cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dncjsxm3h
title: Data for: Chloride-dependent mechanisms of multimodal sensory discrimination and nociceptive sensitization in Drosophila

description: Individual sensory neurons can be tuned to many stimuli, each driving
 unique, stimulus-relevant behaviors, and the ability of multimodal
 nociceptor neurons to discriminate between potentially harmful and
 innocuous stimuli is broadly important for organismal survival. Moreover,
 disruptions in the capacity to differentiate between noxious and innocuous
 stimuli can result in neuropathic pain. Drosophila larval Class III (CIII)
 neurons are peripheral noxious cold nociceptors and innocuous touch
 mechanosensors; high levels of activation drive cold-evoked contraction
 (CT) behavior, while low levels of activation result in a suite of
 touch-associated behaviors. However, it is unknown what molecular factors
 underlie CIII multimodality. Here, we show that the TMEM16/anoctamins
 subdued and white walker (wwk; CG15270) are required for cold-evoked CT,
 but not for touch-associated behavior, indicating a conserved role for
 anoctamins in nociception. We also evidence that CIII neurons make use of
 atypical depolarizing chloride currents to encode cold, and that
 overexpression of ncc69-a fly homologue of NKCC1-results in phenotypes
 consistent with neuropathic sensitization, including behavioral
 sensitization and neuronal hyperexcitability, making Drosophila CIII
 neurons a candidate system for future studies of the basic mechanisms
 underlying neuropathic pain
description: Please see the README document (README.md) and the accompanying
 published article: Himmel, N.J., Sakurai, A., Patel, A.A., Bhattacharjee,
 S., Letcher, J.M., Benson, M.N., Gray, T.R., Cymbalyuk, G.S. and Cox, D.N.
 2023. Chloride-dependent mechanisms of multimodal sensory discrimination
 and nociceptive sensitization in <em>Drosophila. eLife.
 </em>Accepted: DOI: https://doi.org/10.7554/elife.76863
description: Please see the README document (README.md) and the accompanying
 published article: Himmel, N.J., Sakurai, A., Patel, A.A., Bhattacharjee,
 S., Letcher, J.M., Benson, M.N., Gray, T.R., Cymbalyuk, G.S. and Cox, D.N.
 2023. Chloride-dependent mechanisms of multimodal sensory discrimination
 and nociceptive sensitization in <em>Drosophila. eLife.
 </em>Accepted: DOI: https://doi.org/10.7554/elife.76863
DOI: 10.5061/dryad.ttdz08m2p
title: Data for: Diversity and specialization responses to climate and land use differ between deadwood fungi and bacteria

description: This dataset contains data from a field study conducted in 2019 and
 described in the manuscript "Diversity and specialization responses
 to climate and land use differ between deadwood fungi and bacteria".
 To test the effects of land use and climate on diversity and community
 specialization (H2') of deadwood-inhabiting microbes, we exposed
 branches of four different tree species at 179 study sites, distributed
 over a spatial extent of 300 km x 300 km and 1000 m in elevation. Study
 sites were established in four local land-use types: forests, grasslands,
 arable sites, and settlements, embedded in near-natural, agricultural, or
 urban landscapes. We used negative-binomial generalized linear models for
 diversity and calculated community specialization on host trees by using
 the standardized two-dimensional Shannon entropy (H2') and
 beta-regression models. Our results show that host identity and hence
 specialization strongly exceed the effects of climate and land use for
 fungal but not bacterial communities. This suggests contrasting responses
 between microbial taxa to climate change and land-use intensification with
 further consequences on deadwood diversity interactions and hence
 decomposition processes.
description: We used powdery debris of the exposed branches and assessed OTUs
 via high-throughput sequencing Datasets
 "Bac_wide_plot_final.rda" and
 "ITS_wide_plot_final.rda" contain data at study-plot level in a
 wide format; datasets "longdataBac_objects.rda" and
 "longdataITS_objects.rda" contain data at object-level in a long
 format.
description: Files are saved as .rda and can be opened in R.
DOI: 10.5517/ccdc.csd.cc2pbbm0
title: CCDC 2482592: Experimental Crystal Structure Determination

