cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbcm8
title: Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

description: Understanding how geographic and environmental heterogeneity drive local
 patterns of genetic variation is a major goal of ecological genomics and a
 key question in evolutionary biology. The tropical Andes and inter-Andean
 valleys are shaped by markedly heterogeneous landscapes, where species
 experience strong selective processes. We examined genome-wide
 SNP data together with behavioral and ecological traits (mating calls and
 body size) known to contribute to genetic isolation in anurans in the
 emerald-eyed treefrog, Boana platanera, distributed
 across an environmental gradient in Central Colombia (northern South
 America). We analyzed the relationships between
 environmentally (temperature and
 precipitation) associated genetic and phenotypic differentiation
 and the potential drivers of isolation by environment along an
 elevation gradient. We identified candidate SNPs associated with
 temperature and body size, which follow a clinal pattern of genome-wide
 differentiation tightly coupled with phenotypic variation: as
 elevation increases, B. platanera exhibits larger body
 size and longer call duration with more pulses but lower pulse rate and
 frequency. Thus, the environmental landscape has rendered a scenario where
 isolation by environment and candidate loci show
 phenotypic divergence in this tropical
 frog along an elevation gradient in the Colombian
 Andes. Our study sets the basis for evaluating the role of
 temperature in the genetic structure and local adaptation in tropical
 treefrogs and its putative effect on life cycle (embryos, tadpoles,
 adults) along elevation gradients.
description: See methods in the publication.
description: A Readme file is included.
DOI: 10.5061/dryad.f1vhhmgx3
title: Data from: The quiescent centre of the root apical meristem: Conceptual developments from Clowes to modern times

description: This data for the review article "The quiescent centre of
 the root apical meristem: Conceptual developments from Clowes to modern
 times" published in Journal of Experimental Botany by Joseph G.
 Dubrovsky and Victor B. Ivanov (https://doi.org/10.1093/jxb/erab305)
 includes a complete bibliography of Frederick Albert Lionel
 Clowes in chronological order. The referred article is dedicated to the
 100th anniversary of the birth of Clowes, who during his career
 investigated organization, function, and maintenance of the root apical
 meristem in plants and who discovered and formulated a concept of the
 quiescent centre, as a group of cells now considered to be stem cells in
 plant roots. In the main text, the authors discuss how our understanding
 and concepts about the root apical meristem and the quiescent centre
 changed over time, from F.A.L. Clowes to the present times. Before this
 work, the full bibliography of F.A.L. Clowes was unavailable. This data
 fills in this gap.
description: This list is compiled in
 accordance with the list made by F.A.L. Clowes himself, with some
 modifications and corrections. The original list of publications was a
 gift from Mrs D. Winson. The publications starting from 1988 were added by
 the authors.
description: Book reviews by F.A.L. Clowes are not included in this list.
DOI: 10.5061/dryad.x95x69pjc
title: Data from: Increase in leaf organic acids to enhance adaptability of dominant plant species in karst habitats

description: Estimation of leaf nutrient composition of dominant plant species from
 contrasting habitats (i.e. karst and non-karst forests) provides an
 opportunity to understand how plants are adapted to karst habitats from
 the perspective of leaf traits. Here, we measured leaf traits – specific
 leaf area (SLA), concentrations of total carbon ([TC]), nitrogen ([TN]),
 phosphorus ([TP]), calcium ([Ca]), magnesium ([Mg]), manganese ([Mn]),
 minerals ([Min]), soluble sugars, soluble phenolics, lipids, and organic
 acids ([OA]) – and calculated water–use efficiency (WUE), construction
 costs (CC) and N/P ratios, and searched for correlations between these
 traits of 18 abundant plant species in karst and non–karst forests in
 southwesten China. Variation in leaf traits within and across the abundant
 species was both divergent and convergent. Leaf [TC], [Ca], [Min], [OA]
 and CC were habitat–dependent, while the others were not habitat- but
 species-specific. The correlations among [TN], [TP], SLA, [TC], CC, [Min],
 WUE, [OA], and CC were habitat–independent, and inherently associated with
 plant growth and carbon allocation; those between [CC] and [Lip], between
 [Ca] and [Mg], and between [Mg] and [WUE] were habitat–dependent. Habitat
 significantly affected leaf [Ca], and thus indirectly affected leaf [OA],
 [Min], and CC. Our results indicate that plants may regulate leaf [Ca] to
 moderate levels via adjusting leaf [OA] under both high and low soil Ca
 availability, and offer new insights into the abundance of common plant
 species in contrasting habitats.
DOI: 10.5061/dryad.q83bk3jj0
title: Analysis of acoustic index against temperature and barometric pressure

