cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.270600g
title: Data from: Upwelling as the major source of nitrogen for shallow and deep reef-building corals across an oceanic atoll system

description: Oceanographic processes shape coral reefs worldwide by redistributing
 inorganic nutrients and particulate resources over depth. Deep‐water
 upwelling occurs frequently in coral reef ecosystems, but its impact on
 coral nutrition remains unclear. This study investigated the influence of
 upwelling on the trophic ecology of three common reef‐building corals
 (Galaxea fascicularis, Pachyseris speciosa and Pocillopora verrucosa) from
 different reef depths (shallow reef, 10 m, vs. deep reef, 30 m) and reef
 exposures (oceanic rim vs. Inner Sea) across &gt; 250 km of the
 Maldives archipelago, Indian Ocean. Carbon and nitrogen stable isotope
 ratios (δ13C and δ15N) of coral hosts, their symbionts and particulate
 organic matter (POM) were used to characterize coral trophic strategies.
 Across the Maldives, consistent mean δ15N values were recorded in hosts
 (5.5‰) and symbionts (5.2‰) of the three coral species from shallow and
 deep reefs of oceanic and Inner Sea reef exposures. Coral hosts, symbionts
 and POM from both depths had δ15N values that were consistent with the
 isotopic signature of a deep‐water nitrate source transported to surface
 waters via upwelling. In contrast, a wide range of δ13C values (~10‰)
 revealed different trophic strategies and isotopic niches among the coral
 species. Different mean δ13C values of G. fascicularis indicated greater
 symbiont autotrophy in corals from shallow (‐15.5‰) compared to deep reefs
 (‐17.6‰). Conversely, the mean δ13C values of P. speciosa (‐15.1‰) and P.
 verrucosa (‐17.7‰) were not affected by reef depth. These corals
 maintained consistent trophic strategies over depth, with P. speciosa
 relying more on autotrophy compared to P. verrucosa. Despite different
 reef exposure to oceanic waters, coral host and POM δ15N and δ13C values
 did not differ between oceanic and Inner Sea reef exposures. Nutritional
 resources appear to be homogenous in the central Maldives due to
 atoll‐wide water circulation. However, species‐specific trophic strategies
 resulted in diverse patterns of δ13C values over depth. Because
 heterotrophic feeding has been linked to coral host survival through coral
 bleaching events, understanding the trophic ecology of corals within the
 reef assemblage can provide insight into species resilience under ocean
 warming conditions. As a member of the typically competitive
 Pocilloporidae family, the dependence of P. verrucosa on heterotrophy may
 help this coral be a future “winner” under sustained ocean warming.
description: Maldives coral reef
 stable isotope ratiosNatural abundance stable
 isotope ratios of three species of corals and particulate organic matter
 from shallow (10 m) and deep (30 m) coral reefs in the Maldives, Indian
 Ocean. Samples collected from coral reefs of oceanic and Inner Sea reef
 exposures. Samples collected in the spring inter-monsoon period in
 2015.Maldives Isotope data
 Radice.xlsx
DOI: 10.5281/zenodo.18385329
title: GIMtec (2009-2022): processed IGS GIM TEC maps and aligned space-weather drivers

description: Processed Global Ionosphere Map (GIM) TEC data used by PI-GWN experiments. Includes yearly TEC arrays (71x73 grid, 2-hour cadence, 2009-2022) and aligned space-weather drivers (F10.7, Dst, Kp, AE).
DOI: 10.5281/zenodo.18385328
title: GIMtec (2009-2022): processed IGS GIM TEC maps and aligned space-weather drivers

description: Processed Global Ionosphere Map (GIM) TEC data used by PI-GWN experiments. Includes yearly TEC arrays (71x73 grid, 2-hour cadence, 2009-2022) and aligned space-weather drivers (F10.7, Dst, Kp, AE).
DOI: 10.7927/f7bg-3k47
title: IPCC AR6 Synthesis Report LR Figure 3.3 (b) (Left burning embers): Risks on land-based systems

description: Risks of global surface temperature change relative to 1850-1900 for land-based systems. Diagrams shown for each risk assume low to no adaptation. Text bubbles indicate examples of impacts at a given warming level.
DOI: 10.5061/dryad.5120mv4
title: Data from: Conflicting selection on floral scent emission in the orchid Gymnadenia conopsea

