cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9kd51c5cn
title: Gene copy number is associated with phytochemistry in Cannabis sativa

description: Gene copy number variation is known to be important in nearly every
 species where it has been examined. Alterations in gene copy number may
 provide a fast way of acquiring diversity, allowing rapid adaptation under
 strong selective pressures, and may also be a key component of standing
 genetic variation within species. Cannabis sativa plants produce a
 distinguishing set of secondary metabolites, the cannabinoids, many of
 which have medicinal utility. Two major cannabinoids -THCA and CBDA - are
 products of a three-step biochemical pathway. Using whole genome shotgun
 sequence data for 69 Cannabis cultivars from diverse lineages within the
 species, we found that genes encoding the synthases in this pathway vary
 in copy number. Transcriptome sequence data shows that the cannabinoid
 paralogs are differentially expressed among lineages within the species.
 We also found that copy number partially explains variation in cannabinoid
 content levels among Cannabis plants. Our results demonstrate that
 biosynthetic genes found at multiple points in the pathway could be useful
 for breeding purposes, and suggest that natural and artificial selection
 have shaped copy number variation. Truncations in specific paralogs are
 associated with lack of production of particular cannabinoids, showing how
 phytochemical diversity can evolve through a complex combination of
 processes.
DOI: 10.5061/dryad.fxpnvx0nb
title: Mountain biodiversity and ecosystem functions: Interplay between geology and contemporary environments

description: Although biodiversity and ecosystem functions are strongly shaped by
 contemporary environments such as climate and local biotic and abiotic
 attributes, relatively little is known about how they depend on long-term
 geological processes. Here, along a 3000-m elevational gradient with
 tectonic faults on the Tibetan Plateau, we studied the joint effects of
 geological and contemporary environments on biological communities, such
 as the diversity and community composition of plants and soil bacteria,
 and ecosystem functions. We found that these biological communities and
 ecosystem functions generally show consistent elevational breakpoints at
 2000–2800 m, which coincide with Indus-Yalu suture zone fault and are
 similar to the elevational breakpoints of soil bacteria on another
 mountain range 1000 km away. Mean annual temperature, soil pH and moisture
 were the primary contemporary determinants of biodiversity and ecosystem
 functions, which supports previous findings. However, compared to the
 models excluding geological processes, inclusion of geological effects,
 including parent rock and weathering, increased 67.9% and 35.9% of the
 explained variations in plant and bacterial communities, respectively.
 Such inclusion increased 27.6% of the explained variations in ecosystem
 functions. The geological processes thus provide additional links to
 ecosystem properties, which are prominent but show divergent effects on
 biodiversity and ecosystem functions: parent rock and weathering exert
 considerable direct effects on biodiversity, whereas indirectly influence
 ecosystem functions via interactions with biodiversity and contemporary
 environments. Thus, the integration of geological processes with
 environmental gradients could enhance our understanding of biodiversity
 and, ultimately, ecosystem functioning across different climatic zones.
DOI: 10.5061/dryad.sqv9s4n0h
title: Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice

