"Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling.

The main goals and challenges for the life science communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable life science resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European life science research infrastructures, it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable data management according to FAIR (findability, accessibility, interoperability, and reusability) principles, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.

A dataset for assessing phytolith data for implementation of the FAIR data principles.

Phytolith research contributes to our understanding of plant-related studies such as plant use in archaeological contexts and past landscapes in palaeoecology. This multi-disciplinarity combined with the specificities of phytoliths themselves (multiplicity, redundancy, naming issues) produces a wide variety of methodologies. Combined with a lack of data sharing and transparency in published studies, it means data are hard to find and understand, and therefore difficult to reuse. This situation is challenging for phytolith researchers to collaborate from the same and different disciplines for improving methodologies and conducting meta-analyses. Implementing The FAIR Data principles (Findable, Accessible, Interoperable and Reusable) would improve transparency and accessibility for greater research data sustainability and reuse. This paper sets out the method used to conduct a FAIR assessment of existing phytolith data. We sampled and assessed 100 articles of phytolith research (2016-2020) in terms of the FAIR principles. The end goal of this project is to use the findings from this dataset to propose FAIR guidance for more sustainable publishing of data and research in phytolith studies.

On the verge of domestication: Early use of C4 plants in the Horn of Africa.

The earliest evidence of agriculture in the Horn of Africa dates to the Pre-Aksumite period (ca. 1600 BCE). Domesticated C3 cereals are considered to have been introduced from the Near East, whereas the origin (local or not) and time of domestication of various African C4 species such as sorghum, finger millet, or t'ef remain unknown. In this paper, we present the results of the analysis of microbotanical residues (starch and phytoliths) from grinding stones recovered from two archaeological sites in northeastern Tigrai (Ethiopia), namely Mezber and Ona Adi. Together, both sites cover a time period that encompasses the earliest evidence of agriculture in the region (ca. 1600 BCE) to the fall of the Kingdom of Aksum (ca. 700 CE). Our data indicate that these communities featured complex mixed economies which included the consumption of both domestic and wild plant products since the Initial Pre-Aksumite Phase (ca. 1600 to 900 BCE), including C3 crops and legumes, but also C4 cereals and geophytes. These new data expand the record of C4 plant use in the Horn of Africa to over 1,000 y. It also represents the first evidence for the consumption of starchy products in the region. These results have parallels in the wider northeastern African region where complex food systems have been documented. Altogether, our data represent a significant challenge to our current knowledge of Pre-Aksumite and Aksumite economies, forcing us to rethink the way we define these cultural horizons.

Small-scale farming in drylands: New models for resilient practices of millet and sorghum cultivation.

Finger millet, pearl millet and sorghum are amongst the most important drought-tolerant crops worldwide. They constitute primary staple crops in drylands, where their production is known to date back over 5000 years ago. Compared to other crops, millets and sorghum have received less attention until very recently, and their production has been progressively reduced in the last 50 years. Here, we present new models that focus on the ecological factors driving finger millet, pearl millet and sorghum traditional cultivation, with a global perspective. The interaction between environment and traditional agrosystems was investigated by Redundancy Analysis of published literature and tested against novel ethnographic data. Contrary to earlier beliefs, our models show that the total annual precipitation is not the most determinant factor in shaping millet and sorghum agriculture. Instead, our results point to the importance of other variables such as the duration of the plant growing cycle, soil water-holding capacity or soil nutrient availability. This highlights the potential of finger millet, pearl millet and sorghum traditional cultivation practices as a response to recent increase of aridity levels worldwide. Ultimately, these practices can play a pivotal role for resilience and sustainability of dryland agriculture.

Environmental effects on the spread of the Neolithic crop package to South Asia.

The emergence of Neolithic economies and their spread through Eurasia was one of the most crucial transitions of the Holocene, with different mechanisms of diffusion-demic, cultural-being proposed. While this phenomenon has been exhaustively studied in Europe, with repeated attempts to model the speed of Neolithic diffusion based on radiocarbon dates, much less attention has been devoted to the dispersal towards the East, and in particular to South Asia. The Neolithic in the latter region at least partly derived from southwest Asia, given the presence of "founder crops" such as wheat and barley. The process of their eastward diffusion, however, may have been significantly different to the westward dispersal, which was mainly due to demic diffusion, as local domesticates were already available and farming was already practiced in parts of South Asia. Here, we use radiocarbon dates specifically related to the spread of the southwest Asian Neolithic crops to model the speed of dispersal of this agricultural package towards South Asia. To assess potential geographical and environmental effects on the dispersal, we simulate different speeds depending on the biomes being crossed, employing a genetic algorithm to search for the values that most closely approach the radiocarbon dates. We find that the most important barrier to be crossed were the Zagros mountains, where the speed was lowest, possibly due to topography and climate. A large portion of the study area is dominated by deserts and shrublands, where the speed of advance, albeit closer to the range expected for demic diffusion, was lower than observed in Europe, which can also potentially be attributed to environmental constraints in the adaptation of the crops. Finally, a notable acceleration begins in the Indus valley, exceeding the range of demic diffusion in the tropical and subtropical environments east of the Indus. We propose that the latter is due to the rapid diffusion among populations already familiar with plant cultivation.

