Kirsty Elizabeth Helena Penkman's research while affiliated with New York University and other places

In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference. Still, the recovery of protein sequences providing novel phylogenetic insights does not exceed 3.7 Ma (Pliocene). Here, we push this boundary back to 21-24 Ma (early Miocene), by retrieving enamel protein sequences of an early-diverging rhinocerotid (Epiaceratherium sp. - CMNF-59632) from the Canadian High Arctic. We recover partial sequences of seven enamel proteins (AHSG, ALB, AMBN, AMELX, AMTN, ENAM, MMP20) and over 1000 peptide-spectrum matches, spanning over at least 251 amino acids. Authentic endogeneity of these sequences is supported by indicators of protein damage, including several spontaneous and irreversible post-translational modifications accumulated during prolonged diagenesis and reaching near-complete occupancy at many sites. Bayesian tip-dating, across 15 extant and extinct perissodactyl taxa, places the divergence time of CMNF-59632 in the middle Eocene-Oligocene, and identifies a later divergence time for Elasmotheriinae in the Oligocene. The finding weakens alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae. This divergence time of CMNF-59632 coincides with a phase of high diversification of rhinocerotids, and supports a Eurasian origin of this clade in the late Eocene or Oligocene. The findings are consistent with previous hypotheses on the origin of the enigmatic fauna of the Haughton crater, which, in spite of their considerable degree of endemism, also display similarity to distant Eurasian faunas. Our findings demonstrate the potential of palaeoproteomics in obtaining phylogenetic information from a specimen that is ten times older than any sample from which endogenous DNA has been obtained.

Rationale Alkylresorcinols (AR) are cereal‐specific biomarkers and have recently been found in archaeological pots. However, their low concentrations and high susceptibility to degradation make them difficult to detect using conventional gas chromatography mass spectrometry (GC/MS). Here we describe the development of a more sensitive liquid chromatography mass spectrometry (LC/MS) method to detect these compounds. Method A method based on the use of ultra‐high‐performance liquid chromatography (UHPLC) coupled to an Orbitrap mass analyser was established and validated for the detection of low‐concentration ARs in pottery. During the preliminary experiments, UHPLC‐Q/Orbitrap MS (ultra‐high‐performance liquid chromatography‐quadrupole/Orbitrap mass spectrometry) was demonstrated to be more sensitive, and a wide range of AR homologues in cereal extracts were detected, unlike UHPLC‐QTOFMS (ultra‐high‐performance liquid chromatography‐quadrupole time‐of‐flight mass spectrometry) and GC/MS. The developed method was utilised to profile AR homologue distribution in modern cereal samples and reanalyse AR‐containing pots from the archaeological site of Must Farm. Results A highly sensitive LC/MS method with a limit of detection (LOD) of 0.02 μg/g and a limit of quantification (LOQ) of 0.06 μg/g was used to profile ARs in five modern cereal grains. The obtained LOD is 250 times lower than that obtained using the conventional GC/MS approach. AR 21:0 was the most abundant homologue in all four Triticum spp.—einkorn, emmer, Khorasan wheat and common wheat. Meanwhile, AR 25:0 was the predominant homologue in barley, potentially enabling differentiation between wheat and barley. The developed LC/MS‐based method was successfully used to analyse ARs extracted from Must Farm potsherds and identified the cereal species most likely processed in the pots—emmer wheat. Conclusion The described method offers an alternative and more sensitive approach for detecting and identifying ARs in ancient pottery. It has been successfully utilised to detect AR homologues in archaeological samples and discriminate which cereal species—wheat and barley—were processed in the pots.

