cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59966s3
title: Data from: How do soil microorganisms respond to N, P and NP additions? Application of the ecological framework of (co‐)limitation by multiple resources

description: 1.Nitrogen, N, and phosphorus, P, often limit biological processes in
 terrestrial ecosystems. Based on previous studies mainly focusing on
 plants, the concept of resource limitation has evolved towards a theory of
 (co)limitations by multiple‐resources. However, this ecological framework
 has not been applied to analyse how soil microorganisms and plants
 concurrently respond to N and/or P addition, and whether these responses
 are constrained by phylogenetic relatedness. 2.Here, we applied this
 framework to analyse microbial and plant responses at community and taxon
 levels to different fertilization treatments (4 N levels without P; 4 P
 levels without N; and 4 NP levels) in Tibetan grasslands. 3.Total plant
 biomass showed serial limitation by N then P, and most plant species were
 limited by N only. Total archaeal abundance decreased with P addition, but
 diverse nutrient limitation types were observed for archaeal taxa. Closely
 related archaeal taxa tended to similarly respond to N, and functional
 similarity between distant archaeal groups was observed for response to P,
 possibly due to functional convergence. In contrast, total bacteria
 slightly increased with P addition only when plants remained N‐limited,
 whereas without N limitation plants rather than bacteria benefited from P
 addition. Most bacterial taxa were limited by other resources than N and
 P, and no clear phylogenetic signals were observed regarding bacterial
 responses to N/P additions. 4.Synthesis: We propose a novel approach for
 characterizing microbial response types to nutrient addition. It
 demonstrates that in Tibetan meadows, most dominant plant species, archaea
 and bacteria respectively depend on N, both N and P, and other resources.
description: dataIncluding soil archaeal
 and bacterial communities, plant community and soil
 properties.
DOI: 10.5061/dryad.n3t3f8h
title: Data from: Effects of increasing aridity and chronic anthropogenic disturbance on seed dispersal by ants in Brazilian Caatinga

description: 1. Anthropogenic disturbance and climate change are the main drivers of
 biodiversity loss and ecological services around the globe. There is
 concern that climate change will exacerbate the impacts of disturbance and
 thereby promote biotic homogenization, but its consequences for ecological
 services are unknown. 2. We investigated the individual and interactive
 effects of increasing chronic anthropogenic disturbance (CAD) and aridity
 on seed dispersal services provided by ants in Caatinga vegetation of
 northeastern Brazil. 3. The study was conducted in Catimbau National Park,
 Pernambuco, Brazil. Within an area of 214 km2, we established nineteen 50
 x 20 m plots that encompassed gradients of both CAD and aridity. We
 offered diaspores of six plant species, three myrmecochorous diaspores and
 three fleshy fruits that are secondarily dispersed by ants. We then
 quantified the number of interactions, seed removal rate and dispersal
 distances, and noted the identities of interacting ant species. Finally,
 we used pitfall trap data to quantify the abundances of ant disperser
 species in each plot. 4. Our results show that overall composition of ant
 disperser species varied along the gradients of CAD and aridity, but the
 composition of high-quality dispersers varied only with aridity. The total
 number of interactions, rates of removal and mean distance of removal all
 declined with increasing aridity, but they were not related to CAD. These
 same patterns were found when considering only high-quality disperser
 species, driven by the responses of the dominant disperser Dinoponera
 quadriceps. We found little evidence of interactive effects of CAD and
 aridity on seed dispersal services by ants. 5. Our study indicates that
 CAD and aridity act independently on ant-mediated seed dispersal services
 in Caatinga, such that the impacts of anthropogenic disturbance are
 unlikely to change under the forecast climate of increased aridity.
 However, our findings highlight the vulnerability of seed dispersal
 services provided by ants in Caatinga under an increasingly arid climate
 due to low functional redundancy in high-quality disperser species. Given
 the large number of plant species dependent on ants for seed dispersal,
 this has important implications for future plant recruitment and,
 consequently, for the composition of Caatinga plant communities.
description: Number of interaction,
 removal rate and dispersal distance by ants in Brazilian
 CaatingaDryad_data_Oliveira_seed_dispersal.xls
DOI: 10.5061/dryad.tj3gd75
title: Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

