cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.821j0b0
title: Data from: North Atlantic Gateway: test bed of deep-sea macroecological patterns

description: Aim: The deep waters around Iceland, known as the North Atlantic Gateway,
 constitute an ideal location to investigate deep-sea ecological
 hypotheses. Using ostracods, we constructed a comprehensive deep-sea
 macroecological dataset of the North Atlantic Gateway region and
 investigated the controlling factors of large-scale, deep-sea species
 diversity patterns. Location: Sub-polar North Atlantic Ocean Time period:
 Modern Major taxa studied: Ostracoda (Crustacea) Methods: We investigated
 deep-sea biodiversity patterns and applied ecological modeling (multiple
 regression and model averaging) to test whether these patterns are
 governed by environmental factors such as temperature, surface primary
 productivity, and seasonality. Beta diversity analyses were applied to
 evaluate the effect of a geographical barrier (Greenland-Iceland-Faeroe
 Ridge) on deep-sea benthic faunal distributions. Results: We constructed a
 deep-sea macroecological dataset with 32 stations, 5676 specimens, and 122
 species. We confirmed a linear latitudinal diversity gradient with higher
 diversity in the North Atlantic proper than in the Nordic Seas. We report
 a unimodal depth diversity gradient south of the ridge, but a linear
 diversity-decline with depth north of the ridge. The turnover component of
 beta diversity increased toward the ridge. Main conclusions: We found both
 temperature and surface primary production are important for deep-sea
 biodiversity. For the first time, we report a significant
 diversity-temperature relationship in both macroecological (spatial; this
 study) and existing paleoecological (time-series) data for the same taxa.
 In addition to temperature and surface primary production, bathymetric
 features such as a shallow ridge acting as a barrier, are an important
 factor for deep-sea biodiversity distribution. The low diversity of the
 Nordic Seas is likely due to a combination of low temperatures and
 bathymetric barriers. These results substantially expand our understanding
 of the well-known yet poorly understood Greenland-Iceland-Faeroe Ridge
 faunal transition with possible insight to its cause.
description: IceAGE ecological
 modeling dataset from the North Atlantic GatewayDataset used for
 multiple regression modeling of meiobenthic deep-sea ostracod diversity
 from the IceAGE project.IceAGE_ModelingDataset_NAGatewayMS.xlsxRaw census data of Ostracoda of the North Atlantic GatewayInventory of meiobenthic deep-sea ostracods from the IceAGE project.RawCensus_NAGatewayMS.xlsx
DOI: 10.5061/dryad.7465c1j
title: Data from: An alternative approach to reduce algorithm-derived biases in monitoring soil organic carbon changes

description: Quantifying soil organic carbon (SOC) changes is a fundamental issue in
 ecology and sustainable agriculture. However, the algorithm-derived biases
 in comparing SOC status have not been fully addressed. Although the
 methods based on equivalent soil mass (ESM) and mineral-matter mass (EMMM)
 reduced biases of the conventional methods based on equivalent soil volume
 (ESV), they face challenges in ensuring both data comparability and
 accuracy of SOC estimation due to unequal basis for comparison and using
 un-conserved reference systems. We introduce the basal mineral-matter
 reference systems (soils at time zero with natural porosity but no organic
 matter) and develop an approach based on equivalent mineral-matter volume
 (EMMV). To show the temporal bias, SOC change rates were re-calculated
 with the ESV method and modified methods that referenced to soils at time
 t1 (ESM, EMMM, EMMV-t1) or referenced to soils at time zero (EMMV-t0)
 using two datasets with contrasting SOC status. To show the spatial bias,
 the ESV and EMMV-t0 derived SOC stocks were compared using datasets from
 six sites across biomes. We found that, in the relatively C-rich forests,
 SOC accumulation rates derived from the modified methods that referenced
 to t1 soils and from the EMMV-t0 method were 5.7-13.6% and 20.6% higher
 than that calculated by the ESV method, respectively. Nevertheless, in the
 C-poor lands, no significant algorithmic biases of SOC estimation were
 observed. Finally, both the SOC stock discrepancies (ESV vs EMMV-t0) and
 the proportions of this unaccounted SOC were large and site-dependent.
 These results suggest that although the modified methods that referenced
 to t1 soils could reduce the biases derived from soil volume changes, they
 may not properly quantify SOC changes due to using un-conserved reference
 systems. The EMMV-t0 method provides an approach to address the two
 problems and is potentially useful since it enables SOC comparability and
 integrating SOC datasets.
description: dataset for
 re-estimating SOC change rates with new approachHere are the three
 datasets showing how re-estimating SOC change rates with the newly
 proposed approaches based on equivalent mineral-matter volume and what are
 the differences compared to those with the previously approaches based on
 equivalent soil volume and equivalent mass of soil or
 mineral-matter.
DOI: 10.5061/dryad.8qr3090
title: Data from: Compound-specific isotope analysis of amino acids as new tool to uncover trophic chains in soil food webs

