cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bzkh1898t
title: Data from: Effects of climate and topography on the diversity anomaly of plants disjunctly distributed in eastern Asia and eastern North America

description: Aim: Differences in physiography have been proposed to explain
 the diversity anomaly for vascular plants between environmentally similar
 regions of eastern Asia (EAS) and eastern North America (ENA). Here, we
 use plant species within disjunct genera to examine whether differences in
 topography contribute to the diversity anomaly and whether the
 richness–environment relationships differ between regions. Disjuncts are
 used to ensure that the diversity anomaly relates to post-disjunction
 evolution and diversification rather than regional differences in clade
 ages or immigration. Location: EAS and ENA. Time period: Current.
 Major taxa studied: Plant taxa disjunctly distributed in EAS and ENA.
 Method: We compiled county-level plant distribution data, and calculated
 species richness and variables of topography and climate within unit grid
 cells. We compared estimated coefficients of region effects among models,
 where richness was fitted with or without topography and climate.
 Topography and climate were also used to separately model within-region
 spatial diversity patterns using spatial simultaneous autoregressive error
 models. Results: The coefficients of region effects varied from -0.776 for
 the model only including region to -0.309 when topography was controlled
 for, but remained significant. Climate dominated the spatial diversity
 patterns in ENA. In contrast, the influence of climate (14.2%) on species
 richness was weaker than that of topography (18.3%) in warm EAS. Relations
 to elevation and temperature varied between regions, shifting between
 positive and negative relationships in several cases. Main conclusion: Our
 results demonstrate that variability in local topography contributes to
 the strong regional anomaly in plant species richness between EAS and ENA.
 Nevertheless, the diversity anomaly persists after controlling for local
 topography and climate. EAS and ENA also exhibit contrasting
 richness–environment relationships, providing another divergent aspect
 between the EAS-ENA disjunct floras. Our findings highlight that regional
 differences in topography or other environmental factors may underlie the
 diversity anomaly.
description: Explanations of each column are provided in the readme file.
 Details of data sources are shown in the associated manuscript.
 <strong>Data within 100-km and 200-km grid
 cells:</strong>
 Dataset_Effects_of_climate_and_topography_on_the_diversity_anomaly_of_plants_disjunctly_distributed_in_eastern_Asia_and_eastern_North_America.xlsx
DOI: 10.5061/dryad.fqz612jsh
title: Molecular simulation and tyrosinase inhibitory studies of arbutin-6′-undecenoate

description: Arbutin is frequently used as an inhibitor of tyrosinase, a key enzyme in
 the biosynthesis of melanin. Tyrosinase inhibitors are highly sought after
 by the pharmaceutical and cosmetic industries. Given the increasing
 interest in such products, we performed a one-step synthesis of acylated
 arbutin by protease-catalysed transesterification using undecylenic acid
 ester as acyl donor. We simulated the docking of tyrosinase with the
 product using AutoDock Vina and identified its activity as a tyrosinase
 inhibitor by in vitro assay against mushroom tyrosinase. We successfully
 synthesized arbutin-6′-undecenoate by the formation of an ester linkage
 between the carboxyl residue (C1″) of undecylenic acid ester and the C6′
 glucose moiety of arbutin. Results showed that the binding affinity of
 arbutin-6′-undecenoate with tyrosinase was higher than that of arbutin. In
 addition, arbutin-6′-undecenoate inhibits tyrosinase activity effectively
 (IC50 = 0.16 mM). The results of this study strongly suggest that
 arbutin-6′-undecenoate is a promising candidate as tyrosinase inhibitor.
DOI: 10.5061/dryad.v9s4mw6w7
title: Bat-flower interaction networks in Caatinga reveal generalized associations and temporal stability