description: • Floral scent is a crucial trait for pollinator attraction. Yet, only a
 handful of studies have estimated selection on scent in natural
 populations and no study has quantified the relative importance of
 pollinators versus other agents of selection.• In the fragrant orchid
 Gymnadenia conopsea s.s., we used electroantennographic data to identify
 floral scent compounds detected by local pollinators and quantified
 pollinator-mediated selection on emission rates of ten target compounds as
 well as on flowering start, visual display and spur length.• Nocturnal
 pollinators contributed more to reproductive success than diurnal
 pollinators, but there was significant pollinator-mediated selection on
 both diurnal and nocturnal scent emission. Pollinators selected for
 increased emission of two compounds and reduced emission of two other
 compounds, of which none were major constituents of the total bouquet. In
 three cases, pollinator-mediated selection was opposed by
 non-pollinator-mediated selection, leading to weaker or non-detected net
 selection.• Our study demonstrates that minor scent compounds can be
 targets of selection, that pollinators do not necessarily favour strong
 scent signalling, and that some scent compounds are subject to conflicting
 selection from pollinators and other agents of selection. Hence, including
 floral scent traits into selection analysis is important for understanding
 the mechanisms behind floral evolution.
description: Selection analysis
 dataData on morphological
 traits, scent traits, and fitness for all individual Gymnadenia conopsea
 plants included in the study.Data_masterfile_for_publication.xlsx
DOI: 10.5061/dryad.3td78sk
title: Data from: Do riparian forest strips in modified forest landscapes aid in conserving bat diversity?

description: Agricultural practices lead to losses of natural resources and
 biodiversity. Maintaining forests alongside streams (riparian forest
 strips) has been used as a mechanism to minimize the impact of clearing
 for agriculture on biodiversity. To test the contribution of riparian
 forest strips to conserve biodiversity in production landscapes, we
 selected bats as a biodiversity model system and examined two dimensions
 of diversity: taxonomic and functional. We compared bat diversity and
 composition in forest, with and without stream habitat, and in narrow
 forest riparian strips surrounded by areas cleared for agriculture. We
 tested the hypothesis that riparian forest strips provide potential
 conservation value by providing habitat and serving as movement corridors
 for forest bat species. Riparian forest strips maintained 75% of the bat
 species registered in forested habitats. We found assemblage in sites with
 riparian forest strips were dominated by a few species with high abundance
 and included several species with low abundance. Bat species assemblage
 was more similar between sites with streams than between those sites to
 forests without stream habitat. These results highlight the importance of
 stream habitat in predicting presence of bat species. We registered
 similar number of guilds between forest sites and riparian forest strips
 sites. Relative to matrix habitats, stream and edge habitats in riparian
 forest strips sites were functionally more diverse, supporting our
 hypothesis about the potential conservation value of riparian forest
 strips. Results from this study suggest that maintaining riparian forest
 strips within cleared areas for agricultural areas help conserve the
 taxonomic and functional diversity of bats. Also, it provides basic data
 to evaluate the efficacy of maintaining these landscape features for
 mitigating impacts of agricultural development on biodiversity. However,
 we caution that riparian forest strips alone are not sufficient for
 biodiversity maintenance; their value depend on maintenance of larger
 forest areas in their vicinity.
description: Capture data of bats in
 modified forest landscapeCapture data of bats in
 modified forest landscapes. Data was collected in sites with forest
 without streams, forest with streams, and sites where riparian forest
 strips were surrounded by open areas where forest was clear-cut. The file
 includes two sheets: "DataBase" with the capture data and
 "DataDescription" explaining the content of
 "DataBase".Bats_Capture_Database.xlsx
DOI: 10.5061/dryad.st27t1k
title: Data from: Disentangling drivers of the abundance of coral reef fishes in the Western Indian Ocean

