A stable isotope perspective on archaeological agricultural variability and Neolithic experimentation in India

Agriculture has been crucial in sustaining human populations in South Asia across dramatically variable environments for millennia. Until recently, however, the origins of this mode of subsistence in India have been discussed in terms of population migration and crop introduction, with limited focus on how agricultural packages were formulated and utilised in local contexts. Here, we report the first measurements of stable carbon and nitrogen isotope values in well-preserved charred crop remains from sites spanning the Neolithic/Chalcolithic to the Early Historic in two very different environmental zones: tropical East India and the semi-arid Deccan. The results show that this approach offers direct insight into prehistoric crop management under contrasting environmental constraints. Our preliminary results plausibly suggest that early farmers in India experimented with and made strategic use of water and manure resources in accordance with specific crop requirements and under varying environmental constraints. We suggest that the development of modern crop isotope baselines across India, and the application of this methodology to archaeological assemblages, has the potential to yield detailed insight into agroecology in India's past

Ethics and applications of isotope analysis in archaeology

This synthesis explores specific ethical questions that commonly arise in isotopic analysis. For more than four decades, isotope analysis has been employed in archeological studies to explore past human and animal dietary habits, mobility patterns, and the environment in which a human or animal inhabited during life. These analyses require consideration of ethical issues. While theoretical concepts are discussed, we focus on practical aspects: working with descendant communities and other rights holders, choosing methods, creating and sharing data, and working mindfully within academia. These layers of respect and care should surround our science. This paper is relevant for specialists in isotope analysis as well as those incorporating these methods into larger projects. By covering the whole of the research process, from design to output management, we appeal broadly to archaeology and provide actionable solutions that build on the discussions in the general field

Community partnerships are fundamental to ethical ancient DNA research

The ethics of the scientific study of Ancestors has long been debated by archaeologists, bioanthropologists, and, more recently, ancient DNA (aDNA) researchers. This article responds to the article “Ethics of DNA research on human remains: five globally applicable guidelines” published in 2021 in Nature by a large group of aDNA researchers and collaborators. We argue that these guidelines do not sufficiently consider the interests of community stakeholders, including descendant communities and communities with potential, but yet unestablished, ties to Ancestors. We focus on three main areas of concern with the guidelines. First is the false separation of “scientific” and “community” concerns and the consistent privileging of researcher perspectives over those of community members. Second, the commitment of the guidelines’ authors to open data ignores the principles and practice of Indigenous Data Sovereignty. Further, the authors argue that involving community members in decisions about publication and data sharing is unethical. We argue that excluding community perspectives on “ethical” grounds is convenient for researchers, but it is not, in fact, ethical. Third, we stress the risks of not consulting communities that have established or potential ties to Ancestors, using two recent examples from the literature. Ancient DNA researchers cannot focus on the lowest common denominator of research practice, the bare minimum that is legally necessary. Instead, they should be leading multidisciplinary efforts to create processes to ensure communities from all regions of the globe are identified and engaged in research that affects them. This will often present challenges, but we see these challenges as part of the research, rather than a distraction from the scientific endeavor. If a research team does not have the capacity to meaningfully engage communities, questions must be asked about the value and benefit of their research

Adaptability of Millets and Landscapes: Ancient Cultivation in North-Central Asia

Millet is a highly adaptable plant whose cultivation dramatically altered ancient economies in northern Asia. The adoption of millet is associated with increased subsistence reliability in semi-arid settings and perceived as a cultigen compatible with pastoralism. Here, we examine the pace of millet’s transmission and locales of adoption by compiling stable carbon isotope data from humans and fauna, then comparing them to environmental variables. The Bayesian modelling of isotope data allows for the assessment of changes in dietary intake over time and space. Our results suggest variability in the pace of adoption and intensification of millet production across northern Asia.</jats:p

The southern Central Asian mountains as an ancient agricultural mixing zone: new archaeobotanical data from Barikot in the Swat valley of Pakistan

The mountain foothills of inner Asia have served as a corridor of communication and exchange for at least five millennia, using historically documented trade routes such as the Silk Road and the Tea-Horse Road. Recent research has illustrated the important role that this mountain corridor played in the dispersal of crops and farming technology between northeast and southwest Asia 5,000 to 1,000 years ago. However, the role of the mountain valleys along the southern rim of the Pamirs and Himalaya in facilitating crop dispersals has not yet been fully explored. Notably, ongoing debates over secondary dispersals of Hordeum (barley) and Triticum (wheat) into China and the routes of dispersal for the East Asian crops Oryza sativa (rice), Prunus persica (peach) and P. armeniaca (apricot) into northern India are continuing topics of inquiry. In this article, we add to these discussions by focusing on archaeobotanical remains from the Barikot site (ca. 1200 bce–50 ce) in the Swat valley of northern Pakistan. The Swat valley is an ancient settlement zone in the Hindu Kush-Karakoram foothills, whose cultural features have always had a strong link with inner Asia. The archaeobotanical assemblage illustrates that a diverse array of crops, with origins across Asia, were cultivated around the same settlement. Additionally, these farmers likely implemented seasonal cropping cycles and irrigation that required various labour inputs and water management regimes.H2020 European Research Council http://dx.doi.org/10.13039/100010663Max Planck Institute for the Science of Human History (2

The southern Central Asian mountains as an ancient agricultural mixing zone: new archaeobotanical data from Barikot in the Swat valley of Pakistan

