cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31166103.v1
title: Additional file 1 of HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations

description: Additional file 1: Table S1. List of the 49 publications used for blood metabolite list compilation. Table S2. List of 3,950 metabolites included in HUBMet, with HUBMet ID, common name, and category. Table S3. The metabolite-protein associations curated in HUBMet with validated evidence level and validation results based on an independent dataset. Table S4. Metabolite-protein network analysis results, including centrality measurements, functional annotations, and enrichment analysis results of metabolites and proteins within each community. Table S5. Tissue relevance analysis results for metabolite-tissue pairs with high reliability. Table S6. Statistical results for the case study in HUBMet. Table S7. Kappa scores of all the available metabolite sets in HUBMet.
DOI: 10.5061/dryad.c866t1g6s
title: Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics

description: Differences in the geographic scale and depth of phylogeographic structure
 across codistributed taxa can reveal how microevolutionary processes such
 as population isolation and persistence drive diversification. In turn,
 environmental heterogeneity, species’ traits, and historical biogeographic
 barriers may influence the potential for isolation and persistence. Using
 extensive SNP data and a combination of population genetic summary
 statistics and landscape genomic analyses, we explored predictors of the
 scale and depth of phylogeographic structure in codistributed lizard taxa
 from the topographically and climatically complex monsoonal tropics (AMT)
 of Australia. We first resolved intraspecific lineages and then tested
 whether genetic divergence across space within lineages is related to
 isolation by distance, resistance and/or environment and whether these
 factors differ across genera or between rock-related versus habitat
 generalist taxa. We then tested whether microevolutionary processes within
 lineages explain differences in the geographic scale and depth of
 intraspecific phylogeographic lineages. The results indicated that
 landscape predictors of phylogeographic structure differ between taxa.
 Within lineages, there was prevalent isolation by distance, but the
 strength of isolation by distance is independent of the taxonomic family,
 habitat specialization, and climate. Isolation by environment is the
 strongest predictor of landscape-scale genetic divergence for all taxa,
 with both temperature and precipitation acting as limiting factors. The
 strength of isolation by distance does not predict the geographic scale of
 the phylogeographic structure. However, more localized lineages had higher
 mean individual heterozygosity and less negative Tajima's D. This
 result implies that finer-scale phylogeographic structuring within species
 is associated with larger and more stable populations and, hence,
 persistence.
DOI: 10.5061/dryad.cfxpnvx55
title: Data from: Males benefit personally from family life: evidence from a wild burying beetle population

description: Family life in animals is often considered as beneficial for offspring but
 costly for parents. However, parents might also profit from remaining
 aggregated within a family unit, especially if a nutrient-rich resource is
 used for reproduction. We aimed to reveal the potential personal benefits
 of breeding within a family environment for male Nicrophorus vespilloides,
 a species of burying beetles that use small vertebrate cadavers to raise
 their larvae. We previously hypothesized that males obtain an advantage
 from remaining with their family, because they themselves can feed from
 the cadaver. This, in turn, enables them to produce more sex pheromone,
 thereby making them more attractive to females after leaving their brood.
 However, whether such personal benefits arise under natural conditions is
 currently unclear because we have no knowledge of the nutritional
 condition of wild beetles. If carrion is abundant anyways, feeding from a
 vertebrate cadaver during breeding might not have a noticeable positive
 effect on the males’ body condition. In the current study, we caught wild
 males with a natural feeding history and compared their body mass and
 attractiveness before and after participating in family life. We show that
 wild males gain weight during breeding and attract more and larger females
 afterwards. Our study suggests that access to a highly nutrient-rich meal
 can be a driver of the evolution of family life and eventually biparental
 care. Males benefit indirectly from defending the resource and offspring
 against competitors and benefit personally by a higher chance of mating
 again after breeding.
description: Excel file with two spreadsheets. The first spreadsheet contains
 all raw data on male pronotum width, body mass at different time points,
 carcass mass, the number of attracted males and females before and after
 breeding and of the control group, weight change during breeding and the
 time from breeding until second exposure in the field. The second
 spreadsheet contains the pronotum size of each attracted beetle allocated
 to the respective male.
DOI: 10.5061/dryad.jq2bvq88k
title: A trail pheromone mediates the mutualism between ants and aphids