description: Food webs in soil differ fundamentally from those above ground; they are
 based on inputs from both living plants via root exudates, and from
 detritus, which is a complex mixture of fungi, bacteria and dead plant
 remains. Trophic relationships are difficult to disentangle due to cryptic
 lifestyle of soil animals and inevitable microbial contributions to their
 diet. Compound-specific isotope analysis of amino acids (AAs) is
 increasingly used to explore complex food webs. The combined use of AA
 δ13C and δ15N values is a promising new approach to disentangle trophic
 relationships since it provides independent but complementary information
 on basal resource and trophic position of consumers. We conducted a
 controlled feeding study by reconstructing trophic chains from main basal
 resources (bacteria, fungi, plants) to primary consumers (springtails,
 oribatid mites) and predators (gamasid mites, spiders). We analyzed dual
 compound-specific isotope values in AAs of resources and consumers,
 simultaneously applying an approach termed “stable isotope (13C)
 fingerprinting” to identify basal resource, and calculating trophic
 positions using 15N values of trophic and source AAs in consumers. In the
 13C fingerprinting analysis, consumers in general grouped close to their
 basal resources. However, higher than usual offsets in AA δ13C between
 diet and consumers suggest either gut microbial supplementation, or the
 utilization of specific resource fractions. Identification of trophic
 position crucially depends on correct estimates of the trophic
 discrimination factor (TDFGlu-Phe), which was close to the commonly
 applied value of 7.6‰ in primary consumers feeding on microbial resources,
 but considerably lower in arachnid predators (~2.4‰), presumably due to
 higher diet quality, excretion of guanine, and fluid feeding. Primary
 consumers feeding on lime leaf litter were substantially depleted in
 15NPhe, possibly due to selective utilization of more readily available
 nitrogen pools within leaves. Whilst our feeding study demonstrates that
 dual compound-specific AA analyses holds great promise in delineating
 trophic linkages among soil dwelling consumers and their resources, it
 also highlights that a “one-size-fits-all” approach to TDFGlu-Phe does not
 apply to soil food webs.
description: Compound-specific amino
 acid δ13C and δ15N values of resources and consumers from constructed
 trophic chains/feeding trialsThe file contains the
 compound-specific isotope values (13C and 15N) of amino acids from food
 resources and consumers in the trophic chains from the feeding trials.
 Column names include the ID of the sample, the respective species name
 (see "Taxonomic names"), the common name for the species that
 was used in the publication, the prey of predators in the feeding trials,
 the basal resource of consumers, and the trophic level.AA_15N_13C.xlsx
DOI: 10.5061/dryad.bm517c8
title: Data from: Early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: 'Symphyta') may reflect asynchronous switching to angiosperm hosts

