cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4th3p35
title: Data from: Inter-annual dynamics and persistence of small mammal communities in a selectively logged tropical forest in Borneo

description: Understanding temporal change and long-term persistence of species and
 communities is vital if we are to accurately assess the relative values of
 human-modified habitats for biodiversity. Despite a large literature and
 emerging consensus demonstrating a high conservation value of selectively
 logged tropical rainforests, few studies have taken a long-term
 perspective. We resampled small mammals (≤1kg) in a heavily logged
 landscape in Sabah, Borneo between 2011 and 2016 to investigate temporal
 patterns of species-level changes in population density. We found that
 small mammal population density in heavily logged forest was highly
 variable among years, consistent with patterns previously observed in
 unlogged forest, and uncovered evidence suggesting that one species is
 potentially declining towards local extinction. Across nine species,
 population densities varied almost sevenfold during our six-year study
 period, highlighting the extremely dynamic nature of small mammal
 communities in this ecosystem. Strictly terrestrial murid species tended
 to exhibit strong temporal dynamics, whereas semi-arboreal foraging
 species such as treeshrews had more stable dynamics. We found no
 relationships between population density and fruit/seed mass, and
 therefore no evidence that our patterns represent responses to
 inter-annual mast fruiting of the dominant canopy dipterocarp trees. This
 may be due to the removal of most of the canopy during logging, and hence
 the dipterocarp seed resource, although it possibly also reflects
 spatiotemporal limitations of our data. Our results underline the
 importance of understanding long-term variability in animal communities
 before developing conservation and management recommendations for
 human-altered ecosystems.
description: Chapman_capturehistoriesThis is the master file for all the capture history data, used to calculate population density via Spatially Explicit Capture-Recapture modelling in the paper. For background, and details of columns, see the README.Chapman_traplocationsThis is the complete list of trap locations used to provide the spatial element in the Spatially Explicit Capture Recapture models which we used to calculate population density in the paper. The data comprises a grid-specific X- and Y- coordinate for every trap location in our data. For an explanation of how these were derived, see the README .Chapman_seed.dataThis is the seed rain dataset we used to compare against our small mammal density data. It comprises landscape-scale monthly means of pooled seed and fruit mass (g m3) against the relevant grids trapped in each month. For fuller details of how these data were derived, see the README.
DOI: 10.5061/dryad.q749f
title: Data from: Interactions between micro- and macroparasites predict microparasite species richness across primates

description: Most wild animals face concurrent challenges by multiple infectious
 organisms, and immunological responses triggered by some parasites may
 increase susceptibility to other infectious agents. Immune-mediated
 interactions among parasites have been investigated among individuals in a
 population, but less is known about broader comparative patterns. We
 investigated the "macro-micro facilitation hypothesis" that
 higher helminth prevalence in a host species provides greater
 opportunities for intracellular parasites to invade, resulting in higher
 richness of intracellular microparasites. We obtained data on average
 helminth prevalence for 70 primate hosts, along with data on richness of
 intra- and extracellular infectious organisms. Using Bayesian phylogenetic
 methods, we found that primate species with higher overall helminth
 prevalence harbored more species of intracellular microparasites, while
 the positive association between helminth prevalence and extracellular
 microparasite species richness was weaker. The relationships held after
 controlling for potentially confounding variables, but associations were
 not found in focused tests of prevalence for six genera of well-studied
 helminths. The magnitude of support and effect sizes for overall helminth
 prevalence on intracellular microparasite species richness was similar to
 support for other well recognized ecological and life history drivers of
 parasite species richness. Our findings therefore suggest that intra-host
 parasite interactions are as important as some ecological characteristics
 of hosts in accounting for parasite richness across host species.
description: Data-Richness-PrevalenceDatasetsTreeBlock_10kTrees_Primates_Version3-3Block of phylogenies used in comparative analyses
DOI: 10.5061/dryad.8m0q0
title: Data from: Beyond pollinators: evolution of floral architecture with environment across the wild sunflowers (Helianthus, Asteraceae)

