cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.931zcrjqd
title: Evolutionary history of inshore oceanic island land snails diversified in shell colour

description: Aim: Oceanic islands provide an excellent opportunity to study
 the mode and tempo of phenotypic evolution of terrestrial organisms. Many
 studies have focused on oceanic islands far from the mainland. Oceanic
 islands near the mainland may provide distinct perspectives on phenotypic
 evolution, but a comprehensive understanding is still lacking. To address
 this gap, this study aimed to reveal when a land snail species inhabiting
 a volcanic archipelago within 40 km of the mainland diverged and how
 their shell colours evolved. Location: Southern Izu
 Peninsula and five Izu Islands (Oshima, Toshima, Niijima, Shikine, and
 Kozu), Japan. Taxon: Euhadra peliomphala simodae
 Methods: Double-digest restricted-site associated DNA sequencing
 (ddRAD-seq) was conducted using 117 individual snails. Molecular
 phylogenetic and population genomic analyses were performed, including
 Approximation Bayesian computation (ABC). We then examined whether the
 island area, elevation, distance from the surrounding landmasses
 and historical event (bottleneck) explain the shell colour diversity on
 each island using a phylogenetic generalised
 linear mixed model (PGLMM). Results: Snails
 could be genetically categorised according to the island they inhabited,
 and on Niijima, their genetic structure was further divided within the
 island. The divergence times among the extant populations of the snail
 dated back to 2.1 million years ago (Ma), which is older than that of
 other animals occurring in this region. Additionally, island elevation
 positively affected shell colour diversity, and populations with similar
 shell colour profiles were phylogenetically different. Main
 conclusions: Island land snails diversified early in the
 ecosystem of the Izu Islands. This suggests that proximity to the
 mainland, immobility and the physiological
 tolerance of passive dispersal in land snails were the main
 causes of early diversification. Moreover, our study proposes that
 environments covarying with elevation would determine shell colour
 diversity on each island through natural selection.
DOI: 10.5061/dryad.jwstqjqf6
title: Genotyping-by-sequencing data of common quails from the Azores

description: In this study, we focused on common quails (Coturnix coturnix) from the
 Azores archipelago and used morphological, stable isotope, genetic and
 genomic data to characterise this lineage and to assess the divergence
 from neighbouring common quail populations. We detected the presence of a
 large chromosomal inversion that had been already described in other
 populations and we studied its role in this remote archipelago. The
 genotyping-by-sequencing data generated in this project were analysed
 together with those from Sanchez-Donoso et al. 2022
 (https://doi.org/10.1016/j.cub.2021.11.019).  
description: We captured common quail males during the breeding season in
 Spain, Portugal, Morocco, Italy, Netherlands and the Atlantic archipelagos
 of Madeira, Canary Islands and Azores. About 100 µl of blood was extracted
 from each individual from the jugular vein for genomic analyses.
 DNA was extracted by using the DNeasy Blood & Tissue Kit
 of QIAGEN. We built a shotgun genotyping-by-sequencing library from DNA of
 90 common quails from 10 localities, two domestic Japanese quails and
 three hybrids between common and Japanese quails (plus a control) after
 digestion with the restriction enzymeEcoT22I. This library was sequenced
 using Illumina HiSeq 2500 (1x100bp) at Cornell University, Biotechnology
 Resource Center. We called SNPs using the TASSEL-5-GBS
 pipeline52 and mapped them against the Japanese quail genome
 (<em>Coturnix</em> <em>japonica</em>, RefSeq
 assembly accession number: GCF_001577835.2) using bowtie2 v.2.4.1. We
 filtered for biallelic SNPs with minor allele frequency higher than 0.03,
 missing data less than 25% and depth higher than 5 and lower than 100
 using VCFTOOLS v.0.1.13.
DOI: 10.5061/dryad.fqz612jwt
title: Data for: High focus on threatened species and habitats may undermine biodiversity conservation: evidence from the northern Baltic Sea

