L at positions where the ancient sample carried either of those amino acids. To assess the phylogenetic position of the ancient sample, two inference approaches were used: a maximum-likelihood and a Bayesian inference.

Maximum-likelihood approach.

PhyML v. 3.1⁴⁷ was used to infer a maximum-likelihood tree, branch lengths and substitutions rates for each individual protein alignment (SI Fig. 2), and for the concatenated alignment. For each alignment, we started from three random trees (--n_rand_starts 3 -s BEST --rand_start), used the JTT model (-m JTT -f m), and obtained maximum likelihood estimates for the gamma distribution shape parameter (-a e) and the proportion of invariable sites (-v e). Support values were obtained for each bipartition based on 100 non-parametric bootstrap replicates. The bootstrap results per branch split are shown in Extended Data Figure 6b.

Bayesian approach.

As a complementary approach, we used MrBayes⁴⁸ and the concatenated alignment to infer the phylogenetic position of the ancient sample (Fig. 3, Extended Data Fig. 6b). We set an independent bipartition for each gene and estimated: substitution rates, across-site rate variation, and the proportion of invariable sites (unlink Statefreq=(all) Ratemultiplier=(all) Aamodel=(all) Shape=(all) Pinvar=(all)). MrBayes was executed using the CIPRES portal⁴⁹. The MCMC algorithm was set to 5,000,000 cycles with 4 chains and a temperature parameter of 0.2. The convergence of the algorithm was assessed using Tracer v.1.6.0 after discarding 25% of the iterations as burn-in. MrBayes was run against the reference sequence for each species (Extended Data Fig. 6c) or against 162 great ape individuals, one hylobatid, and one cercopithecid (Extended Data Fig. 7). Both of these analyses, as well as the PHyML maximum likelihood approach, resulted in the same topology. The analysis utilizing a large number of individuals shows, however, that resolution within the genus Pongo is limited (Extended Data Fig. 7). Nevertheless, the placement of Gigantopithecus is fully supported.

Divergence time of Gigantopithecus

We estimated the divergence between Gigantopithecus and the Pongo branch first by using a distance-based approach. We used the alignment of the amino acid sequences of reference genome sequences for each species as well as diversity data (see above). A distance matrix was created from the concatenated protein sequences of all individuals using the function dist.ml from the R package phangorn⁵⁰ under the LG amino acid substitution model⁵¹. We used pairwise exclusion to increase the amount of data for the present-day branches. We then calculated the mean difference of all orangutan sequences to all sequences from Homo, Pan, and Gorilla, and the mean difference of all orangutan sequences to Gigantopithecus (Extended Data Fig. 6a). We used the average distance between orangutan and the other extant great apes as a scaling factor, assuming a divergence time between these branches of 23.8 Mya⁵². Under this assumption, the molecular divergence of Gigantopithecus from the Pongo branch is 9.98 Mya. However, since Chuifeng Cave is dated to 1.9 Mya, this branch is likely underestimated and its age needs to be corrected to 11.88 Mya. We combine the 95% confidence interval of the distance matrix with the 95% confidence interval of the mutation rate estimate⁵², and add the upper and lower values of the 95% confidence interval for the Chuifeng Cave dating (1.7-2.1 Mya), and thereby suggest conservative upper and lower boundaries for the divergence time of 8.91 and 15.65 Mya, respectively.

If mutation rates did not substantially differ between extant Pongo and Gigantopithecus, this estimate should reflect the molecular evolution of their common branch. We calculated the divergence between the other great apes, taking into account the mutation rate differences on these lineages as scaling factors⁵². The resulting divergence time between Gorilla and the Homo/Pan branch is estimated at 10.27 Mya (7.9-13.25 Mya, 95% confidence interval), and the divergence between Homo and Pan at 8.72 Mya (8.06-13.81 Mya, 95% confidence interval). These values are in strong agreement with the estimates from Besenbacher et al.⁵², suggesting that these protein sequences represent well the known phylogeny of the great apes. Clearly, all divergence time estimates scale with assumptions on the mutation rates. We also caution that the small number of mutations in the peptide fragments in Gigantopithecus constitutes a severe limitation on the precision of these estimates on this branch. However, the phylogenetic position of Gigantopithecus as a sister clade to orangutans is also well supported in this analysis: a phylogenetic tree from a distance matrix of the reference sequences for these species (neighbor joining tree in phangorn; maximum likelihood computed with the pml function; 1,000 bootstrap replicates) separates Gigantopithecus from orangutans with 100% bootstrap support.

