Prediction of the concentration of cadmium in agricultural soil in the Czech Republic using legacy data, preferential sampling, Sentinel-2, Landsat-8, and ensemble models.

The current study assesses and predicts cadmium (Cd) concentration in agricultural soil using two Cd datasets, namely legacy data (LD) and preferential sampling-legacy data (PS-LD), along with four streams of auxiliary datasets extracted from Sentinel-2 (S2) and Landsat-8 (L8) bands. The study was divided into two contexts: Cd prediction in agricultural soil using LD, ensemble models, 10 and 20 m spatial resolution of S2 and L8 (context 1), and Cd prediction in agricultural soil using PS-LD, ensemble models and 10 and 20 m spatial resolution of S2 and L8 (context 2). In context 1, ensemble 1, L8 with PS-LD was the cumulative optimal approach that predicted Cd in agricultural soil with a higher R2 value of 0.76, root mean square error (RMSE) of 0.66, mean absolute error (MAE) of 0.35, and median absolute error (MdAE) of 0.13. However, with R2 = 0.78, RMSE = 0.63, MAE = 0.34, and MdAE = 0.15, ensemble 1, S2 of PS-LD was the best prediction approach in predicting Cd concentration in agricultural soil in context 2. Overall, the predictions from both contexts indicated that ensemble 1 of S2 combined with PS-LD was the most appropriate and best model for Cd prediction in agricultural soil. The modeling approaches' uncertainty in both contexts was assessed using ensemble-sequential gaussian simulation (EnSGS), which revealed that the degree of uncertainty propagated in the study area was within 5% in both contexts. The combination of the PS dataset and the LD along with ensemble models and the remote sensing dataset, produced promising results. Nonetheless, the results demonstrated that the 20 m spatial resolution band dataset used in the prediction of Cd in agricultural soil outperformed the 10 m spatial resolution. When PS is combined with LD, an appropriate modeling approach, and a well-correlated remote sensing dataset are used, good results are obtained.

Root phenotyping: important and minimum information required for root modeling in crop plants.

As plants cannot relocate, they require effective root systems for water and nutrient uptake. Root development plasticity enables plants to adapt to different environmental conditions. Research on improvements in crop root systems is limited in comparison with that in shoots as the former are difficult to image. Breeding more effective root systems is proposed as the "second green revolution". There are several recent publications on root system architecture (RSA), but the methods used to analyze the RSA have not been standardized. Here, we introduce traditional and current root-imaging methods and discuss root structure phenotyping. Some important root structures have not been standardized as roots are easily affected by rhizosphere conditions and exhibit greater plasticity than shoots; moreover, root morphology significantly varies even in the same genotype. For these reasons, it is difficult to define the ideal root systems for breeding. In this review, we introduce several types of software to analyze roots and identify important root parameters by modeling to simplify the root system characterization. These parameters can be extracted from photographs captured in the field. This modeling approach is applicable to various legacy root data stored in old or unpublished formats. Standardization of RSA data could help estimate root ideotypes.

Four decades of plant community change along a continental gradient of warming.

Many studies of individual sites have revealed biotic changes consistent with climate warming (e.g., upward elevational distribution shifts), but our understanding of the tremendous variation among studies in the magnitude of such biotic changes is minimal. In this study, we resurveyed forest vegetation plots 40 years after the initial surveys in three protected areas along a west-to-east gradient of increasingly steep recent warming trends in eastern Canada (Québec). Consistent with the hypothesis that climate warming has been an important driver of vegetation change, we found an increasing magnitude of changes in species richness and composition from west to east among the three parks. For the two mountainous parks, we found no significant changes in elevational species' distributions in the easternmost park (raw mean = +11.4 m at Forillon Park) where warming has been minimal, and significant upward distribution shifts in the centrally located park (+38.9 m at Mont-Mégantic), where the recent warming trend has been marked. Community Temperature Indices (CTI), reflecting the average affinities of locally co-occurring species to temperature conditions across their geographic ranges ("Species Temperature Indices"), did not change over time as predicted. However, close examination of the underpinnings of CTI values suggested a high sensitivity to uncertainty in individual species' temperature indices, and so a potentially limited responsiveness to warming. Overall, by testing a priori predictions concerning variation among parks in the direction and magnitude of vegetation changes, we have provided stronger evidence for a link between climate warming and biotic responses than otherwise possible and provided a potential explanation for large variation among studies in warming-related biotic changes.

Combining community resurvey data to advance global change research.

More and more ecologists have started to resurvey communities sampled in earlier decades to determine long-term shifts in community composition and infer the likely drivers of the ecological changes observed. However, to assess the relative importance of, and interactions among, multiple drivers joint analyses of resurvey data from many regions spanning large environmental gradients are needed. In this paper we illustrate how combining resurvey data from multiple regions can increase the likelihood of driver-orthogonality within the design and show that repeatedly surveying across multiple regions provides higher representativeness and comprehensiveness, allowing us to answer more completely a broader range of questions. We provide general guidelines to aid implementation of multi-region resurvey databases. In so doing, we aim to encourage resurvey database development across other community types and biomes to advance global environmental change research.