description: Aim: Understanding the drivers of the structure of coral reef fish
 assemblages is vital for their future conservation. Quantifying the
 separate roles of natural drivers from the increasing influence of
 anthropogenic factors, such as fishing and climate change, is a key
 component of this understanding. It follows that the intrinsic role of
 historical biogeographical and geomorphological factors must be accounted
 for when trying to understand the effects of contemporary disturbances
 such as fishing. Location: Comoros, Madagascar, Mozambique and Tanzania,
 western Indian Ocean (WIO). Methods: We modelled patterns in the density
 and biomass of an assemblage of reef-associated fish species from 11
 families, and their association with 16 bio-physical variables. Results:
 Canonical Analysis of Principal Coordinates revealed strong country
 affiliations of reef fish assemblages and distance-based linear modelling
 confirmed geographic location and reef geomorphology were the most
 significant correlates, explaining 32% of the observed variation in fish
 assemblage structure. Another 6-8% of variation was explained by
 productivity gradients (chl_a), and reef exposure or slope. Where spatial
 effects were not significant between mainland continental locations,
 fishing effects became evident explaining 6% of the variation in data. No
 correlation with live coral was detected. Only 37 species, predominantly
 lower trophic level taxa, were significant in explaining differences in
 assemblages between sites. Main Conclusions: Spatial and geomorphological
 histories remain a major influence on the structure of reef fish
 assemblages in the WIO. Reef geomorphology was closely linked to standing
 biomass, with ‘ocean-exposed’ fringing reefs supporting high average
 biomass of ~1,000 kg/ha, while ‘lagoon-exposed fringing’ reefs and ‘inner
 seas patch complex’ reefs yielded substantially less at ~500kg/ha.
 Further, the results indicate the influence of benthic communities on fish
 assemblages is scale dependent. Such insights will be pivotal for managers
 seeking to balance long-term sustainability of artisanal reef fisheries
 with conservation of coral reef systems.
description: Fish density &
 biomass data plus env-benth-anthropogenic variablesPlease see Read Me file
 for description of dataSamoilysetal_Ecol&Evol_2019_fish_&variablesdata.xlsx
DOI: 10.5061/dryad.1v1qf6f
title: Data from: Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection and climate

description: Nuclear and mitochondrial genomes coexist within cells but are subject to
 different tempos and modes of evolution. Evolutionary forces such as
 drift, mutation, selection and migration are expected to play fundamental
 roles in the origin and maintenance of diverged populations; however,
 divergence may lag between genomes subject to different modes of
 inheritance and functional specialization. Herein, we explore whole
 mitochondrial genome data and thousands of nuclear single nucleotide
 polymorphisms to evidence extreme mito-nuclear discordance in the small
 black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja
 California, Mexico and southern California, USA, and discuss potential
 drivers. Results show three deeply divergent mitochondrial lineages dating
 back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that
 likely followed geographic isolation due to trans-peninsular seaways. This
 contrasts with very low levels of genetic differentiation in nuclear loci
 (FST &lt; 0.028) between mtDNA lineages. Analyses of protein-coding
 genes reveal substantial fixed variation between mitochondrial lineages,
 of which a significant portion comes from non-synonymous mutations. A
 mixture of drift and selection is likely responsible for the rise of these
 mtDNA groups, albeit with little evidence of marked differences in
 climatic niche space between them. Finally, future investigations can look
 further into the role that mito-nuclear incompatibilities and mating
 systems play in explaining contrasting nuclear gene flow.
description: Zipped folder with SNP,
 GIS, and phylogenetic data1) VCF folder contains a
 raw and unfiltered VCF file with single nucleotide polymorphisms from
 ddRADseq data assembled de-novo with Stacks. batch_2.vcf.gz 2) biovars
 folder contains the bioclimatic layers used to infer climatic niche
 divergence between mtDNA lineages biovars.grd biovars.gri 3) mtDNA_trees
 folder contains maximum clade credibility (summary) trees that include
 robust counting estimates of dN and dS per branch/node inferred using
 BEAST.Dryad_Bernardo_et_al.zip
DOI: 10.5061/dryad.520q128
title: Data from: Genetic variation and structure of Diaphorina citri (Hemiptera:Liviidae) in populations from México

