cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31151467
title: Genomic datasets for <b><i>Anguilla japonica</i></b>: Male and Female assemblies, annotations, CDS, and protein sequences

description: This dataset contains the chromosome-level genome assemblies and functional annotation files (GFF3, CDS, and Protein sequences) for male and female Japanese eels (<i>Anguilla japonica</i>).<b>Dataset Contents:</b><b>Genomic Sequences:</b> Chromosome-level assemblies (<code>.fasta</code>)<b>Annotations:</b> Gene structure predictions (<code>.gff3</code>)<b>Sequences:</b> Coding sequences (<code>.cds</code>) and protein sequences (<code>.pep</code>)<b>Assembly & Annotation Quality:</b> Both genomes demonstrate exceptional completeness and continuity, evaluated against the <i>actinopterygii_odb10</i> lineage:<b>Male Assembly (1.07 Gb, Scaffold N50: 58.89 Mb):</b>Assembly Completeness (compleasm): <b>99.09%</b>Annotation Completeness (Protein BUSCO): <b>99.00%</b><b>Female Assembly (1.08 Gb, Scaffold N50: 60.98 Mb):</b>Assembly Completeness (compleasm): <b>98.95%</b>Annotation Completeness (Protein BUSCO): <b>97.70%</b><b>Related Data:</b> Raw sequencing reads (HiFi, ONT, Hi-C, WGS, RNA-Seq) are available in the NCBI BioProject database under accession <b>PRJNA1414889</b>.
DOI: 10.6084/m9.figshare.31151467.v1
title: Genomic datasets for <b><i>Anguilla japonica</i></b>: Male and Female assemblies, annotations, CDS, and protein sequences

description: This dataset contains the chromosome-level genome assemblies and functional annotation files (GFF3, CDS, and Protein sequences) for male and female Japanese eels (<i>Anguilla japonica</i>).<b>Dataset Contents:</b><b>Genomic Sequences:</b> Chromosome-level assemblies (<code>.fasta</code>)<b>Annotations:</b> Gene structure predictions (<code>.gff3</code>)<b>Sequences:</b> Coding sequences (<code>.cds</code>) and protein sequences (<code>.pep</code>)<b>Assembly & Annotation Quality:</b> Both genomes demonstrate exceptional completeness and continuity, evaluated against the <i>actinopterygii_odb10</i> lineage:<b>Male Assembly (1.07 Gb, Scaffold N50: 58.89 Mb):</b>Assembly Completeness (compleasm): <b>99.09%</b>Annotation Completeness (Protein BUSCO): <b>99.00%</b><b>Female Assembly (1.08 Gb, Scaffold N50: 60.98 Mb):</b>Assembly Completeness (compleasm): <b>98.95%</b>Annotation Completeness (Protein BUSCO): <b>97.70%</b><b>Related Data:</b> Raw sequencing reads (HiFi, ONT, Hi-C, WGS, RNA-Seq) are available in the NCBI BioProject database under accession <b>PRJNA1414889</b>.
DOI: 10.5061/dryad.qnk98sfg1
title: Simultaneous genotyping of snails and infecting trematode parasites using high-throughput amplicon sequencing.

