cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fj6q573tg
title: Ant exclusion decomposition data

description: Ants play multiple roles in ecosystems, but their ability to affect
 decomposition processes in temperate grasslands is relatively unknown. We
 investigated whether the suppression of ant populations influenced litter
 decomposition in grasslands via predation of some decomposers (e.g., mites
 and springtails) and/or microbial activity and composition. We performed
 two successful ant suppression treatments (seven weeks, 37% suppression,
 year 1, 10 weeks, 70% suppression, year 2) over the course of a 59-week
 experiment.  We then assayed the effects of ant suppression using
 coarse- and fine-mesh litterbags, and evaluated litter chemistry,
 microbial and arthropod communities, and microbial enzyme activity. Ant
 suppression efforts reduced ant abundance, and altered ant, arthropod
 decomposer, and non-ant predator community composition. However, ant
 suppression did not affect decomposer arthropod abundance, litter mass
 loss, microbial composition, or enzyme activity in litterbags. Litterbag
 mesh size did not alter microbial composition, perhaps due to a failure to
 exclude decomposers, as mites and springtails were more or equally
 abundant in fine-mesh bags. Nevertheless, mesh size did change litter
 chemistry, suggesting that mesh size-mediated micro-environments affect
 decomposition environment regardless of invertebrate exclusion.
 Coarse-mesh litterbags had higher concentrations of microbial sugars,
 lignin, and N and lower concentrations of litter C and crystalline
 cellulose than fine-mesh litterbags. Litterbag mesh size may alter
 decomposition processes irrespective of invertebrate abundance. We found
 no evidence that ant predation was an important driver of decomposer
 populations or decomposition in these systems, and we suspect redundancy
 at the top of the detrital food web dilutes the role of ants.
description: Data were collected from a field site in SW over 2015-2016. All
 methods details are given in publication Cates et al. 2021 "No
 evidence of top-down effects by ants on litter decomposition in a
 temperate grassland". The readme tab describes units for each
 column.
description: There are many missing values, as litterbags were lost over time.
 Users should contact catesa@umn.edu with questions.
DOI: 10.15468/dl.ptz75k
title: Occurrence Download

description: A dataset containing 3462 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pterocarpus indicus"
 ]
}

 The dataset includes 3462 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002807-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jm63xsj9g
title: Morrison deer and invasive plants in suburban forests 2021 Ecoscience

description: Fragmented suburban forests of the northeastern US are challenged by
 abundant white-tailed deer and nonindigenous plant invasions. Deer
 browsing/grazing pressure varies among sites, potentially affecting
 herbivory on nonindigenous plants and their invasion success. We aimed to
 identify a useful deer pressure indicator for suburban forests and then
 use it to relate deer pressure to grazing on and abundance of two
 herbaceous invaders, Microstegum viminuem and Alliaria petiolata. We
 compared three indicators: fecal pellet accumulation rate, deer browse on
 indigenous woody plants, and indigenous shrub layer cover. The pellet
 method produced estimates generally far below the region’s known deer
 density. Browse rates and shrub layer cover were negatively correlated,
 and correlations of the three indicators with evidence of deer pressure
 from a subsequent 6.5-year exclosure experiment supported shrub layer
 cover as the better choice. Using that measure in ten forests, we detected
 a weak pattern of more grazed stands under greater deer pressure, but few
 plants per stand were grazed; any negative influence of deer on these
 species was limited to individuals, without population effects. Alliaria
 petiolata abundance was unrelated to deer pressure, but M. vimineum
 abundance was greater in forests with more deer pressure, suggesting
 facilitation of its invasion.
description: Data were collected in field sites in central New Jersey, USA,
 entered and managed in Excel files, and analyzed with SAS and R.
description: A ReadMe file with extensive annotation is provided:
 "README for
 Morrison_DeerAndInvasives_2021_Ecoscience.txt"
DOI: 10.5061/dryad.1rn8pk0sz
title: Head and mandible shapes are highly integrated yet represent two distinct modules within and among worker sub-castes of the ant genus Pheidole