description: The insect order Hymenoptera originated during the Permian nearly 300
 million years ago. Ancestrally herbivorous hymenopteran lineages today
 make up the paraphyletic suborder 'Symphyta,' which encompasses
 circa 8200 species with very diverse host-plant associations. We used
 phylogeny-based statistical analyses to explore drivers of diversity
 dynamics within the 'Symphyta,' with a particular focus on the
 hypothesis that diversification of herbivorous insects has been driven by
 the explosive radiation of angiosperms during and after the Cretaceous.
 Our ancestral-state estimates reveal that the first symphytans fed on
 gymnosperms, and that shifts onto angiosperms and pteridophytes—and
 back—have occurred at different time intervals in different groups.
 Trait-dependent analyses indicate that average net diversification rates
 do not differ between symphytan lineages feeding on angiosperms,
 gymnosperms, or pteridophytes, but trait-independent models show that the
 highest diversification rates are found in a few angiosperm-feeding
 lineages that may have been favored by the radiations of their host taxa
 during the Cenozoic. Intriguingly, lineages-through-time plots exhibit
 signs of an early Cretaceous mass extinction, with a recovery starting
 first in angiosperm-associated clades. Hence, the oft-invoked assumption
 of herbivore diversification driven by the rise of flowering plants may
 overlook a Cretaceous global turnover in insect herbivore communities
 during the rapid displacement of gymnosperm- and pteridophyte-dominated
 floras by angiosperms.
description: Datasets and scripts
 used in the analyses of the articleThis zipped folder
 contains the datasets, R scripts and command files of all analyses of the
 article. Some intermediate results are also included.Dryad
 files.zip
DOI: 10.5061/dryad.tf0s1qg
title: Data from: Combined effects of natural enemies and competition for resources on a forest defoliator: a theoretical and empirical analysis

description: Explanations for the dynamics of insect outbreaks often focus on natural
 enemies, on the grounds that parasitoid and pathogen attack rates are high
 during outbreaks. While natural enemy models can successfully reproduce
 outbreak cycles, experiments have repeatedly demonstrated the importance
 of resource quality and abundance. Experiments, however, are rarely
 invoked in modeling studies. Here we combine mechanistic models,
 observational data, and field experiments to quantify the roles of
 parasitoid attacks and resource competition on the jack pine budworm,
 Choristoneura pinus. By fitting models to a combination of observational
 and experimental data, we show that parasitoid attacks are the main source
 of larval budworm mortality at low and intermediate budworm densities, but
 that resource competition is the main source of mortality at high
 densities. Our results further show that the effects of resource
 competition become more severe with increasing host tree age, and that the
 effects of parasitoids are moderated by strong competition between
 parasitoids for hosts. Allowing for these effects in a model of insect
 outbreaks leads to realistic outbreak cycles, while a host-parasitoid
 model without resource competition produces an unrealistic stable
 equilibrium. The effects of resource competition are modulated by tree
 age, which in turn depends on fire regimes. Our model therefore suggests
 that increases in fire frequency due to climate change may interact in
 complex ways with budworm outbreaks. Our work shows that resource
 competition can be as important as natural enemies in modulating insect
 outbreaks, while demonstrating the usefulness of high-performance
 computing in experimental field ecology.
description: Zip file of
 observational and experimental dataPlease see the readme
 file for a detailed description of the databudworm_data.zip
DOI: 10.5061/dryad.gn8qf6q
title: Data from: Social group signatures in hummingbird displays provide evidence of co-occurrence of vocal and visual learning

description: Vocal learning, in which animals modify their vocalizations based on
 social experience, has evolved in several lineages of mammals and birds,
 including humans. Despite much attention, the question of how this key
 cognitive trait has evolved remains unanswered. The motor theory for the
 origin of vocal learning posits that neural centers specialized for vocal
 learning arose from adjacent areas in the brain devoted to general motor
 learning. One prediction of this hypothesis is that visual displays that
 rely on complex motor patterns may also be learned in taxa with vocal
 learning. While learning of both spoken and gestural languages is
 well-documented in humans, the occurrence of learned visual displays has
 rarely been examined in non-human animals. We tested for geographic
 variation consistent with learning of visual displays in long-billed
 hermits (Phaethornis longirostris), a lek-mating hummingbird that, like
 humans, has both learned vocalizations and elaborate visual displays. We
 found lek-level signatures in both vocal parameters and visual display
 features, including element proportions, sequence syntax, and fine-scale
 parameters of elements. This variation was not associated with genetic
 differentiation between leks. In the absence of genetic differences,
 geographic variation in vocal signals at small scales is most
 parsimoniously attributed to learning, suggesting a significant role of
 social learning in visual display ontogeny. The co-occurrence of learning
 in vocal and visual displays would be consistent with a parallel evolution
 of these two signal modalities in this species.
description: Visual display
 sequencesSequences of visual
 display elements of individual displays by male and lek (first data
 sheet). Column names and element abbreviations are explained in the second
 data sheet.display_sequence_data.xlsxAcoustic data and metadataThis is an R object in the "extended_selection_table" format provided by the R package warbleR. It contains all the acoustic data and associated metadata. See ?selection_table in R for more information about the "extended_selection_table" format. The object was saved as an RDS file. The file can be read (after decompression) using the "readRDS" function in R.extended selection table LBH songs.zip
DOI: 10.5061/dryad.q4fm37m
title: Data from: When spring ephemerals fail to meet pollinators: mechanism of phenological mismatch and its impact on plant reproduction