description: Mutualisms, like the ones between ants and aphids, evolve and persist when
 benefits outweigh the costs from the interactions between the partners. We
 show here that the trail pheromone of the red imported fire ant,
 Solenopsis invicta, can enhance these benefits by suppressing aphid
 walking dispersal and stimulating their reproduction. The cotton aphid,
 Aphis gossypii, was found to readily perceive and respond to two specific
 trail pheromonal components. Both Z,E-a-farnesene and E,E-a-farnesene
 suppressed walking dispersal of apterous aphids, whereas only
 Z,E-a-farnesene also increased aphid reproduction rate. This inter-species
 function of the trail pheromone increases and prolongs the availability of
 honeydew as a key food source for the ants. The aphid colony, meanwhile,
 benefits from faster population growth and continuous ant-provided
 protection. These findings reveal a novel mechanism by which ants and
 aphids both increase the benefits that they provide to each other, thereby
 likely enhancing the stability of their mutualistic relationship.
DOI: 10.5061/dryad.mw6m905wr
title: Scavenging beetles control the temporal response of soil communities to carrion decomposition

description: 1. Carrion is a frequent but overlooked source of nutrients to the soil.
 The decomposition of carrion is accelerated by invertebrate scavengers but
 the impact of the scavengers on below-ground biota and its functions is
 scarcely known. 2. We conducted a laboratory experiment to investigate the
 effects of the burying beetle Nicrophorus vespilloides on the soil
 community of a temperate broadleaved forest. We assembled microcosms from
 soil collected from an oak woodland and treated them with mouse (Mus
 musculus) carcasses and mating pairs of burying beetles (♀+♂) in a
 factorial design with control soils. We sampled independent replicates
 over time to investigate how the beetles affect soil microarthropods and
 microbial biomass (bacteria and fungi) in relation to soil pH and organic
 matter content. 3. The beetle treatment initially reduced total microbial
 biomass and abundance of major groups of microarthropods relative to the
 control soil. At the same time, organic matter increased in the beetle
 treatment and then dropped to the pre-beetle level (i.e. soil baseline) at
 the end of the beetle breeding cycle (2 weeks). The rapid temporal changes
 in organic matter were mimicked by the relative abundances of the dominant
 microarthropod groups, with Oribatida relatively more abundant than
 Collembola and predaceous mites in the beetle treatment. The overall final
 effect of the beetle (relative to the laboratory control) on
 microarthropods was negative but the beetle kept these variables within
 the levels observed for freshly collected soil (baseline), while the final
 effect on pH was positive, and most likely driven by the surplus of
 nutrients from the carcass and biochemical changes triggered by the
 decomposition process. 4. In nature, scavenging invertebrates are
 widespread. Our study demonstrates that beetles breeding in carcasses
 regulate the dynamics of key components of the soil food web, including
 microbial biomass, changes in the relative abundances of dominant
 microarthropods, and soil organic matter and pH. Given the abundance of
 these beetles in nature, the study implies that the distribution of these
 beetles is a key driver of variation in soil nutrient cycling in
 woodlands.
description: See information on the methods of the associated paper in
 Functional Ecology.
DOI: 10.6084/m9.figshare.31166136
title: Additional file 3 of Down the drain: exploring wastewater’s role in coastal microbiome transformations

