cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7m0cfz2g
title: Macroevolution of sexually selected weapons: weapon evolution in chameleons

description: Abstract The evolution of sexually selected traits is a major topic in
 evolutionary biology. However, large-scale evolutionary patterns in these
 traits remain understudied, especially those traits used in male–male
 competition (weapons sensu lato). Here, we analyze weapon evolution in
 chamaeleonid lizards, both within and between the sexes. Chameleons are an
 outstanding model system because of their morphological diversity
 (including 11 weapon types among ~220 species) and a large-scale
 time-calibrated phylogeny. We analyze these 11 traits among 165 species
 using phylogenetic methods, addressing many questions for the first time
 in any group. We find that all 11 weapons have each evolved multiple times
 and that weapon origins are generally more frequent than their losses. We
 find that almost all weapons have each persisted for &gt;30
 million years (and some for &gt;65 million years). Across
 chameleon phylogeny, we identify both hotspots for weapon evolution (up to
 10 types present per species) and coldspots (all weapons absent, many
 through loss). These hotspots are significantly associated with larger
 male body size, but are only weakly related to sexual-size dimorphism. We
 also find that weapon evolution is strongly correlated between males and
 females. Overall, these results provide a baseline for understanding
 large-scale patterns of weapon evolution within clades.
DOI: 10.15468/dl.vyxj3g
title: Occurrence Download

description: A dataset containing 4662088 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta",
 "Year 1981-2023"
 ]
}

 The dataset includes 4662088 records from 928 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0125725-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dz08kps34
title: Data for: Lipid biomarkers recording marine microbial community structure changes through the Frasnian‐Famennian mass extinction event

description: This dataset contains data for a research article published on Geobiology.
 The article is entitled " Lipid biomarkers recording marine microbial
 community structure changes through the Frasnian‐Famennian mass extinction
 event". This study aims to reconstruct changes in the marine
 microbial community structure through the Late Devonian Frasnian‐Famennian
 (F‐F) transition. We performed a multiproxy investigation on a drill core
 of the Upper Devonian New Albany Shale from the Illinois Basin (western
 Kentucky, USA). Detailed information regarding the data collection,
 analysis, and interpretation can be found in the following paper: Chen J.,
 Hogancamp N., Lu M., Ikejiri T., Malina N., Ojeda A., Sun Y., Lu Y. 2023.
 Lipid Biomarkers Recording Marine Microbial Community Structure Changes
 Through the Frasnian‐Famennian Mass Extinction Event. Geobiology
 https://doi.org/10.1111/gbi.12568
description: In May 2019, 61 rock samples
 were collected from the T-6590 drill core of the Upper Devonian New Albany
 Shale curated at the Kentucky Geological Survey. The drill core was
 recovered from well SA-005, McLean County, western Kentucky (N 37.42°, W
 87.28°) by the CNX Gas Company, LLC. Sampling interval is about 1 m. From
 June 2019 to March 2021, element, biomarker, and Tmax data collection was
 performed at the University of Alabama, Zhejiang University, and Source
 Rock Lab, GeoMark Research Inc. From May 2022 to June 2022,
 compound-specific isotope data were collected at the Auburn
 University.
DOI: 10.5517/ccdc.csd.cc2kxz6p
title: CCDC 2381333: Experimental Crystal Structure Determination

description: Related Article: Hongrui Zheng, Qingqing Wang, Xinchao Wang, Fei Wang, Shangda Li, Jian Zhang|2025|Sci.China.Chem.|68|3064|doi:10.1007/s11426-024-2442-0
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.bg79cnpgb
title: Changes in the acoustic structure of Australian bird communities along a habitat complexity gradient