description: Weedy rice (Oryza sativa f. spontanea) is considered to be a pest in
 modern rice production systems because it competes for resources, has poor
 yield characteristics, and subsequently has a negative effect on rice
 grain yield. The evolutionary relationships among weedy rice, landrace
 rice, improved rice cultivars, and wild rice are largely unknown. In this
 study, we conducted a population genetic analysis based on neutral markers
 and gene haplotypes in 524 rice accessions and a comparative
 transcriptomic analysis using 15 representative samples. The results
 showed that weedy rice populations have the highest level of genetic
 diversity (He=0.8386), and can be divided into two groups (japonica-type
 and indica-type). The japonica-type weedy rice accessions from HLJ, JL,
 LN, and NX provinces clustered with the landraces grown in these same
 provinces. The indica-types from JS province also clustered with the
 indica-type landraces from JS province. Comparative transcriptome analysis
 of weedy rice populations, improved rice populations. and landrace rice
 from HLJ, JL and LN provinces showed that the weedy rice still clustered
 with the landrace rice, and that the improved rice lines comprise a single
 population. Thirty-two differentially expressed genes were shared by the
 improved rice and landrace rice groups as well as between the improved
 rice and weedy rice groups. Using GO analysis, we identified 19 shared GO
 terms in the improved rice and landrace rice groups as well as between the
 improved rice and weedy rice groups. Our results suggest that weedy rice
 populations in China have diverse origins, and comparative transcriptome
 analysis of different types of rice from HLJ, JL, and LN 
 suggests that improved rice populations have become a medium or end point
 in the evolution of weedy rice, which provides a new perspective for the
 study of weedy rice origins and lays a solid foundation for rice breeding.
description: The weedy rice samples
 were collected in improved rice fields, and then were planted and
 depuration in experiment fields in Beijing, The depuration samples have
 the stable phenotype to be used to proceed the
 study.
description: These data is the excel documents, and easy to
 understand. The caption of supplemental
 materials: SFig1 The distribution map of 524
 samples<br> SFig2 The structure plot at the best K value of each
 population. <br> Table S1 All primary data based on SSR
 markers.<br> Table S2a The calculation of the best K value for each
 population<br> Table S2 All SNPs from 15 samples.<br> Table S3
 DEG analysis between weedy rice and landrace rice.<br> Table S4 DEG
 analysis between weedy rice and improved rice.<br> Table S5 DEG
 analysis between landrace rice and improved rice.<br> Table S6
 DEG-Go term analysis between weedy rice and landrace rice. <br>
 Table S7 DEG-Go term analysis between weedy rice and improved
 rice.<br> Table S8 DEG-Go term analysis between landrace rice and
 improved rice.
DOI: 10.5061/dryad.rfj6q576m
title: Data from: Ensemble modelling of the potential distribution of the whale shark in the Atlantic Ocean

description: This dataset reports observations of whale shark (Rhincodon typus) in the
 tropical and subtropical Atlantic Ocean. Data were obtained by the Spanish
 Institute of Oceanography (IEO) observers program, and were rescaled to
 the resolution of the Bio-ORACLE 2.0 variables, against which they were
 modelled along with presences from additional online sources. Our data
 include both presence and surveyed absence records – i.e., places where
 observers were active and did not detect whale sharks – within 5
 arc-minute pixels spanning the surveyed area.
description: The Spanish Institute of Oceanography (IEO) observers
 program places one observer on each of the commercial purse seine vessels
 in the industrial fleet targeting tropical tuna. The observers conduct a
 scientific program under the EU Data Collection Framework, to obtain
 direct information on bycaught species as well as the discards of target
 species. We recorded presence (1) and absence (0) of whale shark in each
 observation. We then rescaled these data to the spatial resolution of the
 Bio-ORACLE 2.0 maps of the predictor variables, using the R ‘raster’
 package. We first selected all pixels with at least one presence, and then
 all remaining pixels with at least one absence point. The dataset thus
 includes only coordinates of surveyed pixels.
description: Notice that the coordinates do not mark all points
 with observations, or the exact locations of these points, but rather the
 centroids of the 5 arc-minute pixels within which we had observation
 data.
DOI: 10.5281/zenodo.18357969
title: Sediment Risk Index (SRI) Stream Crossing Surveys - ARSN

description: The Alabama Rivers and Streams Netowrk (ARSN) Sediment Risk Index (SRI) was developed as a model for prioritizing stream crossings (SCs) in the Choctawhatchee watershed within southeast Alabama from 2006 to 2007.  Over seventy-three variables were collected from SCs including information on waterway conditions, crossing structures, road approaches, and roadside soil erosion features that promote sediment delivery.

These findings were summarized into a 12-metric index (the SRI), modeled after Karr’s Index of Biotic Integrity (IBI) for fish and other assemblages (Karr, 1981).  The goal of condensing SC data into an index was to reduce the time and manpower investment of collecting data.

Each metric of the SRI is standardized with scores 1 (most-impacted), 3 (moderately-impacted), or 5 (least-impacted) (Stewart et al., 2006).  The scores for the 12 metrics are summed into a single SRI value ranging from 12 to 60, which is used for determining site rank and condition.
DOI: 10.5281/zenodo.18357968
title: Sediment Risk Index (SRI) Stream Crossing Surveys - ARSN

description: The Alabama Rivers and Streams Netowrk (ARSN) Sediment Risk Index (SRI) was developed as a model for prioritizing stream crossings (SCs) in the Choctawhatchee watershed within southeast Alabama from 2006 to 2007.  Over seventy-three variables were collected from SCs including information on waterway conditions, crossing structures, road approaches, and roadside soil erosion features that promote sediment delivery.