Amino acid geochronology can provide effective relative dating frameworks for the Pleistocene and has enabled correlation of terrestrial deposits to the global climatic fluctuations described by the marine oxygen isotope record. Using methods developed for the analysis of intra-crystalline amino acids in tooth enamel, we aimed to construct an enamel-based amino acid geochronology for the terrace deposits in the valley of the River Thames in southern Britain using different mammalian taxonomic groups: elephant, horse and bison. To achieve this, chiral amino acid analysis was applied to 58 elephantid, 21 horse and 15 bison teeth from 10 horizons in the Upper Thames Valley, three in the Lower Thames Valley and one from a Thames tributary in the Lea Valley. We evaluate differences in the rates of amino acid breakdown between the taxa and establish which species are similar enough to enable comparison for relative dating purposes. The relative dating of the river terrace deposits is in good agreement with the terrace stratigraphy, biostratigraphy, and other independent estimates of age for all three taxonomic groups. These frameworks demonstrate the potential of enamel-based amino acid geochronologies for relative dating of Middle–Late Pleistocene deposits in the UK, and establish an aminostratigraphic framework from which the dating of other tooth material can be refined. Enamel offers an opportunity to evaluate the age of sites where shell material is absent or poorly preserved. It can also, crucially, provide direct relative dating of mammalian fossils, which are often the focus of study in terms of their evolution, distributional changes or extinction. Direct dating negates the risk that the mammal fossils themselves might be reworked, or of different ages to shell, sediments or other dated material in the same deposits; it also enables archived samples with insecure provenance (e.g. from early 17th-19th century collections) to be directly dated.

The bivalve mollusc Arctica islandica can live for hundreds of years, and its shell has provided a valuable resource for sclerochronological studies and geochemical analyses for understanding palaeoenvironmental change. Shell specimens recovered from the seabed need to be dated in order to aid sample selection, but existing methods using radiocarbon dating or crossdating are both costly and time-consuming. We have investigated amino acid geochronology (AAG) as a potential alternative means of providing a less costly and more efficient rangefinding method. In order to do this, we have investigated the complex microstructure of the shells, as this may influence the application of AAG. Each of the three microstructural layers of A. islandica have been isolated and their protein degradation examined (amino acid concentration, composition, racemisation and peptide bond hydrolysis). The intra-crystalline protein fraction was successfully extracted following oxidation treatment for 48 h, and high temperature experiments at 140 °C established coherent breakdown patterns in all three layers, but the inner portion of the outer shell layer (iOSL) was the most appropriate component due to practicalities. Sampling of the iOSL layer in Holocene shells from early and late ontogeny (over 100–400 years) showed that the resolution of AAG is too low in A. islandica for within-shell age resolution. However, analysis of 19 subfossil samples confirmed that this approach could be used to establish a relative geochronology for this biomineral throughout the whole of the Quaternary. In the Late Holocene the temporal resolution is ~1500–2000 years. Relative dating of 160 dredged shells of unknown age were narrowed down using AAG as a range finder, showing that a collection of shells from Iceland and the North Sea covered the Middle Holocene, Late Holocene, post-medieval (1171–1713 CE) and modern day. This study confirms the value of A. islandica as a reliable material for rangefinding and for dating Quaternary deposits.

Proteins are the most stable of the macromolecules that carry genetic information over long periods of time. Closed systems are more likely to retain endogenous proteins or their degradation products. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, Late Cretaceous (Campanian–Maastrichtian) Argentine titanosaurian sauropod eggshells show dark, organic stains under light microscopy/photography and fluorescence imaging. Raman spectroscopy can yield bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, consistent with kerogen formation deriving from eggshell lipids. High-performance liquid chromatography reveals that their intra-crystalline fraction can be enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and are fully racemic (despite being some of the slowest racemising amino acids), indicating ancient origin. This preservation varies across localities, but similar ancient amino acid profiles were also observed in Late Cretaceous Spanish titanosaurians from several localities and Chinese putative hadrosaurid eggshell. These amino acid results are consistent with previous studies on degradation trends deduced from modern, thermally matured, sub-fossil, and ∼3.8–6.5 Ma avian eggshell, as well as ∼30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, and the concentration of free amino acids suggests likely complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation, even if such reactions might be slowed in exceptional circumstances. Future work should survey fossil biocalcite to determine variability in amino acid preservation.