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166136.v1
title: Additional file 3 of Down the drain: exploring wastewater’s role in coastal microbiome transformations

description: Supplementary Material 3.
DOI: 10.6084/m9.figshare.31166139
title: Additional file 4 of Down the drain: exploring wastewater’s role in coastal microbiome transformations

description: Supplementary Material 4.
DOI: 10.6084/m9.figshare.31166139.v1
title: Additional file 4 of Down the drain: exploring wastewater’s role in coastal microbiome transformations

description: Supplementary Material 4.
DOI: 10.5061/dryad.4tmpg4f9m
title: Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations

description: It has been widely hypothesised that the productivity of an ecosystem
 affects the number of species that it can support. Despite decades of
 study, the nature, extent, and underlying mechanisms of this relationship
 are unclear. One suggested mechanism is the “more individuals” hypothesis
 (MIH). This proposes that productivity controls the number of individuals
 in the ecosystem, and that more individuals can be divided into a greater
 number of species before their population size is sufficiently small for
 each to be at substantial risk of extinction. Here, we test this
 hypothesis using REvoSim: an individual-based eco-evolutionary system that
 simulates the evolution and speciation of populations over geological
 time, allowing phenomena occurring over timescales that cannot be easily
 observed in the real world to be evaluated. The individual-based nature of
 this system allows us to remove assumptions about the nature of speciation
 and extinction that previous models have had to make. Many of the
 predictions of the MIH are supported in our simulations: rare species are
 more likely to undergo extinction than common species, and species
 richness scales with productivity. However, we also find support for
 relationships that contradict the predictions of the strict MIH: species
 population size scales with productivity, and species extinction risk is
 better predicted by relative than absolute species size. Furthermore, we
 show that the scaling of species richness with productivity depends upon
 the ability of species to partition niche space. Consequently, we suggest
 that the MIH is applicable only to ecosystems where niches are not already
 saturated with species, and where partitioning is therefore still
 possible. Some hypotheses regarding patterns of biodiversity implicitly or
 explicitly overlook niche theory in favour of neutral explanations, as has
 historically been the case with the MIH. Our simulations demonstrate that
 niche theory exerts a control on the applicability of the MIH. --
description: This datasets consists of data collected from the text files
 output by the REvoSim eco-evolutionary system. These text files were
 processed using several scripts written in the Python programming
 language, which are available as supplementary information alongside the
 related manuscript.
description: The term "Evenness", referred to in these data,
 describes the Shannon's Evenness Index of the population sizes of all
 species sampled in the simulation in question. Some
 values are missing at low energy levels from the analysis of mean
 individual fitness. This is because, as noted in the data, these
 simulations contained no sampled species and, as such, did not have a mean
 individual fitness value.
DOI: 10.5061/dryad.51c59zw88
title: Acute kidney disease among Zambian adults initiating tenoforvir disoproxil fumarate-based antiretroviral therapy