description: Seasonal variation in precipitation regimes influences species composition
 and plant-animal interactions. Such temporal variation is especially
 relevant in the Brazilian Caatinga, the largest Seasonally Dry Tropical
 Forest in South America, where bat pollination is unusually frequent in
 comparison with other tropical plant communities. Here, we describe
 seasonal and annual variations of the interaction networks between
 nectarivorous bats and flower species in the Caatinga. Five species of
 nectar-feeding bats interacted with 30 plant species. Nectarivorous bats
 showed high levels of interaction overlap, which contributed to ecological
 generalization (low specialization and modularity) and lack of nestedness
 in the interaction networks. This pattern was consistent across seasons
 and years. Chiropterophilous and non-chiropterophilous plants were equally
 important components of the interaction network. The generalized
 interaction patterns found may be a necessary condition for the
 persistence of nectarivorous bats and their specialized plants in the
 environmentally harsh and variable Caatinga. The underappreciated
 generalized interactions of bats with plants calls for studies testing the
 effectiveness of bats in pollinating the plants they visit, including
 those not typically categorized as “bat-flowers”.
DOI: 10.5061/dryad.n5tb2rbw2
title: BEE-STEWARD: a research and decision support software for effective land management to promote bumblebee populations

description: The demand for agent-based models to explore the effects of environmental
 change on pollinator population dynamics is growing. However, models need
 a simple yet flexible interface to enable adoption by a wide range of
 stakeholders. We introduce BEE-STEWARD: a research and
 decision-support software tool, enabling researchers, policy-makers, land
 management advisors, and practitioners to predict and compare the
 effects of bee-friendly management interventions on bumblebee populations
 over several years. BEE-STEWARD integrates the BEESCOUT
 and Bumble-BEEHAVE agent-based models of bumblebee behaviour,
 colony growth and landscape exploration into a user-friendly interface,
 with reconstructed code, and expanded functionality. Bespoke automatic
 reports can be created to illustrate how different land management
 interventions can affect the densities of bumblebees and their colonies
 over time. BEE-STEWARD could be an important virtual test-bed for
 scientists exploring the impacts of different stressors on bumblebees and
 used by those with little or no modelling experience, enabling a shared
 methodology between research, policy, and practice.
description: Data for input files, supporting informationa and software for
 the BEE-STEWARD  software tool
DOI: 10.5061/dryad.f7m0cfxw8
title: Diverse arsenic-containing lipids in the surface ocean

description: Arsenic is present at nanomolar levels throughout the ocean, and microbes
 assimilate this potentially toxic element due to its similarity to
 inorganic phosphorus. Although dissolved arsenic has been a focus of
 several oceanographic studies, the size and chemical character of the
 particulate arsenic pool is poorly understood. We measured particulate
 arsenic in five samples from the open ocean and determined the
 contribution of arsenic-containing lipids to this pool. Here we show that
 the accumulation of arsenic into lipids is a widespread phenomenon in the
 surface ocean. Particulate arsenic concentrations were 15 to 42 pmol L−1
 with 7–20% of the particulate arsenic pool within arsenolipids. We found
 that arsenosugar phospholipids dominated the arsenolipid pools in our
 samples with a minor component of arsenohydrocarbons and other
 unidentified lipids. A significant portion of the arsenosugar
 phospholipids (up to 35%) were present as previously undescribed mixed
 acyl ether lipids, suggesting a bacterial source.
description: Surface samples for particulate arsenic speciation and
 quantification were collected from five locations noted in Table 1 (more
 details in Table S1). These samples include two from oligotrophic
 subtropical regions: one from the North Pacific (ALOHA: A Long-Term
 Oligotrophic Habitat Assessment) and one from the North Atlantic (BATS:
 Bermuda Atlantic Time Series). Three additional samples were collected
 from the equatorial upwelling influenced Eastern Tropical North Pacific
 (ETNP), including two offshore samples (ETNP-PS1 and ETNP-PS2) and one
 coastal sample (ETNP-PS3). We took quantitative subsamples for total
 particulate carbon and total particulate arsenic. We extracted samples for
 arsenolipids which we analyzed by liquid chromatography – inductively
 coupled plasma mass spectrometry (LC-ICP-MS, for quantification) and
 liquid chromatography – high resolution electrospray ionization mass
 spectrometry (LC-HR-ESI-MS, for identification of individual lipids).
 Details for each step are in Supplemental Methods of the manuscript and
 preprint on bioRxiv (doi 10.1101/2021.03.22.436501).
DOI: 10.5061/dryad.0zpc866xp
title: Data from: Male reproductive adjustments to an introduced nest predator