description: Avian vocalizations have evolved in response to a variety of abiotic and
 biotic selective pressures. While there is some support for signal
 convergence in similar habitats that is attributed to adaptation to the
 acoustic properties of the environment (the ‘acoustic adaptation
 hypothesis’, AAH), there is also evidence for character displacement as a
 result of competition for signal space among coexisting species (the
 ‘acoustic niche partitioning hypothesis’). We explored the acoustic space
 of avian assemblages distributed along six different habitat types (from
 herbaceous habitats to warm rainforests) in southeastern Queensland,
 Australia. We employed three acoustic diversity indices (acoustic
 richness, evenness, and divergence) to characterize the signal space. In
 addition, we quantified the phylogenetic and morphological structure (in
 terms of both body mass and beak size) of each community. Acoustic
 parameters showed a moderately low phylogenetic signal, indicating labile
 evolution. Although, we did not find meaningful differences in acoustic
 diversity indices among habitat categories, there was a
 significant relationship between the regularity component (evenness) and
 vegetation height indicating that acoustic signals are more evenly
 distributed in dense habitats. After accounting for differences in species
 richness, the volume of acoustic space (i.e., acoustic richness) decreased
 as the level of phylogenetic and morphological resemblance among species
 in a given community increased. Additionally, we found a significantly
 negative relationship between acoustic divergence and divergence in body
 mass indicating that the less different species are in their body mass,
 the more different their songs are likely to be. This implies the
 existence of acoustic niche partitioning at the community level. Overall,
 while we found mixed support for the AAH, our results suggest that
 community-level effects may play a role in structuring acoustic signals
 within avian communities in this region. This study shows that
 signal diversity estimated by diversity metrics of community ecology based
 on basic acoustic parameters can provide additional insight into the
 structure of animal vocalizations.
DOI: 10.5061/dryad.zgmsbcchs
title: Data from: Tool use increases mechanical foraging success and tooth health in southern sea otters (Enhydra lutris nereis)

description: Although it is well documented that tool use can enable the utilization of
 novel resources, the fitness benefits associated with this innovative
 behavior are difficult to test. Using longitudinal data from 196
 radio-tagged southern sea otters, we found that individuals, particularly
 females, with frequent tool use gained access to harder, larger prey
 items. In turn, the mechanical advantages of tool use during food
 processing translated to reduced tooth damage in tool users. We also found
 that tool use diminishes trade-offs between access to different prey
 types, tooth health, and caloric intake that are highly dependent on the
 relative availability of prey in the environment. Overall, tool use allows
 individuals to maintain caloric requirements through the processing of
 alternative prey that are otherwise inaccessible without the use of tools,
 indicating that this innovative behavior is a necessity for the survival
 of southern sea otters in environments with depleted preferred prey.
description: # Tool use increases mechanical foraging success and tooth health in
 southern sea otters (Enhydra lutris nereis)
 [https://doi.org/10.5061/dryad.zgmsbcchs](https://doi.org/10.5061/dryad.zgmsbcchs) ## Description of the data and file structure **dat.Rdata** contains a dataframe "dat" with the follow variables: * otter = individual otter ID * PDE = percent dentine exposure * study = study area * area = study area * hardness = mean prey hardness index of otter (Newton) * sex = sex of individual: F - female; M - male * ageclass = age class of individual: A - adult, J - subadult, AA - aged adult * prey = prey specialization of otter * tool_use = tool use frequency (%) * age = estimated age of otter (years) * mass = body mass of otter (kg) * length = body length of otter (cm) * urchin_num = total number of urchins consumed by otter * crab_num = total number of crabs consumed by otter * mussel_num = total number of mussels consumed by otter * clam_num = total number of crabs consumed by otter * snail_num = total number of snails consumed by otter * abalone_num = total number of abalone consumed by otter * Eintake = caloric intake rate (kcal/min) * Epreycalc = total calories consumed (kcal) * urchin_Nlg = number of large urchins consumed by otter * crab_Nlg = number of large crabs consumed by otter * mussel_Nlg = number of large mussels consumed by otter * clam_Nlg = number of large crabs consumed by otter * snail_Nlg = number of large snails consumed by otter * dietT = prey specialization of otter * lg_Tool = 1 + natural log of tool_use * lg_Tool2 = natural log of Tool^2 * BCI = body mass residuals of each otter * LGI = body length residuals of each otter * size = BCI/5 Model_Terms_LooicWts.xlsx contains a spreadsheet that identifies model terms (used in **2SummarizeAnalyses.R**) ## Code/Software **1AnalyzeData.R** = contains R scripts needed to run models **2SummarizeAnalyses.R** = contains R scripts to summarize data and make plots
DOI: 10.5061/dryad.jq2bvq8fg
title: Data for: Superconductivity in twisted double bilayer graphene stabilized by WSe₂