description: Mosses are a highly diverse lineage of land plants, whose diversification,
 spanning at least 400 million years, remains phylogenetically ambiguous
 due to the lack of fossils, massive early extinctions, late radiations,
 limited morphological variation, and conflicting signal among previously
 used markers. Here, we present phylogenetic reconstructions based on
 complete organellar exomes and a comparable set of nuclear genes for this
 major lineage of land plants. Our analysis of 142 species representing 29
 of the 30 moss orders reveals that relative average rates of
 non-synonymous substitutions in nuclear versus plastid genes are much
 higher in mosses than in seed plants, consistent with the emerging concept
 of evolutionary dynamism in mosses. Our results highlight the evolutionary
 significance of taxa with reduced morphologies, shed light on the relative
 tempo and mechanisms underlying major cladogenic events, and suggest
 hypotheses for the relationships and delineation of moss orders.
description: alignmentstreesrecoverybaits
DOI: 10.5061/dryad.6f60v3q
title: Data from: Spartina alterniflora invasion drastically increases methane production potential by shifting methanogenesis from hydrogenotrophic to methylotrophic pathway in a coastal marsh

description: 1. Plant invasion can strongly influence carbon (C) cycling processes,
 thus it may affect climate change by altering C sequestration and
 greenhouse gas emissions in the invaded ecosystem. Since 1979, the exotic
 Spartina alterniflora has rapidly expanded in China’s coastal areas, where
 significant increase in methane (CH4) emissions has been documented from
 post-invaded sites. However, a mechanistic understanding of the structural
 and functional changes of associated methanogens accompanying this
 invasion remains elusive. 2. Here we conducted integrated biogeochemical
 investigations on methanogenic substrates, activity, and diversity to
 identify implications of S. alterniflora invasion for methanogenesis in
 coastal wetlands. To do this, we collected and analyzed 0–50 cm soil
 profiles from an uncolonized tidal flat (TF) and salt marshes that S.
 alterniflora has invaded for 1 year (SA-1) and 12 years (SA-12) in
 Jiangsu, China. Methanogenic community composition was characterized by
 massive parallel sequencing. The rates and pathways of methanogenesis were
 determined by adding trace concentrations of 13C-labeled substrates to
 anaerobic incubated samples. 3. Our results revealed that 12-year invasion
 of S. alterniflora drastically increased CH4 production potential by one
 order of magnitude over that of TF. This substantial increase was
 primarily attributed to methanogenesis from trimethylamine; its rates
 increased by two orders of magnitude over TF whereas those from acetate
 and H2/CO2 increased far less. Hydrogenotrophic methanogenesis was the
 dominant pathway operating in the TF, but methanotrophic pathway
 contributed most to CH4 production in the surface layer of SA-1 and
 upper-most 40-cm layers of SA-12. Consistent with these observations, the
 dominant methanogens shifted from obligate hydrogenotrophic
 Methanococcales in TF to potential methylamine-utilizing
 Methanosarcinaceae in SA-12. Our Mantel analysis indicated that
 ‘non-competitive’ trimethylamine, derived from cytoplasmic osmolytes of S.
 alterniflora, was the major driver of this change in methanogenic
 community composition. 4. Synthesis. Our results suggest that invasive S.
 alterniflora plants gradually facilitated the local dominance of
 methylotrophic Methanosarcinaceae by changing the key type of methanogenic
 substrate in coastal marshes. Shifts in methanogen communities and
 enhanced availability of trimethylamine elevated the rates and importance
 of methylotrophic methanogenesis, thereby markedly increasing CH4
 production potential and emission rates in this type of ecosystem.
description: Archived data
 JEcol-2018-0791.R1
DOI: 10.5061/dryad.557br15
title: Data from: Extra-pair mating in a socially monogamous and paternal mouthbrooding cardinalfish