Ethical considerations for Forensic Genetic Frequency databases: First Report conception and development.

The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received.

'Nothing new under the sun': Rethinking recycling in the past- Editorial.

Editorial for the Special Issue of Archaeometry 'Tackling Recycling in the Past'. The practice of recycling has undoubtedly become one of the most important strategies to build a long-term sustainable society in the modern world. However, both the perception and practice of recycling can be traced back to prehistory through various archaeological records. Objects made of stone, jade, mortar, textiles, pottery and bones display evidence of physical reshaping and repair, as do objects of metal and glass. Metal and glass, moreover, are materials which can be melted and recast, freeing ancient people from the limitations of the physical form of the original object. Illustrating and understanding patterns of recycling and the underlying social organization can significantly advance our knowledge of ancient people, their economic, political and cultural motivations for recycling, as well as the broad interaction between the social and material world. Though the issue of recycling is not novel in the discussions and debates of the archaeological circle, new theoretical frameworks, methodologies and archaeometric data encourage us to revisit the topic in this special issue. In this editorial, we consider what recycling means in the past, and why these papers are vital.

Interpreting error in the estimation of skeletal growth profiles from past populations: An example demonstrating skeletal growth in historic African American communities.

OBJECTIVES: The study of growth in the past is a critical component of bioarcheological analyses. However, our understanding of growth in the past is subject to a number of methodological challenges. This study aims to model the skeletal growth of past populations by considering the challenges associated with the data collection process and the challenges associated with the age estimation procedures. MATERIALS AND METHODS: We use skeletal remains from two historic African American cemeteries in the American South to model femoral diaphyseal length-for-age. We estimate the age of each individual using dental development techniques and present growth curves as both a product of the maximum likelihood (MLE) age estimate and the estimated posterior age distribution. Growth was compared against a reference sample from the University of Colorado Child Research Council Study. RESULTS: The results of our analyses showed that femoral diaphyseal length in two historic African American communities is small-for-estimated age as compared to a modern reference sample. However, the magnitude and characterization of this difference is variable when taking into account the broader posterior age distribution. DISCUSSION: Both samples may be small-for-age due to physiological stress associated with racism, inequality, and the compounding effects of early urbanization. However, the interpretation of growth in the past is muddled when considering the relationship between the study sample and the reference sample, when accounting for uncertainty in the age estimation procedure, and the error-inducing steps taken during the data collection process. Future interpretation of skeletal growth in the past must include a full account of the possible sources of error in order to present an accurate representation of growth.

Seasonal and annual dynamics of western Canadian boreal forest plant communities: A legacy data set spanning four decades.

As boreal forests rapidly warm due to anthropogenic climate change, long-term baseline community data are needed to effectively characterize the corresponding ecological changes that are occurring in these forests. The combined seasonal dynamics (SEADYN) and annual dynamics (ANNDYN) data set, which documents the vegetative changes in boreal forests during the snow-free period, is one such source of baseline community data. These data were collected by George H. La Roi and colleagues in Alberta, Canada from 1980 to 2015 within permanent sampling plots established in the Hondo-Slave Lake area (eight stands; 1980-2015) in central Alberta and the Athabasca Oil Sands (AOS) region (17 stands; 1981-1984) near Fort McMurray in northeastern Alberta. Various data were collected, with temporal and spatial coverage differing by data set. These data sets include, but are not limited to, cover of each identified vascular plant and bryoid (moss, liverwort, and lichen) species; forest mensuration; forest litter production; and soil temperature and moisture. Notably, permanent sampling plots were set up as a grid, which will facilitate analyses of spatial relations. These data can be used to analyze long-term changes in seasonal dynamics and succession within boreal forest communities and serve as a baseline for comparison with future forest conditions in unmanaged, managed, and reclaimed forests. Data are released under a CC-BY license; please cite this data paper when using the data for analyses.

Different temporal trends in vascular plant and bryophyte communities along elevational gradients over four decades.

Despite many studies showing biodiversity responses to warming, the generality of such responses across taxonomic groups remains unclear. Very few studies have tested for evidence of bryophyte community responses to warming, even though bryophytes are major contributors to diversity and functioning in many ecosystems. Here, we report an empirical study comparing long-term change in bryophyte and vascular plant communities in two sites with contrasting long-term warming trends, using "legacy" botanical records as a baseline for comparison with contemporary resurveys. We hypothesized that ecological changes would be greater in sites with a stronger warming trend and that vascular plant communities, with narrower climatic niches, would be more sensitive than bryophyte communities to climate warming. For each taxonomic group in each site, we quantified the magnitude of changes in species' distributions along the elevation gradient, species richness, and community composition. We found contrasted temporal changes in bryophyte vs. vascular plant communities, which only partially supported the warming hypothesis. In the area with a stronger warming trend, we found a significant increase in local diversity and dissimilarity (ß-diversity) for vascular plants, but not for bryophytes. Presence-absence data did not provide sufficient power to detect elevational shifts in species distributions. The patterns observed for bryophytes are in accordance with recent literature showing that local diversity can remain unchanged despite strong changes in composition. Regardless of whether one taxon is systematically more or less sensitive to environmental change than another, our results suggest that vascular plants cannot be used as a surrogate for bryophytes in terms of predicting the nature and magnitude of responses to warming. Thus, to assess overall biodiversity responses to global change, abundance data from different taxonomic groups and different community properties need to be synthesized.