description: Several methodological issues currently hamper the study of entire
 trematode communities within populations of their intermediate snail
 hosts. Here we develop a new workflow using high-throughput amplicon
 sequencing to simultaneously genotype snail hosts and their infecting
 trematode parasites. We designed primers to amplify 4 snail and 5
 trematode markers in a single multiplex PCR. While also applicable to
 other genera, we focused on medically and economically important snail
 genera within the Superorder Hygrophila and targeted a broad taxonomic
 range of parasites within the Class Trematoda. We tested the workflow
 using 417 Biomphalaria glabrata specimens experimentally infected with
 Schistosoma rodhaini, two strains of Schistosoma mansoni, and combinations
 thereof. We evaluated the reliability of infection diagnostics, the
 robustness of the workflow, its specificity related to host and parasite
 identification, and the sensitivity to detect co-infections, immature
 infections, and changes of parasite biomass during the infection process.
 Finally, we investigated its applicability in wild-caught snails of other
 genera naturally infected with diverse trematode assemblages. After
 stringent quality control the workflow allows the identification of snails
 to species level, and of trematodes to taxonomic levels ranging from
 family to strain. It is sensitive to detect immature infections and
 changes in parasite biomass described in previous experimental studies.
 Co-infections were successfully identified, opening the possibility to
 examine parasite-parasite interactions such as interspecific competition.
 Altogether, these results demonstrate that our workflow provides a
 powerful tool to analyze the processes shaping trematode communities
 within natural snail populations.
description: The dataset includes bash and R script used ot process the output
 of our high-throughput amplicon sequencing experiments from raw reads to
 amplicon sequence variants (ASVs). We also included the R script used to
 further analyze the ASVs profile of each sample, as well as the R
 environment of that script to spare users the need to rerun it. The input
 files required to run the scripts are also included, except for the raw
 reads which were uploaded as fastq files on NCBI SRA: PRJNA743924.
 Finally, the abbreviations and their meaning are listed in the
 README.
DOI: 10.5061/dryad.dfn2z350z
title: Past connections with the mainland structure patterns of insular species richness in a continental-shelf archipelago (Aegean Sea, Greece): Species richness matrixes and shapefiles

description: Recent research in island biogeography has highlighted the important role
 of late Quaternary sea-level fluctuations in shaping biogeographic
 patterns in insular systems but focused on oceanic systems. Through this
 study, we aim investigate how late Quaternary sea-level fluctuations
 shaped species richness patterns in continental shelf island systems.
 Focusing on the Aegean archipelago, we first compiled maps of the area’s
 geography using published data, under three sea-level stands: 1) current;
 2) median sea-level over the last nine Glacial-Interglacial cycles (MSL);
 3) Last Glacial Maximum (LGM). We gathered taxon-island occurrences for
 multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles.
 We investigated the impact of present-day and past geographic settings on
 chorological groups by analysing Island Species-Area Relationships (ISARs)
 and using Generalized Linear Mixed Models (GLMMs) selection based on
 multiple metrics of goodness-of-fit. Our results confirm that the Aegean’s
 geography has changed dramatically since the LGM, whereas the MSL only
 modestly differs from the present configuration. Apart for centipedes,
 paleogeographic changes affected both native and endemic species diversity
 through altering connections between land-bridge islands and the mainland.
 On land-bridge islands, we detected over-representation of native species
 and under-representation of endemics. Unlike oceanic islands, sea-level
 driven increase of isolation and area contraction did not strongly shape
 patterns of species richness. Furthermore, the LGM configurations rather
 than the MSL configuration shaped patterns of endemic species richness.
 This suggests that even short episodes of increased connectivity with
 continental populations are sufficient to counteract the genetic
 differentiation of insular populations. On the other hand, the
 over-representation of native non-endemic species on land-bridge islands
 reflected MSL rather than LGM mainland connections. Our study shows that
 in terms of processes affecting species richness patterns, continental
 archipelagos differ fundamentally from oceanic systems because episodic
 connections with the mainland have profound effects on the biota of
 land-bridge islands.
description: Species richness fils are stored as comma-seperated-value-data
 sheets (csv-files) using the dot (.) as decimal seperator.
 Files containing GIS data (shx, .shp, .qpj, .rj, .dbf, .cpg) can
 be opened using GIS softwares such as QGIS or ArcGIS.
DOI: 10.5281/zenodo.18396670
title: Hydrography30: A 30 m-resolution global hydrography dataset derived from FABDEM using terrain–observation fusion