description: Identifying the essential components of superconductivity in
 graphene-based systems remains a critical problem in 2D materials
 research, connecting this field to the mysteries that underpin
 investigations of unconventional superconductivity throughout
 condensed-matter physics. Superconductivity has been previously observed
 in magic-angle twisted stacks of monolayer graphene but conspicuously not
 in twisted stacks of bilayer graphene, although both systems host
 topological flat bands and symmetry-broken states. Here, we report the
 discovery of superconductivity in twisted double bilayer graphene (TDBG)
 in proximity to WSe2. Samples with twist angles 1.24 and 1.37 degrees
 superconduct in small pockets of the gate-tuned phase diagram within the
 valence and conduction band, respectively. Superconductivity emerges from
 unpolarized phases near van Hove singularities and next to regions with
 broken isospin symmetry, showing the correlation between a high density of
 states and the emergence of superconductivity in TDBG while revealing a
 possible role for isospin fluctuations in the pairing.
DOI: 10.5061/dryad.rbnzs7hhg
title: The raw data of transcriptomes in whole brains when EcR-A was knocked down in pC1 neurons or not

description: The establishment of neural circuits for female sexual receptivity is
 essential to reproduction, but the underlying mechanism of associated
 neurodevelopment is still not fully understood. Here we found that
 neuropeptide prothoracicotropic hormone (PTTH), hormone of the PG axis,
 regulates virgin female receptivity through ecdysone in Drosophila
 melanogaster. PTTH-positive PG neurons are doublesex-expressing neurons,
 they regulate virgin female receptivity before the metamorphosis during
 the 3rd-instar larval stage. Furthermore, the genetic knocking down of
 ecdysone receptor EcR-A in pC1 neurons regulates the morphological
 development of pC1 neurons and further the virgin female copulation rate.
 However, the activity of pC1 neurons did not change, suggesting the
 changes of synaptic connection between pC1 neurons and other neurons.
 Analysis of brain transcriptomes when EcR-A was knocked down in pC1
 neurons reveals that additional genes are regulated downstream of EcR-A in
 pC1 neurons. Our work suggests a mechanism underlying how the
 neurodevelopment of neural circuits regulates virgin female receptivity in
 adults.
DOI: 10.15468/dl.ju32yp
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Material citation, Specimen, Human Observation, Machine Observation, Observation, Fossil, Living Specimen, Occurrence evidence)",
 "Country is Bolivia (Plurinational State of)",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Tremarctos ornatus, Lamellomphalus)",
 "Year 2000-2026"
 ]
}

 The dataset includes 10 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003569-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qv9s4mwm3
title: Phenotype images of the developing heart from wild type and Sox7 mutant mouse embryo

description: The cardiac endothelium influences ventricular chamber development by
 coordinating trabeculation and compaction. However, the
 endothelial-specific molecular mechanisms mediating this coordination are
 not fully understood. Here, we identified the Sox7 transcription factor as
 a critical cue instructing cardiac endothelium identity during ventricular
 chamber development. Endothelial-specific loss of Sox7 function in mice
 results in cardiac ventricular defects similar to non-compaction
 cardiomyopathy, with a change in the proportions of trabecular and compact
 cardiomyocytes in the mutant hearts. This phenotype is paralleled by
 abnormal coronary artery formation. Loss of Sox7 function disrupts the
 transcriptional regulation of the Notch pathway and connexins 37 and 40,
 which govern coronary arterial specification. Upon Sox7
 endothelial-specific deletion, single-nuclei transcriptomics analysis
 identified the depletion of a subset of Sox9/Gpc3 positive endocardial
 progenitor cells and an increase in erythro-myeloid cell lineages. Fate
 mapping analysis revealed that a subset of Sox7-null endothelial cells
 transdifferentiate into hematopoietic but not cardiomyocyte lineages. Our
 findings determine that Sox7 maintains cardiac endothelial cell identity,
 which is crucial to the cellular cross-talk that drives ventricular
 compaction and coronary artery development.
description: Images were captured on a confocal microscope after heart tissue
 sections or whole embryonic hearts were labeled by immunufluorescence
 and/or single molecule FISH.   No processing was
 applied to the raw files, these files corresponds to the original files
 directly taken from the samples.
description: All files can be open using the open source software FIJI.
DOI: 10.5061/dryad.t4b8gtj71
title: Data from: Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application

