cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7v1qg
title: Data from: Predicting bird phenology from space: satellite-derived vegetation green-up signal uncovers spatial variation in phenological synchrony between birds and their environment

description: Population-level studies of how tit species (Parus spp.) track the
 changing phenology of their caterpillar food source have provided a model
 system allowing inference into how populations can adjust to changing
 climates, but are often limited because they implicitly assume all
 individuals experience similar environments. Ecologists are increasingly
 using satellite-derived data to quantify aspects of animals'
 environments, but so far studies examining phenology have generally done
 so at large spatial scales. Considering the scale at which individuals
 experience their environment is likely to be key if we are to understand
 the ecological and evolutionary processes acting on reproductive phenology
 within populations. Here, we use time series of satellite images, with a
 resolution of 240 m, to quantify spatial variation in vegetation green-up
 for a 385-ha mixed-deciduous woodland. Using data spanning 13 years, we
 demonstrate that annual population-level measures of the timing of peak
 abundance of winter moth larvae (Operophtera brumata) and the timing of
 egg laying in great tits (Parus major) and blue tits (Cyanistes caeruleus)
 is related to satellite-derived spring vegetation phenology. We go on to
 show that timing of local vegetation green-up significantly explained
 individual differences in tit reproductive phenology within the
 population, and that the degree of synchrony between bird and vegetation
 phenology showed marked spatial variation across the woodland. Areas of
 high oak tree (Quercus robur) and hazel (Corylus avellana) density showed
 the strongest match between remote-sensed vegetation phenology and
 reproductive phenology in both species. Marked within-population variation
 in the extent to which phenology of different trophic levels match
 suggests that more attention should be given to small-scale processes when
 exploring the causes and consequences of phenological matching. We discuss
 how use of remotely sensed data to study within-population variation could
 broaden the scale and scope of studies exploring phenological synchrony
 between organisms and their environment.
description: DATASET - Predicting
 bird phenology from spaceGreat tit and blue tit
 breeding data and habitat data was collected in the field. The MOD09Q1 and
 MYD09Q1 data products used to calculate EVI are courtesy of the online
 Data Pool at the NASA Land Processes Distributed Active Archive Center (LP
 DAAC), USGS/Earth Resources Observation and Science (EROS) Center, Sioux
 Falls, South Dakota. Cloudiness data is based on the same MODIS sensors as
 in the case of EVI data, this time using the MOD08 product (collection
 5.1, accessed through Level 1 and Atmosphere Archive and Distribution
 System – LAADS, ladsweb.nascom.nasa.gov).
DOI: 10.5061/dryad.4q230
title: Data from: Disentangling the ‘brown world’ faecal-detritus interaction web: dung beetle effects on soil microbial properties

description: Many ecosystem services are sustained by the combined action of
 microscopic and macroscopic organisms, and shaped by interactions between
 the two. However, studies tend to focus on only one of these two
 components. We combined the two by investigating the impact of macrofauna
 on microbial community composition and functioning in the context of a
 major ecosystem process: the decomposition of dung. We compared bacterial
 communities of pasture soil and experimental dung pats inhabited by one
 (Aphodius), two (Aphodius and Geotrupes), or no dung beetle genera.
 Overall, we found distinct microbial communities in soil and dung samples,
 and that the communities converged over the course of the experiment.
 Characterising the soil microbial communities underlying the dung pats
 revealed a significant interactive effect between the microflora and
 macrofauna, where the diversity and composition of microbial communities
 was significantly affected by the presence or absence of dung beetles. The
 specific identity of the beetles had no detectable impact, but the
 microbial evenness was lower in the presence of both Aphodius and
 Geotrupes than in the presence of Aphodius alone. Differences in microbial
 community composition were associated with differences in substrate usage
 as measured by Ecoplates. Moreover, microbial communities with similar
 compositions showed more similar substrate usage. Our study suggests that
 the presence of macrofauna (dung beetles) will modify the microflora
 (bacteria) of both dung pats and pasture soil, including community
 diversity and functioning. In particular, the presence of dung beetles
 promotes the transfer of bacteria across the soil–dung interface,
 resulting in increased similarity in community structure and functioning.
 The results demonstrate that to understand how microbes contribute to the
 ecosystem process of dung decomposition, there is a need to understand
 their interactions with larger co-occurring fauna.
description: LH-PCR, Ecoplate, CO2
 and Dung mass loss dataData_for_Dryad_Slade_Oikos.xlsx
DOI: 10.15468/dl.crn2bd
title: Occurrence Download