description: Hydrography maps constitute a fundamental dataset for hydrological modeling and analysis and are commonly derived from digital elevation models (DEMs). Despite the growing availability of 30-m DEMs, a corresponding global hydrography dataset at 30 m resolution is still lacking, resulting insufficient representation of micro-scale drainage networks and watershed boundaries across a wide range of landscapes. To address these limitations, we develop a terrain–observation fusion framework that integrates Forest And Buildings removed Copernicus DEM (FABDEM) with multi-source surface water data to guide the identification of endorheic basins. We further employ multiple algorithms for flow-direction correction to adjust flow patterns within depressions. Based on this framework, we construct Hydrography30, a 30-m resolution global hydrography map that shows strong consistency with existing observational datasets. Spatial overlap of watershed boundaries exceeds 0.8 for 91% of Global Runoff Data Centre (GRDC) gauges, indicating high geometric accuracy and robust representation of both exorheic and endorheic basins. Validation against observed endorheic data further shows that 80% of the endorheic outlets in the Qiang-tang Basin are captured by the derived hydrography. Moreover, by providing globally consistent 30 m flow direction and flow accumulation data, this dataset establishes a high-resolution hydrography foundation that enables explicit, structure-resolving hydrological analysis at the global scale.
DOI: 10.5061/dryad.05qfttf2g
title: Whiptail lizards (Aspidoscelis exsanguis) recognize invertebrate prey via cuticular hydrocarbons

description: Cuticular hydrocarbons (CHCs) present on the surface of arthropods are
 important mediators of both intraspecific and interspecific interactions.
 They are known to be important chemical cues that help predatory
 arthropods locate prey, yet less is known about if and how vertebrate
 insectivores use these nearly ubiquitous chemical cues. We examined
 behavioral responses of insectivorous lizards (Aspidoscelis exsanguis) to
 the CHCs of three different species of arthropod prey (crickets, ants, and
 spiders). We presented cotton swabs with either extracted CHCs or a
 solvent control to determine if lizards respond to CHCs in the absence of
 visual cues of prey. We found that CHCs not only increased the frequency
 of chemosensory behaviors performed by predatory lizards, but that they
 also elicit feeding‐like behavior from lizards (e.g., biting at the cotton
 swabs). These results indicate that lizards not only respond to arthropod
 CHCs, but that they are sufficient for prey‐recognition by our chosen
 lizard species. This finding lays the groundwork for future studies to
 investigate the precise compounds that are used by foraging lizards, and
 how the chemical communication systems of arthropods respond to selection
 exerted by vertebrate predators.
description: Dataset was collected from cotton swab presentation assays with
 captive wild-caught whiptail lizards at the Southwestern Research Station.
 All units are counts (# of observations during 5min trial) except for
 latencies, which are in seconds. A latency of 300 indicates that the
 behavior was not observed. Latency to escape behavior was not recorded
 during every trial due to human error. to.cue/to.sub/to.air/to.glass
 columns refer to tongue-flick behaviors and specify what the lizard made
 contact with during the behavior. Datasets are already in .csv format and
 ready to be used in the provided R scripts as they are.
DOI: 10.5061/dryad.1vhhmgqs8
title: Data from: Insectivorous bat occupancy is mediated by drought and agricultural land use in a highly modified ecoregion

description: Abstract Aim California’s Central Valley, one of the most productive
 agricultural regions worldwide, is home to a high number of at-risk
 species due to habitat conversion. Amplifying the issue, the Central
 Valley faces severe droughts, creating water scarcity in surrounding
 natural areas. At least 14 insectivorous bat species live in this region,
 and prior studies show mixed results regarding the impact of agriculture
 and drought on bats. The aim of this study was to investigate how bats use
 agricultural areas during drought. Location Central Valley, California,
 United States Methods We deployed ultrasonic acoustic detectors at 274
 sites from March through July of 2016, the final year of an extreme
 drought, and 2017, one of the wettest years on record. We identified bats
 to species, used single-species occupancy models including biologically
 relevant covariates, and created spatial projections of ecoregion-wide
 occupancy for each species. Results We modelled occupancy for eight bat
 species. Long-distance migrants in the study area contracted their
 geographic range during the drought, while resident species did not. Five
 of the eight bats in this analysis were more likely to occupy areas with
 orchard crop cover. Lastly, arid-adapted bats used cultivated landscapes
 during the drought but retracted their range after the drought ended. Main
 Conclusions Migratory bats appeared to shift occupancy more during drought
 than resident bats, possibly because of lower roost fidelity.
 Additionally, the effects of drought on some bat species in the Central
 Valley may be buffered by agricultural landscapes acting as drought
 refugia. Overall, this study demonstrates the benefits of broad-scale
 acoustic studies which can serve as a tool to track changing bat
 distributions on the landscape and provide baseline occupancy for
 acoustically detectable species.
description: We provide the detection histories for 8 bat species at 274 sites
 in the California Central Valley, as well as the covariates and prediciton
 grids that we used to create single species occupancy models. The code
 that uses this data can be found in Appendix S2 in
 https://doi.org/10.1111/ddi.13264.
DOI: 10.5061/dryad.1c59zw3v2
title: Data from: Biocrusts do not differentially influence emergence and early establishment of native and non-native grasses