The mountain foothills of inner Asia have served as a corridor of communication and exchange for at least five millennia, using historically documented trade routes such as the Silk Road and the Tea-Horse Road. Recent research has illustrated the important role that this mountain corridor played in the dispersal of crops and farming technology between northeast and southwest Asia 5,000 to 1,000\ua0years ago. However, the role of the mountain valleys along the southern rim of the Pamirs and Himalaya in facilitating crop dispersals has not yet been fully explored. Notably, ongoing debates over secondary dispersals of Hordeum (barley) and Triticum (wheat) into China and the routes of dispersal for the East Asian crops Oryza sativa (rice), Prunus persica (peach) and P. armeniaca (apricot) into northern India are continuing topics of inquiry. In this article, we add to these discussions by focusing on archaeobotanical remains from the Barikot site (ca. 1200 bce–50 ce) in the Swat valley of northern Pakistan. The Swat valley is an ancient settlement zone in the Hindu Kush-Karakoram foothills, whose cultural features have always had a strong link with inner Asia. The archaeobotanical assemblage illustrates that a diverse array of crops, with origins across Asia, were cultivated around the same settlement. Additionally, these farmers likely implemented seasonal cropping cycles and irrigation that required various labour inputs and water management regimes

SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.

Bacteria within the gut microbiota possess the ability to metabolize a wide array of human drugs, foods, and toxins, but the responsible enzymes for these chemical events remain largely uncharacterized due to the time-consuming nature of current experimental approaches. Attempts have been made in the past to computationally predict which bacterial species and enzymes are responsible for chemical transformations in the gut environment, but with low accuracy due to minimal chemical representation and sequence similarity search schemes. Here, we present an in silico approach that employs chemical and protein Similarity algorithms that Identify MicrobioMe Enzymatic Reactions (SIMMER). We show that SIMMER accurately predicts the responsible species and enzymes for a queried reaction, unlike previous methods. We demonstrate SIMMER use cases in the context of drug metabolism by predicting previously uncharacterized enzymes for 88 drug transformations known to occur in the human gut. We validate these predictions on external datasets and provide an in vitro validation of SIMMER's predictions for metabolism of methotrexate, an anti-arthritic drug. After demonstrating its utility and accuracy, we made SIMMER available as both a command-line and web tool, with flexible input and output options for determining chemical transformations within the human gut. We present SIMMER as a computational addition to the microbiome researcher's toolbox, enabling them to make informed hypotheses before embarking on the lengthy laboratory experiments required to characterize novel bacterial enzymes that can alter human ingested compounds

SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations

Bacteria within the gut microbiota possess the ability to metabolize a wide array of human drugs, foods, and toxins, but the responsible enzymes for these chemical events remain largely uncharacterized due to the time-consuming nature of current experimental approaches. Attempts have been made in the past to computationally predict which bacterial species and enzymes are responsible for chemical transformations in the gut environment, but with low accuracy due to minimal chemical representation and sequence similarity search schemes. Here, we present an in silico approach that employs chemical and protein Similarity algorithms that Identify MicrobioMe Enzymatic Reactions (SIMMER). We show that SIMMER accurately predicts the responsible species and enzymes for a queried reaction, unlike previous methods. We demonstrate SIMMER use cases in the context of drug metabolism by predicting previously uncharacterized enzymes for 88 drug transformations known to occur in the human gut. We validate these predictions on external datasets and provide an in vitro validation of SIMMER’s predictions for metabolism of methotrexate, an anti-arthritic drug. After demonstrating its utility and accuracy, we made SIMMER available as both a command-line and web tool, with flexible input and output options for determining chemical transformations within the human gut. We present SIMMER as a computational addition to the microbiome researcher’s toolbox, enabling them to make informed hypotheses before embarking on the lengthy laboratory experiments required to characterize novel bacterial enzymes that can alter human ingested compounds

Disruptions, restorations and adaptations to health and nutrition service delivery in multiple states across India over the course of the COVID-19 pandemic in 2020: An observational study.

BackgroundModeling studies estimated severe impacts of potential service delivery disruptions due to COVID-19 pandemic on maternal and child nutrition outcomes. Although anecdotal evidence exists on disruptions, little is known about the actual state of service delivery at scale. We studied disruptions and restorations, challenges and adaptations in health and nutrition service delivery by frontline workers (FLWs) in India during COVID-19 in 2020.MethodsWe conducted phone surveys with 5500 FLWs (among them 3118 Anganwadi Workers) in seven states between August-October 2020, asking about service delivery during April 2020 (T1) and in August-October (T2), and analyzed changes between T1 and T2. We also analyzed health systems administrative data from 704 districts on disruptions and restoration of services between pre-pandemic (December 2019, T0), T1 and T2.ResultsIn April 2020 (T1), village centers, fixed day events, child growth monitoring, and immunization were provided by ConclusionsServices to mothers and children were disrupted during stringent lockdown but restored thereafter, albeit not to pre-pandemic levels. Rapid policy guidance and adaptations by FLWs enabled restoration but little remains known about uptake by client populations. As COVID-19 continues to surge in India, focused attention to ensuring essential services is critical to mitigate these major indirect impacts of the pandemic

tardis-sn/tardis: TARDIS v2023.11.05

&lt;p&gt;This release has been created automatically by the TARDIS continuous delivery pipeline.&lt;/p&gt; &lt;p&gt;A complete list of changes for this release is available at &lt;a href="https://github.com/tardis-sn/tardis/blob/master/CHANGELOG.md"&gt;CHANGELOG.md&lt;/a&gt;.&lt;/p&gt