Ancient olive DNA in pits: preservation,amplification and sequence analysis

The olive tree (Olea europaea) was domesticated by vegetative propagation of selected wild individuals with superior fruit. Later, new cultivars were established repeatedly from feral trees or from crosses between wild, feral, and domesticated trees. Thus the genetic background of many contemporary domesticated lines is a mixture of ancient cultivars and local wild trees. Ancient DNA may illuminate the complicated process of olive domestication because such DNA sequences provide data about ancient genomes that existed closer to the domestication events. Well preserved DNA must be available for such studies, even though in the Mediterranean region, where olive cultivation took place, the climatic conditions are not favorable for DNA preservation. To select for well preserved pits we measured their proportions of lignin by IR spectroscopy, and correlated this with parameters of DNA quality such as template length in an olive-specific repeat array, and template quantity as determined by real-time PCR amplification. Archaeological pits that passed these tests did contain high quality ancient DNA. We present the first ancient olive DNA sequences and compare them to modern wild, feral and domesticated lines.     

Bone preservation,decay and its related conditions in ancient human bones from Kuwait

By means of scanning electron microscopy, four out of a series of twelve inhumations from the Hellenistic Period were examined for traces of the decay process. The changes represented the result of erosion and biological decomposition of human bones on a small island in the northern part of the Persian Gulf over a period of ca. 2200 years. Special emphasis was given to bone preservation and blood cell survival, and to bone changes due to physicochemical erosion and fungus, bacterium, insect and plant-root activity. Related soil and climatic conditions were taken into consideration. The observations should be evaluated to understand the unusual state of preservation of the bones and to avoid possible misinterpretation of pseudo-pathological bone changes as ante-mortem pathology.     

On the circumstances surrounding the preservation and analysis of very old DNA

Herein, I discuss the limits and circumstances of DNA preservation in old fossils. The stability of DNA in physiological solution suggests that DNA should be degraded at the latest within 50 000–100 000 years and has convincingly been found in fossil bones of this age. I argue here that particular fossilization conditions can cause exceptional DNA preservation over much longer periods, in an unexpected state. A working hypothesis is proposed stating that DNA can ‘hibernate’—that is, be preserved over long periods—only if it is hidden within molecular ‘niches’ where it is not governed by the rules of aqueous solution chemistry, and that such ‘geological’ DNA cannot be purified using procedures that assume that it behaves like ‘biological’ DNA.     

Bone collagen preservation in the tropics: a case study from ancient Puerto Rico

Bone collagen is a well-characterized and generally robust protein that plays a key role in both radiometric dating and stable isotopic reconstruction of paleodiet. To be useful for such purposes, however, analyzed collagen must be relatively taphonomically unaltered. To date, little research has been conducted to document the taphonomic fate of bone collagen from archaeological sites in the tropics. In the present work, a large (n = 298) dataset of archaeological bone samples from sites on the island of Puerto Rico is examined by means of radiometric, chemical, and elemental analyses. The ultimate conclusion of this work is that while collagen loss may be accelerated in the tropics versus that seen in samples from higher latitudes, what collagen remains is typically sufficiently well-preserved and taphonomically unaltered as to make radiocarbon dating and/or stable isotopic analysis worthwhile.     

Improved methodology for extraction and amplification of DNA from single grains of charred wheat

Comparisons were made between two commonly used methods for the extraction of ancient DNA from charred plant remains. Using artificially charred wheat seeds, we show that silica-binding is the most efficient method for extraction of DNA. We describe a improved silica-binding procedure, including pre-incubation with N-phenacylthiazolium bromide and increased washing of bound DNA, which yields amplifiable DNA from seeds heated at 200 °C for up to 8 h, conditions which promote the formation of Maillard products which often copurify with aDNA and inhibit subsequent PCRs. We believe that this method will be effective in ancient DNA extraction with most types of charred archaeobotanical material. Both cold- and hot-start PCR procedures gave good amplicon yields with extracts prepared in this way, but cold-start PCRs also resulted in synthesis of short artefact products. Addition of bovine serum albumin to PCRs, an inert carrier substance thought to enhance amplification efficiency by binding contaminants, had no advantageous effect and in fact reduced amplicon synthesis.     