description: Many vertebrates form monogamous pairs to mate and care for their
 offspring. However, genetic tools have increasingly shown that many
 offspring arise from matings outside of the monogamous pair bond. Social
 monogamy is relatively common in coral reef fishes, but there have been
 relatively few studies that have confirmed monogamy or extra-pair
 reproduction, either for males or females. Here long-term observations and
 genetic tools were applied to examine the parentage of embryos in a
 paternally mouthbrooding cardinalfish, Sphaeramia nematoptera. Paternal
 care in fishes, such as mouth brooding, is thought to be associated with a
 high degree of confidence in paternity. Two-years of observations
 confirmed that S. nematoptera form long-term pair bonds within larger
 groups. However, genetic parentage revealed extra-pair mating by both
 sexes. Of 105 broods analysed from 64 males, 30.1% were mothered by a
 female that was not the partner and 11.5% of broods included eggs from two
 females. Despite the high paternal investment associated with
 mouthbrooding, 7.5% of broods were fertilised by two males. Extra-pair
 matings appeared to be opportunistic encounters with individuals from
 outside the immediate group. We argue that while pair formation
 contributes to group cohesion, both males and females can maximise
 lifetime reproductive success by taking advantage of extra-pair mating
 opportunities. The results contradict the theory that paternal care is
 associated with a high confidence in paternity.
description: Rueger et al
 2019_Genotypes incl checksThe genotypes of adults
 and juveniles sampled for the study. Including tests for hardy weinberg
 equilibrium ectRueger et al
 2019_Parentage and behaviour dataParentage assignment
 (Colony) and associated behavioural data. Including comparison of genetic
 and behavioural parents for each embryo analysed
DOI: 10.5061/dryad.j3s5v66
title: Data from: Joint attention skills in wild Arabian babblers (Turdoides squamiceps): a consequence of cooperative breeding?

description: Human cooperation strongly relies on the ability of interlocutors to
 coordinate each other’s attentional state: joint attention. One
 predominant hypothesis postulates that this hallmark of the unique
 cognitive system of humans evolved due to the combination of an ape-like
 cognitive system and the prosocial motives that facilitate cooperative
 breeding. Here, we tested this hypothesis by investigating the
 communicative interactions of a cooperatively breeding bird species, the
 Arabian babbler (Turdoides squamiceps). The behaviour of twelve wild
 social groups was observed focusing on two distinct communicative
 behaviours, OBJECT PRESENTATION and BABBLER WALK. The results showed that
 both behaviours fulfilled the criteria for first-order intentional
 communication and involved co-orientation of the recipients'
 attention. In turn, recipients responded with cooperative and
 communicative acts that resulted in coordinated joint travel between
 interlocutors. These findings provide the first evidence that another
 animal species shows several key criteria traditionally used to infer
 joint attention in prelinguistic human infants. Furthermore, they
 emphasize the effect of cooperative breeding on sophisticated
 socio-cognitive performances, while questioning the necessity of an
 ape-like cognitive system underlying joint attentional behaviour.
description: Babbler Walk descriptive
 and duration JABabbler walk signal:
 descriptive statistic, duration of signalling and response
 type.BW
 descriptive and duration JA.xlsxBW use of gaze
 alternationBabbler walk: use of
 gaze alternationOP use of gaze
 alternationObject presentation: use
 of gaze alternation
DOI: 10.5061/dryad.sp10dk0
title: Data from: Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean

description: Trophic networks in small isolated islands are in a fragile balance, and
 their disturbance can easily contribute towards the extinction vortex of
 species. Here we show, in a small Atlantic island (Raso) in the Cabo Verde
 Archipelago, using DNA metabarcoding, the extent of trophic dependence of
 the Endangered giant wall gecko Tarentola gigas on endemic populations of
 vertebrates, including one of the rarest bird species of the world, the
 Critically Endangered Raso lark Alauda razae. We found that the Raso lark
 (27%), Iago sparrow Passer iagoensis (12%), Bulwer's petrel Bulweria
 bulwerii (15%) and the Cabo Verde shearwater Calonectris edwardsii (10%)
 are the most frequent vertebrate signatures found in the faeces of the
 giant wall gecko. This work provides the first integrative assessment of
 their trophic links, an important issue to be considered for the long-term
 conservation of these small and isolated island ecosystems.
description: Final occurrence matrix
 of species in each faecal sampleFinal occurrence matrix
 of species in each faecal sample, ordered by month and classified
 according to their location (C: coastal; I: inland). Also shown the
 frequency of occurrence and upper and lower 95% confidence
 levels.Occurrence Matrix
 1.1.xlsx
DOI: 10.5061/dryad.sk61618
title: Data from: Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