description: Nest predation has a large impact on reproductive success in many taxa.
 Defending offspring from would-be predators can also be energetically and
 physiologically costly for parents. Thus, to maximize their reproductive
 payoffs, individuals should adjust their reproductive behaviors in
 relation to the presence of nest predators. However, effects of nest
 predator presence on parental behaviors across multiple reproductive
 contexts remain poorly understood, particularly in non-avian taxa. We ran
 a series of experiments to test how the presence of an egg predator, the
 invasive rockpool shrimp, Palaemon elegans, influences male
 reproductive decisions and egg survival in a species of fish with
 exclusive paternal care, the three-spined
 stickleback, Gasterosteus aculeatus. We found that, in
 the presence of shrimp, male sticklebacks were less likely to build a
 nest, invested less in territory defense against an intruder and tended to
 fan eggs in their nest less and in shorter bouts, but did not alter their
 investment in courtship behavior. The predators' presence also did
 not affect egg survival rates, suggesting that males effectively defended
 their brood from the shrimp. These results show that reproducing
 individuals can be highly responsive to the presence of nest predators and
 adjust their behavioral decisions accordingly across a suite of
 reproductive contexts.
DOI: 10.5061/dryad.x95x69pjb
title: BACE1 inhibitors from VietHerb

description: An investigation on the potential inhibitors of BACE1 using accurate and
 precise computational approaches was carried out using Autodock4
 package. A shortlist of 20 compounds forming the largest docking energy to
 BACE1 were then refined using steered molecular dynamics (SMD)
 simulations.
description: The 20 studied compounds and the ligand 23I had steered molecular
 dynamics (SMD) simulations performed on them using the GROMACS 5.1.3
 package.
description: Main
 materials: The protein
 target: β-secretase 1 also called BACE1 (PDB ID: 2p4j)
 Steered
 molecular dynamics (SMD) simulation. After docking the compounds by
 using AutoDock Tools, GROMACS was used to parameterize the protein and
 water model, and GAUSSIAN was applied to parameterize the ligands. It
 should be separated in distinct folders with one receptor and one ligand
 for each. It would include these files: rec.pdb (which is protein, but
 here means “receptor”), lig.out (the ligand structure was quantum
 calculated using Gaussian 09 package), top.top, posre.itp.
 After that, use AmberTools
 generate topology to calculate MD by creating a parameter for ligand in
 the form of Amber force field then acpype.py will convert it to
 GROMACS's format. Convert MOL_GMX.top into
 MOL_GMX.itp. Combine the ligand parameter with
 the protein parameter (topology) in top.top file Merge the protein and ligand
 structures together: convert MOL_GMX.gro to MOL_GMX.pdb, concatenate
 MOL_GMX.pdb into rec.pdb. Create PBC triclinic box (box
 with cyclic boundary conditions) surrounding the complex protein-ligand
 and solvate (immerse water in the system). Restraint C-alpha of receptor.
 Then include “CA_restr.itp” into top.top. Using .mdp
 files (which is em.mdp, nvt.mdp, npt.mdp and smd.mdp) to add ions, energy
 minimization, equilibration, and finally performing SMD.
DOI: 10.5061/dryad.79cnp5hvq
title: Data from: Local adaptation, geographical distance and phylogenetic relatedness: assessing the drivers of siderophore-mediated social interactions in natural bacterial communities

