cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dr7sqv9ws
title: Exploring changes in ecosystem service values in strongly human-impacted, contrasting agro-ecological environments

description: Evaluating the impacts of land-use/land-cover (LULC) changes on ecosystem
 service values (ESVs) is essential for sustainable use and management of
 ecosystems. In this study, we evaluated the impact of LULC changes on ESVs
 over the period 1982–2016/17 in contrasting, strongly human-impacted
 agro-ecological environments: Guder (highland), Aba Gerima (midland), and
 Debatie (lowland) watersheds of the Upper Blue Nile basin, Ethiopia.
 During the study period, the continuous expansion of cultivated land at
 the expense of natural vegetation (bushland, forest, and grazing land)
 severely reduced the total ESV by about US$58 thousand (35%) in Aba Gerima
 and US$31 thousand (29%) in Debatie watersheds. In contrast, the
 unprecedented expansion of plantations, mainly through the planting of
 Acacia decurrens, helped the total ESV rebound by about US$71 thousand
 (54%) in Guder watershed after 2006, after it had decreased by about US$61
 thousand (32%) between 1982 and 2006. The reduction in natural forest area
 was the major contributor to the loss of total ESV in the study
 watersheds, ranging from a reduction of US$31 thousand (63%) in Debatie to
 US$96.9 thousand (70%) in Guder between 1982 and 2016/17. On an
 area-specific basis, LULC changes reduced the average ESV from US$560 ha–1
 yr–1 (1982) in Guder to US$306 ha–1 yr–1 (2017) in Debatie watersheds.
 Specific ESVs such as provisioning (mainly as food production) and
 regulating services (mainly as erosion control and climate regulation)
 accounted for most of the total ESVs estimated for the study watersheds.
 In most cases the total and specific ESVs of the watersheds were
 negatively associated with the population growth, which in turn was
 positively associated with the expansion of cultivated land over the study
 period. In Guder watershed, however, ESVs were positively associated with
 population growth, especially after 2012. This resulted primarily from the
 conversion of cultivated land to plantations (predominantly with
 nitrogen-fixing Acacia decurrens trees) because of the farmers’ growing
 desire to rehabilitate degraded cultivated land while simultaneously
 generating income through the sale of charcoal from this fast-growing
 tree. Our results suggest, therefore, that future policy measures and
 directions should focus on improving vegetation cover through planting
 multipurpose trees such as Acacia decurrens to prevent future loss of ESV
 in the midland and lowland regions of the Upper Blue Nile basin and
 beyond.
description: The data were exteracted from high resolution remote sensing
 images by producing multiple land use/land cover maps through ArcGIS 10.4
 software.
DOI: 10.15468/dl.d956e5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chamaecrista fasciculata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002617-260126135527185/datasets/export for details.
DOI: 10.5061/dryad.hmgqnk9f9
title: The Geometry and Genetics of Hybridization

description: When divergent populations form hybrids, hybrid fitness can vary with
 genome composition, current environmental conditions, and the divergence
 history of the populations. We develop analytical predictions for hybrid
 fitness, which incorporate all three factors. The predictions are based on
 Fisher's geometric model, and apply to a wide range of population
 genetic parameter regimes and divergence conditions, including allopatry
 and parapatry, local adaptation and drift. Results show that hybrid
 fitness can be decomposed into intrinsic effects of admixture and
 heterozygosity, and extrinsic effects of the (local) adaptedness of the
 parental lines. Effect sizes are determined by a handful of geometric
 distances, which have a simple biological interpretation. These distances
 also reflect the mode and amount of divergence, such that there is
 convergence towards a characteristic pattern of intrinsic isolation. We
 next connect our results to the quantitative genetics of line crosses in
 variable or patchy environments. This means that the geometrical distances
 can be estimated from cross data, and provides a simple interpretation of
 the ``composite effects''. Finally, we develop extensions to the
 model, involving selectively-induced disequilibria, and variable
 phenotypic dominance. The geometry of fitness landscapes provides a
 unifying framework for understanding speciation, and wider patterns of
 hybrid fitness.
description: Simulated data was generated from individual-based simulations as
 in the code provided.
description: Readme file for simulation code provided. In
 addition, you need to download the following header file and place it in
 the allopatry and parapatry folders before compilation:
 https://github.com/hildeschneemann/Fisher_divergence_simulation/blob/main/allopatry/MersenneTwister.h
DOI: 10.5061/dryad.h9w0vt4gg
title: Data from: The effect of resource limitation on the temperature-dependence of mosquito population fitness