description: Ants use their mandibles for a wide variety of tasks related to substrate
 manipulation, brood transport, food processing, and colony defence. Due to
 constraints involved in colony upkeep, ants evolved a remarkable diversity
 of mandibular forms, often related to specific roles such as specialized
 hunting and seed milling. Considering these varied functional demands, we
 focused on understanding how the mandible and head shape vary within and
 between Pheidole sub-castes. Using x-ray microtomography and 3D geometric
 morphometrics, we tested if these structures are integrated and modular,
 and how ecological predictors influenced these features. Our results
 showed that mandible and head shape of majors and minor workers tend to
 vary from robust to slender, with some more complex changes related to the
 mandibular base. Additionally, we found that head and mandible shapes are
 characterized by a high degree of integration, but with little correlation
 with feeding and nesting habits. Our results suggest that a combination of
 structural (allometric) constraints and the behavioural flexibility
 conferred by caste dimorphism might largely buffer selective pressures
 that would otherwise lead to a fine-tuning between ecological conditions
 and morphological adaptation.
DOI: 10.7272/q66h4fpz
title: Prevalence of elevated liver transaminases and their relationship with alcohol use in people living with HIV on anti-retroviral therapy in Uganda

description: Background: Isoniazid preventive therapy (IPT) reduces tuberculosis
 reactivation and mortality among persons living with HIV (PLWH), yet
 hepatotoxicity concerns exclude “regular and heavy alcohol drinkers” from
 IPT. We aimed to determine the prevalence of elevated liver transaminases
 among PLWH on antiretroviral therapy (ART) who engage in alcohol use.
 Setting: The Immune Suppression Syndrome Clinic of Mbarara, Uganda.
 Methods: We defined elevated liver transaminases as ≥1.25 times
 (X) the upper limit of normal (ULN) for alanine aminotransferase (ALT)
 and/or aspartate aminotransferase (AST). We evaluated the associations of
 current alcohol use and other variables of interest (sex, body mass index,
 and ART regimen) with elevated transaminases at study screening, using
 multivariable logistic regression to obtain adjusted odds ratios (aOR) and
 95% confidence intervals (CI). Results: Among 1301 participants
 (53% female, median age 39 years, 67.4% current alcohol use), 18.8% (95%
 CI: 16.8-21.1) had elevated transaminases pre-IPT, with few (1.1%) severe
 (≥5X the ULN). The proportion with any elevation among those currently
 using alcohol and those abstaining was 22.3% and 11.6%, respectively
 (p&lt;0.01). In multivariable analyses, those currently using alcohol
 had higher odds of elevated transaminases compared to those abstaining
 (aOR 1.65, 95% CI 1.15-2.37) as did males compared to females (aOR 2.68,
 95% CI 1.90-3.78). The data included are the raw data, including the above
 measures, plus the data after multiple imputations. 
 Conclusions: Pre-IPT elevated transaminases among PLWH receiving ART were
 common, similar to prior estimates, but severe elevations were rare.
 Current drinking and male sex were independently associated with elevated
 transaminases. Further research is needed to determine the implications of
 such transaminase elevations and alcohol use on providing IPT.
DOI: 10.5061/dryad.m905qfv0s
title: Changes in above/belowground biodiversity and plant functional composition mediate soil respiration response to nitrogen input

