cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfjfd
title: Data and R code used for the GLMM and NBDA analyses in 'Captive Asian short-clawed otters (Aonyx cinereus) learn to exploit unfamiliar natural prey'

description: Foraging plays a vital role in animal life histories, learning whether
 unfamiliar food items are palatable is a key part of this process. Animals
 that engage in extractive foraging must also learn how to overcome the
 protective measures of their prey. While otters (subfamily Lutrinae) are a
 taxon known for their extractive foraging behaviour, how they learn about
 prey palatability and acquire extractive foraging techniques remains
 poorly understood. Here we investigated: (i) how captive Asian
 short-clawed otters (Aonyx cinereus) learned to interact with, and extract
 meat from, unfamiliar natural prey, and (ii) how their exploitation of
 such prey compared to their ability to overcome artificial foraging tasks
 containing familiar food rewards. Network-based diffusion analysis showed
 that otters learned to interact with unfamiliar natural prey by observing
 their group mates. However, once interacting with the prey, they learned
 to extract the meat mainly asocially. In addition, otters took longer to
 overcome the protective measures of unfamiliar natural prey than those of
 extractive food puzzles. Asian short-clawed otter populations are
 declining in the wild. Increasing our understanding of how they learn to
 overcome novel foraging challenges could help develop pre-release training
 procedures as part of reintroduction programmes for otter conservation.
description: See section 2 in main text of 'Captive Asian short-clawed
 otters (Aonyx cinereus) learn to exploit unfamiliar natural prey' for
 detailed decription of data collection proceedures.
DOI: 10.5061/dryad.ncjsxksxg
title: Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load

description: The evolution of costly traits like deer antlers and peacock trains, which
 drove the formation of Darwinian sexual selection theory, has been
 hypothesised to both reflect and affect patterns of genetic variance
 across the genome, but direct tests are missing. Here, we used an evolve
 and re-sequence approach to reveal patterns of genome-wide diversity
 associated with the expression of a sexually-selected weapon that is
 dimorphic among males of the bulb mite, Rhizoglyphus robini. Populations
 selected for the weapon showed reduced genome-wide diversity compared to
 populations selected against the weapon, particularly in terms of the
 number of segregating non-synonymous positions, indicating enhanced
 purifying selection. This increased purifying selection reduced inbreeding
 depression, but outbred female fitness did not improve, possibly because
 any benefits were offset by increased sexual antagonism. The majority of
 single nucleotide polymorphisms (SNPs) that consistently diverged in
 response to selection were initially rare and overrepresented in exons,
 and enriched in regions under balancing or relaxed selection, suggesting
 they are likely moderately deleterious variants. These diverged SNPs were
 scattered across the genome, further demonstrating that selection for or
 against the weapon and the associated changes to the mating system can
 both capture and influence genome-wide variation. 
description: Experiemntal evolution carried out in large replicated
 populations of R. robini. Artifically selecting for either fighter males
 or scrambler males. Phenotypic assays were perfromed at various
 generations throughtout the experiement - tracking morph proportion,
 fecundity assays, longevity assays and survival assays.
DOI: 10.5061/dryad.sbcc2fr8p
title: Host-parasite interactions between a copepod (Pharodes tortugensis) and small reef-associated gobies (Coryphopterus) in the British Virgin Islands

