cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.80gb5mkr3
title: Microarthropod abundance data of a drought experiment comparing organic and conventional farming

description: In Central Europe summer droughts are increasing in frequency which
 threatens production and biodiversity in agroecosystems. The potential of
 different farming systems to mitigate detrimental drought effects on soil
 animals is largely unknown. We investigated the effects of simulated
 drought on the abundance and community composition of soil microarthropods
 (Collembola, Oribatida, Meso­‑, Pro‑ and Astigmata) in winter wheat fields
 under long-term conventional and organic farming in the DOK trial,
 Switzerland. We simulated drought by excluding 65% of the ambient
 precipitation during the wheat growing season from March to June 2017. The
 abundance of Collembola and Oribatida declined more consistently in
 conventionally compared to organically managed fields under simulated
 drought. The abundance of Collembola as well as Meso‑, Pro‑ and Astigmata,
 but not the abundance of Oribatida, increased in deeper soil layers due to
 simulated drought, suggesting vertical migration as drought avoidance
 strategy. The species composition of Oribatida communities, but not of
 Collembola communities, differed significantly between drought treatments
 as well as between farming systems. Soil carbon content was a major factor
 structuring Oribatida communities. Our results suggest that organic
 farming buffers negative effects of drought on soil microarthropods,
 presumably due to higher soil carbon content, and associated higher soil
 moisture and improved soil structure. This potential of organic farming
 systems to mitigate consequences of future droughts on soil biodiversity
 is promising and needs further exploration across larger climatic and
 spatial scales and should be extended to other groups of soil biota.
DOI: 10.5061/dryad.j0zpc86f2
title: The influence of transpiration on foliar accumulation of salt and nutrients under salinity in poplar (Populus × canescens)

description: Increasing salinity is one of the major drawbacks for plant growth.
 Besides the ion itself being toxic to plant cells, it greatly interferes
 with the supply of other macronutrients like potassium, calcium and
 magnesium. However, little is known about how sodium affects the
 translocation of these nutrients from the root to the shoot. The major
 driving force of this translocation process is thought to be the water
 flow through the xylem driven by transpiration. To dissect the effects of
 transpiration from those of salinity we compared salt stressed, ABA
 treated and combined salt- and ABA treated poplars with untreated
 controls. Salinity reduced the root content of major nutrients like K+,
 Ca2+ and Mg2+. Less Ca2+ and Mg2+ in the roots resulted in reduced leaf
 Ca2+ and leaf Mg2+ levels due to reduced stomatal conductance and reduced
 transpiration. Interestingly, leaf K+ levels were positively affected in
 leaves under salt stress although there was less K+ in the roots under
 salt. In response to ABA, transpiration was also decreased and Mg2+ and
 Ca2+ levels decreased comparably to the salt stress treatment, while K+
 levels were not affected. Thus, our results suggest that loading and
 retention of leaf K+ is enhanced under salt stress compared to merely
 transpiration driven cation supply.
DOI: 10.5061/dryad.hqbzkh1gg
title: Geochemical data for: Intense overpressurization at basaltic open-conduit volcanoes as inferred by geochemical signals: The case of the Mt. Etna December 2018 eruption

description: The reported dataset is annexed to the article “Intense overpressurization
 at basaltic open-conduit volcanoes as inferred by geochemical signals: the
 case of the Mt Etna December 2018 eruption”. It consists of five types of
 parameters: soil CO2 flux from Mt Etna flanks, CO2/SO2 molar ratio of the
 volcano plume, SO2 and HCl fluxes by volcano plume, and He isotope ratio
 in some peripheral gas emissions, all of them recorded in the period
 2017–2019. The data come from continuous monitoring networks installed on
 Mt Etna and from discrete samplings carried out at specific sites, all the
 monitoring facilities being supported by the INGV-Civil Defence joint
 surveillance program.
DOI: 10.5061/dryad.1jwstqjvg
title: Habitat specialization by wildlife reduces pathogen spread in urbanizing landscapes