description: The Asian citrus psyllid, Diaphorina citri Kuwayama, is native to Asia but
 has recently invaded North America. Asian citrus psyllid is a significant
 pest of citrus crops by its direct feeding but, more importantly, as the
 vector of the bacterium ‘Candidatus Liberibacter asiaticus’, which causes
 Huanglongbing disease. Asian citrus psyllid was first found in México in
 2001 and 2002 and, since then, has spread quickly across the country,
 suggesting rapid adaptation to new environments. Yet, we lack information
 on the genetic variation and structure that could facilitate or inhibit
 adaptation. Using six microsatellite markers, we analyzed genetic
 variation and structure among six localities in México: three in western
 states near the Pacific coast and two in the Yucatán Peninsula near the
 Gulf of México. We found low genetic diversity (no more than three alleles
 per locus) and intermediate differentiation between all populations. Asian
 citrus psyllid populations clustered into two genetic groups, but,
 surprisingly, these clusters were present in western populations. The
 first group included El Arenal, and the second group included Autlán de
 Navarro, Colima, and Tecomán. Interestingly, both of the Yucatán
 populations shared variation from the two clusters, suggesting admixture.
 We infer that reproductive isolation, barriers to gene flow, local
 selection, and the possibility of multiple invasions have influenced the
 current genetic structure of Asian citrus psyllid in México.
description: Diaphorina citri for
 Dryadinput file is in
 genealex format. cell A1:No. loci, B1:No. samples, C1:No.pop, D1-?:size of
 each population. ColA: Samples ID, ColB: population, From ColC: codominant
 data as 2 columns per locus
DOI: 10.5061/dryad.4h9170k
title: Data from: Are pheromones key to unlocking cryptic lizard diversity?

description: Animals use mating traits to compete for, attract, and choose mates.
 Because mating traits influence mate choice, the divergence of mating
 traits between populations can result in reproductive isolation. This can
 occur without associated morphological divergence, producing
 reproductively isolated ‘cryptic species’ that are visually
 indistinguishable. Thus, identifying the mating traits in morphologically
 conservative groups is key to resolving diversity and speciation
 processes. Lizards contain many such groups, with phylogeographic studies
 often revealing highly divergent but morphologically cryptic lineages
 within species. Considering that cryptic lizard species can be sympatric
 but morphologically indistinguishable, we hypothesize that candidate
 species will exhibit divergent pheromones and that pheromones will have
 typically diverged more than morphology. To test this, we used gas
 chromatography to characterize pheromones (epidermal pore secretions) from
 10 genetically divergent lineages of the Bynoe’s gecko (Heteronotia
 binoei) species complex in northern Australia. Multivariate analyses of
 pheromone blends and morphology indicate that pheromones are
 lineage-specific and have diverged relatively more than morphology. Such
 specificity suggests that pheromones influence behavioral isolation in
 this morphologically conservative lizard radiation. These results suggest
 that pheromone data may unlock the tremendous ‘cryptic’ diversity
 currently being uncovered in many lizard groups.
description: Heteronotia binoei
 pheromone dataPheromone data for 10
 genetically divergent lineages of the Bynoe's gecko (Heteronotia
 binoei). The data includes raw pheromone peak areas yielded from gas
 chromatography characterization, total ion currents, the proportion of
 each pheromone peak, and log-contrast transformed pheromone
 peaks.H_binoei_pheromone_data.csv
DOI: 10.5281/zenodo.18390345
title: LINF_320010300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5281/zenodo.18390346
title: LINF_320010300

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.bq862p1
title: Data from: Climate is a strong predictor of near-infrared reflectance but a poor predictor of colour in butterflies

description: Colour variation across climatic gradients is a common ecogeographical
 pattern; yet there is long-standing contention over underlying causes,
 particularly selection for thermal benefits. We tested the evolutionary
 association between climate gradients and reflectance of near-infrared
 (NIR) wavelengths, which influence heat gain but are not visible to
 animals. We measured ultraviolet, visible and NIR reflectance from
 calibrated images of 372 butterfly specimens from 60 populations (49
 species, 5 families) spanning the Australian continent. Consistent with
 selection for thermal benefits, the association between climate and
 reflectance was stronger (slope and effect size) for NIR than UVA-visible
 wavelengths. Furthermore, climate predicted reflectance of the thorax and
 basal wing, which are critical to thermoregulation; but did not predict
 reflectance of the entire wing, which has a variable role in
 thermoregulation depending on basking behaviour. These results provide
 evidence that selection for thermal benefits has shaped the reflectance
 properties of butterflies.
description: Complete
 datasetDataset with all
 variables (climatic and colour) used for analyses in manuscript. Some
 variables were log-transformed in the models, details are given in the
 manuscript.Butterfly_dataset.xlsTrees used in analyses4500 phylogenetic trees used in comparative analyses. File that matches tree tips and data rows is found as a tab in the complete dataset file.Meta.subset1.trim1.ingroup.B.10K.pruned.treesXML file used in BEASTXML file with details on BEAST analysesMeta.subset1.trim1.ingroup.B.xml
DOI: 10.6084/m9.figshare.31158136
title: <b>Table S1. Disease-dependent differences between tape-strip and bulk biopsy ssGSEA scores across hair follicle compartments</b>

