Kirsty Penkman

The earliest record of human activity in northern Europe

The colonization of Eurasia by early humans is a key event after their spread out of Africa, but the nature, timing and ecological context of the earliest human occupation of northwest Europe is uncertain and has been the subject of intense debate. The southern Caucasus was occupied about 1.8 million years (Myr) ago, whereas human remains from Atapuerca-TD6, Spain (more than 780 kyr ago) and Ceprano, Italy (about 800 kyr ago) show that early Homo had dispersed to the Mediterranean hinterland before the Brunhes–Matuyama magnetic polarity reversal (780 kyr ago). Until now, the earliest uncontested artefacts from northern Europe were much younger, suggesting that humans were unable to colonize northern latitudes until about 500 kyr ago. Here we report flint artefacts from the Cromer Forest-bed Formation at Pakefield (52° N), Suffolk, UK, from an interglacial sequence yielding a diverse range of plant and animal fossils. Event and lithostratigraphy, palaeomagnetism, amino acid geochronology and biostratigraphy indicate that the artefacts date to the early part of the Brunhes Chron (about 700 kyr ago) and thus represent the earliest unequivocal evidence for human presence north of the Alps.

A chronological framework for the British Quaternary based on Bithynia opercula

Marine and ice-core records show that the Earth has experienced a succession of glacials and interglacials during the Quaternary (last ∼2.6 million years), although it is often difficult to correlate fragmentary terrestrial records with specific cycles. Aminostratigraphy is a method potentially able to link terrestrial sequences to the marine isotope stages (MIS) of the deep-sea record. We have used new methods of extraction and analysis of amino acids, preserved within the calcitic opercula of the freshwater gastropod Bithynia, to provide the most comprehensive data set for the British Pleistocene based on a single dating technique. A total of 470 opercula from 74 sites spanning the entire Quaternary are ranked in order of relative age based on the extent of protein degradation, using aspartic acid/asparagine (Asx), glutamic acid/glutamine (Glx), serine (Ser), alanine (Ala) and valine (Val). This new aminostratigraphy is consistent with the stratigraphical relationships of stratotypes, sites with independent geochronology, biostratigraphy and terrace stratigraphy. The method corroborates the existence of four interglacial stages between the Anglian (MIS 12) and the Holocene in the terrestrial succession. It establishes human occupation of Britain in most interglacial stages after MIS 15, but supports the notion of human absence during the Last Interglacial (MIS 5e). Suspicions that the treeless ‘optimum of the Upton Warren interstadial’ at Isleworth pre-dates MIS 3 are confirmed. This new aminostratigraphy provides a robust framework against which climatic, biostratigraphical and archaeological models can be tested.

Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"

We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of α1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.

Humid periods in southern Arabia: Windows of opportunity for modern human dispersal

Arabia is a key area for the dispersal of anatomically modern humans (AMH, Homo sapiens) out of Africa. Given its modern hostile environment, the question of the timing of dispersal is also a question of climatic conditions. Fresh water and food were crucial factors facilitating AMH expansions into Arabia. By dating relict lake deposits, four periods of lake formation were identified: one during the early Holocene and three during the late Pleistocene centered ca. 80, ca. 100, and ca. 125 ka. Favorable environmental conditions during these periods allowed AMH to migrate across southern Arabia. Between ca. 75 and 10.5 ka, arid conditions prevailed and turned southern Arabia into a natural barrier for human dispersal. Thus, expansion of AMH through the southern corridor into Asia must have taken place before 75 ka, possibly in multiple dispersals.

Is amino acid racemization a useful tool for screening for ancient DNA in bone

Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for ancient DNA from bone.

