In a nutshell: the identification and archaeological application of experimentally defined correlates of Macrozamia seed processing

This paper describes the methods and results of ethnographically-based replicative seed processing experiments conducted on Australian Macrozamia moorei seeds. Archaeological evidence indicates that these seeds were consumed by Australian hunter–gatherers in both the Pleistocene and Holocene. The experiments identified three features indicative of human processing and tested the effect of different processing variables (striking position, indentor type, thermal modification and presence of outer flesh) on the frequency of these diagnostic criteria. The results demonstrate that it is possible to use the physical modifications on individual seed specimens to identify the anthropogenic fracture of seeds and specific methods used to process them. These criteria were used in the analysis of M. moorei seeds from mid-Holocene-aged archaeological sites in central Queensland, Australia. The results indicate that seeds with and without sarcotesta were processed using a wooden indentor via side striking techniques.     

Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early <Emphasis Type="Italic">japonica</Emphasis> in South and Southeast Asia

We report a successful extraction and sequencing of ancient DNA from carbonized rice grains (Oryza sativa) from six archaeological sites, including two from India and four from Thailand, ranging in age from ca. 2500 to 1500 BP. In total, 221 archaeological grains were processed by PCR amplification and primary-targeted fragments were sequenced for comparison with modern sequences generated from 112 modern rice populations, including crop and wild varieties. Our results include the genetic sequences from both the chloroplast and the nuclear genomes, based on four markers from the chloroplast and six from the nuclear genome. These markers allow differentiation of indica rice from japonica rice, the two major subspecies of Asian rice (O. sativa) considered to have separate geographical origins. One nuclear marker differentiates tropical and temperate forms of subspecies japonica. Other markers relate to phenotypic variation selected for under domestication, such as non-shattering, grain stickiness (waxy starch) and pericarp colour. Recovery and identification of sequences from nuclear markers was generally poor, whereas recovery of chloroplast sequences was successful, with at least one of four markers recovered in 61 % of archaeological grains. This allowed for successful differentiation of indica or japonica subspecies variety, with japonica identified in all the Thai material and a mixture of indica and japonica chloroplasts in the two Indian assemblages. Rice subspecies was also assessed through conventional archaeobotanical methods relying on grain metrics, based on measurements from 13 modern populations and 499 archaeological grains. Grain metrics also suggest a predominance of japonica-type grains in the Southeast Asian sites and a mixture of japonica and indica in the Indian sites with indica in the minority. The similar results of grain metrics and ancient DNA (aDNA) affirm that grain measurements have some degree of reliability in rice subspecies identification. The study also highlights the great potential of ancient DNA recovery from archaeological rice. The data generated in the present study adds support to the model of rice evolution that includes hybridization between japonica and proto-indica.     

Essentials in the use of mycolic acid biomarkers for tuberculosis detection: response to “High-throughput mass spectrometric analysis of 1400-year-old mycolic acids as biomarkers for ancient tuberculosis infection” by

High molecular weight long-chain mycolic acids are key structural components of the cell envelope of Mycobacterium tuberculosis and they are established as biomarkers for the identification of both ancient and modern tuberculosis. Mycolic acids from M. tuberculosis have a characteristic profile, reflecting contributions from five major distinct homologous series of mycolate structural types. Diagnosis of tuberculosis in archaeological material, using mycolic acid biomarkers, depends on objective recognition of the key characteristic mycolic acid components. A recent article in this journal claimed that tuberculosis could be confirmed in ancient bones by high throughput mass spectrometric analysis of mycolic acids. Scrutiny of the data presented reveals no convincing evidence for the presence of mycolic acids, characteristic of the M. tuberculosis complex, in the skeletal remains examined. This communication reviews the essential criteria necessary for positive tuberculosis diagnosis, using mycolic acids.     

Diversity of cultivars and other plant resources used at habitation sites in the Llanos de Mojos, Beni, Bolivia: evidence from macrobotanical remains, starch grains, and phytoliths

Although sparsely populated today, the Llanos de Mojos, Bolivia, sustained large sedentary societies in the Late Holocene (ca. 500 to 1400 AD). In order to gain insight into the subsistence of these people, we undertook macrobotanical and phytolith analyses of sediment samples, and starch grain and phytolith analyses of artifact residues, from four large habitation sites within this region. Macrobotanical remains show the presence of maize (Zea mays), squash (Cucurbita sp.), peanut (Arachis hypogaea), cotton (Gossypium sp.), and palm fruits (Arecaceae). Microbotanical results confirm the widespread use of maize at all sites, along with manioc (Manihot esculenta), squash, and yam (Dioscorea sp.). These integrated results present the first comprehensive archaeobotanical evidence of the diversity of plants cultivated, processed, and consumed, by the pre-Hispanic inhabitants of the Amazonian lowlands of Bolivia.     