description: Species delimitation is a major quest in biology and is essential for
 adequate management of the organismal diversity. A challenging example
 comprises the fish species of red snappers in the Western Atlantic. Red
 snappers have been traditionally recognized as two separate species based
 on morphology: Lutjanus campechanus (northern red snapper) and L.
 purpureus (southern red snappers). Recent genetic studies using
 mitochondrial markers, however, failed to delineate these nominal species,
 leading to the current lumping of the northern and southern populations
 into a single species (L. campechanus). This decision carries broad
 implications for conservation and management as red snappers have been
 commercially over-exploited across the Western Atlantic and are currently
 listed as vulnerable. To address this conflict, we examine genome-wide
 data collected throughout the range of the two species. Population
 genomics, phylogenetic and coalescent analyses favor the existence of two
 independent evolutionary lineages, a result that confirms the
 morphology-based delimitation scenario in agreement with conventional
 taxonomy. While we find evidence of introgression in geographically
 neighboring populations in northern South America, the genetic differences
 strongly support isolation and differentiation of these species,
 suggesting that the northern and southern red snappers should be treated
 as distinct taxonomic entities.
description: Selected output SNPs
 datasetsData matrices selected
 to evaluate the effect of the number of individuals and missing data
 included on the sensitivity of the results.Selected_output_datasets.tar.gzMitochondrial haplotype networksNexus files of the mtDNA gene COI and and D-loop mtDNA control region that were used to compute the haplotype networks.Haplotype_networks.tar.gzPhylogenetic treesPhylogenetic trees of the selected matrices using snpsPhylogenetic_trees.tar.gzBayes Factor Delimitationxml files for model testing (one vs two species scenario) with Bayes factor delimitation analyses, using different amount of individuals (58-108) and snps (149-957)BFD.tar.gzDiagnostic SNPsList of character transformations (SNPs) that differentiate populations of L. campechanus from L. purpureusDiagnostic_SNPs.tar.gz
DOI: 10.34740/kaggle/dsv/14639633
title: Valorant VCT Champions 2025 Dataset
DOI: 10.5061/dryad.g4d7p46
title: Data from: Sex-specific selection on plant architecture through 'budget' and 'direct' effects in experimental populations of a wind-pollinated herb

description: Sexual selection may contribute to the evolution of plant sexual
 dimorphism by favoring architecture traits that improve pollen dispersal
 to mates in males. In both sexes, larger individuals may be favored if
 large size allows the allocation of more resources to gamete production (a
 ‘budget’ effect of size). In wind-pollinated plants, large size may also
 benefit males if it allows them to liberate pollen from greater heights,
 fostering its dispersal (a ‘direct’ effect of size). To assess these
 effects and their implications for trait selection, we measured selection
 gradients on plant morphology in both males and females, as well as pollen
 production and dispersal in males, of the wind-pollinated dioecious herb
 Mercurialis annua. In two separate experimental common gardens established
 at different densities, selection strongly favored plants dispersing their
 pollen further. Selection for pollen production was observed in the
 high-density garden only and was weak. In addition, male morphologies
 associated with increased mean pollen dispersal differed between the two
 gardens as elongated branches were favored in the high-density garden
 while shorter plants with longer peduncles bearing inflorescences were
 advantaged the low-density garden. Larger females were selected in both
 gardens. Our results point to the importance of selection on male traits
 that affect pollen dispersal, and to a lesser extent pollen production.
description: Genotype and
 morphological data of Mercurialis annua selection gradient
 analysisIn a common garden at
 low-density and another common garden at high-density, a set of vegetative
 and reproductive traits have been measured in males and females of
 Mercurialis annua. Genotype data on height microsatellites have also been
 produced for all males and females along with respectively 642 and 657
 juveniles for the high- and low-density garden grown from seeds sampled on
 the study females.dryad_Tonnabeletal2019.ods
DOI: 10.5281/zenodo.18389605
title: Sentiment Analysis and Topic Modelling in Indonesian Crypto Application
DOI: 10.5281/zenodo.18389606
title: Sentiment Analysis and Topic Modelling in Indonesian Crypto Application
DOI: 10.5061/dryad.d3n7bs7
title: Data from: Multiple colonizations, hybridization and uneven diversification in Cyrtandra (Gesneriaceae) lineages on Hawai‘i Island