description: Related Article: Jin jingrong|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.5tb2rbp7j
title: Bats of Bangladesh — A systematic review of the diversity and distribution with recommendations for future research

description: Bangladesh is a South Asian country located at the crossroads of the
 Indochina and Indo-Himalayan subregions, making it a country of rich
 faunal diversity. Bangladesh's high population density paired with
 rapid habitat alteration leaving only 6% of its natural habitats threatens
 its faunal diversity. Over 1,455 bat species live on earth, providing
 immense ecological services to maintain biodiversity. The paucity of bat
 research in Bangladesh and the lack of comprehensive work has led us to
 set the goal of checking how many species are present in Bangladesh, and
 the possibility of bat species yet to have occurred. Here we compiled
 species occurrence data on the bats of Bangladesh and states in
 neighboring countries (India – states are West Bengal, Sikkim, Meghalaya,
 Assam, Tripura, Mizoram; Myanmar – states are Chin, Rakhine) from the
 museums (American Museum of Natural History, Smithsonian National Museum
 of Natural History, Natural History Museum at United Kingdom, Field Museum
 of Natural History, Hungarian Natural History Museum, and Royal Ontario
 Museum), Global Biodiversity Information Facility, and literature, and
 constructed distribution maps for each species. The maps depicted both the
 fine-scale and coarse-scale distribution of the species. We confirmed 31
 species are occurring in Bangladesh – among them, 22 species are confirmed
 with the voucher specimen, 15 species are associated with the preserved
 tissues, and one is confirmed with the morphometric data and key
 characteristics. Based on the species occurrence in the states of India
 and Myanmar, along with the habitat preference, an additional 83 species
 are yet to have occurred in Bangladesh. Among them, 38 species are
 categorized as Highly Probable, 33 species are Probable, and 10 species
 are Possible. We recommend bat surveys are urgent in Bangladesh using all
 complementary capture techniques that will contribute to voucher specimen
 collections and confirm the presence of bats. In addition, echolocation
 calls of bats can help establish call libraries.
DOI: 10.5061/dryad.vhhmgqnxq
title: Insights into natal origins of migratory Nearctic hover flies (Diptera: Syrphidae): New evidence from stable isotope (δ2H) assignment analyses

description: Hover flies (Diptera: Syrphidae) are an important group of insects that
 provide a multitude of key ecosystem services including pollination and
 biological control, yet many of their major life history traits are not
 understood. Some Palearctic hover fly species are known to migrate in
 response to changing seasonal conditions, yet this behavior is almost
 entirely unrecognized in Nearctic species. At least one species, Eupeodes
 americanus (Wiedemann 1830), is partially migratory during autumn while
 Allograpta obliqua may be non-migratory, but it is unknown where these
 insects originate and how far they may travel. We examined natal origins
 of two Nearctic hover fly species, Allograpta obliqua and Eupeodes
 americanus, using stable hydrogen isotope (δ2H) measurements of
 metabolically inactive tissues (wings and legs) to derive a hover fly δ2H
 isoscape. While Allograpta obliqua was mostly of local origin, several
 Eupeodes americanus were sourced from northern latitudes in the Midwestern
 United States and Canada, representing travel distances of up to 3,000 km
 likely using seasonally favorable air currents. This phenomenon is
 expected to have major ecological and economic ramifications, especially
 in the realm of plant pollination ecology and biological control.
description: <em>Allograpta</em> <em>obliqua</em> and
 <em>Eupeodes</em> <em>americanus</em> were
 hand-netted from fall-blooming goldenrod (<em>Solidago</em>
 sp.) and frost aster (<em>Symphyotrichum</em>
 <em>pilosum</em>) during September and October 2019 in North
 Alabama (Limestone County), USA, and areas of southern Alabama in November
 2019. Specimens were also captured in Illinois and their offspring were
 used in a laboratory experiment to produce a δ<sup>2</sup>H
 water to hover fly calibration equation. δ<sup>2</sup>H
 isotopes in precipitation were obtained from the GNIP database (https://nucleus.iaea.org/wiser) and processed using the IsoriX protocol (found here: https://bookdown.org/content/782/introduction.html). GNIP data were used to produce geostatistical models which were then used to build precipitation-weighted isoscapes. Isoscapes were then calibrated using the hover fly calibration experiment data and used to assign natal origins of specimens captured in Alabama.
description: R Studio Version 4.1.1 'IsoriX'
 package, version 0.9.0 'dplyr' package,
 version 1.0.7 'ggplot2' package, version
 3.3.5 'Cairo' package, 1.6-0
 Microsoft Excel or other spreadsheet software
DOI: 10.5061/dryad.80gb5mktv
title: Zoo elephant metagenomic Kraken2 reports