description: Urban areas are expanding globally, with far-reaching ecological
 consequences, including for wildlife-pathogen interactions. Wildlife show
 tremendous variation in their responses to urbanization; even within a
 single population, some individuals can specialize on urban or natural
 habitat types. This specialization could alter pathogen impacts on host
 populations via changes to wildlife movement and aggregation. Here, we
 build a mechanistic model to explore how habitat specialization in urban
 landscapes affects interactions between a mobile host population and a
 density-dependent specialist pathogen that confers no immunity. We model
 movement on a network of resource-stable urban sites and
 resource-fluctuating natural sites, where hosts are either urban
 specialists, natural specialists, or generalists that use both patch
 types. We find that, for generalists, natural and partially urban
 landscapes produce the highest infection prevalence and mortality, driven
 by high movement rates at natural sites and high densities at urban sites.
 However, habitat specialization protects hosts from these negative effects
 of partially urban landscapes by limiting movement between patch types.
 These findings suggest that habitat specialization can benefit populations
 by reducing infectious disease transmission, but by reducing movement
 between habitat types could also carry the cost of reducing other
 movement-related ecosystem functions such as seed dispersal and
 pollination.
DOI: 10.5061/dryad.k98sf7m6b
title: Exploring the effects of extreme polyandry on estimates of sexual selection and reproductive success

description: Multiple mating by females can dramatically alter selection on males by
 creating indirect interactions between rivals via sperm competition.
 Exactly how this behavior alters the relationship between male mating and
 fertilization success depends on multiple factors: re-mating frequency,
 sperm usage patterns, and mating assortment (the extent to which the most
 promiscuous individuals mate with each other). Here we explore the role
 these elements play in determining sexual selection in a highly
 polygyandrous species, the squash bug Anasa tristis. Using replicated
 semi-natural enclosures, in which individuals were able to freely interact
 for a two-week period, we tracked matings between individuals and
 subsequent female offspring production. Multiple mating was extremely
 common, resulting in very high levels of sperm competition intensity.
 However, network analysis revealed that the most promiscuous males mated
 with less polyandrous females, and therefore experienced lower levels of
 sperm competition. As a result, estimated male reproductive success
 increased with mating success, but this relationship varied according to
 the mode of sperm utilization with which it was calculated. Furthermore,
 females with more mating partners produced more offspring, suggesting they
 also benefit from mating multiply. Our findings highlight that polyandry
 has numerous and complex effects on sexual selection which may only be
 exposed when examined under naturalistic conditions.
description: Dataset was collected from hourly scan sampling of experimental
 individuals. Dyadic pairs of mating interactions between males and females
 were extracted from images and each experimental individual's
 interactions have been summarised in the uploaded dataset. 
description: ReadMe file included in uploaded Excel sheet.
DOI: 10.5061/dryad.fj6q573v7
title: Adaptive shifts underlie the divergence in wing morphology in bombycoid moths

description: The evolution of flapping flight is linked to the prolific success of
 insects. Across Insecta, wing morphology diversified, strongly impacting
 aerodynamic performance. In the presence of ecological opportunity,
 discrete adaptive shifts and early bursts are two processes hypothesized
 to give rise to exceptional morphological diversification. Here, we use
 the diverse sister-families Sphingidae and Saturniidae to answer how the
 evolution of aerodynamically important traits is linked to clade
 divergence and through what process(es) these traits evolve. The agile
 Sphingidae evolved the hover-feeding behavior, while adult Saturniidae
 lack functional mouth parts and rely on a fixed energy budget. Although
 disparity was established early, we find that Sphingidae undergo an
 adaptative shift in wing morphology coincident with life history and
 behavior divergence, evolving small high aspect-ratio wings advantageous
 for power reduction that can be moved at high frequencies, beneficial for
 flight control. In contrast, Saturniidae, which do not feed as adults,
 evolved large wings and morphology which surprisingly does not reduce
 aerodynamic power, but could contribute to their erratic flight behavior,
 aiding in predator avoidance. We suggest that after the evolution of
 flapping flight, diversification of wing morphology can be potentiated by
 adaptative shifts, shaping the diversity of wing morphology across
 insects.
description: This data set includes several data types.
 First, a phylogenetic tree of bombycoid moths inferred using a
 dataset of 606 loci of 57 species and one outgroup. Here we include the
 raw tree, the dated tree, and the locus recovery data.
 Next, we included the outputs of digitized moth body and wing
 shapes that include data for the forewing, hindwing, and combined wing.
 These data are the raw data used in this paper. All digitized outputs are
 from images of museum specimens from the Florida Museum of Natural
 History. We also include these images as well. Finally,
 we include the output from the analyis of the wing and body data which is
 the data on the functional metrics calculated for the wings and body of
 each species used in this study. These files are .csv files that begin
 with the title Table D and then include an extension in the file name to
 note if it is forewing (FW), hindwind (HW), combined wing (CW) or body
 (BODY).
DOI: 10.6078/d12m6c
title: High throughput measurement of single HeLa cell volume growth and cell cycle progression using FXm