description: Tenofovir disoproxil fumarate (TDF)-based antiretroviral therapy ART is
 the commonest first-line regimen worldwide; however, it causes
 nephrotoxicity that primarily occurs in the first three to six months
 following initiating therapy. The TDF-associated nephrotoxicity can
 manifest as AKI that may lead to direct complications including permanent
 loss of kidney function, chronic kidney disease (CKD), end-stage kidney
 disease (ESKD) requiring dialysis and to indirect complications such as
 cardiovascular diseases.Tenofovir disoproxil fumarate (TDF)-based
 antiretroviral therapy ART is the commonest first-line regimen worldwide;
 however, it causes nephrotoxicity that primarily occurs in the first three
 to six months following initiating therapy. The TDF-associated
 nephrotoxicity can manifest as AKI that may lead to direct complications
 including permanent loss of kidney function, chronic kidney disease (CKD),
 end-stage kidney disease (ESKD) requiring dialysis and to indirect
 complications such as cardiovascular diseases. We prospectively followed
 205 ART-naïve Zambian adults at the adult infectious disease research
 centre (AIDC) in Lusaka for three months from the day of initiating
 TDF-based therapy to determine the incidence of TDF-associated
 nephrotoxicity. We defined TDF-associated nephrotoxicity as meeting any of
 the following criteria: 1) An episode of estimated glomerular filtration
 rate (eGFR)&lt; 60ml/ min/1.73m2 for&lt; 3 months, 2) reduced eGFR
 by&gt; 35% for&lt; 3 months or 3) increased serum creatinine
 by&gt; 50% in 3 months. A total of 45 (22%) developed TDF-associated
 nephrotoxicity; but there was no statistically significant difference in
 the demographics, clinical and laboratory parameters between the patients
 that did and those that did not suffer nephrotoxicity. We concluded that a
 mere assessment of baseline clinical and laboratory characteristics was
 not enough to distinguish or classify patients’ risk for TDF-associated
 nephrotoxicity.
description: Participants were
 systematically randomly sampled to include every other
 Antiretroviral-naive adult that clinicians initiated on tenofovir
 disoproxil fumarate based therapy. The study was a prospective
 observational cohort of 205 participants. The study was done within the
 confines of standard clinical practice, where only candidates that the
 clinicians initiated on TDF-based therapy were invited to participate in
 the study. The investigators had no control over whom the clinicians
 initiated on therapy; they initiated participants based on the Zambian
 national ART treatment guidelines and their expert clinical discretion of
 the risk for TDF-associated nephrotoxicity.
description: 1. There are no missing values in the dataset.
 2. Age has been categorised as below 20, above 50 and the ages in
 between those categorised in 5 years. Ages beyond those extremes may be
 identifiable. 3. BMI categorised as less than 18.5,
 less than 25, less than 30 and above 30
DOI: 10.5061/dryad.cz8w9gj3q
title: A horizontally transmitted Parasitoid Killing Factor protects insects from parasitoids

description: Interkingdom competition occurs between hymenopteran parasitoids and
 insect viruses sharing the same insect hosts. It has been assumed that
 parasitoid larvae die with the death of infected host or as result of
 competition for host resources. Herein we describe a gene family,
 parasitoid killing factor (pkf), that encodes proteins toxic to
 parasitoids of the Microgastrinae group and determines parasitism success.
 Pkfs are found in several entomopathogenic DNA virus families and in some
 lepidopteran genomes. We provide evidence of equivalent and specific
 toxicity against endoparasites for PKFs found in Entomopoxvirus,
 Ascovirus, Baculovirus and Lepidoptera through a mechanism that elicits
 apoptosis in the cells of susceptible parasitoids. This highlights the
 evolutionary arms race between parasitoids, viruses and their insect
 hosts.
DOI: 10.6086/d1pd72
title: Data for: Successful management of invasive rats across a fragmented landscape

description: This dataset is from the manuscript "Successful management of
 invasive rats across a fragmented landscape" and provides
 the details on snap trap and tracking card data in a broadscale rat
 removal effort 2011-2015 in the Upper Waiakea Forest Reserve on
 the Island of Hawai‘i. It describes the successful trapping efforts as
 well as long term tracking data, which allow us to describe patterns of
 habitat use of non-native vertebrate species in these naturally fragmented
 forests in Hawaii.
description: All methodological details are provided in the paper. In short,
 we monitored 34 forest fragments (kipuka) on the windward NE slope of
 Mauna Loa Volcano within the Upper Waiakea Forest Reserve on the Island of
 Hawai‘i. We selected 16 of these kipuka for rat removal using snap traps
 distributed within the kipuka as well as along the fragment edges. We also
 used ink tracking cards to monitor activity.
description: <strong>rat.removal.data.forDRYAD.xlsx
 </strong>provides the snap trap data. Rats worksheet provides data
 as to the number and species of rats collected in snap traps by kipuka
 (including all kipuka details such as size) and date. Rat.size worksheet
 provides detailed data as to the body size details for collected rats in
 snap.traps, including species, sex, and weight, as well as details as to
 the bait type used in the snap trap and date collected. Bycatch worksheet
 provides details as to the number of bycatch collected in snaptraps by
 date and kipuka.
 <strong>tracking.data.forDRYAD.xlsx</strong> provides
 the tunnel data. Tunnels.all worksheet provides the data for the four
 years of quarterly tracking tunnel monitoring with details of what species
 left the tracks kipuka, treatment (control or rat removal), tunnel height
 and height of tunnel. Grids.2012 worksheet provides the same details
 summarized for the ground level extensive trapping in 2012. Location
 indicates whether the tunnels were in the kipuka: 0 is perimeter and 1 is
 grid. Non.rat.tunnels worksheet combines these datasets (summarized by
 kipuka, tunnel height, and dataset (grid.only vs regular quarterly
 monitoring), and looks at the proportion of hits by non-target species,
 bait, and kipuka (including all kipuka details).
DOI: 10.6084/m9.figshare.31166166
title: Additional file 2 of Spatial transcriptomics reveals the spatiotemporal response of garden asparagus stem cells to Phomopsis asparagi infection