description: Background – There is a growing appreciation that the evolution of floral
 traits is shaped by selection not only from pollinators, but also factors
 like abiotic stress, florivory, and disease. Many such pressures impose
 counter-selection for smaller, less attractive flowers. In
 self-incompatible taxa, floral investment in attraction is required to
 ensure cross-pollination, setting up a potential energetic trade-off with
 investment in fecundity through pollen and seeds. Methods – This study
 assesses ecological and evolutionary causes of variation in floral
 morphology across the diverse genus Helianthus (Asteraceae), focusing on
 floral size, colour, water content, and relative investment in attractive
 but sterile ray florets versus non-showy but fertile disc florets. Key
 results – All floral traits were found to be highly evolutionarily labile,
 and the trade-off in relative investment between ray and disc florets was
 found to evolve independently of floral size. Both floral size and disc
 water content were strongly correlated with source site climate and soil
 characteristics, with larger heads and higher water content repeatedly
 evolving in more fertile and drier habitats consistent with aspects of the
 resource-cost and enemy-escape hypotheses of floral trait evolution,
 respectively. The evolution of disc colour and relative ray-disc
 investment was not explained by life history, flowering period, or source
 site environmental characteristics, suggesting that the evolution of these
 traits may instead be driven by other selective pressures, including
 perhaps pollinators. Conclusions – Together the results of this study
 suggest that the macroevolution of sunflower floral architecture is likely
 driven by selective pressures from multiple biotic and abiotic factors,
 with habitat environmental conditions influencing some but not all aspects
 of floral morphology.
description: Electronic Appendix
 1Source information,
 trait data, and environmental metrics used in this
 study.Mason_appendix_1_datasetS1.xlsxElectronic Appendix 2Supplemental figure - phylomorphospace of total flower dry mass and dry mass investment ratio.Mason_appendix_2_figureS1.pdf
DOI: 10.5281/zenodo.18382028
title: The DataSet of the paper : An Adaptive Anomaly Detection Platform for Industrial IoT Streams via LSTM Autoencoders and Human-in-the-Loop Feedback: Supply Chain Application

description: The DataSet of the paper : An Adaptive Anomaly Detection Platform for Industrial IoT Streams via LSTM Autoencoders and Human-in-the-Loop Feedback: Supply Chain Application
DOI: 10.5281/zenodo.18382029
title: The DataSet of the paper : An Adaptive Anomaly Detection Platform for Industrial IoT Streams via LSTM Autoencoders and Human-in-the-Loop Feedback: Supply Chain Application

description: The DataSet of the paper : An Adaptive Anomaly Detection Platform for Industrial IoT Streams via LSTM Autoencoders and Human-in-the-Loop Feedback: Supply Chain Application
DOI: 10.5061/dryad.482f265
title: Data from: Phylogeographic diversification and postglacial range dynamics shed light on the conservation of the kelp Saccharina japonica