description: Laboratory-derived temperature dependencies of life history traits are
 increasingly being used to make mechanistic predictions for how climatic
 warming will affect vector-borne disease dynamics, partially by affecting
 abundance dynamics of the vector population. These temperature-trait
 relationships are typically estimated from juvenile populations reared on
 optimal resource supply, even though natural populations of vectors are
 expected to experience variation in resource supply, including
 intermittent resource limitation. Using laboratory experiments on the
 mosquito Aedes aegypti, a principal arbovirus vector, combined with
 stage-structured population modelling, we show that low-resource supply in
 the juvenile life stages significantly depresses the vector’s maximal
 population growth rate across the entire temperature range (22–32°C) and
 causes it to peak at a lower temperature than at high-resource supply.
 This effect is primarily driven by an increase in juvenile mortality and
 development time, combined with a decrease in adult size with temperature
 at low-resource supply. Our study suggests that most projections of
 temperature-dependent vector abundance and disease transmission are likely
 to be biased because they are based on traits measured under optimal
 resource supply. Our results provide compelling evidence for future
 studies to consider resource supply when predicting the effects of climate
 and habitat change on vector-borne disease transmission, disease vectors
 and other arthropods.
description: The dataset was collected during a laboratory study at Imperial
 College London and has been processed by a series of generalized linear
 models (GLMs) and stage-structured matrix projection
 models (MPMs) in R to produce a MS accepted for publication in Proceedings
 of the Royal Society B: Biological Sciences
description: The readme file contains an explanation of each of the variables
 in the dataset, its measurement units. NA =  values not
 available. Information on how the measurements were done can be found in
 the associated manuscript referenced above.
DOI: 10.15468/dl.6h4tt8
title: Occurrence Download

description: A dataset containing 561 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Geometry POLYGON((-81.74197 -3.29266,-79.14925 -5.2996,-75.30711 -1.59932,-75.24691 -0.08997,-78.29246 1.34262,-79.8134 1.42535,-81.74197 -3.29266))",
 "HasGeospatialIssue is false",
 "TaxonKey is Ara chloropterus"
 ]
}

 The dataset includes 561 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002616-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.08kprr517
title: Identification of Megaselia (Diptera: Phoridae) species using wing vein landmarking

description: A semi-automated identification system using wing venation is described
 for the large, taxonomically challenging genus Megaselia Rondani (Diptera:
 Phoridae). Wing photographs make two-dimensional images that can be
 landmarked and analyzed to produce transformed (standardized) x-y
 coordinates, and are well-suited for a semi-automated approach. We
 landmarked wing photographs of individuals of 108 specimens of Megaselia
 from the ZADBI (Zurqui All Diptera Biodiversity Inventory) project, as
 well as 284 specimens of Megaselia from the Los Angeles based BioSCAN
 (Biodiversity Science: City and Nature) project and ran them against
 libraries of one specimen of each species of the fauna from each site,
 respectively. Accuracy was about 52-67% for the first identification, with
 86-95% of correct identifications in the top 5 candidates list. Expanding
 the library to include all identified specimens raised the likelihood that
 the first identification was correct to 93-96% of specimens, with 97-98%
 correct identifications in the top 5 list. Incorporating major body color
 (dark brown versus yellowish) to the identification system increased
 accuracy to 100% for the ZADBI specimens; other, easily-seen characters
 were used for problematic LA specimens. We suggest that a wing photograph
 be included in all Megaselia species descriptions to allow this
 semiautomation of identification based on morphology, and further that
 this system could provide a bridge to DNA-based species descriptions from
 old holotypes in collections.
DOI: 10.5061/dryad.3xsj3txf5
title: Conservation genetics of an island-endemic lizard: low Ne and the critical role of intermediate temperatures for genetic connectivity