description: The way proliferating animal cells coordinate the growth of their mass,
 volume, and other relevant size parameters is a long-standing question in
 biology. Studies focusing on cell mass have identified patterns of mass
 growth as a function of time and cell cycle phase, but little is known
 about volume growth. To address this question, we improved our
 fluorescence exclusion method of volume measurement (FXm) and obtained
 1696 single cell volume growth trajectories of asynchronous HeLa cells
 expressing hgeminin-GFP. The data were obtained over four independent
 replicates. For each cell, depending on the phase of the cell cycle it was
 observed, the following information is indicated: time of birth (onset of
 cytokinesis), time of G1/S transition (onset of the expression of
 hgeminin-GFP), time of entry into mitosis (onset of mitotic cell
 rounding). All the FXm movies and single cell volume trajectories were
 visually assessed to check and correct any mistake in the automated
 segmentation and lineage tracking that would give false volume
 fluctuations measurements. We thus present a dataset of well curated,
 high-throughput measurement of single cell volume available for the
 investigation of volume growth in animal cells. We find that, during most
 of the cell cycle, volume growth is close to exponential and proceeds at a
 higher rate in S-G2 than in G1. Comparing the data with a mathematical
 model, we establish that the cell-to-cell variability in volume growth
 arises from constant-amplitude fluctuations in volume steps, rather than
 fluctuations of the underlying specific growth rate. We hypothesize that
 such ‘additive noise’ could emerge from the processes that regulate volume
 adaptation to biophysical cues, such as tension or osmotic pressure.
 Future work combining our single cell volume measurements with the
 analysis of single cell mass growth curves will likely provide interesting
 perspectives.
description: The protocol for the experiments and data analysis is described
 in details in the related article (Cadart et al., eLife,
 doi.org/10.7554/eLife.70816)
DOI: 10.25338/b8f33p
title: Reference transcriptomes for three species of sacoglossan sea slug

description: Understanding how species may respond to climate change is of paramount
 importance. Species that occupy highly heterogenous environments such as
 intertidal zone estuarine habitats, provide an ideal test case for
 examining phenotypic and genomic adaptations to different environmental
 conditions, which may influence their response to rapidly shifting
 climatic conditions. The California coast is projected to experience
 changes in both temperature and salinity, which currently vary seasonally
 and latitudinally. Using comparative transcriptomics, I documented
 patterns of positive selection between the northern dwelling
 planktotrophic sacoglossan sea slug Alderia modesta which is remarkably
 tolerant of low temperatures and low salinities and its southern congener
 Alderia willowi which exhibits a striking flexibility for larval type in
 response to seasonally shifting changes in temperature and salinity. Out
 of over four thousand one-to-one orthologous genes, I found a signal of
 positive selection between Alderia willowi and A. modesta for genes
 involved in cell membrane and cell transport, particularly ion homeostasis
 (Aquaporin), cell-cell signal transduction, and phosphorylation (NADH
 dehydrogenase) Positive selection for ion homeostasis in A. modesta has
 implications for its ability to tolerate the lower salinity of its
 northern range and in A. willowi substitutions in NADH may assist in high
 temperature tolerance of its southern California habitats. Identifying
 these candidate genes enables future studies of their functionalization as
 we seek to understand the relationship between phenotype and genotype in
 species whose phenotypes are influenced by environmental conditions.
description: <b>de novo reference transcriptome
 assembly</b> Prior to de novo transcriptome
 assembly, adapters were removed and reads were quality trimmed in
 Trimmomatic using parameters for paired reads, removing leading a trailing
 low quality base pairs (LEADING:2 TRAILING:2), and a sliding window of 4
 base-pairs removing basepairs when quality drops below 15
 (SLIDINGWINDOW:4:15, and keeping reads of a minimum length of 25
 (MINLEN:25)(Faircloth 2013 ). Trimmed reads were assembled in Trinity
 (v2.4.0) using default parameters (Haas et al., 2013). I assessed assembly
 quality with BUSCO (Simão et al., 2015) against the metazoan and eukaryote
 databases.
description: Three reference transcriptomes for the following sacoglossan
 species: Alderia modesta, Alderia willowi, and Olea hansineensis in fasta
 format.
DOI: 10.5061/dryad.zs7h44j8s
title: Millennial-scale change on a Caribbean reef system that experiences hypoxia