Bone preservation in human remains from the Terme del Sarno at Pompeii using light microscopy and scanning electron microscopy

Archaeological bone can show marked and complex alterations depending on the environment in which it was buried. In this study, the state of preservation of 27 femurs recovered from the archaeological site of Pompeii was evaluated by light microscopy and scanning electron microscopy. Most of the bone samples, prepared by the grinding method, showed good histological preservation, although they were characterized by microfissures (microcracking). Nine bone samples showed different states of histological preservation, including worst preservation (two femurs), due to diagenetic processes. Cryostat bone sections stained with thionin or 4′,6′-diamidino-phenylindole (DAPI) revealed the persistence of DNA within some osteocyte lacunae. Scanning electron microscopy analysis showed that ultrastructural characters, such as lamellae and collagen fibres, are recognizable only in unaltered bone. Our results reveal that most Pompeian samples are well preserved since they have a bone microstructure virtually indistinguishable from that of fresh bone. In methodological terms, although each of the various morphological methods used contributes information, histological and histochemical analyses are the most informative for studying the preservation state of bone and allow for rapid essential screening of archaeological bone.     

A pilot study into the effects of X-ray and computed tomography exposure on the amplification of DNA from bone

This research investigates the intersection of radiography and aDNA, two commonly used methods in bioarchaeology. The goal of this project was to investigate the effects of radiation on the ability to amplify DNA from bone. Bones (n = 124) from domestic pig (Sus scrofa) feet were randomly sorted into a control group and four treatment groups: (1) single exposure X-ray; (2) single exposure CT; (3) multiple exposures X-ray; and (4) multiple exposures CT. Number of PCR cycles required to amplify DNA in 100 bp, 200 bp and 400 bp segments were used as a proxy for the amount of available DNA. In the 200 bp CT sample, distal phalanges required significantly more amplification cycles than did the other bones and were removed from analysis. Results suggest that in general radiation exposure fragments DNA thereby decreasing the amount that is amplifiable. While these results are suggestive, further research is required to elucidate the degree to which radiation fragments DNA in archaeological specimens.     

Power,property, and preservation

MacKenzie, Melody Kapilialoha, ed. Native Hawaiian Rights Handbook. Honolulu: Native Hawaiian Legal Corporation, 1991. xi + 320 pp. including notes, glossary, table of cases, and index [distributed by University of Hawaii Press]. $25.00 paper.

Price, H. Marcus. Disputing the Dead: U.S. Law on Aboriginal Remains and Grave Goods. Columbia: University of Missouri Press, 1991. ix + 136 pp. including appendix and bibliography. $37.50 cloth.

West, Patrick C. and Steven R. Brechin, eds. Resident Peoples and National Parks: Social Dilemmas and Strategies in International Conservation. Tucson: University of Arizona Press, 1991. xxiv + 443 pp. including bibliography and index. $29.95 cloth.     

Ancient Iberian horses: a method to recover DNA from archaeological samples buried under sub-optimal conditions for preservation

Existing methods to extract, amplify, and sequence ancient DNA (aDNA) from horse bone and teeth were optimized to recover DNA from a depositional environment of highly permeable acidic soil. DNA was successfully retrieved using 0.10g of bone powder from horse (Equus sp.) remains dating to 25 K years utilizing the methods optimized for this archaeological material. The genetic analyses were performed in a facility that is dedicated to ancient DNA research (Paleo-DNA Laboratory, Thunder Bay, ON, Canada) and has not been previously used to analyse modern or ancient horse DNA. Research was replicated to obtain reliable sequencing results for six samples from the Iberian Peninsula that were consistent with published sequences of Equus caballus. The archaeological sequence data obtained support hypotheses that promote the significance that the Iberian Peninsula has had to the multi-focal centres of origin for horse domestication and distribution of modern horse breeds. The data presented may provide evidence of the existence of an Iberian refugium for Equus during the last glacial period, 10 K years BP. Further molecular data analyses will enhance the ideas presented by this data and our understanding of horse domestication and phylogeny. The optimization of molecular techniques to successfully obtain DNA using minimally destructive, cosmetically sensitive techniques from archaeological remains endeavours to foster further cooperation between museums and researchers.     

Bone chemistry and paleodiet

Bone chemistry paleodietary studies are emerging as important research areas in archaeology, biological anthropology, and paleontology. With appropriate controls, the inorganic and organic chemical composition of bones and teeth can provide information about past diet and habitat use. Chemical signatures are used to address individual dietary variability in early hominid fossils, paleontological remains, and more recent human and faunal populations.     

