cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qjq2bvqgg
title: Data for: Warming rates alter sequence of disassembly in experimental communities

description: This study analyzed patterns of species loss in a community of four
 rotifers and six ciliates exposed to three rates of extreme warming.
 Immediately prior to each +0.5°C increase in temperature, we sampled
 replicate communities and identified all surviving species. The sampling
 temperature at which no further organisms of a given species were observed
 alive represented the temperature of loss for that species and replicate.
 Recording the identity of all surviving species at each incremental change
 in temperature allowed us to both observe the sequence of species loss
 from the community (i.e., the sequence of disassembly) and also generate a
 corresponding table of the distinct communities surviving at each
 temperature. To test the effects of warming rate on the sequence of
 disassembly, we analyzed the sequence (order) of species loss of the ten
 species in each replicate. An order of “1” was assigned to the first
 species lost, “2” to the second, “3” to the third, and so on. To assess
 the contribution of warming rate to variability in community composition,
 we compared all of the distinct communities of surviving species that were
 observed in hourly-, daily- and weekly-rate treatments throughout the
 period of ramping temperature. The percentage of all distinct communities
 that were rate-specific (observed in at least one but not all rate
 treatments) provided a quantitative measure of the contribution of warming
 rate (per se) to variability in community composition. Downloaded files
 include: a) temperature of species loss data for hourly, daily and weekly
 rate replicates, b) order of species loss data for hourly, daily and
 weekly rate replicates, and c) R code for Monte Carlo analyses. 
description: See methods in corresponding paper.
description: Microsoft excel and word.
DOI: 10.5061/dryad.b5mkkwhdd
title: Climate change exacerbates nutrient disparities from seafood

description: Seafood is an important source of bioavailable micronutrients supporting
 human health, yet it is unclear how micronutrient production has changed
 in the past, or how climate change will influence its availability. Here,
 combining reconstructed fisheries databases and predictive models, we
 assess nutrient availability from fisheries and mariculture in the past,
 and project their futures under climate change. Since the 1990s,
 availabilities of iron, calcium and omega-3 from seafood for direct human
 consumption has increased but stagnated for protein. Under climate change,
 nutrient availability is projected to decrease disproportionately in
 tropical low-income countries that are already highly dependent on
 seafood-derived nutrients. At 4 oC of warming, nutrient availability is
 projected to decline by ~30% by 2100 in low income countries, while at 1.5
 - 2.0 oC warming, decreases are projected to be ~10%. We demonstrate the
 importance of effective mitigation to support nutritional security of
 vulnerable nations and global health equity.
DOI: 10.5061/dryad.2ngf1vhnn
title: Floral attraction and flower visitors of a subcanopy tropical rainforest tree, F. picrosperma_Data

description: 1. Flowering plants in tropical rainforests rely heavily on pollen vectors
 for successful reproduction. Research into pollination systems in tropical
 rainforests is dominated by canopy species, while subcanopy
 plant-pollinator interactions remain under-represented. The microclimate
 beneath the rainforest canopy is characterised by low light levels and is
 markedly different from the canopy environment that receives more light
 energy. 2. We studied the floral attractants and floral visitors of a
 dioecious, subcanopy tree, Fontainea picrosperma (Euphorbiaceae) in the
 Wet Tropics bioregion of northern Queensland, Australia. 3. We found that
 wind pollination is rare and male and female flowers do not produce
 nectar. Female flowers are likely pollinated due to their perceptual
 similarity to pollen-offering male flowers. Female flowers had the same
 scent profile as male flowers and floral scent was an important floral
 attractant that acted to regulate pollinator behaviour. The two most
 abundant scent compounds present in the floral bouquet were benzyl alcohol
 and 4-oxoisophorone. These compounds are ubiquitous in nature and are
 known to attract a wide variety of insects. Both day-time and night-time
 pollinators contributed to successful pollen deposition on the stigma and
 diurnal flower visitors were identified from several orders of insects
 including beetles, flies, predatory wasps and thrips. Fontainea
 picrosperma is therefore likely to be pollinated by a diverse array of
 small insects. 4. Synthesis. Our data indicates that F. picrosperma has a
 generalist, entomophilous pollination syndrome. The rainforest subcanopy
 is a distinctive environment characterised by low light levels, low or
 turbulent wind speeds and relatively high humidity. Female flowers of F.
 picrosperma exhibit cost saving strategies by not producing nectar and
 mimicking the smell of reward-offering male flowers. Insects
 opportunistically forage on, or inhabit flowers and pollination occurs
 from a pool of small insects with low-energy requirements that are found
 beneath the rainforest canopy.
description: This data set was collected from a combination of field work and
 laboratory work.
description: The data set is in excel file format and should be easily
 interpreted in combination with the methods section of the related
 publication.
DOI: 10.5061/dryad.6t1g1jwzp
title: Environmental variables and occurrence of 13 fish species