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus , a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa 1,2 and the nature of intraspecific variation ³⁻⁶ are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus , from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus , as previously suggested based on morphology alone ⁶ . Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

Despite the vast array of different geochronological tools available, dating the Paleolithic remains one of the discipline's greatest challenges. This review focuses on two different dating approaches: trapped charge and amino acid geochronology. While differing in their fundamental principles, both exploit time-dependent changes in signals found within crystals to generate a chronology for the material dated and hence, the associated deposits. Within each method, there is a diverse range of signals that can be analyzed, each covering different time ranges, applicable to different materials and suitable for different paleoenvironmental and archaeological contexts. This multiplicity of signals can at first sight appear confusing, but it is a fundamental strength of the techniques, allowing internal checks for consistency and providing more information than simply a chronology. For each technique, we present an overview of the basis for the time-dependent signals and the types of material that can be analyzed, with examples of their archaeological application, as well as their future potential.

This paper presents an updated geological reconstruction of the Quaternary evolution of the River Thames at its downstream extremities, close to the North Sea coast, based on new data from multi-disciplinary and citizen-science sources. In this area, the interaction of the Thames with the MIS 12 (Anglian) glaciation is an important part of the Quaternary archive. The Anglian ice sheet, which reached parts of north and east London, was responsible for diverting the Thames southwards into its present course, although the footprint of the maximum ice sheet(s) does not reach the North Sea coast south of Hollesley, Suffolk. Further south, the coastal zone hosts pre-Anglian and early Anglian river-terrace deposits of the pre-diversion Thames system, superimposed upon which are products of later post-Anglian rivers, of both Middle and Late Pleistocene age. On the peninsula between the Stour and Blackwater–Colne estuaries, the lowest and most recent terrace of the pre-diversion Thames includes evidence directly pertaining to the glacial disruption event, for which geochronological data are reported here for the first time. The first post-diversion terrace of the Thames also reaches this peninsula, the river having essentially re-joined its original valley before crossing the alignment of the modern coastline. This terrace passes beneath Clacton-on-Sea, where it includes the type locality of the Clactonian Palaeolithic Industry. The area of interest to this paper, in NE Essex and southern Suffolk, includes a number of interglacial and Palaeolithic sites, the data from which assist in constraining the chronostratigraphy of the sequence. In some cases, there has been uncertainty as to whether these sites represent pre-Anglian environments and hominin occupations, part of the palaeo-Thames sequence, or whether they are the product of later post-Anglian streams, formed after the Thames had migrated southwards. This paper compiles evidence from a wide range of recent sources, including developer-funded archaeological appraisal and citizen-science activities, to explore and update the evidence from sites at Ipswich, Upper Dovercourt and Thorpe-le-Soken, as well as a number of localities associated with the Clacton Channel Deposits (host to the type-Clactonian), amongst others. The resulting new data are placed within the wider context of the Quaternary fluvial archives in southern Britain, with a discussion of how disparate sources of information, including the work of citizen scientists, have contributed.

Amino acid racemization (AAR) is a geochronological method that uses the ratio of D-to L-configurations in optically active amino acids from carbonate fossils to determine the time elapsed since the death of an organism. Although AAR techniques have been widely applied to foraminiferal tests, there have been limited dedicated assessments of the potential of isolating a bleach-resistant, intra-crystalline fraction of proteins to improve the reliability of AAR in this biomineral system. In this study, we evaluate the effect of two oxidative pre-treatments (hydrogen peroxide and bleach) on amino acid concentrations and D/L values in sub-modern benthic foraminifers (Ammonia spp. and Haynesina germanica) and well-preserved mid Holocene and mid Pleistocene planktic foraminifers (Pulleniatina obliquiloculata, Globorotalia truncatulinoides, and Globorotalia tumida). The oxidative pre-treatments successfully reduced the amino acid content of the foraminiferal tests to a residual fraction, and with the exception of Ammonia spp., neither pre-treatment substantially affected the relative proportion of individual amino acids. The bleaching pre-treatment does not consistently alter D/L values when compared to peroxide pre-treatment, but it does tend to reduce the subsample variability in D/L values, albeit only to a small degree in an inconsistent fashion. Therefore, we recommend that a relatively weak oxidative pre-treatment with 3% hydrogen peroxide is sufficient for foraminifera-based AAR applications.