Correction: Identifying anthropogenic features at Seoke (Botswana) using pXRF: Expanding the record of southern African Stone Walled Sites.

[This corrects the article DOI: 10.1371/journal.pone.0250776.].

Understanding the Relationship between Water Availability and Biosilica Accumulation in Selected C4 Crop Leaves: An Experimental Approach.

Biosilica accumulation in plant tissues is related to the transpiration stream, which in turn depends on water availability. Nevertheless, the debate on whether genetically and environmentally controlled mechanisms of biosilica deposition are directly connected to water availability is still open. We aim at clarifying the system which leads to the deposition of biosilica in Sorghum bicolor, Pennisetum glaucum, and Eleusine coracana, expanding our understanding of the physiological role of silicon in crops well-adapted to arid environments, and simultaneously advancing the research in archaeological and paleoenvironmental studies. We cultivated ten traditional landraces for each crop in lysimeters, simulating irrigated and rain-fed scenarios in arid contexts. The percentage of biosilica accumulated in leaves indicates that both well-watered millet species deposited more biosilica than the water-stressed ones. By contrast, sorghum accumulated more biosilica with respect to the other two species, and biosilica accumulation was independent of the water regime. The water treatment alone did not explain either the variability of the assemblage or the differences in the biosilica accumulation. Hence, we hypothesize that genetics influence the variability substantially. These results demonstrate that biosilica accumulation differs among and within C4 species and that water availability is not the only driver in this process.

A microbotanical and microwear perspective to plant processing activities and foodways at Neolithic Çatalhöyük.

Çatalhöyük is a renowned archaeological site in central Anatolia, best known for its Neolithic occupation dated from 7100 to 6000 cal BC. The site received worldwide attention early on for its large size, well-preserved mudbrick architecture, and elaborate wall paintings. Excavations at the site over almost three decades have unearthed rich archaeobotanical remains and a diverse ground stone assemblage produced by what once was a vibrant farming community. The study presented here adds to our understanding of crops and plant processing at Çatalhöyük by integrating phytoliths and starch analyses on grinding implements found at three domestic contexts attributed to the Middle (6700-6500 cal BC) and Late (6500-6300 cal BC) period of occupation. Our results reveal a rich microbotanical assemblage that testifies the use of a wide range of geophytes and wild seasonal resources previously unknown at the site. Moreover, by comparing results from the microbotanical proxies and microscopic wear patterns on artefacts, we are also able to discern various plant processing practices the analysed artefacts were employed for. In sum, this work further expands our understanding of plants and crop processing activities performed by the inhabitants of Neolithic Çatalhöyük.

Identifying anthropogenic features at Seoke (Botswana) using pXRF: Expanding the record of southern African Stone Walled Sites.

Numerous and extensive 'Stone Walled Sites' have been identified in southern African Iron Age landscapes. Appearing from around 1200 CE, and showing considerable variability in size and form, these settlements are named after the dry-stone wall structures that characterize them. Stone Walled Sites were occupied by various Bantu-speaking agropastoral communities. In this paper we test the use of pXRF (portable X-ray fluorescence analysis) to generate a 'supplementary' archaeological record where evident stratigraphy is lacking, survey conditions may be uneven, and excavations limited, due to the overall site size. We propose herein the application of portable X-ray fluorescence analysis (pXRF) coupled with multivariate exploratory analysis and geostatistical modelling at Seoke, a southern African SWS of historical age (18th century CE). The aim of the paper is twofold: to explore the potential of the application of a low cost, quick, and minimally invasive technique to detect chemical markers in anthropogenic sediments from a Stone Walled Site, and to propose a way to analyse the results in order to improve our understanding of the use of space at non-generalized scales in such sites.

Mapping past human land use using archaeological data: A new classification for global land use synthesis and data harmonization.

In the 12,000 years preceding the Industrial Revolution, human activities led to significant changes in land cover, plant and animal distributions, surface hydrology, and biochemical cycles. Earth system models suggest that this anthropogenic land cover change influenced regional and global climate. However, the representation of past land use in earth system models is currently oversimplified. As a result, there are large uncertainties in the current understanding of the past and current state of the earth system. In order to improve representation of the variety and scale of impacts that past land use had on the earth system, a global effort is underway to aggregate and synthesize archaeological and historical evidence of land use systems. Here we present a simple, hierarchical classification of land use systems designed to be used with archaeological and historical data at a global scale and a schema of codes that identify land use practices common to a range of systems, both implemented in a geospatial database. The classification scheme and database resulted from an extensive process of consultation with researchers worldwide. Our scheme is designed to deliver consistent, empirically robust data for the improvement of land use models, while simultaneously allowing for a comparative, detailed mapping of land use relevant to the needs of historical scholars. To illustrate the benefits of the classification scheme and methods for mapping historical land use, we apply it to Mesopotamia and Arabia at 6 kya (c. 4000 BCE). The scheme will be used to describe land use by the Past Global Changes (PAGES) LandCover6k working group, an international project comprised of archaeologists, historians, geographers, paleoecologists, and modelers. Beyond this, the scheme has a wide utility for creating a common language between research and policy communities, linking archaeologists with climate modelers, biodiversity conservation workers and initiatives.