An aminostratigraphy for the British Quaternary based on Bithynia opercula

Aminostratigraphies of Quaternary non-marine deposits in Europe have been previously based on the racemization of a single amino acid in aragonitic shells from land and freshwater molluscs. The value of analysing multiple amino acids from the opercula of the freshwater gastropod Bithynia, which are composed of calcite, has been demonstrated. The protocol used for the isolation of intra-crystalline proteins from shells has been applied to these calcitic opercula, which have been shown to more closely approximate a closed system for indigenous protein residues. Original amino acids are even preserved in bithyniid opercula from the Eocene, showing persistence of indigenous organics for over 30 million years. Geochronological data from opercula are superior to those from shells in two respects: first, in showing less natural variability, and second, in the far better preservation of the intra-crystalline proteins, possibly resulting from the greater stability of calcite. These features allow greater temporal resolution and an extension of the dating range beyond the early Middle Pleistocene. Here we provide full details of the analyses for 480 samples from 100 horizons (75 sites), ranging from Late Pliocene to modern. These show that the dating technique is applicable to the entire Quaternary. Data are provided from all the stratotypes from British stages to have yielded opercula, which are shown to be clearly separable using this revised method. Further checks on the data are provided by reference to other type-sites for different stages (including some not formally defined). Additional tests are provided by sites with independent geochronology, or which can be associated with a terrace stratigraphy or biostratigraphy. This new aminostratigraphy for the non-marine Quaternary deposits of southern Britain provides a framework for understanding the regional geological and archaeological record. Comparison with reference to sites yielding independent geochronology, in combination with other lines of evidence, allows tentative correlation with the marine oxygen isotope record.

Tuning hardness in calcite by incorporation of amino acids

Structural biominerals are inorganic/organic composites that exhibit remarkable mechanical properties. However, the structure-property relationships of even the simplest building unit-mineral single crystals containing embedded macromolecules-remain poorly understood. Here, by means of a model biomineral made from calcite single crystals containing glycine (0-7 mol%) or aspartic acid (0-4 mol%), we elucidate the origin of the superior hardness of biogenic calcite. We analysed lattice distortions in these model crystals by using X-ray diffraction and molecular dynamics simulations, and by means of solid-state nuclear magnetic resonance show that the amino acids are incorporated as individual molecules. We also demonstrate that nanoindentation hardness increased with amino acid content, reaching values equivalent to their biogenic counterparts. A dislocation pinning model reveals that the enhanced hardness is determined by the force required to cut covalent bonds in the molecules.

Direct terrestrial–marine correlation demonstrates surprisingly late onset of the last interglacial in central Europe

An interdisciplinary study of a small sedimentary basin at Neumark Nord 2 (NN2), Germany, has yielded a high-resolution record of the palaeomagnetic Blake Event, which we are able to place at the early part of the last interglacial pollen sequence documented from the same section. We use this data to calculate the duration of this stratigraphically important event at 3400 ± 350 yr. More importantly, the Neumark Nord 2 data enables precise terrestrial–marine correlation for the Eemian stage in central Europe. This shows a remarkably large time lag of ca. 5000 yr between the MIS 5e ‘peak’ in the marine record and the start of the last interglacial in this region.

Preservation of ancient DNA in thermally damaged archaeological bone

Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.

New faunal analyses and amino acid dating of the Lower Palaeolithic site at East Farm, Barnham, Suffolk

Rich assemblages of non-marine molluscs are described from the Lower Palaeolithic site at East Farm, Barnham, Suffolk. The assemblages from the upper levels of a channel infill (Unit 5c) reflect both aquatic and terrestrial habitats and indicate temperate conditions throughout the fossiliferous sequence. The land snail fauna contains Discus ruderatus , which allows correlation with the lower part of the molluscan succession at the nearby Lower Palaeolithic site at Beeches Pit, West Stow. Palaeontological evidence from both sites suggests attribution to the Hoxnian Stage, broadly equivalent to part of MarineOxygen Isotope Stage (MIS) 11. A tooth of pipistrelle bat ( Pipistrellus pipestrellus ) from the same deposits represents its only known occurrence from the British Hoxnian. The molluscan assemblages from certain levels at Barnham had clearly suffered considerable post-mortem sorting and diagenesis. Not only were there huge differences in the representation of Bithynia shells and their opercula but the apertures of some shells showed evidence of significant recrystallization. Moreover, some of the opercula were slightly folded or even crumpled, indicating that they must once have been soft and deformable rather than hard and brittle. Such diagenetic, effects are likely to have compromised their suitability for amino acid dating. New amino acid analyses were therefore undertaken of the intra-crystalline component of both pristine and distorted opercula. The results indicated that, of 12 opercula analysed, only one showed any serious anomaly, underlining the importance of careful sample selection. The new data from these calcitic opercula support earlier conclusions, based on D-alloisoleucine/L-isoleucine ratios from aragonitic shells, that the fossiliferous sediments at Barnham accumulated during MIS 11.