description: The effects of parasitic copepods on free-living hosts are infrequently
 documented, and the copepod Pharodes tortugensis has remained virtually
 unstudied since described.  For the first time, we document its
 host range in the British Virgin Islands (BVI), the prevalence and
 intensity of infections on wild hosts, and its impacts on host morphology
 and performance.  Infections were observed on four benthic gobies
 in the BVI (Coryphopterus glaucofraenum, C. venezuelae, C. dicrus and C.
 eidolon) but not on other host species previously reported from other
 parts of the western Atlantic.  Infected gobies were widespread
 in the BVI (detected at 33 of 52 sites, prevalence from 1­–25%) but
 extremely rare elsewhere in the Caribbean (detected at 2 of 16 sites,
 prevalence &lt;0.006%).  As is typical of macroparasite
 infections, P. tortugensis was over-dispersed in BVI host populations
 (mean intensity = 4.7, range = 1–17).  Infections were most
 common in juvenile and female hosts, and rarely found in larger male
 hosts.  The copepods attach in the branchial chamber of the goby;
 female copepods show high attachment fidelity to the ventral surface of
 the chamber, while male copepods attached most often to the first two gill
 arches and in the branchial chamber adjacent to the female. 
 Infections caused substantial damage to the host’s branchial chamber and
 gill filaments.  Parasitized gobies also had larger livers and
 smaller gonads than unparasitized individuals of similar length. The
 changes in organ mass of infected gobies were not sizeable enough to
 affect total body mass, and host condition (the body-length vs. body-mass
 relationship) was similar for gobies with and without
 infections.  Parasitized gobies were, however, significantly
 smaller in body mass at a given age, reflecting slower overall growth.
 Effects of P. tortugensis on individual hosts were broadly similar to
 those of other parasitic copepods that infect fish gills and, for unknown
 reasons, the BVI appears to be a persistent hotspot of infections on these
 goby hosts.
description: Pharodes parasites were dissected from Coryphopterus hosts
 collected in the British Virgin Islands
DOI: 10.5281/zenodo.18279327
title: Datensatz "Bücherei des Instituts für Sozialforschung an der Universität Frankfurt (1923–1933)"
DOI: 10.5281/zenodo.18279326
title: Datensatz "Bücherei des Instituts für Sozialforschung an der Universität Frankfurt (1923–1933)"
DOI: 10.5061/dryad.m905qfv3q
title: Aligned DNA sequences of Vanilla

description: Premise Although vanilla is one of the best-known spices, there is a
 limited understanding of its biology and genetics within Mexico, where its
 cultivation originated and where phenotypic variability is high. This
 study aims to augment our understanding of vanilla’s genetic resources by
 assessing species delimitation and genetic, geographic, and climatic
 variability within Mexican cultivated vanilla. Methods Nuclear and plastid
 DNA sequence data from 58 Mexican samples collected from three regions and
 133 ex-situ accessions were used to assess species monophyly using
 phylogenetic analyses and genetic distances. Intra-specific genetic
 variation was summarized through the identification of haplotypes. Within
 the primarily cultivated species, V. planifolia, haplotype relationships
 were further verified using plastome and rRNA gene sequences. Climatic
 niche and haplotype composition were assessed across the landscape. Key
 Results Three species (Vanilla planifolia, V. pompona, and V. insignis)
 and 13 haplotypes were identified among Mexican vanilla. Within V.
 planifolia haplotypes, hard phylogenetic incongruences between plastid and
 nuclear sequences suggest past hybridization events. Eight haplotypes
 exclusively consisted of Mexican samples. The dominant V. planifolia
 haplotype occurred throughout all three regions as well as outside of its
 country of origin. Haplotype richness was found to be highest in regions
 around Papantla and La Chinantla. Conclusions Long histories of regional
 cultivation support the consideration of endemic haplotypes as landraces
 shaped by adaptation to local conditions and/or hybridization. Results may
 aid further genomic investigations of vanilla’s genetic resources and
 ultimately support the preservation of genetic diversity within the
 economically important crop.
description: DNA sequence datasets used for Bayesian and Maximum Likelihood
 phylogenetic analyses and K2P genetic distance analyses. All sequences
 have been aligned and trimmed.
DOI: 10.5281/zenodo.18375661
title: Sequences, metadata, ASVs and soil data for the paper "Underground Lag: Fungal Community and Edaphic Legacies after Disturbance"

description: This dataset includes raw fungal sequencing data (FASTQ), associated metadata, full ASVs dataset, filtered ASVs dataset and chemical soil analysis data derived from the paper "Underground Lag: Fungal Community and Edaphic Legacies after Disturbance".
DOI: 10.5281/zenodo.18375662
title: Sequences, metadata, ASVs and soil data for the paper "Underground Lag: Fungal Community and Edaphic Legacies after Disturbance"

description: This dataset includes raw fungal sequencing data (FASTQ), associated metadata, full ASVs dataset, filtered ASVs dataset and chemical soil analysis data derived from the paper "Underground Lag: Fungal Community and Edaphic Legacies after Disturbance".
DOI: 10.5061/dryad.8cz8w9gt9
title: Data from: Subspecies-level distribution maps for birds of the amazon basin and adjacent areas