Re-evaluating the history of the wheat domestication gene NAM-B1 using historical plant material

The development of agriculture is closely associated with the domestication of wheat, one of the earliest crop species. During domestication key genes underlying traits important to Neolithic agriculture were targeted by selection. One gene believed to be such a domestication gene is NAM-B1, affecting both nutritional quality and yield but with opposite effects. A null mutation, first arisen in emmer wheat, decreases the nutritional quality but delays maturity and increases grain size; previously the ancestral allele was believed lost during the domestication of durum and bread wheat by indirect selection for larger grain. By genotyping 63 historical seed samples originating from the 1862 International Exhibition in London, we found that the ancestral allele was present in two spelt wheat and two bread wheat cultivars widely cultivated at the time. This suggests that fixation of the mutated allele of NAM-B1 in bread wheat, if at all, occurred during modern crop improvement rather than during domestication. We also discuss the value of using archaeological and historical plant material to further the understanding of the development of agriculture.     

Locally diagnostic phytoliths of wild rice (Zizania palustris L.) from Minnesota,USA: comparison to other wetland grasses and usefulness for archaeobotany and paleoecological reconstructions

Wild rice (Zizania spp.) is an important native grain of north-central North America, with spiritual and subsistence significance to many native peoples. Due to lack of suitable proxies, its past distribution and pattern of use are poorly known. This study demonstrates the diagnostic value of silica phytoliths from Z. palustris as a proxy tool to detect its past occurrence in a variety of paleoenvironmental and archaeological contexts. Our main findings are: 1) Dominant wetland grass species in Minnesota produce phytoliths distinct from Zizania phytoliths; 2) Closely related Leersia oryzoides produces a few Zizania-like phytolith morphotypes; however, these potential confusers can be identified based on 2-D and 3-D morphologies; 3) Z. palustris produces a wide variety of phytolith morphotypes, many of which are only found in certain parts of the plant (e.g., Inflorescence Type 1 from the spikelet); 4) Z. palustris produces 23 locally diagnostic phytolith morphotypes that can be used to determine the presence and abundance of wild rice in modern and paleo lake sediments; and 5) Wild rice phytolith Inflorescence Type 1 is the morphotype most likely to be observed in archaeological contexts, and may be unequivocally diagnostic for the genera Zizania.     

DNA analysis in charred grains of naked wheat from several archaeological sites in Spain

In the present work we attempt to recover endogenous ancient DNA from cereal grains preserved under different conditions: charred, partially charred and waterlogged. A total of 126 grains from naked wheat and 18 from barley from different sites on the Eastern Iberian Peninsula ranging from the beginning of agriculture in the region to the turn of the Common Era, were studied. Two different extraction protocols were used, a standard phenol–chloroform method and a silica-based DNA extraction procedure implemented for artificially charred seeds. Amplifications were directed to three markers: the large subunit of ribulose 1,5 biphosphate carboxylase (rbcL) and the microsatellite WCT12 in the chloroplast genome and the x and y subunits of the high molecular weight glutenin gene (Glu-1) in the nucleus. The first two were used to assess the preservation status of the samples, while with the third we tried to identify the wheat grains at species level. It was possible to obtain eleven positive amplifications in 8 partially charred seeds but only two amplifications of the Glu-1 gene from a single sample of the Early Bronze age were genome-specific. Different contamination sources were identified and reported. Cloning and alignment of sequenced clones showed a correspondence of the amplified fragment to modern wheat D genome haplotypes. This result suggests that the sample corresponds to hexaploid wheat (Triticum aestivum L.), thus being the first ancient DNA evidence to date for the cultivation of hexaploid wheat in the prehistoric agriculture of the Iberian Peninsula. Moreover, obtained results highlight contamination problems associated to the study of ancient archaeobotanical charred seeds suggest that the combination of a silica-based extraction method together with the amplification of specific targets is a good strategy for recovering endogenous ancient DNA from this kind of material.     