These findings were summarized into a 12-metric index (the SRI), modeled after Karr’s Index of Biotic Integrity (IBI) for fish and other assemblages (Karr, 1981).  The goal of condensing SC data into an index was to reduce the time and manpower investment of collecting data.

Each metric of the SRI is standardized with scores 1 (most-impacted), 3 (moderately-impacted), or 5 (least-impacted) (Stewart et al., 2006).  The scores for the 12 metrics are summed into a single SRI value ranging from 12 to 60, which is used for determining site rank and condition.
DOI: 10.5061/dryad.8931zcrm0
title: Artificial light at night, in interaction with spring temperature, modulates timing of reproduction in a passerine bird

description: The ecological impact of artificial light at night (ALAN) on phenological
 events such as reproductive timing is increasingly recognized. In birds,
 previous experiments under controlled conditions showed that ALAN strongly
 advances gonadal growth, but effects on egg-laying date are less clear. In
 particular, effects of ALAN on timing of egg-laying are found to be
 year-dependent, suggesting an interaction with climatic conditions such as
 spring temperature, which is known have strong effects on the phenology of
 avian breeding. Thus, we hypothesized that ALAN and temperature interact
 to regulate timing of reproduction in wild birds. Field studies have
 suggested that sources of ALAN rich in short wavelengths can lead to
 stronger advances in egg-laying date. We therefore tested this hypothesis
 in the great tit (Parus major), using a replicated experimental setup
 where eight previously unlit forest transects were illuminated with either
 white, green, or red LED light, or left dark as controls. We measured
 timing of egg-laying for 619 breeding events spread over six consecutive
 years and obtained temperature data for all sites and years. We detected
 overall significantly earlier egg-laying dates in the white and green
 light versus the dark treatment, and similar trends for red light.
 However, there was a strong inter-annual variability in mean egg-laying
 dates in all treatments, which was explained by spring temperature. We did
 not detect any fitness consequence of the changed timing of egg-laying due
 to ALAN, which suggests that advancing reproduction in response to ALAN
 might be adaptive.
description: The dataset was collected in the field by monitor Great tits
 breeding events over 6 consecutive years and in 8 different forest sites
 across the Netherlands. Temperature data was obtained from a published
 dataset (see paper Methods per relevant information).
description: We upload three main scripts with all relevant datasets used
 within them. The three scripts allow to: 1) run
 statistical models and produce figures 1, 2 and 4 - "script for main
 models (figure 1-2-4).R" 2) run statistical models
 and produce figure 3 - "script for models testing temperature and lay
 dates (figure 3).R" 3) run the climwin analysis -
 "script for climwin sliding window.R"
DOI: 10.82294/dvnpllzpp
title: Entrevistas semiestructuradas. Territorio: Cundinamarca. Sector: Cultura. Año: 2025

description: A partir de un proceso de acompañamiento situado, se recopilaron testimonios por medio de entrevistas semiestructuradas durante el año 2025, las cuales indagaron sobre 4 categorías que describían la práctica en educación artística de docentes, cultores, sabedores de la enseñanza del arte, que hacían parte de los programas de formación en educación artística y cultural del sector Cultura (educación informal) en el departamento de Cundinamarca.
DOI: 10.5061/dryad.fbg79cnr4
title: The oxytocin-prostaglandins pathways in the horse (Equus caballus) placenta during pregnancy, physiological parturition, and parturition with fetal membrane retention