description: Studies of postglacial range shifts could enhance our understanding of
 seaweed species’ responses to climate change, and hence facilitate the
 conservation of natural resources. However, the distribution dynamics and
 phylogeographic diversification of the commercially and ecologically
 important kelp Saccharina japonica in the Northwest Pacific (NWP) are
 still poorly surveyed. In this study, we analyzed the evolutionary history
 of S. japonica using two mitochondrial markers and 24 nuclear
 microsatellites. A STRUCTURE analysis revealed two partially isolated
 lineages: lineage H, which is scattered along the coast of Japan; and
 lineage P, which occurs along the west coast of the Japan Sea. Ecological
 niche modeling projections to the Last Glacial Maximum (LGM) revealed that
 the southern coasts of the Japan Sea and the Pacific side of the Oshima
 and Honshu Peninsulas provided the most suitable habitats for S. japonica,
 implying that these regions served as ancient refugia during the LGM.
 Ancient isolation in different refugia may explain the observed divergence
 between lineages P and H. An approximate Bayesian computation analysis
 indicated that the two lineages experienced post‐LGM range expansion, and
 that postglacial secondary contact occurred in Sakhalin. Model projections
 into the year 2100 predicted that S. japonica will shift northwards and
 lose its genetic diversity center on the Oshima Peninsula in Hokkaido and
 Shimokita Peninsula in Honshu. The range shifts and evolutionary history
 of S. japonica improve our understanding of how climate change impacted
 the distribution range and diversity of this species and provide useful
 information for the conservation of natural resources under ongoing
 environmental change in the NWP.
description: data archiving of
 Saccharina japonicaInput files and result
 files for DIYABC, Maxent and STRUCTURE, and the alignment file of
 mitochondrial data.
DOI: 10.5061/dryad.vt82p
title: Data from: Latitudinal and photic effects on diel foraging and predation risk in freshwater pelagic ecosystems

description: 1. Clark & Levy (1988) described an antipredation window for
 smaller planktivorous fish during crepuscular periods when light permits
 feeding on zooplankton, but limits visual detection by piscivores. Yet,
 how the window is influenced by the interaction between light regime,
 turbidity and cloud cover over a broad latitudinal gradient remains
 unexplored. 2. We evaluated how latitudinal and seasonal shifts in diel
 light regimes alter the foraging-risk environment for visually-feeding
 planktivores and piscivores across a natural range of turbidities and
 cloud covers. Pairing a model of aquatic visual feeding with a model of
 sun and moon illuminance, we estimated foraging rates of an idealized
 planktivore and piscivore over depth and time across factorial
 combinations of latitude (0-70º), turbidity (0.1-5 NTU) and cloud cover
 (clear to overcast skies) during the summer solstice and autumnal equinox.
 We evaluated the foraging-risk environment based on changes in the
 magnitude, duration and peak timing of the antipredation window. 3. The
 model scenarios generated up to 10-fold shifts in magnitude, 24-fold
 shifts in duration, and 5.5 h shifts in timing of the peak antipredation
 window. The size of the window increased with latitude. This pattern was
 strongest during the solstice. In clear water at low turbidity (0.1-0.5
 NTU), peaks in the magnitude and duration of the window formed at 57-60º
 latitude, before falling to near zero as surface waters became saturated
 with light under a midnight sun and clear skies at latitudes near 70º.
 Overcast dampened the midnight sun enough to allow larger windows to form
 in clear water at high latitudes. Conversely, at turbidities ≥ 2 NTU,
 greater reductions in the visual range of piscivores than planktivores
 created a window for long periods at high latitudes. Latitudinal
 dependencies were essentially lost during the equinox, indicating a
 progressive compression of the window from early summer into autumn. 4.
 Model results show that diel-seasonal foraging and predation risk in
 freshwater pelagic ecosystems changes considerably with latitude,
 turbidity and cloud cover. These changes alter the structure of pelagic
 predator-prey interactions, and in turn, the broader role of pelagic
 consumers in habitat coupling in lakes.
description: Model code and input
 data filesThis folder provides R
 code (.R file) and all input data files (.csv files). With the information
 and data provided, main results presented in the corresponding manuscript
 can be recreated. See 'ReadMe.txt' file for a description of
 each file in the 'Data files.zip' folder.Data
 files.zip
DOI: 10.5061/dryad.199k8
title: Data from: A test for repertoire matching in eastern song sparrows