description: Conservation policies and environmental impact assessments commonly target
 threatened species and habitats. Nevertheless, macroecological research
 provides reasons why also common species should be considered. We
 investigate the consequences of focusing solely on legally protected
 species and habitats in a spatial conservation planning context using a
 comprehensive, benthic marine dataset from the northern Baltic
 Sea. Using spatial prioritization and surrogacy analysis,
 we show that the common approach in conservation planning, where
 legally listed threatened species and habitats are the focus of
 conservation efforts, could lead to poor outcomes for common species (and
 therefore biodiversity as a whole), allowing them to decline in the
 future.  If conservation efforts were aimed solely at threatened
 species, common species would experience a loss of 62% coverage. In
 contrast, if conservation plans were based only on common species,
 threatened species would suffer a loss of 1%. Threatened species are rare
 and their ecological niches distinct, making them poor surrogates for
 biodiversity. The best results are achieved by unified planning for all
 species and habitats. The minimal step towards acknowledging common
 species in conservation planning would be the inclusion of the richness of
 common species, complemented by information on indicator species or
 species of high importance for ecosystem functioning. The trade-off
 between planning for rare and common species should be evaluated, to
 minimize losses to biodiversity.
DOI: 10.5061/dryad.jwstqjqf7
title: Recorded plant sounds from: Sounds emitted by plants under stress are airborne and informative

description: Stressed plants show altered phenotypes, including changes in color,
 smell, and shape. Yet, airborne sounds emitted by stressed plants have not
 been investigated before. Here we show that stressed plants emit airborne
 sounds that can be recorded from a distance and classified. We recorded
 ultrasonic sounds emitted by tomato and tobacco plants inside an acoustic
 chamber, and in a greenhouse, while monitoring the plant’s physiological
 parameters. We developed machine learning models that succeeded in
 identifying the condition of the plants, including dehydration level and
 injury, based solely on the emitted sounds. These informative sounds may
 also be detectable by other organisms. This work opens new avenues for
 understanding plants and their interactions with the environment and may
 have a significant impact on agriculture.
description: Recordings were done in a soundproof acoustic box, and in a
 greenhouse in Tel-Aviv University. Refer to the article ("Sounds
 emitted by plants under stress are airborne and informative") for
 information on how the recordings were done. The WAV
 files in the dataset are 2ms long, recorded at a sampling rate of 500hKz,
 with the peak of the sound in the middle of the recording. Here is a
 general explanation of the directories in the dataset. For further
 understanding of the recording procedure, read the article.
 <strong>Directories in the
 dataset:</strong> <em>Dry
 Tomato</em> - Tomato plants unwatered for 4-6 days, until the soil
 moisture in the pots decreased below 5%. The recording was held in the
 Acoustic Box. <em>Dry Tobacco</em> -
 Tobacco plants unwatered for 4-6 days, until the soil moisture in the
 pots decreased below 5%. The recording was held in the Acoustic
 Box. <em>Cut Tomato</em> - Tomato plants
 with moist soil, cut with scissors close to the ground right before the
 recording started. The severed part of the plant, disconnected from the
 roots, was recorded. The recording was held in the Acoustic
 Box. <em>Cut Tobacco</em> - Tobacco
 plants with moist soil, cut with scissors close to the ground right before
 the recording started. The severed part of the plant, disconnected from
 the roots, was recorded. The recording was held in the Acoustic
 Box. <em>Empty Pot</em> - Sounds
 recorded from empty pots in the Acoustic Box. These sounds are noise
 generated from the microphones themselves, and only recorded on one
 microphone. <em>Greenhouse Noises </em>-
 Sounds recorded from an empty Greenhouse. These sounds are caught in both
 microphones and are created from unknown sources inside and outside of the
 Greenhouse.
description: The files in the dataset are WAV files and can be opened using
 any sound processing program.
DOI: 10.5061/dryad.7wm37pvxt
title: Nimble code and dataset for: Estimating true density in large, alpine herbivores using Google Earth imagery