description: 1. Biodiversity loss and changes in plant community composition induced by
 anthropogenic nitrogen (N) deposition exert profound effects on ecosystem
 functions. However, limited studies have considered the joint effects of
 plant community composition, plant species richness, plant functional
 diversity and soil biodiversity on the dynamics of soil autotrophic and
 heterotrophic respiration under extra N input. 2. We addressed this issue
 by conducting a multilevel N-manipulation experiment in a Tibetan alpine
 steppe. Based on soil respiration observations as well as biotic and
 abiotic measurements under this N addition experiment, we quantified the
 relative and interactive effects of above/belowground biodiversity, plant
 community composition and other explanatory variables (environmental
 factors, plant and microbial properties) on autotrophic and heterotrophic
 respiration. 3. Our results showed that the effects of N enrichment via
 plant productivity, root amount, the proportion of sedge biomass and plant
 functional diversity explained 71% of the N-induced variations in
 autotrophic respiration. With regard to heterotrophic respiration, the
 combination of N addition, soil pH, plant functional diversity and soil
 biota diversity accounted for 78% of its variations along the N addition
 gradient. Further analyses showed that above/belowground diversity loss
 and changes in plant community composition explained similar variation to
 that contributed by other factors in both autotrophic and heterotrophic
 respiration. The declined plant functional diversity and the increased
 proportion of sedge biomass promoted autotrophic respiration. Conversely,
 the loss of soil biodiversity together with the decreased plant functional
 diversity led to the decline of heterotrophic respiration along the
 experimental N gradient. 4. Our results highlight that the indirect
 regulation of N input on ecosystem function through changes in plant
 community composition and above/belowground biodiversity loss should be
 considered for better understanding the responses of terrestrial
 ecosystems to atmospheric N deposition.
DOI: 10.5061/dryad.zpc866t7v
title: Functional changes in fortified places: Strategy and defensive architecture in the Medieval and Early Modern Era

description: Data for Scott Kirk's Doctoral Dissertation. Dissertation Abstract:
 Defined as fortified elite Houses, castles are a cross-cultural
 phenomenon, best understood by pairing Niche Construction Theory (NCT)
 with the Lévi-Straussian concept of the House. NCT can be thought of as a
 theory of the built environment, thus the material configuration of
 castles and their placement on the landscape reflect elite socio-cultural
 requirements. My dissertation asks: How do changes in castle morphology
 and landscape placement reflect broad shifts in function diachronically
 and cross-culturally? Wherever elites are militarized, castles typically
 appear. Similarities in castle design and function are best understood
 through anthropological frameworks and comparative, interdisciplinary
 approaches. Using a sample of castles from medieval European, western
 colonial, and nonwestern societies, I hypothesize that: (1) castle
 building is a common, cross-cultural behavior, (2) geography and the
 environment constrain castle location, allowing for a landscape-based
 typology of castles, and (3) changes in castle placement and design
 reflect large-scale social competition between elites. These hypotheses
 contradict much of the current regionally-focused work in castle studies,
 which are often grounded in national ideologies. Early 20th century
 studies were more aligned with my hypotheses. Revisiting these earlier
 investigations, my dissertation uses anthropological theories within an
 interdisciplinary approach. It combines architectural, statistical, and
 geospatial analyses to quantitatively test how similar castle placement
 and co-occurring architectural features are cross-culturally, and how
 these attributes change over time in relation to elite competition. This
 research has general and theoretical significance for assessing mechanisms
 of elite status reinforcement, behavior, and decision-making across space
 and time. Building a typology that characterizes castles as resource
 control points, examining how similar architectural features appear in
 disparate cultures, and exploring social change driven by elite
 competition, my dissertation takes aim at nationalistic policies by
 illustrating cross-cultural similarities that are applicable to the modern
 world in terms of increasing wealth disparities and socioeconomic
 inequality.
description: This dataset was collected through a representative literature
 review for each structure followed by ground truthing for 90% of the
 structures.   Data was used in cluster analyses and to
 create indices for two chapters in Scott Kirk's
 dissertation.  
description: Please cite accordingly.
DOI: 10.5061/dryad.xgxd254fv
title: Genome-wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: Implications for coral restoration