description: A dataset containing 6302 records in GBIF matching the query:
SELECT
 '415' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 37.42857426825602
 AND decimalLatitude &lt;= 41.89415215079384
 AND decimalLongitude &gt;= 69.0769461528656
 AND decimalLongitude &lt;= 77.9229717807129
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 6302 records were derived from 139 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001636-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.17209
title: Data from: A characterization of autumn nocturnal migration detected by weather surveillance radars in the northeastern US

description: Billions of birds migrate at night over North America each year. However,
 few studies have described the phenology of these movements, such as
 magnitudes, directions, and speeds, for more than one migration season and
 at regional scales. In this study, we characterize density, direction, and
 speed of nocturnally migrating birds using data from 13 weather
 surveillance radars in the autumns of 2010 and 2011 in the northeastern
 US. After screening radar data to remove precipitation, we applied a
 recently developed algorithm for characterizing velocity profiles with
 previously developed methods to document bird migration. Many hourly radar
 scans contained wind-borne "contamination," and these scans also
 exhibited generally low overall reflectivities. Hourly scans dominated by
 birds showed nightly and seasonal patterns that differed markedly from
 those of low reflectivity scans. Bird migration occurred during many
 nights, but a smaller number of nights with large movements of birds
 defined regional nocturnal migration. Densities varied by date, time, and
 location but peaked in the second and third deciles of night during the
 autumn period when the most birds were migrating. Migration track (the
 direction to which birds moved) shifted within nights from south
 southwesterly to southwesterly during the seasonal migration peaks; this
 shift was not consistent with a similar shift in wind direction. Migration
 speeds varied within nights, although not closely with wind speed.
 Airspeeds increased during the night; groundspeeds were highest between
 the second and third deciles of night, when the greatest density of birds
 was migrating. Airspeeds and groundspeeds increased during the fall
 season, although groundspeeds fluctuated considerably with prevailing
 winds. Significant positive correlations characterized relationships among
 bird densities at southern coastal radar stations and northern inland
 radar stations. The quantitative descriptions of broad-scale nocturnal
 migration patterns presented here will be essential for biological and
 conservation applications. These descriptions help to define migration
 phenology in time and space, fill knowledge gaps in avian annual cycles,
 and are useful for monitoring long-term population trends of migrants.
 Furthermore, these descriptions will aid in assessing potential risks to
 migrants, particularly from structures with which birds collide and
 artificial lighting that disorients migrants.
description: Farnsworth et al 2015
 Data meta_all version 11 August 2015 DRYAD VERSIONPlease see README file
 for description of data headers.
DOI: 10.5061/dryad.f98s6
title: Data from: Transcriptome-wide differential gene expression in Bicyclus anynana butterflies: female vision-related genes are more plastic