description: Island populations are at higher risk of extinction than mainland
 populations. Therefore, understanding the factors that facilitate
 connectivity is particularly pressing for the conservation of island taxa.
 Sceloporus occidentalis becki, the Island Fence Lizard, is an endemic
 taxon restricted to the Northern Channel Islands, part of a nearshore
 archipelago in Southern California, USA. Since the Last Glacial Maximum,
 fence lizard habitat on the Northern Channel Islands has decreased with
 rising sea levels and increasing temperatures that have reduced the
 availability of woody vegetation. More recently, the introduction (and
 subsequent removal) of invasive ungulates over the last 170 years
 and recovery of vegetation has resulted in further dramatic habitat
 modification. Given the potential for genetic bottlenecks, the history of
 habitat alteration, and topographic and landscape complexity, we used
 landscape and population genetic approaches to characterize patterns of
 genetic diversity and structure of Island Fence Lizards on Santa Cruz
 Island, the largest of the Northern Channel Islands. Our analyses revealed
 shallow population structure across the island, low effective population
 size (Ne = ~200), and evidence for a recent genetic bottleneck. Landscape
 genetic analyses showed that connectivity is facilitated by tree canopy
 cover and shrubland, as well as by intermediate temperatures, emphasizing
 the importance of woody vegetation and habitats with variable thermal
 regimes as the climate warms. Combined, these population and landscape
 genetic analyses suggest that the Island Fence Lizard is of greater
 conservation concern than currently appreciated, and increased
 conservation management focus is warranted for this island endemic.
description: Genotyped individuals using primers (in paper). Genotypes scored
 in GeneMapper. Site information provided in file.
DOI: 10.5061/dryad.zkh18938j
title: Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes

description: We determined differential gene expression in response to high glucose in
 lymphoblastoid cell lines derived from matched individuals with type 1
 diabetes with and without retinopathy. Those genes exhibiting the largest
 difference in glucose response were assessed for association to diabetic
 retinopathy in a genome-wide association study meta-analysis. Expression
 Quantitative Trait Loci (eQTLs) of the glucose response genes were tested
 for association with diabetic retinopathy. We detected an enrichment of
 the eQTLs from the glucose response genes among small association p-values
 and identified FLCN as a susceptibility gene for diabetic retinopathy.
 Expression of FLCN in response to glucose was greater in individuals with
 diabetic retinopathy. Independent cohorts of individuals with diabetes
 revealed an association of FLCN eQTLs to diabetic retinopathy. Mendelian
 randomization confirmed a direct positive effect of increased FLCN
 expression on retinopathy. Integrating genetic association with gene
 expression implicated FLCN as a disease gene for diabetic retinopathy.
description: GWAS for EDIC and Gokind was processed using Plink 1.9. Data was
 downloaded from DbGap. Data for GTEX EQTLs was downloaded from their
 website: https://gtexportal.org/home/. Data for GWAS and GTEX was merged in R versions 3.4.0. Meta analysis was performed using http://csg.sph.umich.edu/abecasis/metal/.
DOI: 10.5061/dryad.08kprr518
title: Data from: The effects of ivacaftor on bone density and microarchitecture in children and adults with cystic fibrosis

description: Context: Cystic fibrosis transmembrane conductance (CFTR) dysfunction may
 play a role in CF-related bone disease (CFBD). Ivacaftor is a CFTR
 potentiator effective in improving pulmonary and nutritional outcomes in
 patients with the G551D-CFTR mutation. The effects of ivacaftor on bone
 health are unknown. Objective: To determine the impact of ivacaftor on
 bone density and microarchitecture in children and adults with CF. Design:
 Prospective observational multiple cohort study. Setting: Outpatient
 clinical research center within a tertiary academic medical center.
 Patients or Other Participants: Three cohorts of age-, race-, and
 gender-matched subjects were enrolled: 26 subjects (15 adults and 11
 children) with CF and the G551D-CFTR mutation who were planning to start
 or had started treatment with ivacaftor within three months (Ivacaftor
 cohort); 26 subjects with CF were not treated with ivacaftor (CF Control
 cohort); and 26 healthy volunteers. Interventions: All treatments,
 including ivacaftor, were managed by the subjects’ pulmonologists. Main
 Outcome Measures: Bone microarchitecture by high resolution peripheral
 quantitative computed tomography (HR-pQCT), areal bone mineral density
 (aBMD) by dual-energy X-ray absorptiometry (DXA) and bone turnover markers
 at baseline, 1, and 2 years. Results:  Cortical volume, area, and
 porosity at the radius and tibia increased significantly in adults in the
 Ivacaftor cohort. No significant differences were observed in changes in
 aBMD, trabecular microarchitecture, or estimated bone strength in adults
 or in any outcome measures in children. Conclusions: Treatment with
 ivacaftor was associated with increases in cortical microarchitecture in
 adults with CF. Further studies are needed to understand the implications
 of these findings.
DOI: 10.5061/dryad.4j0zpc893
title: Spatial modulation of visual responses arises in cortex with active navigation

