Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

Rao, Huiyun; Yang, Yimin; Liu, Jinyi; Westbury, Michael V.; Zhang, Chi; Shao, Qingfeng

doi:10.1038/s41598-020-73542-x

Cited by 7 publications

(3 citation statements)

References 64 publications

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“…36 ZooMS analyses are performed on amounts of several tens of milligrams from Pleistocene samples. 17,37,38 To the best of our knowledge, our modified MStern method is the first to describe the identification of bones aged 120,000 years from 1 mg of bones using a MALDI ionization. From this 1 mg digest, up to 10 analyses either by MALDI-MS or LC−MS can be performed.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry

et al. 2023

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Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In the archaeological or paleontological field, PMF is known as zooarchaeology mass spectrometry (ZooMS) and is widely implemented to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to 10-fold the required bone sample amount (down to the milligram scale) and achieves robust deamidation value calculation in a high-throughput manner. These improvements rely on a 96-well plate samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious post-translational modification production, and PMF at high resolution using matrix-assisted laser desorption ionization Fourier transform ion cyclotron resonance (MALDI-FTICR) analysis. This method was applied to the identification of a hundred bones of herbivores from the Middle Paleolithic site of Caours (Somme, France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their osteomorphology, as well as to more challenging samples consisting of small or burned bone fragments. Deamidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry

et al. 2023

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“…Future palaeoproteomic analyses may have the power to provide insights into these questions by providing molecular data from much older specimens [43].…”

Section: (B) Fossil Records In China and Asian Cave Hyenasmentioning

confidence: 99%

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genusCrocuta

Westbury

Yuan

et al. 2021

Proc. R. Soc. B.

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Cave hyenas (genus Crocuta ) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta . Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta . Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

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“…Foram encontrados vários estudos que reivindicaram a presença de sequências de mtDNA e nuDNAem rinocerontes-lanudos, ursosdas-cavernas, camelos-gigantes, cavalos e macrauquênias recuperados de cavernas do Pleistoceno da Europa, Chile, China, Canadá e Estados Unidos (Orlando et al, 2003;Noonan et al, 2005;Lister et al, 2005;Valdiosera et al, 2006;Orstrom et al, 2006;Krause et al, 2008;Dabney et al, 2013;Westbury et al, 2017). Também foram encontrados dados a respeito de amostras de colágenos nesse tipo de ambiente Rao, 2020).…”

Section: Laurasiatheriaunclassified

Exceptional preservation of nonmineralized biomaterials in Cenozoic fossils of the Mammalia clade

Gomes¹,

Machado²,

Alves³

2022

RSD

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The members of the Mammalia class experienced high ecological, morphological and taxonomic diversification during the Cenozoic Era. With technological advances in molecular paleontology in recent decades, many claims for the exceptional preservation of nonmineralized biomaterials have been made for this clade. However, these data are scattered in the literature and have associated such reports with unique and rare events. This study presents a review of the literature published in the last six decades, aiming to investigate the frequency with which vestigial of nonmineralized biomaterials are found in Mammalia fossils. The results identified 79 published studies describing endogenous biocomponents in Metatheria and Theria members. Of these, protein fragments were more frequent in sedimentary deposits (33.3%), and ancient DNA sequences were more frequent in depositional environments more favorable to exceptional preservation (53.1%), such as ice and cave deposits. The data on organic material for mammalian fossils are geographically and taxonomically comprehensive, with the superordinates Laurasiatheria and Afrotheria presenting the largest number of reports. With the emergence and improvement of new techniques for the recovery of organic material, it is believed that paleomolecular information for fossil mammals should increase, in addition to broadening the understanding of taphonomic factors related to exceptional preservation.

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Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

Cited by 7 publications

References 64 publications

Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry

Robust High-Throughput Proteomics Identification and Deamidation Quantitation of Extinct Species up to Pleistocene with Ultrahigh-Resolution MALDI-FTICR Mass Spectrometry

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genusCrocuta

Exceptional preservation of nonmineralized biomaterials in Cenozoic fossils of the Mammalia clade

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