description: cave-adapted species down-regulate the expression of vision genes or even
 lose their eyes and associated eye genes entirely. Alternatively,
 organisms that live in fluctuating environments, with different
 requirements for vision at different times, may evolve phenotypic
 plasticity for expression of vision genes. Here we use a global
 transcriptomic and candidate gene approach to compare gene expression in
 the heads of a polyphenic butterfly. Bicyclus anynana have two seasonal
 forms that display sexual dimorphism and plasticity in eye morphology, and
 female-specific plasticity in opsin gene expression. Non-choosy dry season
 females down-regulate opsin expression, consistent with the high
 physiological cost of vision. To identify other genes associated with
 sexually dimorphic and seasonally plastic differences in vision we
 analyzed RNA-Sequencing data from whole head tissues. We identified two
 eye development genes (klarsicht and warts homologs) and an eye pigment
 biosynthesis gene (henna) differentially expressed between seasonal forms.
 By comparing sex-specific expression across seasonal forms, we found that
 klarsicht, warts, henna, and another eye development gene (domeless) were
 plastic in a female-specific manner. In a male-only analysis, white (w)
 was differentially expressed between seasonal forms. RT-PCR confirmed that
 warts and white are expressed in eyes only, whereas klarsicht, henna and
 domeless are expressed in both eyes and brain. We find that differential
 expression of eye development and eye pigment genes is associated with
 divergent eye phenotypes in B. anynana seasonal forms, and that there is a
 larger effect of season on female vision-related genes.
description: Bicyclus_anynana_transcriptome.fastaBicyclus anynana de novo transcriptome created using Trinity. The assembly was made using four trimmed and parsed RNA-Seq libraries: 1 dry season female, 1 wet season female, 1 dry season male, and 1 wet season male.Trinity_4_trimmed.fasta.gz
DOI: 10.6084/m9.figshare.31158151
title: Original data of seasonal peat frozen ground

description: This dataset is related to the geotechnical characteristics and formation processes of seasonal peat frozen ground in the Western Sichuan Plateau, China, consisting mainly of two parts: laboratory tests and DEM simulations.
DOI: 10.6084/m9.figshare.31158151.v1
title: Original data of seasonal peat frozen ground

description: This dataset is related to the geotechnical characteristics and formation processes of seasonal peat frozen ground in the Western Sichuan Plateau, China, consisting mainly of two parts: laboratory tests and DEM simulations.
DOI: 10.5061/dryad.38578
title: Data from: Spatial structure of above-ground biomass limits accuracy of carbon mapping in rainforest but large scale forest inventories can help to overcome

description: Precise mapping of above-ground biomass (AGB) is a major challenge for the
 success of REDD+ processes in tropical rainforest. The usual mapping
 methods are based on two hypotheses: a large and long-ranged spatial
 autocorrelation and a strong environment influence at the regional scale.
 However, there are no studies of the spatial structure of AGB at the
 landscapes scale to support these assumptions. We studied spatial
 variation in AGB at various scales using two large forest inventories
 conducted in French Guiana. The dataset comprised 2507 plots (0.4 to 0.5
 ha) of undisturbed rainforest distributed over the whole region. After
 checking the uncertainties of estimates obtained from these data, we used
 half of the dataset to develop explicit predictive models including
 spatial and environmental effects and tested the accuracy of the resulting
 maps according to their resolution using the rest of the data. Forest
 inventories provided accurate AGB estimates at the plot scale, for a mean
 of 325 Mg.ha-1. They revealed high local variability combined with a weak
 autocorrelation up to distances of no more than10 km. Environmental
 variables accounted for a minor part of spatial variation. Accuracy of the
 best model including spatial effects was 90 Mg.ha-1 at plot scale but
 coarse graining up to 2-km resolution allowed mapping AGB with accuracy
 lower than 50 Mg.ha-1. Whatever the resolution, no agreement was found
 with available pan-tropical reference maps at all resolutions. We
 concluded that the combined weak autocorrelation and weak environmental
 effect limit AGB maps accuracy in rainforest, and that a trade-off has to
 be found between spatial resolution and effective accuracy until adequate
 “wall-to-wall” remote sensing signals provide reliable AGB predictions.
 Waiting for this, using large forest inventories with low sampling rate
 (&lt;0.5%) may be an efficient way to increase the global coverage of
 AGB maps with acceptable accuracy at kilometric resolution.
description: Forest Inventories used
 for AGB estimates in French GuianaThe xls file contains
 one readme and two datasets derived from two forest surveys :
 "inventaire papetier" inventory done by CTFT between 1974 and
 1976 (coded "pap"), and "inventaire habitat" inventory
 done by ONF between 2006 and 2013 (coded "hab").The datasets
 include plots coordinates and areas, estimates of mean wood specific
 gravity (WSG) for each plots, and the number of trees per DBH classes for
 each plots.DataAGB.xlsx
DOI: 10.5061/dryad.g28c8
title: Data from: Phylogenetic analysis reveals positive correlations between adaptations to diverse hosts in a group of pathogen-like herbivores