description: Species-environment relationships were studied between the occurrence of
 13 fish and lamprey species and 9 mainly map-based environmental variables
 of Finnish boreal small streams. A self-organizing map (SOM) analysis
 showed strong relationships between the fish species and environmental
 variables in a single model (explained variance 55.9%). Besides basic
 environmental variables such as altitude, catchment size, and mean
 temperature, landcover variables were also explored. A logistic regression
 analysis indicated that the occurrence probability of brown trout, Salmo
 trutta L., decreased with an increasing percentage of peatland ditch
 drainage in the upper catchment. Ninespine stickleback, Pungitius
 pungitius (L.), and three-spined stickleback, Gasterosteus aculeatus L.,
 seemed to benefit from urban areas in the upper catchment. Discovered
 relationships between fish species occurrence and land-use attributes are
 encouraging for the development of fish-based bioassessment for small
 streams. The presented ordination of the fish species in the mean
 temperature gradient will help in predicting fish community responses to
 climate change.
description: Electrofishing data from small Finnish streams were gathered
 mainly from a national database.
DOI: 10.5061/dryad.hqbzkh1gj
title: Tree water uptake enhances nitrogen acquisition in a fertilized boreal forest – but not under nitrogen poor conditions

description: Understanding how plant water uptake interacts with acquisition of soil
 nitrogen (N) and other nutrients is fundamental for predicting plant
 responses to a changing environment, but it is an area where models
 disagree. We present a novel isotopic labelling approach which reveals
 spatial patterns of water and N uptake, and their interaction, by trees.
 The stable isotopes 15N and 2H were applied to a small
 area of the forest floor in stands with high and low soil N availability.
 Uptake by surrounding trees was measured. The sensitivity of N acquisition
 to water uptake was quantified by statistical modelling. Trees in the
 high-N stand acquired twice as much 15N as in the low-N stand and
 around half of their N uptake was dependent on water uptake (2H
 enrichment). In contrast, in the low-N stand there was no positive effect
 of water uptake on N uptake.  We conclude that tree N acquisition
 was only marginally dependent on water flux toward the root surface under
 low N conditions but under high-N conditions, the water-associated N
 uptake was substantial. The results suggest a fundamental shift in N
 acquisition strategy under high-N conditions. 
description: Isotopic labelling (deuterium and 15N) in boreal forests (one
 annually N-fertilized, and one N-poor reference stand). One square meter
 of forest floor was labelled (below the moss layer) using 5g
 <sup>15</sup>N (potassium nitrate) and 2x200 ml
 D<sub>2</sub>O. All trees growing within a 14 meter radius of
 the labelled square meter were sampled. In total, 6 plots were labelled
 and sampled (3 in the fertilized stand, and 3 in the reference
 stand). 15N uptake by trees detected via mass
 spectroscopy of needle samples. 2H uptake by trees
 detected via mass spectroscopy of current year stem wood.
 Statistical modelling performed to test connection between water
 uptake and nitrogen uptake. Hypotheses based on
 conclusions from McMurtrie & Näsholm (2018).
DOI: 10.5061/dryad.1g1jwstwf
title: CLSM data of CLE40, CLV3, WUS, BAM1, and CLV1 reporter lines in Arabidopsis thaliana