description: Available distribution datasets used to assess the range extantion of
 biological species are often at a species-level taxonomy. Because
 different taxonomy biases, many bird subspecies from the Neotropical
 region may deserve full species status. We provide range polygons
 for 3,990 subspecies of birds, representing 2,043 species from 65
 families. All taxa are from the Amazon region, which includes the entire
 Amazon basin, the east slope of tropical Andes, French Guiana, Suriname,
 Guyana, south Venezuela (Bolivar and Amazonas departments), parts of the
 Brazilian Cerrado, and the Araguaia-Tocantins basin. These new maps of
 Amazonian bird subspecies distributions will improve and refine analyses
 on biodiversity studies (e.g. macroecology, evolution, conservation), and
 facilitate biogeographic, ecological, evolutionary, and conservation
 research on birds in the most biologically diverse region in the world.
description: To build the distribution maps we compiled a point-locality
 database of 620,000 records, 90% of which represent specimens vouchered in
 research collections. After manually cleaning and optimising the quality
 of the point localities, we generated extent-of-occurrence polygons at the
 subspecies level using a concave hull function. We corrected each polygon
 based on the literature and expert knowledge.
description: In this supplement you will find a shape file corresponding to the
 distribution of bird taxa occurring in Amazonia and adjacent areas. This
 dataset represents the distribution of bird taxa in the format of range
 polygons, thus no exact location for any threatened taxa is provided.
DOI: 10.6086/d1r38z
title: Secondary brown carbon from photooxidation of 1-methylnaphthalene and longifolene

description: An improved understanding of the optical properties of secondary organic
 aerosol (SOA) particles is needed to better predict their climate impacts.
 Here, SOA was produced by reacting 1-methylnaphthalene or longifolene with
 hydroxyl radicals (OH) under variable ammonia (NH3), nitrogen oxide (NOx),
 and relative humidity (RH) conditions. In the presence of NH3 and NOx,
 longifolene-derived aerosols had relatively high single scattering albedo
 (SSA) values and low absorption coefficients at 375 nm independent of RH,
 suggesting that the longifolene SOA is mostly scattering. In
 1-methylnaphthalene experiments, the resulting SSA and SOA mass absorption
 coefficient (MACorg) values suggest the formation of light-absorbing SOA,
 and the addition of high NOx and high NH3 enhanced the SOA absorption.
 Under intermediate-NOx dry conditions, the MACorg values increased from
 0.13 m2 g−1 in NH3-free conditions to 0.28 m2 g−1 in high-NH3 conditions.
 Under high-NH3 conditions, the MACorg value further increased to 0.36 m2
 g−1 with an increase in RH. Under dry high-NOx conditions, the MACorg
 value increased from 0.42 to 0.67 m2 g−1 with the addition of NH3, while
 with elevated RH, the MACorg value reached 0.70 m2 g−1. The time series of
 MACorg showed increasing trends only in the presence of NH3. Composition
 analysis of SOA suggests that organonitrates, nitroorganics, and other
 nitrogen-containing organic compounds (NOCs) are potential chromophores in
 the 1-methylnaphthalene SOA. Significant formation of NOCs was observed in
 the presence of high-NOx and NH3 and was enhanced under elevated RH.
description: The data have been collected in an environmental chamber,
 oxidizing 30-100 ppbv of 1-methylnaphthalene and 70-100 ppbv of
 longifolene under different levels of nitrogen oxides, ammonia, and
 relative humidity. Microphysical properties (size distribution and
 absorption and scattering coefficients) of SOA along with its composition
 were monitored throughout the experiment. Submitted data include the time
 series of the calculated mass absorption coefficient and single scattering
 albedo at 375 nm, derived real and imaginary components of the refractive
 index, organic nitrate to organic ratio, and organic and nitrate mass
 concentrations. The data have been analyzed using
 Wavemetrics Igor Pro, specifically the software written specifically to
 analyze the data obtained from Aerodyne's aerosol mass spectrometers
 (i.e., Squirrel and Pika). Other calculations were also carried out in
 Igor Pro. More details are provided in the related manuscripts.
description: Please see README file.
DOI: 10.5061/dryad.h70rxwdmn
title: Determination of mean effective shore level to delineate periods of emersion and immersion for intertidal rocky shores