description: During navigation, the visual responses of neurons in mouse primary visual
 cortex (V1) are modulated by the animal’s spatial position. Here we show
 that this spatial modulation is similarly present across multiple higher
 visual areas but negligible in the main thalamic pathway into V1. Similar
 to hippocampus, spatial modulation in visual cortex strengthens with
 experience and with active behavior. Active navigation in a familiar
 environment, therefore, enhances the spatial modulation of visual signals
 starting in the cortex.
description: 2 photon imaging Raw data were preprocessed
 with Suite2p (image registration, ROI detection, deconvolution)
 Corrected traces were used for estimating response profile
 patterns as described in Methods and in Readme file.
description: Plese see the Readme file for full description of the datasets
 and any additional notes.
DOI: 10.5061/dryad.7m0cfxpsd
title: Phenological changes offset the warming effects on biomass production in an alpine meadow on the Qinghai-Tibetan Plateau

description: 1. Phenology is an important indicator of plant response to environmental
 changes and is closely correlated with biomass production. However, how
 changes of phenological events affect plant biomass production when
 exposed to changing temperature and precipitation remains unclear. 2. We
 conducted a four-year manipulative experiment of warming and precipitation
 addition to explore phenology-biomass interactions under climate change in
 a dry alpine meadow on the central Qinghai-Tibetan Plateau from 2015 to
 2018. 3. In dry and warm years, warming delayed phenology and
 precipitation addition advanced them. Warming decreased biomass of
 Kobresia pygmaea in 2018 and biomass of Poa pratensis in 2015, 2017 and
 2018. However, precipitation addition significantly increased the biomass
 of Poa pratensis and Potentilla multifida in most of the experimental
 years. Phenological changes regulated the responses of biomass to
 treatments. Specifically, delay of green up of P. pratensis and delay of
 withering of K. pygmaea induced by warming can increase biomass
 production, but it can be offset by the direct negative effects of warming
 on biomass. 4. Synthesis. Here we show how warming induced drought tend to
 decrease biomass production of graminoids and the negative effects of
 warming on biomass of P. pratensis and K. pygmaea were partially offset by
 green up postponement and withering postponement, respectively. Our
 results highlights phenology is a crucial regulator for biomass production
 under climate change. Hence, both direct and indirect effects of warming
 and precipitation addition on phenology and biomass cannot be ignored when
 predicting biomass responses to climate change.
DOI: 10.5061/dryad.xwdbrv1c7
title: Thermal tolerance and cardiac phenotypes