description: Stem cell homeostasis in plant shoot meristems requires tight coordiantion
 between stem cell proliferation and cell differentiation. In Arabidopsis,
 stem cells express the secreted dodecapeptide CLAVATA3 (CLV3), which
 signals through the leucine-rich repeat (LRR)–receptor kinase CLAVATA1
 (CLV1) and related CLV1-family members to downregulate expression of the
 homeodomain transcription factor WUSCHEL (WUS). WUS protein moves from
 cells below the stem cell domain to the meristem tip and promotes stem
 cell identity, together with CLV3 expression, generating a negative
 feedback loop. How stem cell activity in the meristem centre is
 coordinated with organ initiation and cell differentiation at the
 periphery is unknown. We show here that the CLE40 gene, encoding a
 secreted peptide closely related to CLV3, is expressed in the SAM in
 differentiating cells in a pattern complementary to that of CLV3. CLE40
 promotes WUS expression via BAM1, a CLV1-family receptor, and CLE40
 expression is in turn repressed in a WUS-dependent manner. Together,
 CLE40-BAM1-WUS establish a second negative feedback loop. We propose that
 stem cell homeostasis is achieved through two intertwined pathways that
 adjust WUS activity and incorporate information on the size of the stem
 cell domain, via CLV3-CLV1, and on cell differentiation via CLE40-BAM1.
description: Z-Stacks from the top of inflorescence meristems of Arabidopsis
 thaliana plants were taken with a LSM780/880. Images (z-stacks) were
 analysed using ImageJ.
DOI: 10.5061/dryad.kwh70rz3v
title: Data for: Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus

description: Efforts to understand the genetic underpinnings of phenotypic variation
 are becoming more and more frequent in molecular ecology. Such efforts
 often lead to the identification of candidate regions showing signals of
 association and/or selection. These regions may contain multiple genes and
 therefore validation of which genes are actually responsible for the
 signal is required. In Atlantic salmon (Salmo salar), a large‐effect locus
 for maturation timing, an ecologically important trait, occurs in a
 genomic region including two
 genes, vgll3 and akap11, but data for clearly
 determining which of the genes (or both) contribute to the association
 have been lacking. Here, we take advantage of natural recombination events
 detected between the two candidate genes in a salmon broodstock to reduce
 linkage disequilibrium at the locus, thus enabling delineation of the
 influence of variation at these two genes on early maturation. By rearing
 5,895 males to maturation age, of which 81% had
 recombinant vgll3/akap11 allelic combinations, we found
 that vgll3 single nucleotide polymorphism (SNP)
 variation was strongly associated with early maturation, whereas there was
 little or no association between akap11 SNP variation
 and early maturation. These findings provide strong evidence
 supporting vgll3 as the primary candidate gene in the
 chromosome 25 locus for influencing early maturation. This will
 help guide future research for understanding the genetic processes
 controlling early maturation. This also exemplifies the utility of natural
 recombinants to more precisely map causal variation underlying
 ecologically important phenotypic diversity.
DOI: 10.5061/dryad.ht76hdrg2
title: Knowledge and attitude of infection prevention and control practices among health care workers caring for patients with suspected or confirmed COVID-19