description: This nimble code will estimate elk density from the count data
 (DO_data_list.RData) and covariates (DO_constants_list.RData). 
 Data and covariates include: a 'y' matrix of double observer
 counts with 3315 rows (1 for each 250 m square plot) and 3 columns for the
 observer 1's exclusive counts, observer 2's exclusive counts,
 and the count of elk detected by both observers. The double-observe
 protocol was only employed in 372 random cells. 'n' is a vector
 of total counts – the total number of uniquely detected elk in each
 plot.  'obs1tot' is a vector of the total count of elk
 by just observer 1, who counted elk in all 3315 cells. There are two dummy
 indicator variables that are all 1's ('obs1constraint' and
 'obs2constraint') to constrain unobserved but estimated counts
 to sum to expected totals. For example, observer 1 was the only observer
 in 2943 plots. This single count would be the equivalent of the sum of the
 exclusive observer 1 counts and the joint observer 1 and 2 counts in a
 double-observer protocol. Additionally, the sum of observer 2s exclusive
 counts and observer 1's total counts must equal the total count of
 unique individuals in a cell. The covariates 'meadow' and
 'deadfall' are the additive log-ratio transformations of the
 proportion of open meadow and burned forest, respectively, in each 250-m
 plot. The 'nonforest' covariate is the number of hectares in
 each plot that was not conifer forest.  'M' is the
 total number of plots. 'firstsearch' is an indicator variable,
 indicating which plots were part of the first search area in the alpine
 &gt;2750 m above sea level. 'domethod' is an indicator
 variable, indicating which plots were searched using the double-observer
 protocol. 
description: Counts and covariates were obtained according to the methods
 outlined in "Estimating true density in large, alpine herbivores
 using Google Earth imagery." by Christianson, David; Winnie, John,
 Wildlife Biology 10.1002/wlb3.01089. The nimble code for the
 double-observer model of counts and model fitting was based partly on
 excerpts from Kery and Royle 2016. Code was adapted to accommodate the
 partial application of double-observer to the study area.
description: This code was built in R version 4.2.2 and nimble version
 0.13.1.
DOI: 10.15468/dl.6a8y8x
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sus cebifrons"
 ]
}

 The dataset includes 69 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003474-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcjjk9
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.33647 48.7553,2.37307 48.7553,2.37307 48.78369,2.33647 48.78369,2.33647 48.7553))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 12 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003479-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b2rbnzskw
title: Target-capture probes for phylogenomics of the Caenogastropoda

description: Target-capture approaches have facilitated a rapid growth in the field of
 phylogenomics but few probe sets exist for mollusks, an exceptionally rich
 phylum with unparalleled ecological and morphological diversity. We
 designed and tested the first universal probe set using Phyluce to capture
 ultraconserved elements (UCEs) and exon loci from the Subclass
 Caenogastropoda – one of six major lineages of gastropods. The probe set
 consists of 29,441 probes (8,872 for UCEs and 20,569 for exons) designed
 to target 1,142 UCE loci and 1,933 exon loci (3,075 total). In silico
 analyses of our probe set yielded an average of 2,110 loci from genomes
 and 1,389 loci from transcriptomes of diverse caenogastropods,
 respectively. After screening these loci to remove those that matched
 multiple contigs, an average of 1,686 loci from genomes and 785 loci from
 transcriptomes were retained. Phylogenetic analyses of the loci extracted
 from transcriptomes produced well-supported trees very similar to those
 published based on transcriptomic analyses. Although there are few
 caenogastropod genomes to analyze, phylogenetic relationships estimated
 from the analysis of loci extracted from genomes recover similar
 phylogenetic relationships and indicate that the loci targeted with this
 probe set are informative for resolving deep phylogenetic relationships.
 An in vitro analysis of the probe set with the Epitoniidae, a diverse
 caenogastropod family of uncertain affinity and with poorly resolved
 evolutionary relationships, recovered an average of 1,710 loci and
 produced a well-resolved phylogeny. Although preliminary, the analysis of
 loci captured by our probe set for a small number of epitoniid taxa
 produced a well-resolved tree indicating that this probe set is also able
 to resolve relationships at shallower hierarchical scales. Together, the
 in silico and in vitro analyses indicate that target-capture enrichment
 with this probe set is a useful tool for reconstructing phylogenetic
 relationships across taxonomic levels and evolutionary time scales.
description: Please see the README document
 ("README_Caenogastropod_probeset.md") and the accompanying
 published article: Goulding, T.C., Strong, E.E., and Quattrini, A. 2023.
 Target-capture probes for phylogenomics of the Caenogastropoda. Molecular
 Ecology Resources. Accepted.
DOI: 10.5281/zenodo.18401581
title: Properties of peat samples collected from Estonian peatlands