We used the program MrBayes⁴⁸ to estimate divergence time estimates in a Bayesian framework using the reference genome sequences. We defined Macaca mulatta as outgroup, grouped Pan, Homo and Gorilla together as well as Pongo and Gigantopithecus, and set the divergence time of the two groups with a uniform distribution of 17.739-26.061 Mya, using the estimate from Besenbacher et al.⁵². Furthermore, we set the divergence time of the macaques and apes at 26.061-39.9 Mya (from the maximum divergence time of the hominids to a very high divergence time of the apes). We used a variable mutation rate and the VT amino acid substitution model⁵³ in 5 million iterations. This results in a divergence time of Gigantopithecus–Pongo of 10.14 Mya (4.76-15.79 Mya, 95% HPD interval). The divergence of Gorilla from the Homo/Pan branch is estimated at 8.59 Mya (4.62-13.56 Mya, 95% HPD interval), and the divergence of Homo and Pan at 5.78 Mya (2.64-9.53 Mya, 95% HPD interval). These are largely consistent with, but somewhat younger than, previous estimates^52,54, possibly due to a mutation slowdown on these lineages compared to the Pongo lineage, which is not taken into account here. However, they seem in agreement with the fossil record indicating the origin of hominins around 6-8 Mya and the dating of a possible early Gorillini (Chororapithecus) around 7-9 Mya^54-58. Therefore, we conclude that the relative branch lengths of the tree (Fig. 3b) are concordant with the overall phylogeny and the estimates presented above.

DATA AVAILABILITY

All the mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the data set identifier PXD013838. Generated ancient protein consensus sequences for both hominins can be found in SI File 2.

Extended Data

Extended Data Figure 1. The current environment of Chuifeng Cave.

a, Landscape outside Chuifeng Cave. b, Elevated altitude of Chuifeng Cave (arrow points to the entrance). Photo credit: Wei Wang.

Extended Data Figure 2. Excavations in Chuifeng Cave.

a, Main entrance of the Chuifeng Cave. b, Well-preserved deposits before excavation. c, The stratigraphic profile (1.3 m in height) of Area D. d, W.W. excavating in Area D. e, Excavated channel. f and g, In situ Gigantopithecus blacki teeth (the scale bars are 3 cm). Photo credit: Wei Wang.

Extended Data Figure 3. Total ion current (TIC) chromatograms of the analysed samples.

a, HCl extract. b, TFA extract. Note differences in maximum TIC on the y-axis. Each extract was analysed only once.

Extended Data Figure 4. Comparison of HCl and TFA extraction protocols.

a, Summed and normalized peptide intensities for each combination of peptide length and number of acidic residues (D, E, deamidated N, deamidated Q). b, Summed and normalized intensities by peptide length. c, Summed and normalized peptide intensities across peptide hydrophobicity. Insets show peptide count distribution across peptide hydrophobicity. d, Extraction performance for various categories of the data. Values scaled to one and compared to the best-performing extraction method for each category independently. SAPs refer to those SAPs informative within Hominoidea. e, Proportional Venn diagram of unique peptide sequences identified in the two demineralization methods. All comparisons based on MaxQuant LFQ data only.

Extended Data Figure 5. Damage characteristics of HCl and TFA extraction protocols.

a, Comparison of mean peptide lengths, showing an identical distribution for the TFA (n=305) and HCl (n=191) extractions (two-sided t-test(394)=−0.599, p=0.5495). b, Comparison of asparagine deamidation. c, Comparison of glutamine deamidation. For b and c, violin plots describe the distribution of bootstrap replicates (n=1,000) of intensity-based peptide deamidation³². For some proteins, only deamidated asparagines or glutamines were observed (for example, AMBN), while DCD is included as an example of a non-deamidated contaminant. All comparisons based on MaxQuant data only. For a-c, boxplots define the range of the data (whiskers extending to 1.5 the interquartile range), outliers (beyond 1.5 the interquartile range) 25th and 75th percentiles (boxes), and medians (dots).

Extended Data Figure 6. Unconstrained phylogenetic analysis of Gigantopithecus blacki.

a, Pairwise distances between groups of selected Hominoids and Pongo estimated using the concatenated protein alignments and the phangorn R package. n=number of pairwise comparisons. b, Maximum-likelihood tree computed on a distance matrix using pml R function. Support values were obtained from 1,000 bootstrap replicates. c, Rooted phylogenetic tree obtained using MrBayes. For each bipartition, we show the posterior probability (0-1) obtained from the Bayesian approach and the support values obtained from 100 non-parametric bootstrap replicates in a PHyML maximum-likelihood (0-100) tree. PHyML and MrBayes recover the same topology. Both b and c are based on the same concatenated alignment of the five proteins retrieved from Gigantopithecus, and resulted in the same tree topology.