description: Background: COVID-19 pandemic is growing rapidly, accounting for an
 increasing proportion of cases worldwide. Infection in healthcare
 facilities enhances very likely the local outbreaks, impacting mainly the
 elderly and vulnerable populations. All activities used to minimize the
 risk of infection spread are referred to as infection control measures.
 Therefore, this study aimed to; determine the proportion of SARS-COV2
 infection among heath care workers (HCWs) caring for patients with
 suspected or confirmed COVID-19, assess their knowledge and attitude to
 infection control practices and recommend strategies to decrease the risk
 of SARS-COV2 infection among them. Methods: This is an electronic-based
 cross-sectional analytical study conducted in Egypt to assess the
 knowledge, attitude of HCWs to infection control practices for patients
 with suspected or confirmed COVID-19 infection. A purposive sample of 520
 participants was targeted through electronic data collection, and they
 were asked to fill a structured questionnaire form and submit it. Results:
 The study revealed that 11% of the HCWs were infected with SARS-Cov2.
 Their mean knowledge percent score regarding infection control prevention
 practices was 36.19 ± 11.26. The higher rate of infection was among
 Internal Medicine specialists (75%) with little experience (76.7%),
 affiliated with the Ministry of Health (46.7%). About (89%) mentioned that
 the leading cause of infection was the shortage in Personal Protective
 Equipment PPE. Conclusion: There was a high proportion of SARS-COV2
 infection among HCWs in EGYPT, especially among those working in Cairo
 governorate in Internal Medicine Departments, with fewer years of
 experience, due to lack of knowledge about infection prevention and
 control measures and shortage of Personal Protective Equipment in their
 working facilities.
description: An online data collection
 method was used in line with lockdown measures conducted in Egypt to
 achieve social distancing. A Google form was created, and participants
 were requested to complete and submit it. A questionnaire link was shared
 with groups for HCWs on social media forums (Facebook, Twitter, and
 WhatsApp). Furthermore, authors have shared the link personally to HCWs in
 their network areas The data was coded and exported on a
 data sheet prepared on Microsoft Excel program, version 2013. (SPSS
 version 24) was used for data analysis. Simple descriptive statistics were
 used for the summary of quantitative data and frequencies used for
 qualitative data. The bivariate relationship was displayed in
 cross-tabulations, and a comparison of proportions was performed using the
 chi-square and Fisher's exact tests where appropriate. Independent
 T-test was used to compare normally distributed quantitative data. The
 level of significance was set at P-value &lt;0.05.
DOI: 10.5061/dryad.p2ngf1vqw
title: Maintenance of phenotypic plasticity is linked to oxidative stress in spadefoot toad larvae

description: Phenotypic plasticity allows organisms to improve the match between their
 phenotype and heterogeneous environments. Theoretical models have argued
 that costs of maintaining the sensory and response machinery necessary for
 adaptive phenotypic plasticity are important determinants to the evolution
 of plasticity. Despite recurrent arguments invoking putative metabolic
 costs associated with maintenance of cellular machinery, no studies have
 yet attempted to quantify it from a molecular standpoint. Here we
 experimentally examine physiological differences across genotypes
 (sibships) of spadefoot toad larvae with different degrees of plasticity
 in response to predator cues. We observed marked differences across
 sibships in developmental, growth and morphological responses to
 predators, and tested whether increased plasticity was associated with
 oxidative stress or immune suppression. We observed that more plastic
 sibships experienced higher antioxidant enzymatic activity when reared in
 the absence of predator cues, i.e. not expressing their plastic responses.
 The degree of plasticity was also associated with higher lipid
 peroxidation and slightly greater granulocyte-to-lymphocyte ratio. Higher
 antioxidant activity in highly plastic sibships suggests that maintenance
 of phenotypic plasticity may be linked to energy demanding metabolic
 processes. Our findings suggest that having the potential to produce
 plastic responses may incur oxidative and immunological costs. In the long
 term, such maintenance costs may erode individual fitness and even
 constrain the evolution of plasticity. To our knowledge, this is the first
 empirical evidence indicating the existence of a physiological cost to the
 maintenance of phenotypic plasticity.
DOI: 10.5061/dryad.9s4mw6mgs
title: Data and code for Winter conditions structure extratropical patterns of species richness of amphibians, birds, and mammals globally

description: This repository contains the dataset analyzed in 'Winter conditions
 structure extratropical patterns of species richness of amphibians, birds,
 and mammals globally' - published in the journal Global Ecology and
 Biogeography - and the R code used to generate the correlations,
 generalized additive models, and related figures presented in the
 manuscript. Column descriptions for the data can be found in the
 associated README.txt file. Please refer to the manuscript for further
 detail on the variables and how they were derived. The Winter Indices
 (WIs) were derived using satellite remote sensing data from optical
 (MODIS, snow cover) and microwave (MEaSUREs freeze/thaw, frozen ground)
 sensors. The species richness maps were derived using IUCN range maps for
 individual species of amphibians, birds, and mammals (data requests can be
 made here: https://www.iucnredlist.org/resources/spatial-data-download).
 Climatic varibales were derived from WorldClim v2.0 data, elevation from
 USGS GMTED2010 data, and primary productivity from the cumulative dynamic
 habitat index available here: http://silvis.forest.wisc.edu/maps-data/.
DOI: 10.5061/dryad.wpzgmsbn7
title: Verification of CcpA gene knockout