description: Repertoire matching occurs when one songbird replies to another with a
 song type that the two birds share. Repertoire matching has previously
 been demonstrated to occur at well above chance levels in a western
 population of song sparrows, where it is hypothesized to serve as a low
 level threat in a hierarchy of aggressive signals. Here we test for
 repertoire matching in an eastern population of song sparrows. Previous
 work indicates that this eastern population differs from the western one
 in having lower levels of song sharing between neighboring males and in
 showing no association between song sharing and territory tenure. Here we
 confirm that males in this eastern population on average share few whole
 songs with their neighbors. The eastern males are familiar with their
 neighbors’ repertoires, as evidenced by a stronger singing response to
 stranger song than to neighbor song. Males in the eastern population did
 not repertoire match: when played an unshared song type from a specific
 neighbor, they did not reply with a song type shared with that neighbor
 more often than expected by chance or more often than in response to
 playback of a control song (an unshared stranger song). The results thus
 demonstrate a qualitative difference in vocal signaling strategies between
 two populations of the same species.
description: Sharing Analysis
 2013-14Data on the sharing
 metric for whole song sharing and introductory phrase sharing. For each
 male (identified by color band combination) the sharing metric is averaged
 across his adjacent neighbors. Also given are song repertoire sizes and
 number of songs recorded.Song sharing per dyad of
 adjacent male song sparrowsFor each pair of
 adjacent territorial male song sparrows, the file gives the number of
 whole song types shared and the number of introductory phrases
 shared.Dyad
 analysis.xlsxPARTIAL MATCHING
 ANALYSISFor each focal male,
 whether he did (YES) or did not (NO) repertoire match playback of an
 unshared neighbor song and whether he sang the same target song(s) for
 playback of an unshared stranger song, counting partially shared songs as
 a repertoire match.WHOLE SONG MATCHING
 ANALYSISFor each focal male,
 whether he did (YES) or did not (NO) repertoire match playback of an
 unshared neighbor song and whether he sang the same target song(s) for
 playback of an unshared stranger song, counting only wholly shared songs
 as a repertoire match.neighbor:strangerNumber of songs given by subjects in response to playback of neighbor song and to playback of stranger song.
DOI: 10.5061/dryad.95262
title: Data from: Comparing rates of springtail predation by web-building spiders using Bayesian inference

description: A major goal of gut-content analysis is to quantify predation rates by
 predators in the field, which could provide insights into the mechanisms
 behind ecosystem structure and function, as well as quantification of
 ecosystem services provided. However, percent-positive results from
 molecular assays are strongly influenced by factors other than predation
 rate, and thus can only be reliably used to quantify predation rates under
 very restrictive conditions. Here, we develop two statistical approaches,
 one using a parametric bootstrap and the other in terms of Bayesian
 inference, to build upon previous techniques that use DNA decay rates to
 rank predators by their rate of prey consumption, by allowing a
 statistical assessment of confidence in the inferred ranking. To
 demonstrate the utility of this technique in evaluating ecological data,
 we test web-building spiders for predation on a primary prey item,
 springtails. Using these approaches we found that an orb-weaving spider
 consumes springtail prey at a higher rate than a syntopic sheet-weaving
 spider, despite occupying microhabitats where springtails are less
 frequently encountered. We suggest that spider-web architecture (orb web
 vs sheet web) is a primary determinant of prey-consumption rates within
 this assemblage of predators, which demonstrates the potential influence
 of predator foraging behaviour on trophic web structure. We also discuss
 how additional assumptions can be incorporated into the same analysis to
 allow broader application of the technique beyond the specific example
 presented. We believe that such modelling techniques can greatly advance
 the field of molecular gut-content analysis.
description: Data file for field and
 laboratory assays of web-building spidersExcel file containing 5
 sheets: (1) field data on spider webs collected in alfalfa in Lexington,
 Ky, in 2009, along with results of PCR gut-content assays, (2) sticky-trap
 data collected in the same location and year; (3) laboratory trials
 determining how many springtails encountered were consumed; and (4)
 laboratory feeding trials to determine retention times of springtail DNA
 in spider guts. Sheet (5) is a key.Welch MolEcol
 Data.xlsx
DOI: 10.5061/dryad.d5j4m
title: Data from: River network architecture, genetic effective size and distributional patterns predict differences in genetic structure across species in a dryland stream fish community