description: Adaptation to local environments involves the evolution of ecologically
 important traits and underlying physiological processes. Here, we used low
 coverage whole-genome resequencing (lcWGR) on individuals to identify
 genome regions involved in thermal adaptation in wild redband trout
 Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits
 ecosystems ranging from cold montane forests to high elevation deserts.
 This study includes allele frequency-based analyses for selective sweeps
 among populations, followed by multiple association tests for
 specific sets of phenotypes measured under thermal stress (acute and
 chronic survival/mortality; high or low cardiac performance groups).
 Depending on the groups in each set of analyses, sequencing reads covered
 between 43-75% of the genome at ≥15X and each analysis included millions
 of SNPs across the genome. In tests for selective sweeps among
 populations, a total of six chromosomal regions were significant. However,
 association tests for specific phenotypes revealed that the region on
 chromosome 4 was consistently the most significant and contains the cerk
 gene (ceramide kinase). This study provides insight into a potential
 genetic mechanism of local thermal adaptation and suggests cerk may be an
 important candidate gene. However, further validation of this cerk gene is
 necessary to determine if the association with cardiac performance results
 in a functional role to influence thermal performance when exposed to high
 water temperatures and hypoxic conditions. 
description: Acute and chronic thermal tolerance was measured by rearing fish
 under daily temperature cycled between 17.5°C (evening) to 28.5°C
 (afternoon) that mimic the 24-h water temperature fluctuation in natural
 desert streams during the hottest summer days Cardiac
 phenotypes was measured using a custom-built electrocardiogram (ECG)
 system, where its heart rate were pharmacologically stimulated to maximum
 (maximum heart rate or <i>f</i><sub>H,max</sub>)
 by atropine sulphate and isoproterenol.
DOI: 10.5061/dryad.h18931zjd
title: The smell of cooperation: rats increase helpful behaviour when receiving odour cues of a conspecific performing a cooperative task

description: Reciprocity can explain cooperative behaviour among non-kin, where
 individuals help others depending on their experience in previous
 interactions. Norway rats (Rattus norvegicus) cooperate
 reciprocally according to direct and generalized reciprocity. In a
 sequence of four consecutive experiments, we show that odour cues from a
 cooperating conspecific are sufficient to induce altruistic help of rats
 in a food-exchange task. When rats were enabled to help a non-cooperative
 partner while receiving olfactory information from a rat helping a
 conspecific in a different room, they helped their non-cooperative partner
 as if it was a cooperative one. We further show that the cues inducing
 altruistic behaviour are released during the act of cooperation
 and do not depend on the identity of the cue provider.
 Remarkably, olfactory cues seem to be more important for cooperation
 decisions than experiencing a cooperative act per se. This suggests that
 rats signal their cooperation propensity to social partners, which
 increases their chances to receive help in return.
description: To test for reciprocal cooperation, we used wild-type Norway rats
 that were capable of producing food for a partner . In addition, we
 manipulated the availability of olfactory information by controlling the
 airflow between social partners. We performed a series of four consecutive
 experiments to stepwise clarify which information rats consider when
 deciding to provision a social partner with food
DOI: 10.5061/dryad.pk0p2ngkx
title: Strong foraging preferences for Ribes alpinum (Saxifragales: Grossulariaceae) in the polyphagous caterpillars of Buff tip moth Phalera bucephala (Lepidoptera: Notodontidae)

description: Herbivorous insects such as butterflies and moths are essential to natural
 and agricultural systems due to pollination and pest outbreaks. However,
 our knowledge of butterflies’ and moths’ nutrition is fragmented and
 limited to few common, charismatic, or problematic species. This gap
 precludes our complete understanding of herbivorous insects’ natural
 history, physiological and behavioural adaptations that drive how species
 interact with their environment, the consequences of habitat destruction
 and climate change to invertebrate biodiversity, and pest outbreak
 dynamics. Here, we first report a population of the Buff tip moth Phalera
 bucephala (Lepidoptera: Notodontidae) feeding on a previously unknown
 family of hostplants, the mountain currant Ribes alpinum (Saxifragales:
 Grossulariaceae). This is the first report of a Notodontid moth feeding on
 Grossulariaceae hosts. Using no-choice and choice assays, we showed that
 P. bucephala has strong foraging preferences for a previously unknown
 hosts, the R. alpinum but also, although to a smaller extent, R.
 uva-crispa compared with a previously known host (the maple Acer sp.).
 These findings demonstrate that P. bucephala feed on – and show strong
 preference for Grossulariaceae hostplants, indicating flexible
 physiological mechanisms to accommodate hosts plants from various
 families. This makes this species a potential model organism to study the
 behavioural and physiological mechanisms underpinning insect-plant
 interactions and diet breadth evolution. We discuss the broad ecological
 implications of this observations to the biology of the species, the
 potential negative effects of interspecific competition with endemic
 specialist moths, and highlight questions for future research.
description: Detailed methods provided in the publication.
description: ReadMe file uploaded with the data