description: Non-invasive biological samples benefit studies that investigate rare,
 elusive, endangered, and/or dangerous species. Integrating genomic
 techniques that use non-invasive biological sampling with advances in
 computational approaches can benefit and inform wildlife conservation and
 management. We use non-invasive fecal DNA samples to generate low- to
 medium-coverage genomes (e.g., &gt;90% of the complete nuclear genome
 at 6 X-fold coverage) and metagenomic sequences, combining widely
 available and accessible DNA collection cards with commonly used DNA
 extraction and library-building approaches. DNA preservation cards are
 easy to transport and can be stored non-refrigerated, avoiding cumbersome
 and/or costly sample methods. The genomic library construction and shotgun
 sequencing approach did not require enrichment or targeted DNA
 amplification. The utility and potential of the generated data generated
 were demonstrated through genome-scale analysis and metagenomics of zoo
 and free-ranging African savanna elephants (Loxodonta africana). Fecal
 samples collected from free-ranging individuals contained an average of
 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these
 elephants with others from the same geographic region was demonstrated by
 principal component analysis of genetic variation using nuclear
 genome-wide SNPs. Metagenomic analyses generated compositional taxon
 classifications that included Loxodonta, green plants, fungi, arthropods,
 bacteria, viruses, and archaea, showcasing the utility of this approach
 for addressing complementary questions based on host-associated DNA, e.g.,
 pathogen and parasite identification. The molecular and bioinformatic
 analyses presented here contribute towards the expansion and application
 of genomic techniques to conservation science and practice.
description: These files contain the Kraken2 output for each of the zoo
 elephants included in the manuscript, "Blending methods for
 non-invasive fecal DNA opens whole genome and metagenomic analyses in
 wildlife biology".
DOI: 10.5061/dryad.00000006j
title: Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection

description: Within-host parasite interactions can be mediated by the host and changes
 in host phenotypes often serve as indicators of the presence or intensity
 of parasite interactions. Parasites like helminths induce a range of
 physiological, morphological, and immunological changes in hosts that can
 drive bottom-up (resource-mediated) or top-down (immune-mediated)
 interactions with co-infecting parasites. Although top-down and bottom-up
 interactions are typically studied in isolation, the diverse phenotypic
 changes induced by parasite infection may serve as a useful tool for
 understanding if, and when, these processes act in concert. Using an
 anthelmintic treatment study of African buffalo (Syncerus caffer), we
 tracked changes in host immunological and morphological phenotypes during
 helminth-coccidia co-infection to investigate their role in driving
 independent and combinatorial bottom-up and top-down parasite
 interactions. We also examined repercussions for host fitness. Clearance
 of a blood-sucking helminth, Haemonchus, from the host gastrointestinal
 tract induced a systemic Th2 immune phenotype, while clearance of a
 tissue-feeding helminth, Cooperia, induced a systemic Th1 phenotype.
 Furthermore, the Haemonchus-associated systemic Th2 immune phenotype drove
 simultaneous top-down and bottom-up effects that increased coccidia
 shedding by changing the immunological and morphological landscapes of the
 intestine. Higher coccidia shedding was associated with lower host body
 condition, a lower chance of pregnancy, and older age at first pregnancy,
 suggesting that coccidia infection imposed significant condition and
 reproductive costs on the host. Our findings suggest that top-down and
 bottom-up interactions may commonly co-occur and that tracking key host
 phenotypes that change in response to infection can help uncover complex
 pathways by which parasites interact.
description: The zip directory (Data.zip) contains data reported in the
 associated publication.
DOI: 10.5061/dryad.v9s4mw70g
title: Quantifying the effects sizes of common controls on methane emissions from an ombrotrophic peat bog