Extended Data Figure 7. Bayesian phylogenetic tree of Gigantopithecus blacki including 162 modern genomes of great apes, and a single hylobatid (Nomascus leucogenys).

Tree obtained from the concatenated alignment using MrBayes. Macaca mulatta was used as an outgroup. The internal nodes corresponding to Gorilla, Pan and Homo clades are collapsed for visualisation purposes. The number of individuals in each of these nodes is indicated in parentheses.

Extended Data Figure 8. Sequence conservation and structural relevance of retrieved AHSG peptides.

All AHSG-specific peptides, identified by PEAKS and MaxQuant, derive from a single sequence region bridging cystatin domain 1 and 2. The surviving sequence region is evolutionary conserved across Catarrhini. It contains a regular repeat of acidic amino acid (aspartic acids, D, on positions 133, 137, and 141) residues that enable binding of basic calcium phosphate (residues highlighted in green), similarly to a conserved region just N-terminal (glutamic acid, E, on position 111, and aspartic acids, D, on position 113 and 115). At the bottom, a fragment ion alignment is given of MaxQuant-identified AHSG peptides. The serine is phosphorylated in all matching spectra. The consensus sequence for Catarrhini is shown at the top for amino acid positions 100-149 (amino acid coordinates following UniProt accession P02765 FETUA_HUMAN).

Extended Data Table 1. Mean annual temperature (MAT) estimation at Chuifeng Cave.

The 10 geographically closest meteorological weather stations included in publicly available WMO data are used to estimate current MAT at Chuifeng Cave. Correlation of online altitude estimation and WMO provided altitude is R²=0.99 (Pearson correlation).

WMO station ID	WMO station name	Longitude	Latitude	WMO altitude (m)	Estimated altitude (m)	First month	Last month	MAT	Altitude source used	Chuifeng Cave MAT
5920901	Ching His	106.42E	23.13N	740	743	February 1981	October 1990	19.5	WMO	22.8
5698505	Hekou	103.95E	22.5N	137	114	January 1961	December 1970	22.6	WMO	22.1
5791601	Tien-O	107.17E	25.0N	305	245	January 1981	October 1990	19.7	WMO	20.0
5904602	Ta Wan	109.42E	23.85N	76	81	January 1981	October 1990	20.8	WMO	20.0
5963201	Tung Hsing	107.97E	21.55N	13	10	February 1981	October 1990	23.0	WMO	22.0
5921100	Bose	106.6E	23.9N	na	154	January 1961	October 1990	22.5	Estimated altitude	22.2
5920901	Napo	105.95E	23.3N	na	1214	January 1981	October 1990	19.6	Estimated altitude	24.5
5900700	Guangnan	105.07E	24.07N	na	1257	January 1981	October 1990	17.6	Estimated altitude	22.8
5943100	Nanning	108.35E	22.82N	na	81	January 1922	November 1993	22.0	Estimated altitude	21.2
5902300	Hechi	108.05E	24.7N	na	204	January 1981	October 1990	21.2	Estimated altitude	21.1

Extended Data Table 2. Enamel proteome sequence coverage.

Only proteins with 2 unique peptides in at least either MaxQuant or PEAKS searches were accepted. No protein matches in the dentine or blank extractions fulfilled this criterion. Primary entry refers to the Pongo abelii entry in UniProt for reference purposes. Protein sequence coverage in the final column indicates the coverage obtained after combining PEAKS and MaxQuant peptide recovery. For amino acid columns, numbers in brackets refer to amino acid positions uniquely identified in PEAKS or MaxQuant searches.

Protein	Primary entry	Protein accession	MaxQuant peptides (all unique)	MaxQuant amino acids	PEAKS peptides (all unique)	PEAKS amino acids	Combined sequence coverage (%)
AMELX	H2PUX0_PONAB	H2PUX0	149	135 (4)	270	141 (10)	70.7
AMBN	H2PDI5_PONAB	H2PDI5	55	105 (15)	79	107 (11)	27.5
AMTN	H2PDI4_PONAB	H2PDI4	2	18 (0)	2	18 (0)	8.6
ENAM	H2PDI6_PONAB	H2PDI6	125	129 (5)	189	181 (57)	16.3
MMP20	H2NF32_PONAB	H2NF32	2	9 (0)	1	9 (0)	1.9
AHSG	H2PC98_PONAB	H2PC98	7	13 (0)	12	13 (0)	3.5
ALB	ALBU_Bovin	P02769	2
DCD	DCD_human	P81605	3		8
B2MG	B2MG_human	P61769	2
K1C9	K1C9_human	P35527			3