description: Coastal hypoxia has become an increasingly acknowledged threat to coral
 reefs that is potentially intensifying because of increased input of
 anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a
 semi-enclosed system that experiences hypoxia in deeper waters which
 occasionally expand into shallow coral reefs, suffocating most aerobic
 benthic life. To explore the long-term history of reefs in the bay we
 extracted reef matrix cores from two reefs that today experience
 contrasting patterns of oxygenation. We constructed a 1800-year-long
 record of gastropod assemblages and isotope compositions from six U-Th
 chronologically-constrained reef matrix cores. We extracted two cores from
 each reef at 3 m water depth and two additional cores from a deeper part
 (4.8 m) of the hypoxia-exposed reef. Results show that the deeper part of
 the hypoxic reef slowed in growth and stopped accreting approximately 1500
 years BP while the shallow part of the reef continued to accrete to the
 present day, in agreement with a model of expanding hypoxia at this time.
 Our proxy-based approach suggests that the patterns of increasing
 herbivores and decreasing carbon isotope values in the deeper part of the
 hypoxic reef may have been driven by an increase in hypoxia via
 eutrophication caused by either natural changes or human impacts. Similar
 patterns in these paleoindicators occurred in the shallow part of the
 hypoxic reef during the last few decades. This suggests that hypoxia may
 be expanding to depths as shallow as 3 m and that shallow reefs are
 experiencing greater risk due to increased human activity.
DOI: 10.5061/dryad.b8gtht7cp
title: Plotting receiver operating characteristic and precision-recall curves from presence and background data

description:     The receiver operating characteristic (ROC) and
 precision-recall (PR) plots have been widely used to evaluate the
 performances of species distribution models. Plotting the ROC/PR curves
 requires a traditional test set with both presence and absence data
 (namely PA approach), but species absence data are usually not available
 in reality. Plotting the ROC/PR curves from presence-only data while
 treating background data as pseudo absence data (namely PO approach) may
 provide misleading results. In this study we propose a new approach to
 calibrate the ROC/PR curves from presence and background data with
 user-provided information on a constant c, namely PB approach. Here c
 defines the probability that species occurrence is detected (labeled), and
 an estimate of c can also be derived from the PB-based ROC/PR plots given
 that a model with good ability of discrimination is available. We used
 five virtual species and a real aerial photography to test the
 effectiveness of the proposed PB-based ROC/PR plots. Different models (or
 classifiers) were trained from presence and background data with various
 samples sizes. The ROC/PR curves plotted by PA approach were used to
 benchmark the curves plotted by PO and PB approaches. Experimental results
 show that the curves and areas under curves by PB approach are more
 similar to that by PA approach as compared with PO approach. The PB-based
 ROC/PR plots also provide highly accurate estimations of c in our
 experiment. We conclude that the proposed PB-based ROC/PR plots can
 provide valuable complements to the existing model assessment methods, and
 they also provide an additional way to estimate the constant c (or species
 prevalence) from presence and background data.
description: Data were collected and
 analyzed as described
 in https://doi.org/10.22541/au.161648888.85984872/v1
DOI: 10.5061/dryad.zcrjdfnc8
title: Data for: The association between personalities, alternative breeding strategies, and reproductive success in dunnocks