description: Northern wetlands and bogs are a large source of biogenic methane (CH4) to
 the atmosphere and shape climate. There is then substantial interest in
 quantifying the effect sizes of controls on bog CH4 emissions.
 Yet quantification is complicated because wetland emissions are, like the
 controls that regulate them, spatially and temporarily heterogeneous
 within individual wetland systems. To account for this heterogeneity, we
 established 55 measurement plots in a sampling design that had extensive
 spatial, and repeated temporal, coverage over one ombrotrophic bog. This
 coverage allowed us to robustly estimate the effect sizes of known
 environmental controls on CH4 emissions such as temperature,
 water table depth (WTD), and plant functional composition. As expected,
 89% of the cumulative measured flux came from 16% of the plots, with
 consistently high CH4 emissions over two consecutive growing
 seasons. Soil temperature exhibited the strongest control on emissions,
 while WTD and vegetation composition had much smaller relative effects
 compared to temperature. Interestingly, at high temperatures, WTD was a
 strong determinant of whether a plot had high vs. lower emissions. Despite
 temperature’s large effect size, the controls we measured only explained
 ~29% of the variance in CH4 fluxes. Overall, our data confirm
 observations from other wetlands that CH4 emissions are highly
 variable at local scales, and yet our data also reveal that effect sizes
 can be quantified robustly within this heterogeneity. Highly-replicated,
 local designs may therefore be useful for generating data that can serve
 to help refine wetland CH4 emissions uncertainties.
description: This dataset is comprised of three tabs in an Excel file. The
 “metadata tab contains information about the variables measured. The “GHG
 flux data” tab contains daily CH<sub>4</sub> and
 CO<sub>2</sub> flux information and environmental variables
 measured simultaneously to flux measurements. The “Plot vegetation data”
 tab has percent cover data for each subplot in the experiment.
 The code file is named ‘TayloretalJGRBCode.txt’ and contains all
 R (the statistical freeware package) code used for data analysis in the
 manuscript. Analytical steps are explained ahead of each section of code
 within the code file.
DOI: 10.5061/dryad.bcc2fqzgx
title: Sweepstakes reproductive success via pervasive and recurrent selective sweeps

description: Highly fecund natural populations characterized by high early mortality
 abound, yet our knowledge about their recruitment dynamics is somewhat
 rudimentary. This knowledge gap has implications for our understanding of
 genetic variation, population connectivity, local adaptation, and the
 resilience of highly fecund populations. The concept of sweepstakes
 reproductive success, which posits a considerable variance and skew in
 individual reproductive output, is key to understanding the distribution
 of individual reproductive success. However, it still needs to be
 determined whether highly fecund organisms reproduce through sweepstakes
 and, if they do, the relative roles of neutral and selective sweepstakes.
 Here we use coalescent-based statistical analysis of population genomic
 data to show that selective sweepstakes likely explain recruitment
 dynamics in the highly fecund Atlantic cod. We show that the Kingman
 coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling
 random sweepstakes), including complex demography and background
 selection, do not provide an adequate fit for the data. The
 Durrett-Schweinsberg coalescent, in which selective sweepstakes result
 from recurrent and pervasive selective sweeps of new mutations, offers
 greater explanatory power. Our results show that models of sweepstakes
 reproduction and multiple-merger coalescents are relevant and necessary
 for understanding genetic diversity in highly fecund natural populations.
 These findings have fundamental implications for understanding the
 recruitment variation of fish stocks and general evolutionary genomics of
 high-fecundity organisms.
description: The data described in Árnason et al. 2023 are unfolded site
 frequency spectra of two populations of Atlantic cod (<em>Gadus
 morhua</em>) from Iceland. The site frequency spectra are estimated
 from whole-genome sequence results using ANGSD (Korneliussen et. al 2014).
 The estimation uses genotype likelihood (Samtools likelihood, gl1, and
 GATK likelihood, gl2) and returns 100 bootstrap estimates. An estimate is
 provided for each of the 23 chromosomes. Pacific cod (<em>G.
 macrocephalus</em>) was used as an outgroup to polarize the
 variation at sites. Reference
 Árnason E, Koskela J, Halldórsdóttir K, and Eldon B. 2023.
 Sweepstakes reproductive success via pervasive and recurrent selective
 sweeps. eLife 2023;12:e80781. DOI:
 https://doi.org/10.7554/eLife.80781. Korneliussen TS,
 Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing
 Data. BMC Bioinformatics. 2014 nov; 15(1).
 http://dx.doi.org/10.1186/s12859-014-0356-4, doi:
 10.1186/s12859-014-0356-4.
description: The data are presented as zipped archives of plain text files of
 site frequency spectrum and 100 bootstrap values for each chromosome and
 both likelihoods. The data are readable, for example, with R.
DOI: 10.5061/dryad.5dv41ns92
title: Species interactions and diversity: a unified framework using Hill numbers