description: A jack of all trades can be master of none – this intuitive idea underlies
 most theoretical models of host-use evolution in plant-feeding insects,
 yet empirical support for trade-offs in performance on distinct host
 plants is weak. Trade-offs may influence the long-term evolution of host
 use while being difficult to detect in extant populations, but host-use
 evolution may also be driven by adaptations for generalism. Here we used
 host-use data from insect collection records to parameterize a
 phylogenetic model of host-use evolution in armored scale insects, a large
 family of plant-feeding insects with a simple, pathogen-like life history.
 We found that a model incorporating positive correlations between
 evolutionary changes in host performance best fit the observed patterns of
 diaspidid presence and absence on nearly all focal host taxa, suggesting
 that adaptations to particular hosts also enhance performance on other
 hosts. In contrast to the widely invoked trade-off model, we advocate a
 “toolbox” model of host-use evolution in which armored scale insects
 accumulate a set of independent genetic tools, each of which is under
 selection for a single function but may be useful on multiple hosts.
description: Diaspidid_host_use_binary_byHostSpeciesPresence/absence data for armored scale insects on host genera compiled from the Hemiptera Tri-Trophic Database (https://research.amnh.org/pbi/locality/)Diaspidid_host_use_binary_byHostGenusPresence/absence data for armored scale insects on host species compiled from the Hemiptera Tri-Trophic Database (https://research.amnh.org/pbi/locality/)Diaspidid_phylogenyPhylogenetic tree of armored scale insects used in the paper.Analysis_R_scriptsR scripts for running the analyses from this paper.
DOI: 10.5061/dryad.td570
title: Data from: Preservational bias controls the fossil record of pterosaurs

description: Pterosaurs, a Mesozoic group of flying archosaurs, have become a focal
 point for debates pertaining to the impact of sampling biases on our
 reading of the fossil record, as well as the utility of sampling proxies
 in palaeo-diversity reconstructions. The completeness of the pterosaur
 fossil specimens themselves potentially provides additional information
 that is not captured in existing sampling proxies, and might shed new
 light on the group's evolutionary history. Here we assess the quality
 of the pterosaur fossil record via a character completeness metric based
 on the number of phylogenetic characters that can be scored for all known
 skeletons of 172 valid species, with averaged completeness values
 calculated for each geological stage. The fossil record of pterosaurs is
 observed to be strongly influenced by the occurrence and distribution of
 Lagerstätten. Peaks in completeness correlate with Lagerstätten deposits,
 and a recovered correlation between completeness and observed diversity is
 rendered non-significant when Lagerstätten species are excluded. Intervals
 previously regarded as potential extinction events are shown to lack
 Lagerstätten and exhibit low completeness values: as such, the apparent
 low diversity in these intervals might be at least partly the result of
 poor fossil record quality. A positive correlation between temporal
 patterns in completeness of Cretaceous pterosaurs and birds further
 demonstrates the prominent role that Lagerstätten deposits have on the
 preservation of smaller bodied organisms, contrasting with a lack of
 correlation with the completeness of large-bodied sauropodomorphs.
 However, we unexpectedly find a strong correlation between sauropodomorph
 and pterosaur completeness within the Triassic–Jurassic, but not the
 Cretaceous, potentially relating to a shared shift in environmental
 preference and thus preservation style through time. This study highlights
 the importance of understanding the relationship between various
 taphonomic controls when correcting for sampling bias, and provides
 additional evidence for the prominent role of sampling on observed
 patterns in pterosaur macroevolution.
description: Appendix
 S1Excel file containing
 all data on pterosaur completeness, proxies, groupings, and model
 outputs.
DOI: 10.5061/dryad.4061p
title: Data from: Inter- and Intraspecific Conflict between Parasites over Host Manipulation