description: Although consistent between-individual differences in behaviour (i.e.
 animal personality) are ubiquitous in natural populations, relatively few
 studies have examined how personalities influence the formation of social
 relationships. Yet, behavioural characteristics of both sexes might be key
 when it comes to pair-bond formation, and the cooperation with partners to
 successfully rear offspring. We here use a wild population of dunnocks
 (Prunella modularis) to first investigate whether individuals mate
 non-randomly (i.e. assortative mating) with regard to four behavioural
 traits – flight-initiation distance (FID), provisioning, activity, and
 vigilance – that differ in repeatability and have previously been
 associated with mating patterns and fitness in other species. Second, we
 test whether an individual’s FID is associated with variability in the
 dunnocks’ mating system (i.e. monogamous pairs vs. polygamous groups).
 Finally, we determine whether FID and provisioning of males and females
 associate with their reproductive success. We found no statistical support
 for assortative mating in FID between males and females. Interestingly, in
 polygamous groups, co-breeding males differed in their FIDs with dominant
 alpha-males having significantly shorter FIDs compared to subordinate
 beta-males. Moreover, there was evidence for assortative mating in
 provisioning for alpha-males and females in polygamous groups. We also
 found that male provisioning influenced reproductive success of both
 sexes, while female provisioning rates only positively correlated with her
 own but not their partner(s) reproductive output. Our results suggest that
 personality differences may have important implications for social
 relationships, the emergence of different mating patterns and ultimately
 reproductive success within populations.
description: This research was conducted as part of a long-term study on a
 wild population of dunnocks (<i>Prunella modularis</i>) at the
 Dunedin Botanic Garden, Dunedin, New Zealand between 2012-2014. The data
 and accompanied R-scripts for the following statistical analyses are
 included: 01. Repeatability (activity,
 flight-initiation-distance, vigilance, provisioning)
 02. Assortative mating (flight-initiation-distance,
 provisioning) 03. Association between FID and mating
 system 04. Associations between FID or provisioning and
 reproductive success We conducted all data analyses in
 <i>R</i> v. 4.0.2 (R Core Team, 2020), and all models were
 fitted within a Bayesian framework using Markov chain Monte Carlo (MCMC)
 methods in the <i>MCMCglmm</i> package (Hadfield, 2010).
 Please also refer to the Methods section of the main manuscript for a
 detailed description of behavioural traits and conducted
 analyses.
DOI: 10.5061/dryad.d2547d82z
title: Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas

description: Populations of large wildlife have declined in many landscapes around the
 world, and have been replaced or displaced by livestock. The consequences
 of these changes on the transfer of organic matter (OM) and nutrients from
 terrestrial to aquatic ecosystems are not well understood. We used
 behavioural data, excretion and egestion rates and C: N: P stoichiometry
 of dung and urine of zebu cattle, to develop a metabolism-based estimate
 of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We
 also directly measured the deposition of OM and urine by cattle into the
 river during watering. Per head, zebu cattle excrete and/or egest 25.6 g
 dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of
 OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To
 replace loading rates OM of an individual hippopotamus by cattle, around
 100 individuals will be needed, but much less for different elements. In
 parts of the investigated sub-catchments loading rates by cattle were
 equivalent to or higher than that of the hippopotamus. Changing these
 patterns of OM and nutrients transport and cycling are having significant
 effects on the structure and functioning of both terrestrial and aquatic
 ecosystems.
description: The data was collected by monitoring and observing animal
 behaviour in streams and rivers. Insitu physico-chemical and nutrient
 parameters were also determined at livestock watering points. Samples from
 field sampling were also analyzed in the laboratory.
DOI: 10.6084/m9.figshare.31166539
title: Warming-enhanced soil methane uptake is suppressed by nitrogen deposition in a saline-alkali grassland

description: The data for the study of Warming-enhanced soil methane uptake is suppressed by nitrogen deposition in a saline-alkali grassland
DOI: 10.6084/m9.figshare.31166539.v1
title: Warming-enhanced soil methane uptake is suppressed by nitrogen deposition in a saline-alkali grassland

description: The data for the study of Warming-enhanced soil methane uptake is suppressed by nitrogen deposition in a saline-alkali grassland