description: In heterogenous, spatially structured habitats, individuals within
 populations can become adapted to the prevailing conditions in their local
 environment. Such local adaptation has been reported for animals and
 plants, and for pathogens adapting to hosts. There is increasing interest
 in applying the concept of local adaptation to microbial populations,
 especially in the context of microbe-microbe interactions. Here, we tested
 whether cooperation and cheating on cooperation can spur patterns of local
 adaptation in soil and pond communities
 of Pseudomonas bacteria, collected across a geographical
 scale of 0.5 to 50 meters. We focused on the production of pyoverdines, a
 group of secreted iron-scavenging siderophores that often differ among
 pseudomonads in their chemical structure and the receptor required for
 their uptake. A combination of supernatant-feeding and competition assays
 between isolates from four distance categories revealed tremendous
 variation in the extent to which pyoverdine non- and low-producers can
 benefit from pyoverdines secreted by producers. However, this variation
 was not explained by geographical distance, but primarily depended on the
 phylogenetic relatedness between interacting isolates. A notable exception
 occurred in local pond communities, where the effect of phylogenetic
 relatedness was eroded in supernatant assays, probably due to the
 horizontal transfer of receptor genes. While the latter result could be a
 signature of local adaptation, our results overall indicate that common
 ancestry and not geographical distance is the main predictor of
 siderophore-mediated social interactions among pseudomonads.
DOI: 10.5061/dryad.jh9w0vtbx
title: Influence of microhabitat on the distribution of tadpoles of three endemic Nyctibatrachus species (Nyctibatrachidae) from the Western Ghats, India

description: Amphibians show a high amount of species richness and endemism. Such
 diversity can be attributed to their microenvironment as amphibians
 display fine-scale heterogeneity depending on the microhabitats they
 inhabit. Tadpoles are considered as good indicators for
 understanding microhabitat-species association as they reflect
 the breeding sites and signify species survival potential. In this study,
 we assessed the microhabitat factors influencing the distribution
 of tadpoles of three endemic frogs of the
 genus Nyctibatrachus namely N. jog, N.
 kempholeyensis, and N. kumbara from central
 Western Ghats, India.  Forty-three streams were sampled
 from three river basins and stream characteristics were analysed using
 Generalized Linear Models. The results indicate that the tadpoles
 show specific microhabitat preferences and spatial niche partitioning.
 Among microhabitat variables, the slope significantly influenced the
 distribution of tadpoles of N. jog and N. kempholeyensis. The
 tadpoles of N. jog preferred steep slopes while N. kempholeyensis tadpoles
 were found in gradual slopes with low water depth. For N. kumbara
 tadpoles, water temperature significantly influenced their distribution in
 the streams. Such spatial heterogeneity promotes the co-existence of these
 species supporting the niche theory. The study advances the understanding
 of how amphibian diversity from the Western Ghats is shaped at the
 microhabitat scale. The perennial streams that
 the Nyctibatrachus tadpoles inhabit are at risk due to
 anthropogenic activities. The findings of this study provide important
 baseline data that could be useful for the conservation of the endemic
 anurans in the Western Ghats, India.
description: The data has been collected from the field and is a raw
 dataset.
DOI: 10.5061/dryad.1ns1rn8th
title: Air temperature influences early Covid-19 outbreak as indicated by worldwide mortality

description: The Covid-19 outbreak has triggered a global crisis that is challenging
 governments, health systems and the scientific community worldwide. A
 central question in the Covid-19 pandemic is whether climatic factors have
 influenced its progression. To address this question, we used mortality
 rates during the first three weeks of recorded mortality in 144 countries,
 during the first wave of the pandemic. We examined the effect of climatic
 variables, along with the proportion of the population older than 64 years
 old, the number of beds in hospitals, and the timing and strength of the
 governmental travel measures to control the spread of the disease. Our
 first model focuses on air temperature as the central climatic factor and
 explains 67% of the variation in mortality rate, with 37% explained by the
 fixed variables considered and 31% explained by country-specific
 variations. We show that mortality rate is negatively influenced by warmer
 air temperature. Each additional Celsius degree decreases mortality rate
 by ~5%. Our second model is centred on the UV Index and follows the same
 trend as air temperature, explaining 69% of the variation in mortality
 rate. These results are robust to the exclusion of countries with low
 incomes, as well as to the exclusion of low- and medium-income countries.
 We also show that the proportion of vulnerable age classes and access to
 healthcare are critical factors impacting the mortality rate of this
 disease. The effects of air temperature at an early stage of the Covid-19
 outbreak is a key factor to understand the primary spread of this
 pandemic, and should be considered in projecting subsequent waves.
DOI: 10.5061/dryad.p8cz8w9qq
title: Mutual mate choice and assortative mating in relation to a carotenoid-based color trait in blue tits