description: Aim The diversity and composition of species pools within oceanic
 archipelagos is determined by a combination of colonization, abiotic
 tolerance, in situ diversification, biotic interactions, and extinction.
 The signature of biogeographic events and evolutionary processes, however,
 may be masked by recent coalescence and hybridization between closely
 related species. We used the species-rich plant genus Cyrtandra
 (Gesneriaceae) to investigate the roles of colonization and hybridization
 in shaping community assemblages on the geologically young Hawaii Island.
 Location Hawaiian Islands. Taxon Cyrtandra (Gesneriaceae). Methods We
 sampled 29 Cyrtandra taxa and putative hybrids across the main Hawaiian
 Islands and generated single nucleotide polymorphisms (SNPs) from nine
 single-copy nuclear genes. Maximum likelihood and Bayesian inference were
 used to reconstruct phylogenetic relationships, divergence times were
 estimated using secondary calibrations and island ages, and ancestral area
 estimation was done using likelihood models. Lastly, we used a Bayesian
 population assignment test and principal components analysis to infer
 population genetic structure. Results Cyrtandra colonization of the main
 Hawaiian Islands appears to have followed the progression rule, whereby
 the oldest high Hawaiian Islands (Kauai and Oahu) were colonized first,
 followed by colonization of the younger islands as habitat became
 available. Hawaii Island was colonized four times, with two dispersal
 events from Oahu and two from Maui Nui. The different colonization events
 gave rise to significantly uneven numbers of species, and hybridization
 among the incipient lineages was detected in the form of intermediate
 genotypes. Main Conclusions Our investigation into community assembly in a
 species-rich plant genus on a geologically young oceanic island revealed a
 history of multiple colonizations and hybridization among colonizing
 lineages. The rapid diversification (3.5 species/My) of one of four
 Cyrtandra lineages on Hawaii Island may be the result of hybridization
 between genetically diverse lineages that stem from independent
 colonization events. Multiple colonization events followed by a merging of
 lineages may be particularly common during early-stage community assembly
 on islands and, through the generation of genetic variation, may be
 especially important for species diversification.
description: Hawaiian Cyrtandra
 genotypesGenotypes based on SNPs
 for nine single-copy nuclear genes in Hawaiian Cyrtandra species and
 hybrids.HawaiianCyrtandra_genotypes.xlsx
DOI: 10.5061/dryad.t7874hd
title: Data from: Altitude effects on spatial components of vascular plant diversity in a subarctic mountain tundra

description: Environmental gradients are caused by gradual changes in abiotic factors,
 which affect species abundances and distributions, and are important for
 the spatial distribution of biodiversity. One prominent environmental
 gradient is the altitude gradient. Understanding ecological processes
 associated with altitude gradients may help us to understand the possible
 effects climate change could have on species communities. We quantified
 vegetation cover, species richness, species evenness, beta diversity, and
 spatial patterns of community structure of vascular plants along altitude
 gradients in a subarctic mountain tundra in northern Sweden. Vascular
 plant cover and plant species richness showed unimodal relationships with
 altitude. However, species evenness did not change with altitude,
 suggesting that no individual species became dominant when species
 richness declined. Beta diversity also showed a unimodal relationship with
 altitude, but only for an intermediate spatial scale of 1 km. A lack of
 relationships with altitude for either patch or landscape scales suggests
 that any altitude effects on plant spatial heterogeneity occurred on
 scales larger than individual patches but were not effective across the
 whole landscape. We observed both nested and modular patterns of community
 structures, but only the modular patterns corresponded with altitude. Our
 observations point to biotic regulations of plant communities at high
 altitudes, but we found both scale dependencies and inconsistent magnitude
 of the effects of altitude on different diversity components. We urge for
 further studies evaluating how different factors influence plant
 communities in high altitude and high latitude environments, as well as
 studies identifying scale and context dependencies in any such influences.
description: Naud-et-al-DataRaw data for Naud et al. Ecology and evolution. File includes a data table containing % vegetation cover, plant species richness, plant Shannon evenness, and three distances to centroids (which have been used as measurements of beta diversity on three different spatial scales), as well as a binary presence - absence matrix used for community structure calculations.