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 Pleistocene 1. 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 drugstore 11. The entire Gigantopithecus blacki fossil record, dated between the Early Pleistocene (~2.0 Mya) and the late Middle Pleistocene (~0.3 Mya 12), 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 proteomes 17 (Methods). Enamel demineralization was replicated using two different acids, trifluoroacetic acid (TFA) and hydrochloric acid (HCl). Welker et ...

A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation

“…The proteins are cleaved into peptides in situ, as part of enamel formation during tooth biogenesis 50 , 72 , 73 . In order to extract and analyze this peptide population, researchers need to demineralize the enamel and most use acid-based 33 – 36 , 45 , 46 , 55 , 58 , 74 approaches. There are two analytical options: a targeted approach focused on a limited number of specific amelogenin peptides 34 , 36 , 54 , or a shotgun proteomics approach that seeks to identify all proteins in the proteome and then selectively measure all amelogenin peptides bioinformatically after peptide spectral matching 35 , 45 , 46 , 54 , 55 .…”

“…Proteins can be useful targets for analysis in many archaeological settings as their molecular structure is more favorable for preservation relative to DNA 41 – 44 . Moreover, because amelogenin peptides are incorporated within the mineral phase of tooth enamel, the hardest and most durable material in the human body, such peptides may be particularly stable and persistent over long periods of time 45 – 47 .…”

Palaeoproteomics gives new insight into early southern African pastoralism

“…In addition to ancient DNA studies, the past few years have witnessed a multiplicity of analyses based on the extraction and characterisation of long-term persistent biomolecules: proteins [56][57][58][59][60][61] . Since their amino acid sequence is coded for by the DNA, proteins carry genetically derived features that allow researchers to propose phylogenetic relationships of extinct species [62][63][64][65] , sex attribution 66,67 or even characterisation of palaeopathogens 68 . The major protein of bone and teeth, type I collagen (constituting 90% of the organic phase of these materials), is composed of amino acid sequences that carry taxon-related differences in their order, allowing species discrimination 69 .…”

Tooth Enamel and Its Dynamic Protein Matrix

“…Tooth enamel has been used as a record of ontogeny, health history and as a proxy record for behavior and environment in archeological research and for forensic purposes. The degradation-resistant proteins remain well preserved within the densely packed and mineralized tissues, including the highly mineralized tooth enamel [ 19 , 20 , 21 , 22 , 23 , 24 ]. Proteins located within highly mineralized remains, such as tooth enamel, appear to be well preserved for millions of years and withstand postmortem diagenetic alteration better compared to proteins in more porous mineralized tissues such as bone.…”