description: Dendritic ecological network (DEN) architecture can be a strong predictor
 of spatial genetic patterns in theoretical and simulation studies. Yet,
 interspecific differences in dispersal capabilities and distribution
 within the network may equally affect species’ genetic structuring. We
 characterized patterns of genetic variation from up to ten microsatellite
 loci for nine numerically dominant members of the upper Gila River fish
 community, New Mexico, USA. Using comparative landscape genetics, we
 evaluated the role of network architecture for structuring populations
 within species (pairwise FST) while explicitly accounting for
 intraspecific demographic influences on effective population size (Ne).
 Five species exhibited patterns of connectivity and/or genetic diversity
 gradients that were predicted by network structure. These species were
 generally considered to be small-bodied or habitat specialists. Spatial
 variation of Ne was a strong predictor of pairwise FST for two species,
 suggesting patterns of connectivity may also be influenced by genetic
 drift independent of network properties. Finally, two study species
 exhibited genetic patterns that were unexplained by network properties and
 appeared to be related to nonequilibrium processes. Properties of DENs
 shape community-wide genetic structure but effects are modified by
 intrinsic traits and nonequilibrium processes. Further theoretical
 development of the DEN framework should account for such cases.
description: Riverscape genetics of
 Gila River fishesMicrosatellite
 gentotypes for nine fish species sampled in October-November 2010.
 Microsatellite loci were amplified using PCR and analyzed on an ABI 3130
 automated DNA sequencer. Peaks were scored using ABI software
 GeneMapper.Gila_2010_msat_genotypes_Dryad.xlsx
DOI: 10.15468/dl.jzh7nv
title: Occurrence Download

description: A dataset containing 21912 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phryma"
 ]
}

 The dataset includes 21912 records from 405 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000692-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kb830
title: Data from: Does genetic variation maintained by environmental heterogeneity facilitate adaptation to novel selection?

description: Environmental heterogeneity helps maintain genetic variation in fitness.
 Therefore, one might predict that populations living in heterogeneous
 environments have higher adaptive potential than populations living in
 homogeneous environments. Such a prediction could be useful in guiding
 conservation priorities without requiring detailed genetic studies.
 However, this prediction will be true only if the additional genetic
 variation maintained by environmental heterogeneity can be used to respond
 to novel selection. Here we examine the effect of environmental
 heterogeneity on future adaptability using replicated experimental
 Drosophila melanogaster populations that had previously evolved for ∼100
 generations under one of four selective regimes: constant salt-enriched
 larvae medium, constant cadmium-enriched larvae medium, and two
 heterogeneous regimes that vary either temporally or spatially between the
 two media. Replicates of these experimental populations were subjected to
 a novel heat stress while being maintained in their original larval diet
 selection regimes. Adaptation to increased temperature was measured with
 respect to female productivity and male siring success after ∼20
 generations. For female productivity, there was evidence of adaptation
 overall and heterogeneous populations had a larger adaptive response than
 homogeneous populations. There was less evidence of adaptation overall for
 male siring success and no support for faster adaptation in heterogeneous
 populations.
description: female productivity for
 control population at standard temperatureFemale productivity for
 control population at standard 25 °C. Description for each column in the
 data sheet can be found in a separate sheet named "Variables" in
 the file.female productivity at
 high temperatureFemale productivity for
 both heat selection and control population at high temperature.
 Description for each column in the data sheet can be found in a separate
 sheet named "Variables" in the file.male siring
 success_generation24Male siring success
 assayed in generation 24 at high temperature. Description for each column
 in the data sheet can be found in a separate sheet named
 "Variables" in the file.Supplementary male
 siring success_generation9Male siring success
 assayed in generation 9. Description for each column in the data sheet can
 be found in a separate sheet named "Variables" in the file. The
 data is not included in the analysis in the main
 manuscript.