cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wdbrv15tk
title: Ecological, genetic and geographical divergence explain differences in sunbird (Nectariniidae) colouration

description: Bird plumages are among the most elaborate ornaments, displaying almost
 all colours of the rainbow. Why and how birds are so colourful remains an
 open question with multiple and sometimes competing hypotheses. Different
 colours in different patches might have different functions and thus
 result from different forms of selection (e.g., natural vs. sexual
 selection). Here we test three hypotheses that might explain colour
 differences: (1) species isolation, (2) light environment, and (3)
 Brownian motion. We show that both natural and sexual selection affect the
 evolution of sunbird colouration, but that their extent and direction
 differs between sexes, by species interactions, and for different patches
 across the body. Even though overlap in the light environment explains
 part of colour differences in species, no colour metric (brightness and
 chroma) correlates to the light environment. It is likely that these
 results, where multiple forms of selection influence colouration in
 different ways, are more general across birds, highlighting the need to
 investigate bird colouration as a network of individual but
 inter-connected colour patches.
description: # Ecological, genetic and geographical divergence explain differences in
 sunbird (Nectariniidae) colouration This dataset comprises the following
 files: 1. An R file called coldist_vs_sympatry_final.R calculates how
 colour divergences relate to allopatry/sympatry, ecological overlap and
 genetic distances. * This file requires an: *  input tree
 (beautifile_v3_uncorrelated_MCC) (see below) * input file distances3 which
 contains species names (sp1/2), the degree of overlap, whether or not they
 are sympatric and then colour distances for CR, MA, TH, BA, BD, and BE
 (all in JND units), as well as genetic distances (in my), NDVI (Normalized
 Difference Vegetation Index) overlap and minimal distances between
 distributions (in km). 2. Two R files called habitat_type, which look at
 the relationship between colour metrics and NDVI and this for female
 (dataset called habitat_type_F2) and male colours (dataset called
 habitat_type2). * This file requires an: * input tree
 (beautifile_v3_uncorrelated_MCC) --
 see [https://doi.org/10.5061/dryad.7h44j0zxp](https://doi.org/10.5061/dryad.7h44j0zxp) * input colour data sunbirds_ave.csv (see below) * input habitat data habitat_2 (see below) 3. Phylogenetic tree of sunbirds (beautifile_v3_uncorrelated_MCC). 4. A file (distances.txt) containing geographic distances (km), colour distances (JND), NDVI overlap, genetic distances (mya) and geographic overlap between species pairs. 5. A file (habitat_2.csv) with average NDVI values per species. 6. A file (sunbrids_ave.csv) with raw colour measurements. 7. Several output files that were created by the code (coldist_vs_sympatry.txt, NDVI_col_x_M/F.txt). These are added to easily compare results. In all files, NAs/? correspond to missing data. In all files CR, MA, TH, BA, BD, and BE stand for Crown, Mantle, Throat, Breast 1, Breast 2 and Belly.
DOI: 10.5061/dryad.n5tb2rc1h
title: Data from: Environmental correlates of molluscan predator-prey body size in the northern Gulf of Mexico