Molecular genetic basis of determining subspecies of ancient rice using the shape of phytoliths

The presence of phytoliths derived from motor cells of rice (Oryza sativa L.) in archaeological sites could provide strong evidence for cultivation of rice in ancient times. The shape of phytoliths is now considered an effective criterion for determining subspecies of ancient rice. To understand the molecular genetic basis of determining subspecies of ancient rice based on the shape of phytoliths, and to analyze the quantitative trait loci (QTLs) controlling the shape of the silica body, which is the predecessor of phytoliths, we used 68 recombination inbred lines (RIL) from progeny of a combination of a cross between japonica variety, Asominori and indica variety, IR24. Knowledge of the positions of QTLs for the shape of the silica body would contribute to the study on the differentiation and evolution of rice at the molecular level. A total of 16 QTLs associated with the shape of the silica body were detected. Of these, five QTLs for vertical length of the silica body were mapped to chromosome 2, 3, 4, 8 (two QTLs) and accounted for 7.1–10.7% of the total phenotypic variation. Six QTLs for the horizontal length were detected on chromosome 1, 2, 3, 4 (two QTLS), 8 and accounted for 8.1–10.7% of the total phenotypic variation. Five QTLs controlling the lateral length on chromosome 1 (two QTLs), 2, 11 (two QTLs) were detected and explained 7.3–8.6% of the phenotypic variation. The genetic linkage relationships between QTLs for the shape of the silica body and taxonomic traits for classifying subspecies of rice showed feasibility of classifying subspecies of rice based on the shape of phytoliths in archaeological sites.     

Archaeobotanical inference of Bronze Age land use and land cover in the eastern Mediterranean

Charcoal and charred seeds at five Bronze Age archaeological sites discern ancient land use in the eastern Mediterranean. Seed frequencies of orchard crops, annual cereals and pulses, and wild or weedy plants are used to characterize plant utilization at different archaeological sites on the island of Cyprus, in the Rift Valley of Jordan, and in the Jabbul Plain and along the upper Euphrates River valley in Syria. Seed to charcoal ratios provide proxies to determine the relative usage of dung versus wood for fuel across the ancient Mediterranean landscape. Greater charcoal and lower charred seed values are interpreted to represent a wooded environment, while higher amounts of charred seeds and minimal wood charcoal suggest a much great use of dung as a fuel source. Interestingly, Politiko-Troullia (Cyprus, Cypriot archaeological sites are, by convention, named for the nearest modern village (Politiko), followed by an italicized toponym (Troullia) referring to the plot of land that incorporates the site) has the lowest seed to charcoal ratio, suggesting its residents primarily burned wood and that the landscape surrounding Troullia remained relatively wooded during the Bronze Age. In contrast, villagers at Tell el-Hayyat (Jordan) utilized a mixture of wood and dung, in contrast to Tell Abu en-Ni’aj (Jordan), and especially Umm el-Marra and Tell es-Sweyhat (Syria), where inhabitants relied solely on dung fuel. Comparative analysis and interpretation of seed and charcoal evidence thus illustrates the variety of fuel use strategies necessitated by the dynamic and diverse Bronze Age landscapes of the Eastern Mediterranean.     

Amplification and sequencing of Trichuris trichiura ancient DNA extracted from archaeological sediments

Despite high prevalence of Trichuris trichiura infection, PCR-based analysis on T. trichiura from archaeological samples has not been established so far. In the present study, we sought to perform PCR-based amplification of T. trichiura aDNA using the sediments from medieval tomb of Korea. The presence of Trichuris eggs were first detected by microscopic observation; then confirmed by PCR-based aDNA analysis. Obtained sequence showed 100% homology to that of the small subunit ribosomal RNA (SSUrRNA) gene of T. trichiura but distinct from that of other Trichuris species. PCR-based aDNA analysis in this study can serve as effective method to confirm the presence of T. trichiura eggs in the soils or coprolites collected from archaeological sites.     

Red abalone collecting and marine water temperature during the Middle Holocene occupation of Santa Cruz Island,California

Oxygen isotope values derived from prehistoric mussel (Mytilus californianus) shell calcite are used to determine whether sea-surface temperatures in the vicinity of the Punta Arena site (CA-SCRI-109) on Santa Cruz Island, California, were cooler than present between 6300 and 5300 cal BP. This site and others in the western sector of the island dating to this period are distinctive because of the presence of large red abalone (Haliotis rufescens) shells, a species that historically has been subtidal around Santa Cruz and the other northern Channel Islands. Comparison of temperature values derived from archaeological shells with those from modern mussel shells, along with water temperatures derived from satellites, indicates that waters were cooler during the 6300 to 5300 cal BP period. These results are consistent with a previous study and support the interpretation that collection of red abalone during the 6300–5300 cal BP period was partly the result of cooler water temperatures that made this large mollusk more available to foragers in the intertidal or shallow subtidal zone.     

