Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts

Polymerase chain reaction (PCR) inhibitors are often co-extracted with ancient DNA (aDNA) and when present make the analysis of aDNA difficult, if not impossible. In this study we review previous research on PCR inhibitors and techniques that address their co-extraction with DNA from sub-optimal samples. Additionally, we introduce a simple extraction technique, “repeat silica extraction,” that effectively removed PCR inhibitors from extracts of 7000–8000-year-old human skeletal remains from the Windover archaeological site in Florida and 700–2000-year-old human coprolites excavated from Fish Slough Cave in southern California. A series of tests on these same samples demonstrates that N-phenacylthiazolium bromide is largely ineffective, despite previously reported success using this compound as part of the DNA extraction process. We also describe a method for demonstrating the presence as well as successful removal of PCR inhibitors by use of a “positive aDNA control,” a test necessary to conclude that negative PCR amplification is the result of the absence of preserved DNA.     

Temporal Patterns and Effects of Surface‐Water Diversions on Daily Flows and Aquatic Habitats: Bega‐Bemboka River,New South Wales,Australia

An understanding of the nature and magnitude of hydrological, physical habitat and physico‐chemical effects resulting from surface‐water diversions in river systems is essential for effective management of water resources. For most coastal‐draining rivers in New South Wales, however, there are few data available on irrigation diversions, their hydrological impacts and environmental effects. This paper therefore presents an analysis of mean daily surface‐water diversions for pasture irrigation from approximately three years of metered data and the resultant effects on daily flows and aquatic habitats in the Bega‐Bemboka River. The period of analysis of the hydrological effects of irrigation diversions is extended to the full length of record (approximately five years) for gauging stations most affected by irrigation diversions, using Maintenance of Variance Extension Type 1 (MOVE.1) modelling techniques. The annual mean, median and peak daily rates of water diversion by metered surface‐water licences used to irrigate 925 ha of dairy pasture are 10.5 Ml d^?1, 7.3 Ml d^?1 and 41.5 Ml d^?1, respectively. Diversion effects on flow duration statistics are such that the measured 90th and 95th daily flow duration percentiles at the gauging station most affected by upstream irrigation diversions are equivalent to the 97th and 99th flow duration percentiles, respectively, under MOVE.1 modelled natural flow conditions. While diversions for irrigation over the three‐year data period account for only 6.6% of total flow volumes, diversions as a proportion of daily surface‐water inflows increase exponentially under decreasing flow rates. Median and maximum daily diversion rates attain 91% and 118%, respectively, of total surface‐water inflows to the diversion‐affected reach when upstream inflows range from 15 to 20 Ml d^?1. This exponentially‐increasing relationship between daily diversion rates and declining surface‐water inflows suggests that ‘rule of thumb’ guidelines on sustainable diversion limits based on mean or median annual percentage diversion volumes need to be applied cautiously to river systems with no or limited capacity to manipulate flows to meet downstream consumptive demands.     

Human impact around settlement sites: a phytolith and mineralogical study for assessing site boundaries,phytolith preservation,and implications for spatial reconstructions using plant remains

Defining the extent of human activity around settlement sites is of particular significance in archaeology as it may define peripheral activity areas and thus the site's boundary. In Near Eastern archaeology, site boundaries are usually defined by the presence of architectural and other macroscopic archaeological remains. Here we use the phytolith concentrations and morphotype assemblages, as well as changes in the mineralogical composition of the sediments in and around the small Iron Age site of Izbet Sartah in central Israel to determine the site boundaries. The site has a shallow stratigraphy and highly bioturbated sediments. Coincidental changes in the clay/quartz ratio and phytolith concentrations define the boundary between high and low impact anthropogenic activities. This boundary is generally some 20 m away from the architectural remains. In addition, we note that the phytoliths in the site's core show clear evidence of having been affected by chemical dissolution (i.e., diagenesis), while those in the vicinity of the site's boundary have undergone severe diagenesis. These observations indicate that phytolith diagenesis will affect site boundaries determination, as well as phytolith-based reconstructions of activity areas. We propose that phytolith preservation depends on the initial amount of available silica, the depth of burial with respect to the active root area of modern vegetation, and the presence of fresh phytoliths in the soil.     

Examining Indigenous perspectives on the health implications of large‐scale agriculture in Jalisco,Mexico

In Mexico, as in many other parts of the world, industrial agriculture is dramatically changing rural landscapes and altering relationships with the land. This paper draws on community‐based research from a collaborative international research project that examined the perceived health implications of the agricultural industry for Indigenous peoples in the state of Jalisco, Mexico. Thirty interviews were conducted in a Nahuas community experiencing expanding agribusiness industries. The results of this study show that the implications of export‐oriented agricultural industry for this Nahuas community are complex and, at times, contradictory: employment in the agricultural industry provides community members with much‐needed sources of income, but it is precarious work. At the same time, community members are concerned about the long‐term health and environmental implications, such as increased exposure to chemicals, depletion of the soil and water, and loss of traditional food and lifeways. These results suggest that to better understand the costs and benefits of large‐scale agriculture for Indigenous health, a broad lens of health that is situated in the context of colonial legacies and the particularities of relationships with the land is required.     