description: Biological soil crusts (biocrusts) cover the soil surface of global
 drylands and interact with vascular plants. Biocrusts may influence the
 availability and nature of safe sites for plant recruitment and the
 susceptibility of an area to invasion by non-native species. Therefore, to
 investigate the potential role of biocrusts in invasive species
 management, we sought to determine if native and non-native grass
 recruitment in two North American deserts were differentially affected by
 biocrusts. We conducted a series of coordinated experiments in field,
 semi-controlled and controlled environment settings in the Colorado
 Plateau and Sonoran Desert using contrasting biocrust and grass functional
 types. Experiments in field environments focused on early establishment of
 grass seedlings whereas controlled environment experiments focused on
 seedling emergence. Within each experiment, we compared responses
 (frequency, magnitude, and timing of emergence/establishment) both across
 species (biocrust types pooled) and across species and levels of biocrust
 development. Native grasses varied by experiment and included Aristida
 purpurea, A. purpurea var. longiseta, Bouteloua gracilis, and Vulpia
 octoflora. Emergence of non-native Bromus tectorum was similar to that of
 native grasses on the Colorado Plateau. Differences in emergence of native
 vs. non-native grasses in the Sonoran Desert were species- and
 response-specific. Emergence of the non-native Bromus rubens was
 comparable to that of native grasses whereas emergence frequency and
 magnitude of the non-native Pennisetum ciliare was lower compared to two
 of four native species. Within a grass species, emergence was higher and
 faster on bare soil compared to biocrusts in the Sonoran Desert
 semi-controlled and greenhouse environment experiments. However, the
 pattern was not consistent across other experiments. When comparing across
 Colorado Plateau and Sonoran Desert biocrusts in greenhouse experiments,
 we found that emergence of native grasses was higher on Colorado Plateau
 biocrusts. Based on the lack of consistent results across our experiments,
 grass recruitment on biocrusts appears to be driven more by
 species-specific traits than species provenance. Our greenhouse
 experiments suggest that biocrust topographic relief is an important safe
 site trait influencing plant recruitment.
description: Dataset includes four files used in analyses in McIntyre et al.
 2021 and each file contains a ReadMe tab with field
 definitions. <br> FieldData.xlsx contains data from field
 trials. <br> HoopHouseData.xlsx contains data from hoop house
 trials. <br> GreenhouseData.xlsx contains data from greenhouse
 emergence trials, excluding water absorption trials. <br>
 GreenhouseWA.xlsx contains data from water absorption trials.
DOI: 10.5061/dryad.0k6djhb0c
title: Conspecific and congeneric interactions shape increasing rates of breeding dispersal of northern spotted owls