description: Host manipulation is a common strategy by which parasites alter the
 behaviour of their host to enhance their own fitness. In nature, hosts are
 usually infected by multiple parasites. This can result in a conflict over
 host manipulation. Studies of such a conflict in experimentally infected
 hosts are rare. The cestode Schistocephalus solidus (S) and the nematode
 Camallanus lacustris (C) use copepods as their first intermediate host.
 They need to grow for some time inside this host before they are infective
 and ready to be trophically transmitted to their subsequent fish host.
 Accordingly, not yet infective parasites manipulate to suppress predation.
 Infective ones manipulate to enhance predation. We experimentally infected
 lab-bred copepods in a manner that resulted in copepods harbouring (1) an
 infective C plus a not yet infective C or S or (2) an infective S plus a
 not yet infective C. An infective C completely sabotaged host manipulation
 by any not yet infective parasite. An infective S partially reduced host
 manipulation by a not yet infective C. We hence show experimentally that a
 parasite can reduce or even sabotage host manipulation exerted by a
 parasite from a different species.
description: data_experiment_1basic data: Data on each copepod used in the experiment. latency: results for each copepod on each day for how long it took to resume moving after a simulated predator attack. Behavioral data: Data on the position of each copepod during each two second interval and whather or not it moved for all days on which behavior was recordeddata_experiment_2basic data: Data on each copepod used in the experiment. latency: results for each copepod on each day for how long it took to resume moving after a simulated predator attack. Behavioral data: Data on the position of each copepod during each two second interval and whather or not it moved for all days on which behavior was recorded
DOI: 10.5061/dryad.m8q78
title: Data from: Effect of soil pH increase by biochar on NO, N2O and N2 production during denitrification in acid soils

description: Biochar (BC) application to soil suppresses emission of nitrous- (N2O) and
 nitric oxide (NO), but the mechanisms are unclear. One of the most
 prominent features of BC is its alkalizing effect in soils, which may
 affect denitrification and its product stoichiometry directly or
 indirectly. We conducted laboratory experiments with anoxic slurries of
 acid Acrisols from Indonesia and Zambia and two contrasting BCs produced
 locally from rice husk and cacao shell. Dose-dependent responses of
 denitrification and gaseous products (NO, N2O and N2) were assessed by
 high-resolution gas kinetics and related to the alkalizing effect of the
 BCs. To delineate the pH effect from other BC effects, we removed part of
 the alkalinity by leaching the BCs with water and acid prior to
 incubation. Uncharred cacao shell and sodium hydroxide (NaOH) were also
 included in the study. The untreated BCs suppressed N2O and NO and
 increased N2 production during denitrification, irrespective of the effect
 on denitrification rate. The extent of N2O and NO suppression was
 dose-dependent and increased with the alkalizing effect of the two BC
 types, which was strongest for cacao shell BC. Acid leaching of BC, which
 decreased its alkalizing effect, reduced or eliminated the ability of BC
 to suppress N2O and NO net production. Just like untreated BCs, NaOH
 reduced net production of N2O and NO while increasing that of N2. This
 confirms the importance of altered soil pH for denitrification product
 stoichiometry. Addition of uncharred cacao shell stimulated
 denitrification strongly due to availability of labile carbon but only
 minor effects on the product stoichiometry of denitrification were found,
 in accordance with its modest effect on soil pH. Our study indicates that
 stimulation of denitrification was mainly due to increases in labile
 carbon whereas change in product stoichiometry was mainly due to a change
 in soil pH.
description: Biochar pH effects on
 denitrification in acid soilsThe data was generated
 through lab incubation. Each excel file has many sheets. The sheet
 labelled "Materials" has information that is important for
 understanding the data in other sheets in the same excel
 file.Biochar_Denitrification
 paper.zip