description: Despite their importance in mammalian reproduction, substances in the
 oxytocin-prostaglandins pathways have not been investigated in the horse
 placenta during most of pregnancy and parturition. Therefore, we
 quantified placental content of oxytocin (OXT), oxytocin receptor (OXTR),
 and prostaglandin E2 and F2 alpha during days 90–240 of pregnancy (PREG),
 physiological parturition (PHYS), and parturition with fetal membrane
 retention (FMR) in heavy draft horses (PREG = 13, PHYS = 11, FMR = 10). We
 also quantified OXTR and prostaglandin endoperoxide synthase-2 (PTGS2)
 mRNA expression and determined the immunolocalization of OXT, OXTR, and
 PTGS2. For relative quantification of OXT and OXTR, we used western
 blotting with densitometry. To quantify the prostaglandins, we used enzyme
 immunoassays. For relative quantification of OXTR and PTGS2, we used
 RT-qPCR. For immunolocalization of OXT, OXTR, and PTGS2, we used
 immunohistochemistry. We found that OXT was present in cells of the
 allantochorion and endometrium in all groups. PTGS2 expression in the
 allantochorion was 14.7-fold lower in FMR than in PHYS (p = 0.007). These
 results suggest that OXT is synthesized in the horse placenta. As PTGS2
 synthesis is induced by inflammation, they also suggest that FMR in heavy
 draft horses may be associated with dysregulation of inflammatory
 processes.
description: For relative quantification of mRNA, we used RT-qPCR. For
 relative quantification of oxytocin peptide and oxytocin receptor protein,
 we used western blotting with densitometry. To quantify prostaglandin E2
 and PGF<sub>2α</sub> content, we used enzyme
 immunoassays.
description: This
 dataset contains two files (please download both of them):
 -‘Rapacz-Leonard_data.csv’ contains the data -‘Rapacz-Leonard_script.txt’ contains instructions and the script for replicating the statistical analyses  Required packages for R:<br> To use the script in 'Rapacz-Leonard_script.txt' file, you will need to have the following packages installed:<br> - the tidyverse family of packages (can be installed with command install.packages("tidyverse"))<br> - WRS (download the Rallfun file from the author's website, https://dornsife.usc.edu/labs/rwilcox/software/)
DOI: 10.5061/dryad.sxksn02zj
title: Data from: Environmental and spatial effects on coastal stream fishes in the Atlantic rainforest

description: Contemporary and historical factors influence assemblage structure. The
 environmental and spatial influences acting on fish organization of
 rainforest coastal streams in the Atlantic rainforest of Brazil were
 examined. Fish (and functional traits such as morphology, diet, velocity
 preference, body size), environmental variables (pH, water conductivity,
 dissolved oxygen, temperature, stream width, flow, depth, substrate) and
 altitude were measured from 59 stream reaches. Asymmetric eigenvector maps
 were used to model the spatial structure considering direction of fish
 movements. Elevation played an important role – fish abundance, biomass,
 and richness all decrease with increasing elevation. Fish communities are
 influenced by both environmental and spatial factors, but downstream
 movements were shown to be more important in explaining the observed
 spatial variation than were bidirectional and upstream movements. Spatial
 factors, as well as environmental variables influenced by the spatial
 structure, explained most of the variation in fish assemblages. The strong
 spatial structuring is probably attributable to asymmetric dispersal
 limitation along the altitudinal profile: dispersal is likely to be more
 limiting moving upstream than downstream. These fish assemblages reflect
 scale-dependent processes: at the stream reach-scale, fish respond to
 local environmental filters (habitat structure, water chemistry, and food
 supply), which are in turn influenced by a larger scale, namely the
 altitudinal gradient expected in steep coastal mountains. Thus,
 environmental drivers are not independent of spatial factors, and the
 effects of local factors can be confounded across the altitudinal
 gradient. These results may have implications for conservation, because
 downstream reaches are often neglected in management and conservation
 plans.
DOI: 10.5061/dryad.fj6q573qd
title: Repositories for taxonomic data: Where we are and what is missing