description: This table reports single-sample gene set enrichment analysis (ssGSEA) scores for anatomically defined hair follicle compartments across diseases and sampling modalities (tape strip vs bulk biopsy). Mean scores, delta values (tape minus bulk), Wilcoxon p values, directionality (favours tape strip or bulk biopsy), and statistical significance are provided. For atopic dermatitis, bulk-biopsy data were unavailable.<b>Abbreviations:</b> AA, alopecia areata; AD, atopic dermatitis; PSO, psoriasis; HC, healthy controls; IFE, interfollicular epidermis; INF, infundibulum; IST, isthmus; ORS, outer root sheath; IRS, inner root sheath; DP, dermal papilla; CTS, connective tissue sheath; ssGSEA, single-sample gene set enrichment analysis; Δ, delta (tape-strip minus bulk biopsy score).<b>Source data</b>: This table integrates ssGSEA scores derived from tape-strip and bulk RNA-seq data, including publicly available datasets from the Gene Expression Omnibus (GEO): <b>GSE160501, GSE178197, and GSE262827</b>.
DOI: 10.6084/m9.figshare.31158136.v1
title: <b>Table S1. Disease-dependent differences between tape-strip and bulk biopsy ssGSEA scores across hair follicle compartments</b>

description: This table reports single-sample gene set enrichment analysis (ssGSEA) scores for anatomically defined hair follicle compartments across diseases and sampling modalities (tape strip vs bulk biopsy). Mean scores, delta values (tape minus bulk), Wilcoxon p values, directionality (favours tape strip or bulk biopsy), and statistical significance are provided. For atopic dermatitis, bulk-biopsy data were unavailable.<b>Abbreviations:</b> AA, alopecia areata; AD, atopic dermatitis; PSO, psoriasis; HC, healthy controls; IFE, interfollicular epidermis; INF, infundibulum; IST, isthmus; ORS, outer root sheath; IRS, inner root sheath; DP, dermal papilla; CTS, connective tissue sheath; ssGSEA, single-sample gene set enrichment analysis; Δ, delta (tape-strip minus bulk biopsy score).<b>Source data</b>: This table integrates ssGSEA scores derived from tape-strip and bulk RNA-seq data, including publicly available datasets from the Gene Expression Omnibus (GEO): <b>GSE160501, GSE178197, and GSE262827</b>.
DOI: 10.5061/dryad.dv44mg0
title: Data from: Diversifying livestock promotes multidiversity and multifunctionality in managed grasslands

description: Increasing plant diversity can increase ecosystem functioning,stability,
 and services in both natural and managed grasslands,but the effects of
 herbivore diversity, and especially of livestock diversity, remain
 underexplored. Given that managed grazing is the most extensive land use
 worldwide, and that land managers can readily change livestock diversity,
 we experimentally tested how livestock diversification (sheep, cattle, or
 both) influenced multidiversity (the diversity of plants, insects, soil
 microbes, and nematodes) and ecosystem multifunctionality (including plant
 biomass production, plant leaf N and P, above-ground insect abundance,
 nutrient cycling, soil C stocks, water regulation, and plant–microbe
 symbiosis) in the world’s largest remaining grassland. We also considered
 the potential dependence of ecosystem multifunctionality on
 multidiversity. We found that livestock diversification substantially
 increased ecosystem multifunctionality by increasing multidiversity. The
 link between multidiversity and ecosystem multifunctionality was always
 stronger than the link between single diversity components and functions.
 Our work provides insights into the importance of multitrophic diversity
 to maintain multifunctionality in managed ecosystems and suggests that
 diversifying livestock could promote both multidiversity and ecosystem
 multifunctionality in an increasingly managed world.
description: Diversifying livestock
 promotes multidiversity and multifunctionality in managed
 grasslandsDiversifying livestock
 promotes multidiversity and multifunctionality in managed
 grasslandsLing's data for
 PNAS2.19.xlsx