description: The Mississippi River watershed drains 40% of the continental United
 States, and the tremendous primary productivity in the adjacent
 north-central Gulf of Mexico has created one of the most extensive dead
 zones on Earth. In contrast, smaller watersheds deliver less nutrients to
 the northeastern Gulf, and consequently productivity is limited and
 hypoxia is uncommon. How has variation in primary productivity, oxygen
 availability, and sea surface temperature, affected coastal food webs?
 Here, we investigate environmental controls on the size of molluscan
 predators and prey in the northern Gulf of Mexico using Holocene death
 assemblages. Linear mixed models indicate that bivalve size and the
 frequency of drilling predation are affected by dissolved oxygen
 concentrations; drilling frequency declines with declining oxygen, whereas
 bivalve size increases. In contrast, sea surface temperature is positively
 associated with the size of molluscan predators and prey. Net primary
 productivity contributes relatively little to predator or prey size, and
 predator-to-prey size ratios do not vary consistently with environmental
 conditions across the northern Gulf. Larger bivalves in areas of oxygen
 limitation may be due to decreased predation pressure and consequently
 greater prey longevity. The larger size of bivalves and predatory
 gastropods in warmer waters may reflect enhanced growth under these
 conditions, provided dissolved oxygen concentrations exceed a minimum
 threshold. Holocene death assemblages can be used to test long-standing
 hypotheses regarding environmental controls on predator-prey body size
 distributions through geologic time and provide baselines for assessing
 the ongoing effects of anthropogenic eutrophication and warming on coastal
 food webs.
DOI: 10.25345/c5dj58w51
title: MassIVE MSV000100620 - 2026_PSU_HFTuber-extracts_POS-LCMS
title: hydnophytum formicarum tuber extracts 1) methanol 2) Non-Anionic fraction 3)10% anionic fraction 4) 30% Anionic fraction 5) 50% Anionic fraction
DOI: 10.5061/dryad.fbg79cp14
title: Data for: Meta analysis reveals impacts of disturbance on reptile and amphibian body condition

description: Ecosystem disturbance is increasing in extent, severity, and frequency
 across the globe. To date, research has largely focused on the impacts of
 disturbance on animal population size, extinction risk, and species
 richness. However, individual responses, such as changes in body
 condition, can act as more sensitive metrics and may provide early warning
 signs of reduced fitness and population declines. We conducted the first
 global systematic review and meta-analysis investigating the impacts of
 ecosystem disturbance on reptile and amphibian body condition. We collated
 384 effect sizes representing 137 species from 133 studies. We tested how
 disturbance type, species traits, biome, and taxon moderate the impacts of
 disturbance on body condition. We found an overall negative effect of
 disturbance on herpetofauna body condition (Hedges’ g = -0.37, 95%CI:
 -0.57, -0.18). Disturbance type was an influential predictor of body
 condition response and all disturbance types had a negative mean effect.
 Drought, invasive species, and agriculture had the largest effects. The
 impact of disturbance varied in strength and direction across biomes, with
 the largest negative effects found within Mediterranean and temperate
 biomes. In contrast, taxon, body size, habitat specialisation, and
 conservation status were not influential predictors of disturbance
 effects. Our findings reveal the widespread effects of disturbance on
 herpetofauna body condition and highlight the potential role of
 individual-level response metrics in enhancing wildlife monitoring. The
 use of individual response metrics alongside population and community
 metrics would deepen our understanding of disturbance impacts by revealing
 both early impacts and chronic effects within affected populations. This
 could enable early and more informed conservation management.
DOI: 10.5061/dryad.0p2ngf25z
title: Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates

description: Environmental DNA (eDNA) methods complement traditional monitoring and can
 be configured to detect multiple species simultaneously. One such
 approach, eDNA metabarcoding, uses high-throughput DNA sequencing to
 indirectly detect many different organisms, spanning broad taxonomic
 boundaries, from water samples. We are optimizing a non-invasive, low cost
 eDNA metabarcoding protocol to be used in conjunction with existing
 monitoring programs. One resource that is currently lacking for
 metabarcoding studies in general, including those in the San Francisco
 Estuary (SFE), is a comprehensive database of DNA barcode reference
 sequences. Without this foundational data, many species go undetected or
 misidentified in metabarcoding studies. To meet this need, we generated a
 custom barcode sequence database for the SFE by DNA sequencing and mining
 of public DNA seqeunce data for estuarine and freshwater species of
 interest to monitoring programs and ecological studies. Here we present
 custom reference sequence databases for three barcodes: Cytochrome C
 Oxidase I (COI), 12S MiFish and 16S.
description: Data were collected from two sources. Specimens of fish and
 invertebrates collected from the San Francisco Estuary were used for
 Sanger DNA sequencing. DNA extractions were performed using the Qiagen
 Blood and Tissue kit and PCR was performed using primers to amplify the
 entire barcode sequence. Raw chromatogram data files were manually
 examined for quality control, aligned, and flanking and primer sequences
 were trimmed using CodonCode Aligner. For species without physical
 specimens, or for those specimens that failed PCR/sequencing/QC, publicly
 available DNA sequences were downloaded from GenBank, and aligned and
 trimmed to the barcode region using CodonCode Aligner. The combined
 experimental and downloaded sequences for each barcode were placed into a
 single .txt file formatted for use with the DADA2 metabarcoding software.
 For all sequences, an additional verification step was performed by
 querying the BLASTn database. A separate metadata file (.csv) was also
 generated for each barcode that includes the specimen name (if
 applicable), GenBank Accession numbers (if applicable), taxonomic
 information, common name, and specimen locality, US state, and collection
 date, if available.
description: The barcode sequence databases (.txt) files can be opened with
 any text editor program (e.g., Notepad, TextEdit). The .csv metadata files
 can be opened with any text editor (e.g., Notepad, TextEdit) or
 spreadsheet software (e.g., Microsoft Excel).
DOI: 10.5061/dryad.2fqz612v8
title: Ecosystem stability is determined by plant defense functional traits and population stability under mowing in a semi-arid temperate steppe

