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An increasing number of researchers support reproducibility by including pointers to and descriptions of datasets, software and methods in their publications. However, scientific articles may be ambiguous, incomplete and difficult to process by automated systems. In this paper we introduce RO-Crate, an open, community-driven, and lightweight approach to packaging research artefacts along with their metadata in a machine readable manner. RO-Crate is based on Schema$.$org annotations in JSON-LD, aiming to establish best practices to formally describe metadata in an accessible and practical way for their use in a wide variety of situations. An RO-Crate is a structured archive of all the items that contributed to a research outcome, including their identifiers, provenance, relations and annotations. As a general purpose packaging approach for data and their metadata, RO-Crate is used across multiple areas, including bioinformatics, digital humanities and regulatory sciences. By applying "just enough" Linked Data standards, RO-Crate simplifies the process of making research outputs FAIR while also enhancing research reproducibility. An RO-Crate for this article is available at https://www.researchobject.org/2021-packaging-research-artefacts-with-ro-crate/ Comment: 42 pages. Submitted to Data Science

Abstract We propose connections between long-term persistent use of landscapes, anthropogenic landform modifications, and the production of systems of territorial ownership/proprietorship. Exploring the case of the socio-politically complex cultures of the Northwest Coast, we argue that while tenure and proprietorship were mediated by historical precedent of use (proprietorship-through-endowment), investments in places through physical engagement with or transformation of coastal landforms could be used to make explicit these endowed rights or to assert or negotiate new rights (proprietorship-through-investment). A key ingredient in negotiating proprietorship was an engagement with the dynamic coast itself, an active agent in landscape transformation perceived as being spiritually powerful. Using the archaeological landscape of the Prince Rupert Harbour area, we assess the timing and tempo of measurable investments in the physical landscape at village sites and the occurrence of independent archaeological proxies for restricted or unequal access to territory or resources. Systems of territorial proprietorship existed there by at least the mid-Holocene, though we document increasingly institutionalized proprietorship systems coincident with increased investments into the built environment beginning ~3000 years ago. Our approach has broad applicability, and encourages archaeologists to explore the role of human engagement with dynamic landscapes in the generation of senses of identity and social or political organization.

Past research has greatly improved our understanding of palaeoenvironmental changes in the Lake Baikal Region, but at the same time has indicated intra-regional variations in this vast study area. Here we present a new AMS-dated late glacial-middle Holocene (ca. 13,500-4000 cal. yr BP) pollen record from Lake Ochaul (54 degrees 14'N, 106 degrees 28'E; altitude 641 m a.s.l.) situated in the less-studied area of Cis-Baikal and compare reconstructed vegetation and climate dynamics with the published environmental history of Trans-Baikal based on the pollen record from Lake Kotokel (52 degrees 47'N, 108 degrees 07'E; altitude 458 m a.s.l.). Although both records show comparable major long-term trends in vegetation, there are considerable differences. Around Ochaul the landscape was relatively open during the Younger Dryas stadial, but forest vegetation started to spread at the late glacial/Holocene transition (ca. 11,650 cal. yr BP), thus ca. 1000 years earlier than around Kotokel. While in both regions taiga forests spread during the early and middle Holocene, the marked increase in Scots pine pollen in the Kotokel record after ca. 6800 cal. yr BP is not seen in that from Ochaul, where birch and coniferous taxa, such as Siberian pine, larch, spruce and fir, dominate, indicating different environmental conditions and driving forces in both study regions. However, the pollen data from Ochaul emphasizes that the Cis-Baikal area also saw a continuous increase in forest cover and in the proportion of conifers over birch trees and shrubs during the early-middle Holocene, which may have contributed to a decrease in the number of large herbivores, the main food resource of the Early Neolithic hunter-gatherer groups. This and rather abrupt reorganization of atmospheric circulation, which affected atmospheric precipitation distribution resulting in thicker and longer-lasting snow cover, may have led to a collapse of Early Neolithic Kitoi populations ca. 6660 cal. yr BP followed by a cultural "hiatus" in the archaeological records during the Middle Neolithic phase (ca. 6660-6060 cal. yr BP). The results stress the importance of sub-regional palaeoenvironmental studies and the need for a representative network of well-dated, high-resolution sediment archives for a better understanding of environmental changes and their potential impacts on the hunter-gatherer populations in the archaeologically-defined micro-regions.