description: Natural history collections are leading successful large-scale projects of
 specimen digitization (images, metadata, DNA barcodes), transforming
 taxonomy into a big data science. Yet, little effort has been directed
 towards safeguarding and subsequently mobilizing the considerable amount
 of original data generated during the process of naming 15–20,000 species
 every year. From the perspective of alpha-taxonomists, we provide a review
 of the properties and diversity of taxonomic data, assess their volume and
 use, and establish criteria for optimizing data repositories. We surveyed
 4113 alpha-taxonomic studies in representative journals for 2002, 2010,
 and 2018, and found an increasing yet comparatively limited use of
 molecular data in species diagnosis and description. In 2018, of the 2661
 papers published in specialized taxonomic journals, molecular data were
 widely used in mycology (94%), regularly in vertebrates (53%), but rarely
 in botany (15%) and entomology (10%). Images play an important role in
 taxonomic research on all taxa, with photographs used in &gt;80% and
 drawings in 58% of the surveyed papers. The use of omics (high-throughput)
 approaches or 3D documentation is still rare. Improved archiving
 strategies for metabarcoding consensus reads, genome and transcriptome
 assemblies, and chemical and metabolomic data could help to mobilize the
 wealth of high-throughput data for alpha-taxonomy. Because long term —
 ideally perpetual — data storage is of particular importance for taxonomy,
 energy footprint reduction via less storage-demanding formats is a
 priority if their information content suffices for the purpose of
 taxonomic studies. Whereas taxonomic assignments are quasi-facts for most
 biological disciplines, they remain hypotheses pertaining to evolutionary
 relatedness of individuals for alpha-taxonomy. For this reason, an
 improved re-use of taxonomic data, including machine-learning-based
 species identification and delimitation pipelines, requires a
 cyberspecimen approach—linking data via unique specimen identifiers, and
 thereby making them findable, accessible, interoperable, and reusable for
 taxonomic research. This poses both qualitative challenges to adapt the
 existing infrastructure of data centers to a specimen-centered concept and
 quantitative challenges to host and connect an estimated ≤2 million images
 produced per year by alpha-taxonomic studies, plus many millions of images
 from digitization campaigns. Of the 30–40,000 taxonomists globally, many
 are thought to be non-professionals, and capturing the data for online
 storage and reuse therefore requires low-complexity submission workflows
 and cost-free repository use. Expert taxonomists are the main stakeholders
 able to identify and formalize the needs of the discipline; their
 expertise is needed to implement the envisioned virtual collections of
 cyberspecimens.
DOI: 10.5061/dryad.n02v6wwss
title: Data from: Urbanization and population genetic structure of the Panama City crayfish (Procambarus econfinae)

description: For species with geographically restricted distributions, the impacts of
 habitat loss and fragmentation on long-term persistence may be
 particularly pronounced. We examined the genetic structure of Panama City
 crayfish (PCC), Procambarus econfinae, whose historical distribution is
 limited to an area approximately 145 km2, largely within the limits of
 Panama City and eastern Bay County, Florida, USA. Currently, PCC occupy
 approximately twenty-eight percent of its historical range, with suitable
 habitat composed of fragmented patches in the highly urbanized western
 portion of the range and managed plantations in the more contiguous
 eastern portion of the range. We used 1,640 anonymous single nucleotide
 polymorphisms to evaluate the effects of anthropogenic habitat
 modification on the genetic diversity and population structure of 161 PCC
 sampled from across it known distribution. First, we examined the urban
 habitat patches in the west compared to less-developed habitat patches in
 the east. Second, we used Approximate Bayesian Computation to model
 inferences on the demographic history of eastern and western populations.
 We found anthropogenic habitat modifications explain the genetic structure
 of PCC range-wide. Clustering analyses revealed significant genetic
 structure between and within eastern and western regions. Estimates of
 divergence between east and west were consistent with urban growth in the
 mid-20th Century. PCC have low genetic diversity and high levels of
 inbreeding and relatedness, indicating populations are small and isolated.
 Our results suggest that PCC have been strongly affected by habitat loss
 and fragmentation and management strategies, including legal protection,
 translocations, or reintroductions, may be necessary to ensure long-term
 persistence.
DOI: 10.5061/dryad.zpc866t59
title: Underwater caustics disrupt prey detection by a reef fish

description: Natural habitats contain dynamic elements, such as varying local
 illumination: can such features mitigate the salience of organism
 movement? Dynamic illumination is particularly prevalent in coral reefs,
 where reticulate patterns known as ‘water caustics’ play chaotically in
 the shallows. In behavioural experiments with a wild-caught reef fish, the
 Picasso triggerfish (Rhinecanthus aculeatus), we demonstrate that the
 presence of dynamic water caustics negatively affects the detection of
 moving prey items, as measured by attack latency. Manipulating two
 features of water caustic form (sharpness and scale) implies that the
 masking effect should be most effective in shallow water. Due to the
 direct impact upon foraging efficiency, we expect the presence of water
 caustics to influence decisions about habitat choice and foraging by wild
 prey and predators.