description: To verify whether the CcpA gene was successfully deleted, we designed the
 primer for PCR. The primer was designed across the upstream and
 downstream sequences of the CcpA gene, with a size of about
 1827bp. Results showed that two (1827bp and 1985bp) PCR products
 (WT2 and KO2) were produced, then the amplified DNA products of
 WT2 and KO2 were electrophoresed on a 1% (wt/vol) agarose gel, and
 sequenced by Shanghai Sangon Biological Engineering Technology and
 Services Co., Ltd. for further verification. The results of DNA sequencing
 confirmed that the CcpA deletion strain was successfully constructed.
DOI: 10.5061/dryad.wh70rxwnp
title: The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

description: The robustness and sensitivity of gene networks to environmental changes
 is critical for cell survival. How gene networks produce specific,
 chronologically ordered responses to genome-wide perturbations, while
 robustly maintaining homeostasis, remains an open question. We analysed if
 short- and mid-term genome-wide responses to shifts in RNA polymerase
 (RNAP) concentration are influenced by the known topology and logic of the
 transcription factor network (TFN) of Escherichia coli. We found that, at
 the gene cohort level, the magnitude of the single-gene, mid-term
 transcriptional responses to changes in RNAP concentration can be
 explained by the absolute difference between the gene’s numbers of
 activating and repressing input transcription factors (TFs).
 Interestingly, this difference is strongly positively correlated with the
 number of input TFs of the gene. Meanwhile, short-term responses showed
 only weak influence from the TFN. Our results suggest that the global
 topological traits of the TFN of E. coli shape which gene cohorts respond
 to genome-wide stresses.
description: Collection and data generation are described in the Methods
 sections of the main manuscript. Data processing
 methods and the software packages used are described in the Methods
 sections of the main manuscript.
DOI: 10.5061/dryad.rn8pk0p9w
title: Taxonomic and functional homogenization of farmland birds along an urbanization gradient in a tropical megacity

description: Urbanization is a major driver of land use change and biodiversity
 decline. While most of the ongoing and future urbanization hot spots are
 located in the Global South, the impact of urban expansion on agricultural
 biodiversity and associated functions and services in these regions has
 widely been neglected. Additionally, most studies assess biodiversity
 responses at local scale (α-diversity), however, ecosystem functioning is
 strongly determined by compositional and functional turnover of
 communities (β-diversity) at regional scales. We investigated taxonomic
 and functional β-diversity of farmland birds across three seasons on 36
 vegetable farms spread along a continuous urbanization gradient in
 Bangalore, a South Indian megacity. Increasing amount of grey area in the
 farm surroundings was the dominant driver affecting β-diversity and
 resulting in taxonomic and functional homogenization of farmland bird
 communities. Functional diversity losses were higher than expected from
 species declines (i.e. urbanization acts as an environmental filter), with
 particular losses of functionally important groups such as insectivores of
 crop pests. Moreover, urbanization reduced functional redundancy of bird
 communities, which may further weaken ecosystems resilience to future
 perturbations. Our study underscores urbanization as a major driver of
 taxonomic and functional homogenization of species communities in
 agricultural systems, potentially threatening crucial ecosystem services
 for food production.
DOI: 10.5061/dryad.4qrfj6q9r
title: Infanticide by females is a leading source of juvenile mortality in a large social carnivore

description: Social animals benefit from their group-mates, so why do they sometimes
 kill each other’s offspring? Using 30 years of data from multiple groups
 of wild spotted hyenas, we address three critical aims for understanding
 infanticide in any species: (1) quantify the contribution of infanticide
 to overall mortality (2) describe the circumstances under which
 infanticide occurs and (3) evaluate hypotheses about the evolution of
 infanticide. We find that, although observed only rarely, infanticide is
 in fact a leading source of juvenile mortality. Infanticide accounted for
 24% of juvenile mortality, and 1 in 10 hyenas born in our population
 perished due to infanticide. In all observed cases of infanticide, killers
 were adult females, but victims could be of both sexes. Of four hypotheses
 regarding the evolution of infanticide, we found the most support for the
 hypothesis that infanticide in spotted hyenas reflects competition over
 social status among matrilines.