description: This dataset contains data described in the paper entitled
 "Environmental filtering causes increasingly negative effects towards
 the range limit of an invasive mussel". Data include: the R script to
 estimate temperature thresholds and calculate effective shore levels
 (esl_function.R); data files associated with this R script
 (material.RData); mean effective shore levels determined for the five
 South African rocky-shore sites where submersible temperature data loggers
 were installed (esl_overall_results.csv); measurements of mussel shell
 lengths, level of endolithic infestation, and counts of epibionts on the
 basibiont mussel Mytilus galloprovincialis (mussel_data.csv); counts of
 barnacles (Chthamalus dentatus) and mussels (Mytilus
 galloprovincialis and Perna perna) on emersed rocks
 using 50 × 50 cm quadrats and counts of mussels (Mytilus galloprovincialis
 and Perna perna) in mono-layer mixed-species mussel patches using 25 × 25
 cm quadrats (quadrat_data.csv); hourly temperatures recorded by
 submersible temperature data loggers (EnvLogger Version 2.4; precision of
 ≤ 0.1 ºC and accuracy  of ≤ 0.2 ºC) from September 2019 to
 September 2020 at the five South African rocky-shore sites
 (temperature_data.csv); and 2019 and 2020 hourly tidal predictions
 (courtesy of the South African Navy Hydrographic Office) for the closest
 maritime port to the sites where the temperature data loggers were
 installed (tide_data.csv).
description: The readme file provides a description of each column in the
 dataset. NA =  values not available.
DOI: 10.5061/dryad.tx95x6b10
title: Patterns of ferns community assemblages in some Malaysian and Nigerian tropical forests

description: Research on fern ecology has gained attention in the last decade, yet
 there is a paucity of information on the comparison of ferns communities
 across continents. This study focused on comparing the ferns community
 assemblages in some tropical forests of Malaysia and Nigeria, thereby
 assessing the patterns of species richness (SR) and phylogenetic
 diversity(PD) in relation to the bioclimatic drivers across the
 continents. The diversity and taxonomic compositions of ferns were
 assessed using 180 plots of 10 m x 10 m in each country. The species
 richness and other diversity indices were determined using the combined
 forests data for each country and for the individual forests. Also, the
 phylogenetic diversity of the ferns was assessed using the genus-based
 molecular sequences downloaded from the GeneBank. The patterns of the
 ferns SR and PD in the two countries as driven by some bioclimatic factors
 were evaluated using the regression analysis. The observed and
 rarefied–extrapolated fern species richness is significantly higher in
 Malaysian forests than in Nigerian forests. Also, the other diversity
 indices are significantly higher in Malaysian forests except for the
 Shannon index which showed no significant difference between the two
 biogeographic regions. There is a very low similarity (7.41%) in the
 taxonomic composition of ferns between the two biogeographic areas,
 although the similarity in composition increased with increasing taxonomic
 levels (species: 7.41%, genus: 12.77%, family: 70.96%). Terrestrial and
 epiphytic ferns are more dominant than the other life forms in the two
 countries. The precipitation variables drive the phylogenetic structure of
 ferns in Nigeria whereas both precipitation and temperature variables
 drive the phylogenetic structure of ferns in Malaysia. This indicates that
 ferns assemblages in Nigeria and Malaysia are driven by both climatic
 variables. Besides, we also hypothesize that these observed differences
 could be due to other historical and evolutionary processes.
DOI: 10.5061/dryad.9kd51c5kp
title: 15N recovery under ambient and deepened snow treatments