description: Biodiversity describes the variety of organisms on planet earth.
 Ecologists have long hoped for a synthesis between analyses of
 biodiversity and analyses of biotic interactions among species, such as
 predation, competition, and mutualism. However, it is often unclear how to
 connect details of these interactions with complex modern analyses of
 biodiversity. To resolve this gap, we propose a unification of models of
 biotic interactions and measurements of diversity. We show that analyses
 of biodiversity obscure details about biotic interactions. For example,
 identical changes in biodiversity can arise from predation, competition or
 mutualism. Our approach indicates that traditional models of community
 assembly miss key facets of diversity change. Instead, we suggest that
 analyses of diversity change should focus on partitions, which measure
 mechanisms that directly shape changes in diversity, notably species level
 selection and immigration, rather than traditional analyses of biotic
 interactions.
description: The code is used to generate the figures presented in the paper,
 including a re-analysis of a previously published dataset concerning
 competiton among fruitflies.
DOI: 10.5061/dryad.2fqz612sp
title: Species list of vascular plants observed on Peberholm 1999–2020

description: Peberholm is a constructed Danish island in the Øresund strait. It was
 primarily constructed by calcareous clay from the seafloor and is
 traversed by a highway and a railway. Being constructed from material
 without a seed bank, Peberholm constituted a good opportunity to study
 primary succession in an anthropogenic context. In this study, data from a
 survey of the vascular plant community of Peberholm was studied. The data
 span a 22-year period, between 1999 and 2020. The development of the flora
 was analysed with regards to indicators for environmental factors and
 vegetation types, as well as occurrence of alien species or species of
 conservation concern. Peberholm experienced a rapid succession during its
 first 5 years. The effects of the initial ground disturbance quickly wore
 off, resulting in a relative decline in plant communities associated with
 ruderal land. These highly anthropogenic habitats were replaced with
 grasslands. The shrubification also began early on. The rapid initial
 changes were then replaced with a much slower but also more continuous
 change, resulting in the development of both more natural grasslands and
 an increased shrubification. Although several rare or threatened species
 colonized Peberholm from the beginning, the conservation value of the
 flora on a whole increased during the succession process of forming more
 natural vegetation types. The succession process demonstrated at Peberholm
 has more in common with the succession at urban soils than with naturally
 occurring primary succession.
description: The survey of Peberholm was
 arranged by Lund Botanical Society and conducted by yearly visits to the
 island, usually five times each year during the main plant season between
 May and September. Usually, each visit lasted a full workday with 3–5
 experienced botanists partaking. Bengt Örneberg initiated the study and
 took part during the entire period; Staffan Nilsson was responsible for
 the project 2013–2020. Each year, the island was systematically monitored
 for vascular plants, resulting in a species list indicating presence and
 absence for each taxon. For most taxa, voucher specimens have been
 collected and examined at Lund Botanical Museum. Over the years, several
 subspecies and hybrids have been registered. However, many of these have
 not been treated consistently over the years and they are thus excluded
 from this analysis.