description: Fumigants and fungicides are effective at controlling soil-borne pathogens
 but might also adversely affect soil beneficial microbes, such as soil
 phosphorus (P) solubilizing microbes, further altering nutrient cycling
 processes. Therefore, this study investigated the effects of the fumigant
 chloropicrin (CP) and the fungicide azoxystrobin (AZO) on soil
 microeukaryotes and P-cycling related soil bacteria through a greenhouse
 experiment. Soil microeukaryotic communities and bacterial communities
 containing two phosphomonoesterase encoding genes
 (phoC and phoD) were analysed using high-throughput
 sequencing methods. Results showed that, when applied at the field
 recommended application dosage, the fungicide AZO had no significant
 influence on the community structure of soil microeukaryotes
 and phoD-containing bacteria. However, in CP-fumigated soils, the
 soil microeukaryotic community composition changed from fungi-dominated to
 protist-dominated. CP fumigation significantly decreased the
 total phoC/phoD gene copy number but increased the
 relative abundance of some phoC/phoD-containing bacteria (such
 as Sinorhizobium and Streptomyces), which are
 significantly positively correlated to available P compositions in soil.
 The structural equation model (SEM) confirmed that CP fumigation could
 affect soil available P content directly by
 altering phoC-/phoD-containing bacteria, or indirectly by
 affecting phoC/phoD gene abundance and acid/alkaline
 phosphatases activity in soil. The inconsistent changes
 in phoC/phoD-containing bacteria, phoC/phoD gene number,
 and the phosphomonoesterase activities indicated that enzyme secretion may
 not be the only way for P solubilizing soil microorganisms to regulate P
 availability after soil fumigation. The outcome of this study can provide
 theoretical support for the design of soil beneficial microorganism
 recovery strategies and the regulation of phosphate fertilizer after soil
 fumigation.
description: Methods for dataset collection and process can be found in the
 publication: Wang, Y., Yang, X., Harkes, P., van Steenbrugge, J. J., Xu,
 M., & Geissen, V. (2024). Soil microeukaryotic communities and
 phosphorus-cycling microorganisms respond to chloropicrin fumigation and
 azoxystrobin application. <em>Science of The Total
 Environment</em>, 172871.
description: # Data from: Soil microeukaryotic communities and phosphorus-cycling
 microorganisms respond to chloropicrin fumigation and azoxystrobin
 application We uploaded all the original OTU data for soil microeukaryotes
 and phoC-/phoD-containing bacteria, as well as the gene copy number of
 phoC and phoD genes. All of our analyses and figures were based on **these
 two tables (CSV files)**. The analysis methods and software can be found
 in our publication. The script for the R code can be accessed on request.
DOI: 10.15139/s3/qrxu7n
title: Data Management and Sharing Plan for: The Role of C1-Metabolism in the Estuarine Carbon Cycle: A Microbe to Ecosystem Study