Evaluating bone collagen extraction methods for stable isotope analysis in dietary studies

The specific purpose of this study was to compare three different collagen extraction methods commonly used in isotope laboratories conducting dietary studies. We evaluated their resultant differences in δ¹³C and δ¹⁵N, collagen quality and collagen yield. Our study was based on well-preserved skeletal material from the medieval period in Denmark. Our study shows that there is a systematic significant difference in the yield and the δ¹³C values between the three methods. Using the method of DeNiro and Epstein [DeNiro, M.J., Epstein, S., 1981. Influence of diet on the distribution of nitrogen isotopes in animals. Geochimica et Cosmochimica Acta 45, 341–351] with NaOH as cleaning agent, will, according to our study, give δ¹³C values that are on average ±0.32‰ more positive than using the ultra-filtration method [Brown, T.A., Nelson, D.E., Vogel, J.S., Southon, J.R., 1988. Improved collagen extraction by modified Longin method. Radiocarbon 30 (2), 171–177, modified in Richards, M.P., Hedges R.E.M., 1999. Stable isotope evidence for similarities in the types of marine foods used by late Mesolithic humans at sites along the Atlantic coast of Europe. Journal of Archaeological Science 26, 717–722]. The third method, which is a modified version of the second method, excluded the ultra-filtration step. This method seems to give δ¹³C values that lie in between the other methods. Our study did not show any significant difference in δ¹⁵N values. Although the differences between the methods are very small, we conclude that the use of stable isotope analysis in food determination studies requires adherence to routine methods for preparing and measuring samples.     

中国北方史前遗址稻作遗存的植物硅酸体判别标准

利用植物硅酸体方法鉴定考古遗址中的栽培稻遗存,关键之一就是确立鉴定标准。通过对野生稻生长的环境背景进行综合分析,提出在中国北方地区,在全新世时期,特别是仰韶时代和龙山时代,不具备野生稻生长的气候条件;在考古遗址中发现的稻属植物硅酸体可以被看成是栽培稻的遗存。     

Phytolith taphonomy: a comparison of dry ashing and acid extraction on the breakdown of conjoined phytoliths formed in Triticum durum

Durum wheat plants grown under optimum irrigation conditions in Jordan were processed in three different ways: 1) using a dry ashing method, 2) using acid extraction and 3) using both these methods, first dry ashing and then acid extraction. The aim was to determine if the laboratory processing method employed has an impact on the number of conjoined phytoliths recovered. This is important because it has been proposed that the number of conjoined phytoliths, or multi cells, can be an indication of water availability in arid and semi-arid regions (Rosen and Weiner 1994). The results showed that the processing method does have an impact on the resulting assemblage, with dry ashing producing a greater number of multi-cells than acid extraction. It is proposed that either the more violent oxidation of organic matter during acid extraction causes the breakup of conjoined phytoliths, or that the silica dehydrates during dry ashing resulting in a slight fusion between the individual phytoliths and hence more conjoined forms.     

Phytoliths and microcharcoal at Jinluojia archeological site in middle reaches of Yangtze River indicative of paleoclimate and human activity during the last 3000 years

A variety of phytoliths, together with prolific microcharcoal particles, sponge spicules and diatoms were extracted and identified in four cultural layers from an archeological site at Jinluojia, Macheng, Hubei Province, Central China. The warmth (Iw) and aridity (Iph) indices calculated from grass phytoliths reveal warm and wet periods during the West Zhou, early East Zhou, Tang and Song Dynasties whilst cool and dry periods occurred during the late East Zhou, Ming and Qing Dynasties. The paleoclimate conditions reconstructed on the basis of grass phytoliths extracted from archeological sediments are in agreement with those from natural sediments in the Middle Yangtze region. In contrast, the woody phytoliths show a positive correlation with microcharcoal particles, suggesting an anthropogenic contribution to the woody phytoliths from the use of woody plants for fuel during cooking and heating. Two episodes of the enhanced abundance of woody phytoliths and microcharcoal particles were found to occur at East Zhou Dynasty and from Ming and Qing Dynasties to the Present, proposed to be a consequence of the population expansion and/or the frequent wars.     

Digital extraction: Blockchain traceability in mineral supply chains

Digital data — including technologically-mediated data generated by blockchain-enabled traceability — is performing an increasingly integral role in extractive operations, but scarce attention has been paid to the structuring effect of these digital technologies or the socio-economic spatiality of data-driven mining operations. Drawing on extensive qualitative research (interviews, participant observation, and two sets of survey data among actors relevant to these mineral supply chains), this article advances the notion of “digital extraction” to describe the collection, analysis, and instrumentalization of digital data generated under the banner of blockchain-based due diligence, chain of custody certifications, and various transparency mechanisms, situated alongside and in support of mineral extraction. The article mobilizes concepts from political geography and political ecology to argue that digital technologies of traceability in extractive processes potentially create new forms of control and exclusion or exacerbate existing social, political, and territorial dispossession through asymmetric relations of power and knowledge in mineral supply chains. Despite industry efforts to make mineral supply chains more sustainable by resorting to digital certification and traceability, the strategic uses of uncertainty, ignorance, and ambiguity undergirding blockchain-enabled traceability systems fail to challenge existing inequalities in resource use and access or fulfill the promise of transparency and accountability.