description: Seasonal differences in plant and microbial nitrogen (N) acquisition are
 believed to be a major mechanism that maximizes ecosystem N retention.
 There is also a concern that climate change may interrupt the delicate
 balance in N allocation between plants and microbes. Yet, convincing
 experimental evidence is still lacking. Using a 15N tracer, we assessed
 how deepened snow affects the temporal coupling between plant and
 microbial N utilization in a temperate Mongolian grassland. We found that
 microbial 15N recovery peaked in winter, accounting for 22% of the total
 ecosystem 15N recovery, and then rapidly declined during the
 spring thaw. By stimulating N loss via N2O emission and leaching, deepened
 snow reduced the total ecosystem 15N recovery by 42% during the
 spring thaw. As the growing season progresses, the 15N released
 from microbial biomass was taken up by plants, and the competitive
 advantage for N shifted from microbes to plants.
 Plant 15N recovery reached its peak in August,
 accounting for 17% of the total ecosystem 15N recovery. The
 Granger causality test showed that the temporal dynamics of
 plant 15N recovery can be predicted by microbial 15N
 recovery under ambient snow but not under deepened snow. In addition,
 plant 15N recovery in August was positively correlated with and
 best explained by microbial 15N recovery in March. The lower
 microbial 15N recovery under deepened snow in March reduced
 plant 15N recovery by 73% in August. Together, our results
 provide direct evidence of seasonal differences in plant and microbial N
 utilization that are conducive to ecosystem N retention, however, deepened
 snow disrupted the temporal coupling between plant-microbial N use and
 turnover. These findings suggest that changes in snowfall patterns may
 significantly alter ecosystem N cycling and N-based greenhouse gas
 emissions under future climate change. We highlight the importance of
 better representing winter processes and their response to winter climate
 change in biogeochemical models when assessing N cycling under global
 change.
DOI: 10.57903/uj/8tzlxw
title: Understanding the Morphological Evolution of Anodic Tantalum Oxide Nanostructures in Acidic Medium - replication data
DOI: 10.5061/dryad.8w9ghx3pw
title: Concordance and discordance in the phylogenomics of the wrasses and parrotfishes (Teleostei: Labridae)

description: Phylogenomic analysis of large genome-wide sequence data sets can resolve
 phylogenetic tree topologies for large species groups, help test the
 accuracy of and improve resolution for earlier multilocus studies, and
 reveal the level of agreement or concordance within partitions of the
 genome for various tree topologies. Here we used a target-capture approach
 to sequence more than 1,000 single-copy exons for more than 200 labrid
 fishes together with more than 100 outgroup taxa to generate a new
 data-rich phylogeny for the family Labridae. Our time-calibrated
 phylogenetic analysis of exon-capture data pushes the root node age of the
 family Labridae back into the Cretaceous to about 79 Ma years ago. The
 monotypic Centrogenys vaigiensis, and the order Uranoscopiformes
 (stargazers) are identified as the sister lineages of Labridae. The
 phylogenetic relationships among major labrid subfamilies and within these
 clades was largely congruent with prior analyses of select mitochondrial
 and nuclear datasets. However, the position of the tribe Cirrhilabrini
 (fairy and flame wrasses) showed discordance, resolving either as the
 sister to a crown julidine clade or alternatively sister to a group formed
 by the labrines, cheilines and scarines. Exploration of this pattern using
 multiple approaches leads to slightly higher support for this latter
 hypothesis, highlighting the importance of genome-level data sets for
 resolving short internodes at key phylogenetic positions in large,
 economically important groups of coral reef fishes.
description: See ReadMe.docx for an explanation of Supplemental Tables,
 Figures, and Appendices.
description: # Concordance and discordance in the phylogenomics of the wrasses and
 parrotfishes (Teleostei: Labridae) --- Phylogenetic trees and matrices
 from: Concordance and Discordance in the Phylogenomics of Wrasses and
 Parrotfishes (Teleostei: Labridae). ## Description of the Data and file
 structure Supplemental Tables and Figures (Zenodo) Supplemental Tables
 S1-S2: SupplementaryTables_S1-S2.docx Table S1: Voucher Information Table
 S2: Genome & transcriptome accession numbers Supplemental Figures
 S1-S28: SupplementalFigures_S1-S28.pdf Appendices
 Appendix1_FossilCalibrations.docx (Zenodo) * Contains all references and
 justifications for fossil placements. See also Fig. S1. *
 Labridae_Hedman2010.R: R code for determining soft upper bounds of fossil
 calibrations. (Zenodo) Appendix2_Alignments&Trees.zip * Contains all
 concatenated alignments, ML and ASTRAL trees, and concordance factors.
 Appendix3_BEASTFiles.zip * Contains all .xml files and MCC trees from the
 four BEAST runs. Appendix4_GeneTrees.zip * Contains gene alignments,
 partitioned models, and trees for all loci, used as input for ASTRAL.
 Appendix5_Introgression.zip * Contains all resampled trees and observed
 concordance factors. R code for calculating Delta is hosted on Zenodo. ###
 Change Log Jan 2025: Added Labridae_Hedman2010.R which was previously
 missing