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.vq83bk3zm
title: Not only hedgerows, but also flower fields can enhance bat activity in intensively used agricultural landscapes

description: Agri-environment schemes (AES) have become important tools for farmland
 biodiversity conservation, providing suitable habitats, resources, and
 connectivity within agricultural landscapes. Bats are rarely studied in
 relation to AES effectiveness in contrast to birds, even though their
 presence and activity as biological control agents on insects, especially
 pest species, can be important for agricultural crops. While the role of
 hedgerows for bat occurrence and activity, as well as for their
 prey's diversity and abundance has been widely studied, the role of
 other AESs such as flower fields remains unclear. We monitored the
 activity of the main functional groups (edge, narrow and open space
 foragers) using ultrasound recorders, as well as potential prey abundances
 using light traps, across 35 study sites representing different AES in
 Central Germany from late July to September 2018. The sampled AES
 consisted of annual flower fields, mixed flower fields (with annual and
 biennial vegetation), perennial flower fields (sown every 5 years),
 hedgerows (surrounded by meadows and agricultural fields), and were
 compared to winter wheat (control) in a balanced design. Bat activity over
 hedgerows increased threefold for edge space foragers and sevenfold for
 narrow space foragers compared to wheat fields. Compared to wheat fields,
 narrow space forager activity increased fourfold over perennial flower
 fields, threefold over annual and twofold over mixed flower fields. This
 group's activity over hedgerows also increased almost threefold
 compared to mixed flower fields. However, the number of feeding buzzes and
 prey abundance did not differ significantly between AES. We detected
 foraging group-specific differences in bat activity between the studied
 AES. Thus, to promote bats in agricultural landscapes and to ensure their
 biological control services, it is important to establish more AES, such
 as hedgerows and flower fields, to increase their diversity and
 connectivity in intensively used agricultural landscapes.
description: Bats were recorded with ultrasound recorders (Song Meter SM2Bat +
 model, Wildlife Acoustics, Inc.) Potential insect prey
 was collected using light traps, each lamp possessed four small LED
 lights: green, blue and two UV (ELEKON AG, 2018), with wavelengths of
 λ<sub>max</sub> ∼530 nm, 465 nm, 340 nm, and 348 nm, and a
 total illuminance of 5 lx, powered by two AA NiMH batteries (Villarroya-Villalba <em>et al.,</em> 2021). We used QGIS 3.6 (Development Team, 2019) and information obtained from land use maps (SLA, 2018) to digitise agricultural fields and landscape elements based on satellite images (Map data ©2019 Google based on GoogleSatellite plugin). All statistical analyses were conducted in R 3.6.0 (R Development Core Team, 2019). 
description: The datasets are in .csv format, which open in the R Software (R
 Development Core Team, 2019).
DOI: 10.5061/dryad.wpzgmsbt0
title: Can cryptic female choice prevent invasive hybridization in external fertilizing fish?

description: Polyandrous mating systems result in females mating with multiple males,
 generating opportunities for strong pre-mating and post-mating sexual
 selection. Polyandry also creates the potential for unintended matings and
 subsequent sperm competition with hybridizing species. Cryptic female
 choice allows females to bias paternity towards preferred males under
 sperm competition and may include conspecific sperm preference when under
 hybridization risk. The potential for hybridization becomes particularly
 important in context of invasive species that can novelly hybridize with
 natives, and by definition, have evolved allopatrically. We provide the
 first examination of conspecific sperm preference in a system of three
 species with the potential to hybridize: North American native Atlantic
 salmon (Salmo salar) and brook char (Salvelinus fontinalis), and invasive
 brown trout (Salmo trutta) from Europe. Using naturalized populations on
 the island of Newfoundland, we measured changes in sperm swimming
 performance, a known predictor of paternity, to determine the degree of
 modification in sperm swimming to female cues related to conspecific sperm
 preference. Compared to water alone, female ovarian fluid, in general, had
 a pronounced effect and changed sperm motility (by a mean of 53%) and
 swimming velocity (mean 30%), but not linearity (mean 6%). However,
 patterns in the degree of modification suggest there is no conspecific
 sperm preference in the North American populations. Furthermore, female
 cues from both native species tended to boost the sperm of invasive males
 more than their own. We conclude that cryptic female choice via ovarian
 fluid mediated sperm swimming modification is too weak in this system to
 prevent invasive hybridization and is likely insufficient to promote or
 maintain reproductive isolation among the native North American species.