'Not all that burns is wood'. A social perspective on fuel exploitation and use during the Indus urban period (2600-1900 BC).

Ancient civilisations depended heavily on natural fuel resources for a wide array of activities, and this had an impact on such resources that can be traced in the archaeological record. At its urban apex, the populations of the Indus Civilisation (2600-1900 BC) produced a wide range of objects and crafts, several of which involved highly specialised pyrotechnology. In the wake of increasing aridity and a period of weakened monsoon rainfall that affected South Asia from 2100 BC, these activities potentially put pressure on the natural resource base that may have had to be counterbalanced by differentiation in fuel use. The combined analysis of archaeobotanical and geoarchaeological remains from four Indus urban phase archaeological sites, has enable an assessment of the mechanisms through which people exploited wood, and diversified their fuel resources to adapt to the arid to semi-arid environments in which they lived. The combined use of local wood species with alternative fuels, such as dung and crop-processing leftovers, are evidence for resilient socio-ecological practices during the 700 years of Indus urbanism and perhaps beyond.

Chimpanzee diet: phytolithic analysis of feces.

Most primate populations remain unobservable; therefore, researchers depend on the analyses of indirect evidence encountered at a study-site in order to understand their behavioral ecology. Diet can be determined through the analyses of scats or feeding remains encountered on-site. This allows aspects of their dietary repertoire to be established, which has implications both for conservation efforts (by locating food resources), and for understanding the evolution of hominin diet (if used as referential models). Macroscopic inspection of fecal samples is a common method applied to ascertain a primate population's diet. However, new approaches are required to identify food-items unrecognizable at this level. We applied a dry ash extraction method to fecal samples (N=50) collected from 10 adult chimpanzees in Kanyawara, Kibale National Park, Uganda and also to plant parts (N=66) from 34 species known to be included in the diet of this community of apes. We recovered phytoliths in 26 of the 34 plant species. Fifteen phytolith morphotypes were only detected in 14 plant species (termed "distinct" phytoliths). We used these distinct phytoliths to identify plant foods (i.e., that they were associated with) in fecal samples. We then validated findings by checking if the 10 chimpanzees had eaten parts of these plants ∼24 hr prior to fecal sample collection; six plant species associated with five distinct phytoliths had been eaten. Finally, we compared plant foods identified in fecal samples from phytolith analyses with plants that had been identified from macroscopic inspection of the same fecal samples. Findings from phytolith analyses corroborate with those from macroscopic inspection by expanding the total number of plant species identified per fecal sample (i.e., we identified certain plant parts that remained unrecognizable at macroscopic level). This study highlights the potential of phytolith analyses of feces to increase our knowledgebase of the dietary repertoire of primate populations.

Squaring the circle. Social and environmental implications of pre-pottery neolithic building technology at Tell Qarassa (South Syria).

We present the results of the microstratigraphic, phytolith and wood charcoal study of the remains of a 10.5 ka roof. The roof is part of a building excavated at Tell Qarassa (South Syria), assigned to the Pre-Pottery Neolithic B period (PPNB). The Pre-Pottery Neolithic (PPN) period in the Levant coincides with the emergence of farming. This fundamental change in subsistence strategy implied the shift from mobile to settled aggregated life, and from tents and huts to hard buildings. As settled life spread across the Levant, a generalised transition from round to square buildings occurred, that is a trademark of the PPNB period. The study of these buildings is fundamental for the understanding of the ever-stronger reciprocal socio-ecological relationship humans developed with the local environment since the introduction of sedentism and domestication. Descriptions of buildings in PPN archaeological contexts are usually restricted to the macroscopic observation of wooden elements (posts and beams) and mineral components (daub, plaster and stone elements). Reconstructions of microscopic and organic components are frequently based on ethnographic analogy. The direct study of macroscopic and microscopic, organic and mineral, building components performed at Tell Qarassa provides new insights on building conception, maintenance, use and destruction. These elements reflect new emerging paradigms in the relationship between Neolithic societies and the environment. A square building was possibly covered here with a radial roof, providing a glance into a topologic shift in the conception and understanding of volumes, from round-based to square-based geometries. Macroscopic and microscopic roof components indicate buildings were conceived for year-round residence rather than seasonal mobility. This implied performing maintenance and restoration of partially damaged buildings, as well as their adaptation to seasonal variability.