description: Properties of peat samples, collected and measured at the University of Tartu. All the samples are taken from peatlands in Estonia. Most of the sampling has been done using the Russian type corer, some surficial samples were cut using a serrated knife. The bulk density, ash content, and humification (as light absorbance at 540 nm) were measured using the laboratory protocol of Chambers et al., 2011. The von Post score and visible botanical components were assessed in the field.
DOI: 10.5281/zenodo.18401582
title: Properties of peat samples collected from Estonian peatlands

description: Properties of peat samples, collected and measured at the University of Tartu. All the samples are taken from peatlands in Estonia. Most of the sampling has been done using the Russian type corer, some surficial samples were cut using a serrated knife. The bulk density, ash content, and humification (as light absorbance at 540 nm) were measured using the laboratory protocol of Chambers et al., 2011. The von Post score and visible botanical components were assessed in the field.
DOI: 10.15468/dl.r4q6xp
title: Occurrence Download

description: A dataset containing 22933 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Occurrence Data of Vascular Plants collected or compiled for the Flora of Bavaria",
 "Geometry POLYGON((9.82611 49.70003,10.09414 49.70003,10.09414 49.85788,9.82611 49.85788,9.82611 49.70003))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1500-2024"
 ]
}

 The dataset includes 22933 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003475-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8tzjnk
title: Occurrence Download

description: A dataset containing 445 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Mongolia)",
 "Geometry POLYGON((38.99608 13.92284,177.00392 13.92284,177.00392 69.07716,38.99608 69.07716,38.99608 13.92284))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Geranium dahuricum"
 ]
}

 The dataset includes 445 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003477-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.18931zd2f
title: Data for: rtrees: An R package to assemble phylogenetic trees from megatrees

description: Despite the increasingly available phylogenetic hypotheses for multiple
 taxonomic groups, most of them do not include all species. In phylogenetic
 ecology, there is still strong demand to have phylogenies with all species
 in a study included. The existing software tools to graft species to
 backbone megatrees, however, are mostly limited to a specific taxonomic
 group such as plants or fishes. Here, I introduce a new user-friendly R
 package `rtrees` that can assemble phylogenies from existing or
 user-provided megatrees. For most common taxonomic groups, users can only
 provide a vector of species' scientific names to get a phylogeny or a
 set of posterior phylogenies from megatrees. It is my hope that `rtrees`
 can provide an easy, flexible, and reliable way to assemble phylogenies
 from megatrees, facilitating the progress of phylogenetic ecology.
DOI: 10.5061/dryad.kh18932bc
title: Erosional exhumation of carbonate rock facilitates dispersal-mediated allopatric speciation in freshwater fishes