description: As a common grassland management practice in many high-latitude regions
 worldwide, mowing has great impacts on grassland functioning and
 stability. Species richness, species asynchrony and species stability have
 been suggested as central in responses to environmental change. Mowing can
 evoke plant defense systems due to physical damages to plants. However, no
 studies have comprehensively evaluated the role of plant defense
 functional traits, species richness, species asynchrony and stability in
 ecosystem functioning under mowing regimes across time-scales. In the
 present study, we set up short-term (4-years) and long-term (16-years)
 mowing experiments with three stubble heights (control, 10 cm, 2 cm) in a
 temperate steppe of Inner Mongolia. We investigated the effects of
 mowing-induced changes in distribution metrics associated with plant
 defense traits, i.e. mean, variance, skewness and kurtosis of trait
 distribution, on ecosystem stability of grassland communities using
 structural equation modeling. We found that grassland ecosystem stability
 was enhanced by increasing mowing duration and decreasing stubble height.
 Mowing-induced increases in abundance and diversity of plant defense
 traits contributed to greater ecosystem stability by enhancing species
 asynchrony and population stability. Moreover, we found that mowing
 enhanced the abundance and diversity of plant defense traits of dominant
 species and contributed to population stability and species asynchrony,
 thus enhancing temporal stability of grassland ecosystems. These results
 demonstrate the important roles of plant defense traits in maintaining
 stability of grasslands under mowing, and highlight that, in addition to
 species richness, asynchrony and population stability, plant functional
 defense trait act in stabilizing ecosystem functions under human-induced
 environmental changes.
DOI: 10.5281/zenodo.18392064
title: Dataset for the BIA Belgium study

description: This dataset contains the data produced in the Business Impact Assessment for Obesity and Population Nutrition and the Business Impact Assessment for Sustainability that were conducted in Belgium in 2023–2024, following the protocols established by INFORMAS (INFORMAS | International Network for Food and Obesity/non-communicable Disease Research, Monitoring and Action Support). A total of thirty-five companies were assessed. The dataset includes each company’s score across all BIA domains and indicators, together with screenshots documenting the publicly available information used to assess company commitments. In some cases, relevant information was identified in company publications such as annual reports, sustainability reports, or policy documents. These publications cannot be posted publicly but can be made available on request; where applicable, a list of these documents is included in the dataset. The full report of the BIAs conducted in Belgium and the corresponding executive summary are available via 10.5281/zenodo.14860171
DOI: 10.5281/zenodo.18392063
title: Dataset for the BIA Belgium study