description: It is essential to consider genetic composition for both conventional
 coral restoration management and for expanding new interventions to
 counter the significant global decline in living corals. Population
 genetic structure at fine spatial scale should be carefully evaluated
 before implementing strategies to achieve self-sustaining ecosystems via
 coral restoration. Here, we investigated the population genetic structure
 of two acroporid species at Kume Island, Okinawa, Japan. 140 colonies of
 Acropora digitifera from 7 study sites, and 81 colonies of Acropora tenuis
 from 6 sites were collected. We obtained 384 SNP loci for A. digitifera
 and 470 SNPs for A. tenuis using a comparatively economical technique,
 Multiplexed ISSR Genotyping by sequencing (MIG-seq). Observed
 heterozygosity was significantly lower than expected heterozygosity at all
 SNP sites in both acroporid species, suggesting deficient genetic
 diversity possibly caused by past massive coral bleaching. Even though
 both species are broadcast spawners, we found different population
 structure in the two species. No detectable structure was evident in A.
 digitifera, but two distinct clades were found in A. tenuis. The genetic
 homogeneity of A. digitifera at Kume Island suggests that this species
 could be used as focal species for active restoration in terms of genetic
 differentiation at this island. On the other hand, A. tenuis unexpectedly
 included two distinct clades with no or little admixture within a small
 spatial study area, possibly representing two reproductively isolated
 cryptic species. Thus, when using A. tenuis, it would be prudent to avoid
 disturbing genetic composition of wild populations until this question is
 answered.
DOI: 10.5061/dryad.vhhmgqnsk
title: Supplemental Materials: Duration of poverty and subsequent cognitive function and decline among older adults in China, 2005-2018

description: Objective To investigate the relationship between late-life duration of
 poverty exposure and cognitive function and decline among older adults in
 China. Methods Data were from 3,209 participants aged ≥64 in the Chinese
 Longitudinal Healthy Longevity Survey (CLHLS). Duration of poverty,
 defined according to urban and rural regional standards from the China
 Statistical Yearbook, was assessed from 2005-2011 (never in
 poverty; 1/3 of the period in poverty; ≥2/3 of the
 period in poverty). Cognitive function was measured by the Chinese Mini
 Mental State Exam (CMMSE) from 2011 to 2018. We used attrition-weighted,
 multivariable mixed-effects Tobit regression to examine the association of
 duration of poverty with cognitive performance and rate of decline.
 Results A total of 1,162 individuals (36.21%) were never in poverty over
 the period from 2005 to 2011, 1,172 (36.52%) were in poverty 1/3 of the
 period, and 875 (27.27%) were in poverty ≥2/3 of the period. A longer
 poverty duration was associated with lower subsequent CMMSE scores with a
 dose-response relationship (1/3 vs. never in poverty: β = -0.98; 95% CI:
 -1.61 to -0.35; ≥2/3 vs. never in poverty: β = -1.55; 95% CI: -2.29 to
 -0.81). However, a longer duration of poverty was associated with a slower
 rate of CMMSE score decline over time. Conclusion These findings provide
 valuable evidence on the role of cumulative late-life poverty in relation
 to cognitive health among older adults in a rapidly urbanizing and aging
 middle-income country. Our findings may support a compensation hypothesis
 for cognitive reserve in this setting.
DOI: 10.15468/dl.zrnup9
title: Occurrence Download

description: A dataset containing 279 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dalbergia cochinchinensis"
 ]
}

 The dataset includes 279 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002808-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9p8cz8wfr
title: Input files of various genomic analyses used to unravel the domestication history of Cannabis

description: Cannabis sativa has long been an important source of fiber extracted from
 hemp and both medicinal and recreational drugs based on cannabinoid
 compounds. Here, we investigated its poorly known domestication history
 using whole-genome resequencing of 110 accessions from worldwide origins.
 We show that C. sativa was first domesticated in early Neolithic times in
 East Asia and that all current hemp and drug cultivars diverged from an
 ancestral gene pool currently represented by feral plants and landraces in
 China. We identified candidate genes associated with traits
 differentiating hemp and drug cultivars, including branching pattern and
 cellulose/ lignin biosynthesis. We also found evidence for loss of
 function of genes involved in the synthesis of the two major biochemically
 competing cannabinoids during selection for increased fiber production or
 psychoactive properties. Our results provide a unique global view of the
 domestication of C. sativa and offer valuable genomic resources for
 ongoing functional and molecular breeding research.
DOI: 10.5061/dryad.wpzgmsbmj
title: Defining and quantifying effective connectivity of landscapes for species' movements

