Identification of dyes on ancient Chinese paper samples using the subtracted shifted Raman spectroscopy method

The Stein Collection in the British Library contains the Diamond Sutra, the world's oldest, dated, printed document. The paper of the Diamond Sutra and other documents from the Stein collection is believed to be dyed yellow by a natural extract, called huangbo, from the bark of Phellodendron amurense, which contains three major yellow chromophores: berberine, palmatine, and jatrorrhizine, Conservation of these documents requires definite information on the chemical composition of the dyes but no suitable, completely noninvasive analytical method is known. Here we report resonance Raman studies of a series of prate dyes, of plant materials and extracts, and of dyed ancient and modern paper samples. Resonance Raman spectroscopy is used to enhance the spectra of the dyes over the signals from the paper matrixes in which they are held. The samples an give resonance Raman spectra which are dominated by intense fluorescence, but by using SSRS (subtracted shifted Raman spectroscopy) we have obtained reliable spectra of the pure dyes, native bark from the Phellodendron amurense, modern paper dyed with huangbo extracted from this bark, and ancient paper samples. For both ancient paper samples whose pigment bands were detected, the relative intensities of the bands due to berberine and palmatine suggest that the ancient paper is richer in berberine than its modern counterpart, This is the first nondestructive in situ method for detection of these pigments in manuscripts, and as such has considerable potential benefit for the treatment of irreplaceable documents that are believed to be dyed with huangbo but documents on which conservation work cannot proceed without definite identification of the chemical compounds that they contain.

Ancient manuring practices pollute arable soils at the St Kilda World Heritage Site, Scottish North Atlantic

The impact of ancient fertilization practices on the biogeochemistry of arable soils on the remote Scottish island of Hirta, St Kilda was investigated. The island was relatively unusual in that the inhabitants exploited seabird colonies for food, enabling high population densities to be sustained on a limited, and naturally poor, soil resource. A few other Scottish islands, the Faeroes and some Icelandic Islands, had similar cultural dependence on seabirds. Fertilization with human and animal waste streams (mainly peat ash and bird carcases) on Hirta over millennia has led to over-deepened, nutrient-rich soils (plaggen). This project set out to examine if this high rate of fertilization had adversely impacted the soil, and if so, to determine which waste streams were responsible. Arable soils were considerably elevated in Pb and Zn compared to non-arable soils. Using Pb isotope signatures and analysis of the waste streams, it was determined that this pollution came from peat and turf ash (Pb and Zn) and from bird carcases (Zn). This was also confirmed by (13)C and (15)N analysis of the profiles which showed that soil organic matter was highly enriched in marine-derived C and N compared to non-arable soils. The pollution of such a remote island may be typical of other 'bird culture' islands, and peat ash contamination of marginal arable soils at high latitudes may be widespread in terms of geographical area, but less intense at specific locations due to lower population densities than on Hirta.

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Causes of late Quaternary extinctions of large mammals (" megafauna") continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or con-fined to refugia. Here we report an alternative approach to detect 'ghost ranges' of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.

Phylogenetic and phylogeographic analysis of the genus Orestias (Teleostei: Cyprinodontidae) in the southern Chilean Altiplano: The relevance of ancient and recent divergence processes in speciation

This study presents phylogenetic molecular data of the Chilean species of Orestias to propose an allopatric divergence hypothesis and phylogeographic evidence that suggests the relevance of abiotic factors in promoting population divergence in this complex. The results reveal that diversification is still ongoing, e.g. in the Ascotán salt pan, where populations of Orestias ascotanensis restricted to individual freshwater springs exhibit strong genetic differentiation, reflecting putative independent evolutionary units. Diversification of Orestias in the southern Altiplano may be linked to historical vicariant events and contemporary variation in water level; these processes may have affected the populations from the Plio-Pleistocene until the present.

The Death Cults of prehistoric Malta:Mysteries of the Ancient Ones

reprinted

Care and Management of Ancient Stone Monuments During Environmental Change

Ancient stone monuments (ASMs), such as standing stones and rock art panels, are powerful and iconic expressions of Britain’s rich prehistoric past that have major economic and tourism value. However, ASMs are under pressure due to increasing anthropogenic exposure and changing climatic conditions, which accelerate their rates of disrepair. Although scientific data exists on the integrity of stone monuments, most applies to “built” systems; therefore, additional work specific to ASMs in the countryside is needed to develop better-informed safeguarding strategies. Here, we use Neolithic and Bronze Age rock art panels across Northern England as a case study for delineating ASM management actions required to enhance monument preservation. The state of the rock art is described first, including factors that led to current conditions. Rock art management approaches then are described within the context of future environments, which models suggest to be more dynamic and locally variable. Finally, a Condition Assessment and Risk Evaluation (CARE) scheme is proposed to help prioritise interventions; an example of which is provided based on stone deterioration at Petra in Jordon. We conclude that more focused scientific and behavioural data, specific to deterioration mechanisms, are required for an ASM CARE scheme to be successful.

Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called "wild" pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region. © 2007 by The National Academy of Sciences of the USA.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.