description: Additional file 2: Table S1. Spatial transcriptome data quality reports Table S2. Characteristics of distinct clusters and gene expression. Table S3. The list of 74 marker genes and their average expression levels across 5 cell types. Table S4. Primers for RT-qPCR.
DOI: 10.6084/m9.figshare.31166166.v1
title: Additional file 2 of Spatial transcriptomics reveals the spatiotemporal response of garden asparagus stem cells to Phomopsis asparagi infection

description: Additional file 2: Table S1. Spatial transcriptome data quality reports Table S2. Characteristics of distinct clusters and gene expression. Table S3. The list of 74 marker genes and their average expression levels across 5 cell types. Table S4. Primers for RT-qPCR.
DOI: 10.5061/dryad.nzs7h44rg
title: Migration and tolerance shape host behavior and response to parasites infection

description: Numerous theoretical models have demonstrated that migration, a seasonal
 animal movement behavior, can minimize the risks and costs of parasite
 infection. Past work on migration-infection interactions assumes migration
 is the only strategy available to organisms for dealing with the parasite
 infection, that is they migrate to a different environment to recover or
 escape from infection. Thus, migration is similar to the non-spatial
 strategy of resistance, where hosts prevent infection or kill parasites
 once infected. However, an alternative defense strategy is to tolerate the
 infection and experience a lower cost to the infection. To our knowledge,
 no studies have examined how migration can change based on combining two
 host strategies (migration and tolerance) for dealing with parasites. In
 this paper, we aim to understand how both parasite transmission and
 infection tolerance can influence the host’s migratory behavior. We
 constructed a model that incorporates two host strategies (migration and
 tolerance) to understand whether allowing for tolerance affects the
 proportion of the population that migrates at equilibrium in response to
 infection. We show that the benefits of tolerance can either decrease or
 increase the host’s migration. Also, if the benefit of migration is great,
 then individuals are more likely to migrate regardless of the presence of
 tolerance. Finally, we find that the transmission rate of parasite
 infection can either decrease or increase the tolerant host’s migration,
 depending on the cost of migration. These findings highlight that adopting
 two defense strategies is not always beneficial for the hosts. Instead, a
 single strategy is often better, depending on the costs and benefits of
 the strategies and infection pressures. Our work further suggests that
 multiple host-defense strategies as a potential explanation for the
 evolution of migration to minimize the parasite infection. Moreover,
 migration can also affect the ecological and evolutionary dynamics of
 parasite-host interactions. 
description: Figure 2 folder [files] 
 gammas_only_cm.R - codes for creating a figure (2a)
 alpha_only_cm.R - codes for creating a figure (2b)
 figure2.Rmd - codes for combining all the figures (2a, 2b, 2c)
 together Figure 3 folder [files]
 cT_cM.R - codes for creating a figure (3a)
 figure3.Rmd - codes for creating a figure 3 including code for
 figure (3b). Figure 4 folder
 [files] figure4.Rmd - codes for creating a
 figure 4. Figure 5 folder
 [files] fig5a.R- codes for creating a
 figure (5a) fig5b.R- codes for creating a figure
 (5b) figure5.Rmd - codes for combining all the
 figures (5a & 5b) together