Creative preservation: The development of an artistic approach to the preservation and presentation of the past

Abstract

The article proposes “Creative Preservation” as an artistic approach to contemporary questions concerning the preservation and presentation of archaeological sites. By examining critically the role of cultural heritage today, it attempts to search for alternative perspectives and to retrieve forgotten sensibilities such as Diderot's “Poetics of Ruins”. It first examines concepts of time and authenticity, especially in archaeological sites, as interpreted by various authors from Poincare, von Schiller, Bergson and Simmel to Choay and Jokilehto.

Dedicated to immaterial qualities of places, “Creative Preservation” suggests the refinement of “images of authenticity” in an attempt to penetrate and to communicate with deeper levels in the complex reality of ancient places – actual and specific locations which anchor and root memory in material.

A first realization of this approach is presented in the form of the spiral viewpoint recently constructed at the northwest part of the archaeological site of Ramat Rachel near Jerusalem.     

Fruit and seed biomineralization and its effect on preservation

Mineralised fruits and seeds are frequently found in archaeological sediments but their chemical nature has not been often examined. The nature and the origin of these archaeobotanical remains have to be investigated to understand their taphonomic history. Fruits or seeds can be mineralised not only by replacement mineralisation but also by biomineralisation during the plant life. The mineral components of three fossil fruits sampled on the Pleistocene site of Dmanisi were analysed and compared with their modern analogues. Analyses were carried out by means of an environmental scanning electron microscope, equipped with an energy dispersive X-ray device and by means of a Fourier transform infrared spectrometer. Biogenic carbonates and/or biogenic silica were identified in the fossil and modern fruits of some taxa. Comparison between fossil and modern specimens has shown that molecular reorganisation occurred in carbonate and in biogenic silica during fossilisation, through diagenetic processes. The resulting stable mineral structures confer an exceptional preservation to fruits in sediments. Taking into account these taphonomic specificities (transformation and differential preservation), the chronological and palaeoenvironmental aspects of the mineralised fruits are discussed.     

Ancient DNA in archaeological wheat grains: preservation conditions and the study of pre-Hispanic agriculture on the island of Gran Canaria (Spain)

The recovery of ancient DNA from archaeological wheat samples under different preservation conditions was assessed using a number of genetic markers. It was possible to amplify nuclear DNA from desiccated grains but not from charred. The desiccated grain was from a pre-Hispanic grain silo in Gran Canaria and showed excellent DNA preservation, enabling the amplification of the ribosomal DNA markers IGS and ITS, the upstream region of the HMW-glutenin locus and single-locus nuclear microsatellites. Our results demonstrated the presence of both durum and bread wheat in an assemblage of naked grain. We were also able to identify different genotypes in durum wheat and compare these with extant landraces, providing insights into the agrarian practices of the ancient Canarians and the origin of their crops.     

Neogene crinoids of southeast Asia: preservation,systematics and significance

Donovan, S.K. &; Helwerda, R.A., August 2016. Neogene crinoids of southeast Asia: preservation, systematics and significance. Alcheringa 41, xxx–xxx. ISSN 0311-5518.

The Cenozoic record of fossil crinoids is poor. In part, this is because the stalked taxa have moved into deep water (>100–150 m water depth) since the Cretaceous, but also results from the propensity for the crinoid endoskeleton to disarticulate soon after death. Despite this, we report two new, small crinoid faunas of moderate diversity from the Pliocene of East Kalimantan and the Philippines. Included taxa are columnals of the isocrinid Metacrinus? sp.; a bourgueticrinid cup and columnal, Democrinus? sp.; and cirral and brachial ossicles (isocrinids and comatulids). The preservation of these Pliocene crinoids is not conducive to classification to the level of species, although some taxa are easier to determine than others, but the precise reason for this dearth of complete specimens remains uncertain. Because of our knowledge of extant crinoids, this Cenozoic ‘gap’ has been poorly appreciated. Rather than denigrating the Pliocene crinoids documented herein for being fragmentary and difficult to accurately determine, we instead report them as a rare set of data points, filling, in part, the Cenozoic ‘gap’.

Stephen K. Donovan [steve.donovan@naturalis.nl] and Renate Helwerda [renate.helwerda@naturalis.nl], Naturalis Biodiversity Center, Postbus 9517, 2300 RA Leiden, The Netherlands. Received 03.05.2016; revised 16.06.2016; accepted 21.6.2016.