Abstract Hyponymy is a semantic relation of class inclusion (e.g., a cat is an animal; a wildcat is a cat). Compound words are often, but not always, in a hyponymic relationship with the second constituent of the compound, as in wildcat and cat. This paper introduces a set of human ratings of hyponymy for over 2500 English compound words, which will facilitate research on the role of hyponymy in compound word processing and related areas. In the compound word processing literature, the semantic transparency of the compound (i.e., the extent to which the meaning of the constituents is maintained in the compound) is a critical theoretical construct. We investigate the role that hyponymy plays in the semantic transparency of compound words, as well as in the processing of compound words. We find that hyponymy is a critical component of the semantic transparency of both the second constituent (e.g., cat) and the compound as a whole (e.g., wildcat) and somewhat surprisingly also of the first constituent (e.g., wild). Hyponymy also affects the speed of processing of compound words in both lexical decision and naming.

AbstractDespite the longstanding significance of North America's Great Lakes, little is known about their preindustrial ecology. Here, we report on when and how humans first became a main driver of Lake Ontario's nutrient dynamics. Nitrogen isotope analyses of archaeological fish show that, prior to the 1830s, Lake Ontario's nitrogen cycle and the trophic ecology of its top predators had remained stable for at least 800 yrs, despite Indigenous and historical European agricultural land management across the region. An abrupt shift in the nitrogen isotope composition of Lake Ontario's fish community is evident in the early to mid‐19th century and reflects the initiation of industrial‐scale forest clearance. These data show how the nitrogenous nutrient regimes of even the world's largest freshwater ecosystems can be highly sensitive to short‐term watershed forest cover disturbances and indicate a profound shift in the relationship between humans and their environment.

Abstract Three archaeological surveys in central Cyprus have recovered lithic artifacts from a variety of chert sources, isolated findspots and sites. Typological analyses of these finds and 14C results from one site suggest that they date to the Late Epi-Palaeolithic and very early Neolithic periods. Previous research ( McCartney et al., 2006 , McCartney et al., 2007 , McCartney et al., 2008 , Murphy et al., 2019 , Stewart et al., 2017 ) of the spatial relationships between these finds suggests ways that these early settlers to the island entered into and explored this new landscape to access a variety of resources, with chert artifacts leaving a lasting record of this behaviour. A previous pilot test of Instrumental Neutron Activation analysis (INAA) further supported our initial observations. Here we expand this research to include a much larger sample size. While this study was only able statistically to isolate one group of artifacts, it does indicate that all the other artifacts in the study originated in the circum-Troodos Lefkara sedimentary formation chert deposits. The single anomaly, a group of dark, silicified umber artifacts, may reflect early use of this distinctive raw material, judging by its restricted location along the central south coast and into the interior by way of the Tremithos River valley.

Pacific salmonid (Oncorhynchus spp.) remains are routinely recovered from archaeological sites in northwestern North America but typically lack sexually dimorphic features, precluding the sex identification of these remains through morphological approaches. Consequently, little is known about the deep history of the sex-selective salmonid fishing strategies practiced by some of the region’s Indigenous peoples. Here, we present a DNA-based method for the sex identification of archaeological Pacific salmonid remains that integrates two PCR assays that each co-amplify fragments of the sexually dimorphic on the Y chromosome (sdY) gene and an internal positive control (Clock1a or D-loop). The first assay co-amplifies a 95 bp fragment of sdY and a 108 bp fragment of the autosomal Clock1a gene, whereas the second assay co-amplifies the same sdY fragment and a 249 bp fragment of the mitochondrial D-loop region. This method’s reliability, sensitivity, and efficiency, were evaluated by applying it to 72 modern Pacific salmonids from five species and 75 archaeological remains from six Pacific salmonids. The sex identities assigned to each of the modern samples were concordant with their known phenotypic sex, highlighting the method’s reliability. Applications of the method to dilutions of modern DNA samples indicate it can correctly identify the sex of samples with as little as ~39 pg of total genomic DNA. The successful sex identification of 70 of the 75 (93%) archaeological samples further demonstrates the method’s sensitivity. The method’s reliance on two co-amplifications that preferentially amplify sdY helps validate the sex identities assigned to samples and reduce erroneous identifications caused by allelic dropout and contamination. Furthermore, by sequencing the D-loop fragment used as a positive control, species-level and sex identifications can be simultaneously assigned to samples. Overall, our results indicate the DNA-based method reported in this study is a sensitive and reliable sex identification method for ancient salmonid remains.