description: Breeding dispersal, the movement from one breeding territory to another,
 is rare for philopatric species that evolved within relatively stable
 environments, such as the old-growth coniferous forests of the Pacific
 Northwest. While dispersal is not inherently maladaptive, the consequences
 of increased dispersal on population dynamics in populations whose
 historical dispersal rates are low could be significant, particularly for
 a declining species. We examined rates and possible causes of breeding
 dispersal based on a sample of 4,118 northern spotted owls (Strix
 occidentalis caurina) monitored in seven study areas over 28 years, 1990
 to 2017, in Oregon and Washington, USA. Using a multistate mark-resight
 analysis, we investigated the potential impacts of an emergent congeneric
 competitor (barred owl Strix varia) and forest alteration (extrinsic
 factors), and social and individual conditions (intrinsic factors) on 408
 successive and 1372 non-successive dispersal events between years. The
 annual probability of breeding dispersal increased for individual owls
 that had also dispersed in the previous year and decreased for owls on
 territories with historically high levels of reproduction. Intrinsic
 factors including pair status, prior reproductive success, and experience
 at a site, were also associated with breeding dispersal movements. The
 percent of monitored owls dispersing each year increased from ~7% early in
 the study to ~25% at the end of the study, which coincided with a rapid
 increase in numbers of invasive and competitively dominant barred owls. We
 suggest that the results presented here can inform spotted owl
 conservation efforts as we identify factors contributing to changing rates
 of demographic parameters including site fidelity and breeding dispersal.
 Our study further shows that increasing rates of breeding dispersal
 associated with population declines contribute to population instability
 and vulnerability of northern spotted owls to extinction, and the
 prognosis is unlikely to change unless active management interventions are
 undertaken.
description: DataS1 contains a csv file (annual observations.csv) with 21175
 annual observations of breeding age northern spotted owls (<i>Strix
 occidentalis occidentalis) </i>on 7 study areas in Oregon and
 Washington monitored between 1990 and 2017. This data was used to generate
 2-state detection histories for all owls that included time-varying
 individual covariates specific to each owl. We did not include
 observations of owls from outside study area boundaries.
DOI: 10.5061/dryad.6hdr7sr0c
title: Quantitative assessment of agricultural sustainability reveals divergent priorities among nations

description: Agriculture is fundamental to all three pillars of sustainability,
 environment, society, and economy. However, the definition of sustainable
 agriculture and capacities to measure it remain elusive. Independent and
 transparent measurements of national sustainability are needed to gauge
 progress, encourage accountability, and inform policy. Here, we developed
 a Sustainable Agriculture Matrix (SAM) to quantify national performance
 indicators in agriculture and to investigate the tradeoffs and synergies
 based on historical data for most countries of the world. The results
 reveal priority areas for improvement by each country and show that the
 trade-offs and synergies among indicators often differ. Exceptions to
 common economic-versus-environmental trade-offs, for example, offer
 opportunities to learn from countries with synergistic pathways for
 multiple sustainability indicators. These SAM indicators will improve as
 data become more available, but this version offers a useful starting
 point for evaluating progress, identifying priorities for improvement, and
 informing national policies and actions towards sustainable agriculture.
description: Please
 see https://github.com/yaoguolin/SustainableAgricultureMatrix for scripts
 that prepare the data.
DOI: 10.5061/dryad.v41ns1rvm
title: Adaptive immune response and resting metabolism are unaffected by manipulation of flight intensity, but negatively related to each other

description: Activation of an immune response (IR) upon exposure to pathogens is
 crucial to ensure adequate organismal performance and is directly linked
 to survival. Fitness benefits of the response may be associated with costs
 in terms of increased energy expenditure and may compete for resources and
 compromise such fitness benefits. Trade-offs between immune function and
 other traits relevant for fitness are well documented, however, it remains
 unknown if such trade-offs are energetically mediated. We manipulated the
 flight activity of 70 zebra finches (Taeniopygia guttata) to investigate
 the energy reallocation to the immune system in rested and exercised
 birds. Four experimental groups exhibiting different flight intensity were
 used: trained, untrained, and birds that either stopped or started flight
 training after the immune challenge. If costs associated with the IR and
 flight activity compete for energy, we predicted the extent of inhibition
 of IR would be dependent on energy allocated to physical activity. Daytime
 resting metabolic rate was measured before and after the immune challenge,
 induced using sheep red blood cells (SRBC). Strength of the response was
 measured as the concentration of anti-SRBC antibodies 6 days
 post-challenge. We found no evidence for the predicted inhibition of the
 immune function between trained and untrained birds, as there was no
 difference in resting metabolic rate between experimental groups. However,
 resting metabolic rate following the challenge was negatively correlated
 with the IR. Surprisingly, individuals with relatively low resting
 metabolic rates following immune challenge were able to up-regulate their
 IR, indicating a trade-off in the use of the energy resource independent
 of flight activity levels. Our results suggest that energy allocation to
 mount the IR may represent a constraint that is possibly linked to the
 circadian pattern of the energy budget but appears to be independent of
 energetic challenges brought on by different levels of flight activity.
description: Please see Materials and Methods section in Bryla et al. 2021
 (DOI: 10.1111/jav.02764)
description: All important information related to this dataset are described
 in "info" spreadsheet of the file.