description: This dataset contains the data produced in the Business Impact Assessment for Obesity and Population Nutrition and the Business Impact Assessment for Sustainability that were conducted in Belgium in 2023–2024, following the protocols established by INFORMAS (INFORMAS | International Network for Food and Obesity/non-communicable Disease Research, Monitoring and Action Support). A total of thirty-five companies were assessed. The dataset includes each company’s score across all BIA domains and indicators, together with screenshots documenting the publicly available information used to assess company commitments. In some cases, relevant information was identified in company publications such as annual reports, sustainability reports, or policy documents. These publications cannot be posted publicly but can be made available on request; where applicable, a list of these documents is included in the dataset. The full report of the BIAs conducted in Belgium and the corresponding executive summary are available via 10.5281/zenodo.14860171
DOI: 10.5061/dryad.rjdfn2zhx
title: Transition to organic farming negatively affects bat activity

description: The effectiveness of organic farming on biodiversity has been widely
 documented especially for plants, arthropods and birds; however, the
 effects of the transition period required to become an organic farm on
 wildlife remain poorly understood. We assessed the effects of organic
 farming on insectivorous bats in citrus orchards in the Republic of Cyprus
 employing two matched designs (conventional vs. 3-years
 organic-transitional and conventional vs. organic-certified) and a third
 unmatched design (3-years organic-transitional vs. organic-certified). We
 specifically investigated whether the transition period prior to full
 organic certification influenced bat activity with a special focus on any
 moderation effects from surrounding semi-natural areas. The activity of
 three (Pipistrellus kuhlii, Hypsugo savii and Miniopterus schreibersii) of
 four bat species was significantly lower in farms undergoing the
 transitional period than in conventional farms, and P. kuhlii and H. savii
 were significantly less active in organic transitional farming systems
 that in organic-certified ones. Furthermore, the activity of the most
 dominant species (P. kuhlii) was significantly higher on organic than
 transitional and conventional citrus orchards, thus suggesting a time-lag
 effect. Landscape complexity measured as the amount of semi-natural areas
 did not moderate the effects of farming system for any study species.
 Synthesis and application. The transition to organic farming had
 persistent detrimental effects on bats and potentially on the pest
 suppression services they provide. Future agri-environmental policy should
 consider the transition period and implement measures to mitigate any
 negative effects on biodiversity, alongside promoting asynchronous
 transition of nearby farms. Our findings further highlight the crucial
 need to consider the time since transition to organic farming when
 assessing potential benefits of organic management on biodiversity.
DOI: 10.5061/dryad.3j9kd51q9
title: Supplementary datasets to: Molecular species delimitation and morphometry in the Melampus bidentatus (Panpulmonata, Ellobiidae) cryptic species complex

description: The coffee bean snail Melampus bidentatus occurs in coastal salt marshes
 along the North American Atlantic and Gulf coasts and in the Caribbean. It
 was recently found that this large geographical span is actually occupied
 by a complex of three apparently cryptic species (preliminarily called
 “North”, “South”, and “Gulf”) with partially overlapping distributions.
 Until now, it was not clear whether there are any morphological
 differences between the three species or which of the available names can
 be applied to each of the cryptic species. We used the already-known
 distribution patterns of the cryptic species as well as new barcode
 sequences to assign available names to the three cryptic species. We then
 compared morphological characters from 264 specimens using two approaches:
 an analysis based on 11 landmark points on the shell and another based on
 the entire shell outline. We were able to assign a nominal name to each of
 the three cryptic species: Melampus bidentatus for “North”, Melampus
 jaumei for “South”, and Melampus gundlachi for “Gulf”. The morphometric
 analyses did not yield any diagnostic differentiating features; these
 cryptic species are hence diagnosable solely by genetic analysis but may
 phenotypically differ in some unseen internal features or in their
 physiology.
DOI: 10.5061/dryad.z08kprrjj
title: Data from: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections

description: Bacterial infections are often polymicrobial, leading to intricate
 pathogen-pathogen and pathogen-host interactions. There is increasing
 interest in studying the molecular basis of pathogen interactions and how
 such mechanisms impact host morbidity. However, much less is known about
 the ecological dynamics between pathogens and how they affect virulence
 and host survival. Here we address these open issues by co-infecting
 larvae of the insect model host Galleria mellonella with one, two, three,
 or four bacterial species, all of which are opportunistic human pathogens.
 We found that host mortality was always determined by the most virulent
 species regardless of the number of species and pathogen combinations
 injected. In certain combinations, the more virulent pathogen simply
 outgrew the less virulent pathogen. In other combinations, we found
 evidence for negative interactions between pathogens inside the host,
 whereby the more virulent pathogen typically won a competition. Taken
 together, our findings reveal positive associations between a
 pathogen's growth inside the host, its competitiveness towards other
 pathogens, and its virulence. Beyond being generalizable across species
 combinations, our findings predict that treatments against polymicrobial
 infections should first target the most virulent species to reduce host
 morbidity, a prediction we validated experimentally.
DOI: 10.5061/dryad.76hdr7t29
title: Population dynamics and social organization of sambar (Rusa unicolor unicolor) in Horton Plains National Park, Sri Lanka

description: We estimated the population density and investigated the social
 organization of sambar (Rusa unicolor unicolor) in Horton Plains National
 Park (HPNP), Sri Lanka. Distance sampling was conducted along six strip
 transects every month for a period over three years (2018–2020) to
 estimate the density of the sambar population in grasslands of HPNP (9.4
 km2), while the antler stage of males and the behaviour of individuals
 were recorded to describe the population’s reproductive stage and hence
 the social organization. Population density estimates showed relative
 stability over the three years and varied over the seasons but with
 consistent peaks from year to year with the highest population densities
 recorded in November-December (212.93 ± 25.38 animals/km2 in 2018, 187.91
 ± 28.51 in 2019, and 179.76 ± 31.85 in 2020). The highest percentage of
 males in hard antlers was observed from November through January, while
 the percentage of antlers cast sambar peaked from March to April each
 year. Hinds were observed with newborn calves throughout the year, but the
 highest number of newborn calves were recorded from July to August each
 year, while the number of calves counted each year varied from 210–267
 individuals. The mean group size was variable throughout each year with
 the largest groups recorded from September to December (up to 52), the
 period accompanied by the most observations of mating and sparring
 behaviour. Although on a tropical island, HPNP is situated on a rolling
 plateau landscape in the highlands, where sambar showed a degree of
 reproductive seasonality somewhat similar to temperate cervid species.
description: The study was conducted within the grasslands of HPNP (Figure 1)
 using transects to count sambar deer and to estimate their density using a
 distance sampling technique  (Buckland et al., 2013). However, our
 methodology was biased on the grassland habitat that provides high-quality
 feeding grounds for sambar, with no distance transect counts taken in
 patches of cloud forests within HPNP, and the counts were conducted in
 peak grazing hours of sambar during the dusk, with the assumption that the
 entire population is in the grasslands during that time. Hence, the
 resulting density estimation is only valid for the grassland habitat and
 presented here as the ecological density of sambar in grasslands of
 HPNP.
DOI: 10.15468/nnmfg3
title: Occurrence records from agroforestry, livestock and beekeeping activities in Mushenyi village, South Kivu, DRC

description: This dataset contains initial occurrence records collected as part of agroforestry, livestock, and beekeeping activities implemented by ADE‑CLIMATERRA in Mushenyi village, Walungu Territory, South Kivu Province, Democratic Republic of the Congo.The records include observations of cultivated plant species (such as Grevillea robusta, Eucalyptus spp., and Musa spp.), domestic animals (Sus scrofa domesticus), and managed honey bee colonies (Apis mellifera). These observations were documented during routine field activities carried out by ADE‑CLIMATERRA staff in agroforestry plots, nurseries, livestock facilities, and beekeeping sites.Each occurrence record provides information on species presence, geographic coordinates (WGS84), date of observation, and organism quantity. The dataset is structured according to the Darwin Core standard to ensure compatibility with GBIF and international biodiversity data repositories.This dataset contributes to biodiversity monitoring in agroecological systems, supports sustainable land management, and enhances the visibility of local practices through open data sharing.