Macrobotanical food remains from a trans-Holocene sequence at Daisy Cave (CA-SMI-261), San Miguel Island, California

Carbonized macrobotanical remains from a trans-Holocene archaeological and paleontological sequence at Daisy Cave provide important insights into the use of food plants by Paleocoastal people as well as later groups on California’s Northern Channel Islands. Small seeds are rare among the macrobotanical remains recovered in the cultural strata at Daisy Cave, which are dominated by charcoal from woody plants used as fuel. The recovery of Brodiaea-type corms from the Early and Late Holocene strata suggests, however, that geophytes were an important source of carbohydrates and calories for Channel Islanders throughout the Holocene. The proposed importance of geophytes is consistent with the abundance of Brodiaea in island vegetation communities recovering from more than a century of overgrazing, as well as the large numbers of digging stick weights found in island sites.     

The origins of agriculture in North-West Africa: macro-botanical remains from Epipalaeolithic and Early Neolithic levels of Ifri Oudadane (Morocco)

This research aims to shed light on the early stages of agricultural development in Northern Africa through the analysis of the rich macro-botanical assemblages obtained from Ifri Oudadane, an Epipalaeolithic–Early Neolithic site from North-East Morocco. Results indicate the presence of domesticated plants, cereals (Hordeum vulgare, Triticum monococcum/dicoccum, Triticum durum and Triticum aestivum/durum) and pulses (Lens culinaris and Pisum sativum) in the Early Neolithic. One lentil has been dated to 7611 ± 37 cal BP representing the oldest direct date of a domesticated plant seed in Morocco and, by extension, in North Africa. Similarities in both radiocarbon dates and crop assemblages from Early Neolithic sites in Northern Morocco and the Iberian Peninsula suggest a simultaneous East to West maritime spread of agriculture along the shores of the Western Mediterranean. Wild plants were abundantly collected in both the Epipalaeolithic and the Early Neolithic periods pointing to the important role of these resources during the two periods. In addition to fruits and seeds that could have been consumed by both humans and domesticated animals, fragments of esparto grass (Stipa tenacissima) rhizomes have been identified. This is a western Mediterranean native plant that may have been used as a source of fibres for basketry.     

Archaeobotany of fruit seed processing in a monsoon savanna environment: evidence from the Keep River region,Northern Territory,Australia

We analyse archaeobotanical remains from three excavated rockshelter sites, Jinmium, Granilpi and Punipunil, in the Keep River region, northwestern Australia. The record is dominated by burnt fragmented seed remains from the fruit trees Persoonia falcata and Buchanania obovata, consistent with ethnographic records of whole fruits being pounded into pastes and cakes at the beginning of the summer wet season. Surface seed samples of non-cultural origin are mostly whole and unburnt, and contain higher proportions of grass seeds. Sustained processing of fruit seeds is first visible in the archaeological record about 3500 years ago. Spatial and temporal variation in its intensity is evident since that time until it declines following European colonisation. The decline does not represent total site abandonment, but a reorientation of activities following the ecological and social changes that came with pastoralism. The former included the local decline of P. falcata with more intense fire regimes.     

Methodologies for assessment of the state of preservation of pollen and plant macrofossil remains in waterlogged deposits

Abstract

Methodologies are proposed for assessing the state of preservation of pollen and plant macrofossil remains based on the investigation of known prehistoric waterlogged sites in the Somerset Levels, under threat from peat extraction and peat wastage. For each sample assessed, a fixed number of pollen grains and macrofossil seeds was classified according to deterioration type and scored for intensity of deterioration. The principal deterioration types recognised for pollen were biochemical (corrosion and degradation) and mechanical (breakage and crumpling). For seeds two main categories of deterioration were adopted, fragmentation and erosion/corrosion of the seed testa. The calculation of preservation indices for pollen and macrofossils allowed comparisons to be made within and between sites. A range of factors which may have influenced variations in preservation are briefly discussed. These methodologies are potentially valuable where there is a need to assess the survival of the archaeobotanical record, particularly where sites are sensitive to environmental change.     