description: Choosing an appropriate partner is a critical decision for many animal
 species. However, many mechanisms involved in mate choice are still poorly
 understood. Do both males and females choose their sexual partners, do
 both sexes use the same criteria for choosing, and do their own phenotype
 influence the choices they make, are questions that need further
 investigation. Over two successive experiments conducted in captivity with
 hand-reared blue tits (Cyanistes caeruleus), we manipulated the color of
 the chest plumage, a secondary sexual trait that reflects an
 individual's condition, to create two different color morphs (one
 pale and one colored). We then tested whether both sexes express a
 preference, whether they are attracted to the same morphs, and if the
 subjects' own chest color influences the preference they show. Our
 data reveal that both sexes are choosy, with females tending to be
 slightly choosier than males. We also show that both sexes preferentially
 select individuals with a pale chest plumage over colorful individuals,
 and this was again more pronounced in females. Finally, paler individuals
 tend to be selected by birds that are themselves pale, even if this
 phenotype matching was not very robust. Such a preference for paler
 individuals is intriguing since mates are predicted to associate with
 individuals displaying higher, not lower, value of quality signals. It
 could result from adaptive mechanisms related to avoidance of
 aggressiveness in confined environment, avoidance of conflicting sexual
 signals within individuals, or from cultural mechanisms leading to
 preference for individuals that match its own phenotype.
DOI: 10.5061/dryad.vq83bk3sn
title: Demographic, physiological, and genetic factors linked to poleward range expansion along the shoreline of China

description: Distribution range expansion is one of the most significant
 consequences of climate change in the Anthropocene. During range
 expansion, the former biogeographic barrier can be broken and then a new
 biogeographic pattern might appear. A comprehensive study, including
 demographic pattern, physiological performance and genetic features, is
 crucial for understanding how the expanding population occupies and
 survives in the new habitat, within which it formerly did not occur. In
 the present study, we investigated the demographic, physiological, and
 genetic features of the intertidal gastropod Nerita yoldii, which
 has extended its northern limit by ~200 km into areas that are warming up
 faster than the historical distribution over the former biogeographic
 break of the Yangtze River Estuary (YRE) during recent decades. The
 neutral SNPs data showed that the new marginal populations formed a
 distinct cluster established by a few founders. Demographic modeling
 analysis revealed that the new marginal populations experienced strong
 genetic bottlenecks followed by recent demographic expansion. Successful
 expansion that overcomes the founder effect (reduced genetic variation)
 might be attributed to its high capacity of rapid population growth and
 multiple introductions. According to the non-neutral SNPs under
 diversifying selection, there were high levels of heterozygosity in the
 new marginal populations, which might be beneficial for adapting to the
 novel thermal conditions. The common garden experiment showed that the new
 marginal populations have evolved divergent transcriptomic and
 physiological responses to heat stress, allowing them to occupy and
 survive in the novel environment. Our study also reveals a fast loss
 of transcriptional plasticity in the new marginal
 populations, potentially contributing to local adaptation. These results
 suggest a new biogeographic pattern for the snail N.
 yoldii has formed with the occurrence of demographic, physiologic
 and genetic changes, and emphasize the roles of adaptation of marginal
 populations during distribution range expansion.