description: A fundamental goal of evolutionary biology is to understand the mechanisms
 that generate and maintain biodiversity. Discovery and delimitation of
 species represent essential prerequisites for such investigations. We
 investigate a freshwater fish species complex comprising Etheostoma
 bellator and the endangered E. chermocki which is endemic to the Black
 Warrior River system in Alabama, USA, a global hotspot of temperate
 freshwater biodiversity. Phylogenomic analyses delimit five geographically
 disjunct species masquerading as E. bellator. Three of these new species
 exhibit microendemic distributions comparable to that of E. chermocki
 raising the possibility that they also require protection. The species of
 the complex are found in streams flowing over carbonate rock and they are
 separated by waterways flowing over siliciclastic rock, a geographic
 pattern dictated by the underlying stratigraphy and structural geology.
 Over time, rivers have eroded downward through layers of siliciclastic
 rocks in the basin, gradually exposing underlying carbonate rock, the
 substrate of suitable habitat today. Our results suggest that episodic
 dispersal to patches of suitable habitat set the stage for allopatric
 speciation in the species complex. Our study suggests that the presence of
 heterogeneous rock can facilitate dispersal-mediated allopatric speciation
 in freshwater organisms in the absence of external tectonic or climatic
 perturbations.
DOI: 10.7291/d1m97z
title: Upwelling intensity and source water properties drive high interannual variability of corrosive events in the California Current

description: Ocean acidification is progressing rapidly in the California Current
 System (CCS), a region already susceptible to reduced aragonite saturation
 state due to seasonal coastal upwelling. Results from a high-resolution
 (~ 3 km), coupled physical-biogeochemical model highlight that the
 intensity, duration, and severity of undersaturation events exhibit high
 interannual variability along the central CCS shelfbreak. Variability in
 dissolved inorganic carbon (DIC) along the bottom of the 100-m isobath
 explains 70–90% of event severity variance over the range of latitudes
 where most severe conditions occur. An empirical orthogonal function (EOF)
 analysis further reveals that interannual event variability is explained
 by a combination of coastal upwelling intensity and DIC content in
 upwelled source waters. Simulated regional DIC exhibits low-frequency
 temporal variability resembling that of the Pacific Decadal Oscillation,
 and is explained by changes to water mass composition in the CCS. While
 regional DIC concentrations and upwelling intensity individually explain 9
 and 43% of year-to-year variability in undersaturation event severity,
 their combined influence accounts for 66% of the variance. The mechanistic
 description of exposure to undersaturated conditions presented here
 provides important context for monitoring the progression of ocean
 acidification in the CCS and identifies conditions leading to increased
 vulnerability for ecologically and commercially important species.
description: This dataset is a subset of a coupled
 physical-biogeochemcial model for the central California Current upwelling
 system. The physical model is an implementation of the Regional Ocean
 Modelling System (ROMS; www.myroms.org) coupled to NEMUCSC, a customized
 version of the North Pacific Ecosystem Model for Understanding Regional
 Oceanography (NEMURO). The NEMUCSC biogeochemical model includes three
 limiting macro-nutrients, two phytoplankton functional groups, three
 zooplankton size-classes, three detritus pools, as well as oxygen cycling
 and carbonate chemistry. To better represent the combined effects of
 regional circulation patterns and local upwelling intensity on physical
 and biogeochemical properties, the model downscales a data-assimilative
 physical reanalysis at 1/10° (~10 km) resolution for the broader
 California Current system to a higher 1/30° (~3 km) resolution domain for
 the central California Current region. Ferret V7.1 (http://ferret.pmel.noaa.gov/Ferret) was used to extract a subset of variables along the 100-m isobath and on the 26.0 kg/m3 isopycnal for 1988–2010. The dataset is in NetCDF4 format (CF-1.4 compliant) with metadata describing each variable name and associated units on the native 1/30° ROMS grid.
description: Any software capable of reading
 NetCDF4 format can be used to open the data file. All necessary
 information to use this dataset is contained in the metadata (variable
 name, units, missing value flag, etc).
DOI: 10.15468/dl.5s8qd9
title: Occurrence Download

description: A dataset containing 12193 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.13.12_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (December, January, February)",
 "OccurrenceStatus is Present",
 "Year 2020-2025"
 ]
}

 The dataset includes 12193 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003478-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.