Oxygen isotopic composition of limpet shells from the Beagle Channel: implications for seasonal studies in shell middens of Tierra del Fuego

Shell middens distributed along the coastal areas of the Beagle Channel (Tierra del Fuego) testify the primary role of marine resources in the successful social dynamic of hunter–gatherer–fisher societies (HGF) in extreme high latitude environmental conditions. Intertidal and subtidal limpet species are frequently identified taxa of these archaeological deposits. We investigated whether shell δ¹⁸O of the limpet species Nacella deaurata is a valuable record of local sea surface temperature (SST) and ambient water δ¹⁸O (δ¹⁸Ow) fluctuations, and in turn can be used to estimate the season of its exploitation by Holocene HGF. Sequential shell δ¹⁸O of modern species track seasonal changes of SST and δ¹⁸Ow. The comparison of shell δ¹⁸O profiles of N. deaurata and Nacella magellanica (a coexisting species) suggests the occurrence of distinct growth rate and physiological adaptations between species. Shell δ¹⁸O of zooarchaeological specimens of N. deaurata from Lanashuaia II suggests that animals were exploited predominantly in winter and that experienced similar environmental conditions of present day at ∼1320 years BP. Results also indicate that N. deaurata is a valuable candidate for studying past seasonal changes in SST and δ¹⁸Ow in this southernmost part of South America.     

Ectopic paragonimiasis from 400-year-old female mummy of Korea

Of the parasite eggs discovered in ancient samples from Korean archaeological sites, Paragonimus spp. are of particular importance in that they are regarded as one of the most insidious trematode infection sources. Although their infection prevalence decreased rapidly in the early 20th century, archaeoparasitological studies on the species are still required, as historical knowledge of paragonimiasis remains far from comprehensive. Fortunately, we recently were given a chance to examine a medieval Korean mummy in a good state of preservation. Using morphological techniques, we discovered evidence of ectopic paragonimiasis in the sample from the 17th-century female. When the ITS 2 gene was extracted, amplified and sequenced from Paragonimus eggs, it showed 100% homology to the sequences of modern Paragonimus westermani reported from Korea and Japan, forming a cluster distinct from South Asian P. westermani. Our report is the first-ever analysis of ancient Paragonimus DNA from any archaeological field in the world. The ectopic paragonimiasis diagnosis made in this study, especially involving the liver sample, also is the first of its kind in archaeoparasitology.     

A parasitological paradox: Why is ascarid infection so rare in the prehistoric Americas?

Ascaris lumbricoides (giant roundworm) and Trichuris trichiura (whipworm) are the most common intestinal parasites found in humans worldwide today and they almost always co-occur. However, we find two distinct patterns in archaeological material. In historical North American and Old World contexts, the association of A. lumbricoides and T. trichiura is similar to the modern epidemiological picture. In contrast, the co-occurrence of A. lumbricoides and T. trichiura eggs in prehistoric South America is rare. For prehistoric contexts, T. trichiura is the most common parasite found in archaeological material. Recently molecular biology techniques pointed to a subdiagnosis of roundworm infection in pre-Columbian South American populations. This is contrary to the modern epidemiological picture in which A. lumbricoides infection is predominant. This is a paradox, especially when one considers the number of eggs laid by female daily, 200,000 and 20,000 thousand per day, for A. lumbricoides and T. trichiura respectively. By reviewing the records of these parasites, this paradox is presented and explanations for the paradox are explored. Taphonomy, prehistoric behavior patterns and medicinal plant use seem to be most relevant to the explanation of the paradox. Nematophagous fungi is a less likely factor creating the near absence of A. lumbricoides eggs in the prehistoric New World.     

The Preservation and Interpretation of δ34S Values in Charred Archaeobotanical Remains

The measurement of sulphur isotope (δ³⁴S) values in charred plant remains has the potential to inform understanding of the spatial configuration and ecology of crop production. We investigated the effects of charring, manuring, oxidation and anaerobic soil conditions on modern cereal grain/pulse seed δ³⁴S values, and assessed the effect of chemical pre‐treatment on charred modern and archaeobotanical grain/seed δ³⁴S values. We used these results to interpret δ³⁴S values in archaeobotanical material from Neolithic Çatalhöyük. Our results suggest that δ³⁴S values can be reliably preserved in charred grain/seeds but are subject to influence by anaerobic soil conditions, the effect depending on the timing of flooding in relation to S assimilation.     

Early cat taming in Egypt: a correction

A cat skeleton from a Predynastic burial in Egypt that was previously labelled as Felis silvestris is re-identified as Felis chaus. This means that the previous claim needs to be withdrawn that the specimen represents early evidence for taming of Felis silvestris that ultimately led to domestication. However, the statement that the small felid has been held in captivity for several weeks, based on the presence of healed fractures, is still valid.