description: The flowering phenology of early-blooming plants is largely determined by
 snowmelt timing in high-latitude and high-altitude ecosystems. When the
 synchrony of flowering and pollinator emergence is disturbed by climate
 change, seed production may be restricted due to insufficient pollination
 success. We revealed the mechanism of phenological mismatch between a
 spring ephemeral (Corydalis ambigua) and its pollinator (overwintered
 bumble bees), and its impact on plant reproduction, based on 19 years of
 monitoring and a snow removal experiment in a cool-temperate forest in
 northern Japan. Early snowmelt increased the risk of phenological mismatch
 under natural conditions. Seed production was limited by pollination
 success over the three years of pollination experiment and decreased when
 flowering occurred prior to bee emergence. Similar trends were detected on
 modification of flowering phenology through snow removal. Following
 snowmelt, the length of the pre-flowering period strongly depended on the
 ambient surface temperature, ranging from 4 days (at &gt;7ºC) to 26
 days (at 2.5ºC). Flowering onset was explained with an accumulated surface
 degree-day model. Bumble bees emerged when soil temperature reached 6ºC,
 which was predictable by an accumulated soil degree-day model, although
 foraging activity after emergence might depend on air temperature. These
 results indicate that phenological mismatch tends to occur when snow melts
 early but subsequent soil warming progresses slowly. Thus, modification of
 the snowmelt regime could be a major driver disturbing spring phenology in
 northern ecosystems.
description: Kudo&Cooper_Source
 Data of Figs.1-4Source data of Figs.1-4
 are included in each spread sheet of the excel file.Kudo&Cooper_SourceData.xlsx
DOI: 10.5061/dryad.vb76300
title: Data from: Host sexual dimorphism affects the outcome of within-host pathogen competition

description: Natural infections often consist of multiple pathogens of the same or
 different species. When co-infections occur, pathogens compete for access
 to host resources and fitness is determined by how well a pathogen can
 reproduce compared to its competitors. Yet not all hosts provide the same
 resource pool. Males and females, in particular, commonly vary in both
 their acquisition of resources and investment in immunity, but their
 ability to modify any competition between different pathogens remains
 unknown. Using the Daphnia magna - Pasteuria ramosa model system, we
 exposed male and female hosts to either a single genotype infection or
 co-infections consisting of two pathogen genotypes of varying levels of
 virulence. We found that co-infections within females favoured the
 transmission of the more virulent pathogen genotype, while co-infections
 within male hosts resulted in the equal transmission of competing pathogen
 genotypes. This contrast became less pronounced when the least virulent
 pathogen was able to establish an infection first, suggesting that the
 influence of host sex is shaped by priority effects. We suggest that sex
 is a form of host heterogeneity which may influence the evolution of
 virulence within co-infection contexts and that one sex may be a reservoir
 for pathogen genetic diversity in nature.
description: Spore loads and
 virulence dataData showing the
 influence of host sex on pathogen spore production (i.e. proliferation)
 and pathogen-induced reduction in host lifespan (i.e. virulence) in each
 of the single and co-infection treatments.gipson-vir-spores-data.csvIndividual pathogen fitness in co-infectionsThe predicted (based on instantaneous replication rates) and observed spore loads for each pathogen genotype competing in a co-infection (estimated using quantitative microsatellite analysis).Gipson-coinfection-fitness.csv
DOI: 10.5061/dryad.285s287
title: Data from: MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils

description: Mate choice contributes to driving evolutionary processes when animals
 choose breeding partners that confer genetic advantages to offspring, such
 as increased immunocompetence. The major histocompatibility complex (MHC)
 is an important group of immunological molecules, as MHC antigens bind and
 present foreign peptides to T-cells. Recent studies suggest that mates may
 be selected based on their MHC profile, leading to an association between
 an individual’s MHC diversity and their breeding success. In conservation,
 it may be important to consider mate choice in captive breeding programs,
 as this mechanism may improve reproductive rates. We investigated the
 reproductive success of Tasmanian devils in a group housing facility to
 determine whether increased MHC-based heterozygosity led individuals to
 secure more mating partners and produce more offspring. We also compared
 the breeding success of captive females to a wild devil population. MHC
 diversity was quantified using 12 MHC-linked microsatellite markers,
 including 11 previously characterised markers and one newly identified
 marker. Our analyses revealed that there was no relationship between
 MHC-linked heterozygosity and reproductive success either in captivity or
 the wild. The results of this study suggest that, for Tasmanian devils,
 MHC-based heterozygosity does not produce greater breeding success, and
 that no specific changes to current captive management strategies are
 required with respect to preserving MHC diversity.
description: GenotypesComma-separated file containing MHC genotype data (two-column format) for individuals included in the study. Missing data indicated with blanks.1 genotypes.csvIndividual reproductive successData for analysis of individual male and female reproductive success in captivity.2 captive repro.csvPairwise reproductive successData for analysis of pairwise reproductive success in a competitive captive setting.3 captive pairwise.csvCaptive vs wild femalesData for comparison of reproductive success of captive versus wild females.4 females captive vs wild.csv
DOI: 10.5061/dryad.m225sc0
title: Data from: Ecosystem services and disservices by birds, bats and monkeys change with macadamia landscape heterogeneity

description: 1.The relative importance of ecosystem services and disservices can change
 with landscape structure in a poorly understood way. 2.We compare the
 impact of biocontrol, provided by bats and birds, with that of crop
 raiding by vervet monkeys on yield in South African macadamia orchards.
 Insectivorous bats and birds are known to feed on macadamia pest insect
 species, like the macadamia nut borer or the green vegetable bug. Vervet
 monkeys move into the orchards during the day to feed on premature
 macadamia nuts. Bats, birds and monkeys benefit from patches of natural
 vegetation adjacent to orchards. 3.With exclusion experiments (four
 treatments: day, night, day & night, control) we quantified the
 relative importance of biocontrol and crop raiding on yield, comparing two
 different landscape settings of the orchards, a natural and a
 human‐modified. 4.Crop raiding occurred only close to natural vegetation
 and caused yield losses of about 26%. Biocontrol by bats and birds was
 higher near natural vegetation, but still significant in human‐modified
 landscapes, at up to 530m distance to forest patches. Prevented biocontrol
 through the exclusion of bats and birds resulted in yield losses of up to
 60%. 5.Effects of biocontrol by bats and birds (USD ~5000/ha/yr) were
 economically more important than the losses of crop raiding (USD
 ~1600/ha/yr). As both are linked to the vicinity of forest patches, the
 removal of natural vegetation to limit monkey abundances would also limit
 biocontrol service provision. 6.Synthesis and applications. This study
 highlights the high economic benefits of biocontrol by bats and birds,
 which outweighed negative impacts through yield losses caused by
 crop‐raiding monkeys. Management practices to prevent crop damage, such as
 guarding, excluding vertebrates or removal of adjacent natural vegetation,
 would also limit access for bats and birds and the great economic benefits
 provided by their biocontrol. Ecosystem services by bats and birds can be
 promoted by the exposure of artificial roost and nest sites, but research
 into species‐specific preferences is needed. The education of farmers is
 crucial, as many are unaware of the benefits from birds and bats and the
 fact that these benefits can outweigh the disadvantages of the monkeys’
 crop‐raiding.
description: Linden-JAPPL-2019Excel file with raw data sheets for nut quality and yield measures.