Data models, representation and adequacy-for-purpose.

We critically engage two traditional views of scientific data and outline a novel philosophical view that we call the pragmatic-representational (PR) view of data. On the PR view, data are representations that are the product of a process of inquiry, and they should be evaluated in terms of their adequacy or fitness for particular purposes. Some important implications of the PR view for data assessment, related to misrepresentation, context-sensitivity, and complementary use, are highlighted. The PR view provides insight into the common but little-discussed practices of iteratively reusing and repurposing data, which result in many datasets' having a phylogeny-an origin and complex evolutionary history-that is relevant to their evaluation and future use. We relate these insights to the open-data and data-rescue movements, and highlight several future avenues of research that build on the PR view of data.

Seeing beyond the trees: a comparison of tropical and temperate plant growth forms and their vertical distribution.

Forests are the most diverse and productive terrestrial ecosystems on Earth, so sustainably managing them for the future is a major global challenge. Yet, our understanding of forest diversity relies almost exclusively on the study of trees. Here, we demonstrate unequivocally that other growth forms (shrubs, lianas, herbs, epiphytes) make up the majority of vascular plant species in both tropical and temperate forests. By comparing the relative distribution of species richness among plant growth forms for over 3,400 species in 18 forests in the Americas, we construct the first high-resolution quantification of plant growth form diversity across two ecologically important regions at a near-continental scale. We also quantify the physical distribution of plant species among forest layers, that is, where among the vertical strata plants ultimately live their adult lives, and show that plants are strongly downshifted in temperate forests vs. tropical forests. Our data illustrate a previously unquantified fundamental difference between tropical and temperate forests: what plant growth forms are most speciose, and where they ultimately live in the forest. Recognizing these differences requires that we re-focus ecological research and forest management plans to encompass a broader suite of plant growth forms. This more holistic perspective is essential to conserve global biodiversity.

Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt's Farm, Cradle of Humankind (South Africa).

Bolt's Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner's rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947-1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke's map to try and relocate the original fossil deposits. However, Peabody's map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody's original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt's Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt's Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of Equus in some pits implying ages of <2.3 Ma, whereas more primitive suids (Metridiochoerus) hint at a terminal Pliocene age for other deposits. This study highlights that Bolt's Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material.

A story of data won, data lost and data re-found: the realities of ecological data preservation.

This paper discusses the process of retrieval and updating legacy data to allow on-line discovery and delivery. There are many pitfalls of institutional and non-institutional ecological data conservation over the long term. Interruptions to custodianship, old media, lost knowledge and the continuous evolution of species names makes resurrection of old data challenging. We caution against technological arrogance and emphasise the importance of international standards. We use a case study of a compiled set of continent-wide vegetation survey data for which, although the analyses had been published, the raw data had not. In the original study, publications containing plot data collected from the 1880s onwards had been collected, interpreted, digitised and integrated for the classification of vegetation and analysis of its conservation status across Australia. These compiled data are an extremely valuable national collection that demanded publishing in open, readily accessible online repositories, such as the Terrestrial Ecosystem Research Network (http://www.tern.org.au) and the Atlas of Living Australia (ALA: http://www.ala.org.au), the Australian node of the Global Biodiversity Information Facility (GBIF: http://www.gbif.org). It is hoped that the lessons learnt from this project may trigger a sober review of the value of endangered data, the cost of retrieval and the importance of suitable and timely archiving through the vicissitudes of technological change, so the initial unique collection investment enables multiple re-use in perpetuity.

Soil legacy data rescue via GlobalSoilMap and other international and national initiatives.

Legacy soil data have been produced over 70 years in nearly all countries of the world. Unfortunately, data, information and knowledge are still currently fragmented and at risk of getting lost if they remain in a paper format. To process this legacy data into consistent, spatially explicit and continuous global soil information, data are being rescued and compiled into databases. Thousands of soil survey reports and maps have been scanned and made available online. The soil profile data reported by these data sources have been captured and compiled into databases. The total number of soil profiles rescued in the selected countries is about 800,000. Currently, data for 117, 000 profiles are compiled and harmonized according to GlobalSoilMap specifications in a world level database (WoSIS). The results presented at the country level are likely to be an underestimate. The majority of soil data is still not rescued and this effort should be pursued. The data have been used to produce soil property maps. We discuss the pro and cons of top-down and bottom-up approaches to produce such maps and we stress their complementarity. We give examples of success stories. The first global soil property maps using rescued data were produced by a top-down approach and were released at a limited resolution of 1km in 2014, followed by an update at a resolution of 250m in 2017. By the end of 2020, we aim to deliver the first worldwide product that fully meets the GlobalSoilMap specifications.