description: Demonstration of the workflow and supplementary information on
 the randomized shortest paths framework for "Defining and quantifying
 effective connectivity of landscapes for species’ movements" by Van
 Moorter B, Kivimäki I, Panzacchi M, Saerens M. (2021) in Ecography
 44(6):1–15.  Ecosystem functioning depends on multiple successful
 interactions, many supported by individual movements. The degree to which
 the landscape allows these interactions to take place has been referred to
 as ‘effective connectivity' (EC). Many of the cumulative impacts of
 anthropogenic activities on ecosystem functioning arise from changes in
 EC. Therefore, a coherent framework to quantify EC is urgently needed.
 Recent theoretical developments propose that studying EC requires the
 simultaneous consideration of spatial, environmental and species intrinsic
 characteristics (SEI framework). In the paper we further expand
 the SEI framework by integrating advances in geographic information
 science, ecological niche modelling, movement ecology, island biogeography
 and network sciences to develop a comprehensive three-step methodological
 approach for quantifying EC. First, using niche modelling and movement
 ecology, we quantify the species movement probabilities with respect to
 local environmental conditions. Second, we quantify ecological distances
 between non-adjacent locations by integrating species movement responses
 to the local environment with the spatial configuration of the landscape
 using the expected cost obtained from the randomized shortest paths (RSP)
 framework. This expected cost generalizes the two most frequently used
 ecological distance metrics, i.e. least-cost distance and resistance
 distance. Moreover the ‘absorbing random walk' properties of RSP
 allow the integration of new developments in connectivity research, i.e.
 spatial absorbing Markov chains, to account for movement-related
 mortality. Third, drawing from island biogeography and metapopulation
 ecology, we scale ecological distances by relevant species- and
 area-specific parameters to estimate EC for the ecological process of
 interest, e.g. migration, dispersal or gene flow. The integrative and
 highly interdisciplinary approach we propose can lead to increasingly more
 realistic measures of EC at different organizational levels. Moreover
 efficient computation allows its application to large-scale
 high-resolution landscapes for theoretical studies, conservation planning
 and sustainable management of real landscapes.
description: Supplementary Information for "Defining and Quantifying
 Effective Connectivity of Landscapes for Species'
 Movements" 1) Demonstration of the workflow in R
 (SupportingInformation_DemonstrationInR.pdf) 2) Brief
 review of the Randomized Shortest Pathsframework
 (SupportingInformation_RandomizedShortestPathsFramework.pdf)
DOI: 10.5061/dryad.w9ghx3fp0
title: Seasonal release from competition explains partial migration in European moose

description: Partial migration, whereby a proportion of a population migrates between
 distinct seasonal ranges, is common throughout the animal kingdom.
 However, studies linking existing theoretical models of migration
 probability, with empirical data are lacking. The competitive release
 hypothesis for partial migration predicts that due to density-dependent
 habitat selection, the proportion of migrants increases as the relative
 quality and size of the seasonal range increases, but decreases with
 increasing migration cost and population density. To test this prediction,
 we developed a quantitative framework to predict the proportion of
 migrants, using empirical data from 545 individually GPS-marked moose
 (Alces alces) from across Fennoscandia, spanning latitudes of 56° to 68°N.
 Moose contracted their ranges to common and spatially limited winter areas
 (typically at lower elevation), but expanded them during summer due to an
 increase in suitable habitat (at highland ranges). As predicted from our
 model, a better and larger highland range relative to the lowland range
 corresponded to a higher proportion of migrants in an area. Quantitative
 predictions coupling the balance of habitat availability of seasonal
 ranges with the probability of migrating in a large herbivore is a
 necessary step towards an enhanced understanding of the mechanisms
 underlying migration at the population level.