description: 1. New low-cost options to long-term acoustic monitoring in terrestrial
 ecology are becoming increasingly available. However, integration of
 acoustic stations with sensors for logging of additional data, such as
 temperature and barometric pressure is rare. Separate environmental
 loggers often come at a cost of &gt; US$100 whereas the same sensors
 for use with microprocessors come at a cost between US$. 1-15 The cost
 savings integration entails as well as the crucial need for the recording
 of some of these variables in acoustic studies mean that this is an
 important development avenue. 2. Overcoming these issues is important to
 enable insights into the long-term dynamics of ecological systems and how
 they respond to changes in the environment at varying temporal scales and
 is especially important for studies involving species that are
 microclimate dependent. 3. Here we present a hardware system for both
 acoustic and environmental data logging where the board design is released
 under a creative commons license. The system has been field tested in a
 tropical setting and is called the Kinabalu Recorder. The presented
 configuration came at a cost of less than US$100 per station. This cost is
 for professional manufacture and assembly of the boards, temperature and
 barometric sensor, two batteries, water-proof housing and two 64 GB micro
 SD cards. 4. The system has been extensively tested in a tropical setting
 along an altitude gradient and with over 1.3 TB of data (&gt; 2,000
 hours of data with over 10 months in the field) presents a robust solution
 to long term acoustic monitoring integrated with environmental data
 sensors. 5. Work on hardware and software systems are an important part of
 the technological development of field biology as it allows greater
 flexibility in terms of cost and configuration of systems whilst promoting
 cross-field collaboration and information flow.
description: This data was collected using the Kinabalu Recorder in Kinabalu
 Park, Malaysia, a station for acoustic and abiotic environmental
 recording. The data was then processed in the software R and the
 bioacoustic index and normalised difference index was extracted. The data
 contained is from March until September 2020. The data was used for
 figures and mixed model analysis in the MEE manuscript.
description: There are missing values as these stations were field tested
 during the 2020 pandemic and movement control orders in Malaysia
 interrupted the schedule for battery replacement.
DOI: 10.5061/dryad.tht76hf04
title: Water availability influences thermal safety margins for leaves

description: One application of plant physiological heat tolerance measurements is the
 assessment of vulnerability to increasing environmental temperatures under
 climatic change. A thermal safety margin, the difference between
 physiological tolerance and environmental temperature, is a common metric
 for the assessment of plant thermal vulnerability. However, there are
 biological and methodological aspects to consider when evaluating thermal
 vulnerability that have the potential to substantially alter assessments.
 Two such aspects include the leaf to air temperature relationship and the
 scale at which air temperature data are collected. We grew plants of a
 desert species, Myoporum montanum, in situ under water- stressed and
 well-watered conditions, measured their leaf temperatures and
 photosynthetic heat tolerance (T50 threshold) every third day over 12 days
 in summer. Thermal safety margins were calculated based on leaf
 temperatures and compared to those calculated with local and regional air
 temperatures. We found that heat tolerance and the thermal vulnerability
 assessment of a plant changed with water status. When water was readily
 available, plants maintained wide leaf temperature safety margins and
 displayed partial-homeothermy. When cooling via transpiration was limited,
 increasing leaf temperature corresponded with occurrences of leaf poikilo-
 and megathermy, higher heat tolerance, and narrower safety margins. Our
 study shows high physiological heat thresholds are not necessarily
 reflective of wide safety margins, but instead can indicate a greater
 vulnerability and increased risk of heat stress exposure. Calculating
 thermal safety margins using air temperatures can also substantially alter
 margin widths. Where possible, the use of leaf temperatures in assessments
 of thermal vulnerability will lead to more meaningful vulnerability
 assessments. We recommend considering the source and temporal pairing of
 temperature measurements as well as plant water status, when measuring and
 interpreting plant thermal safety margins.
description: Leaf temperature, air temperature, leaf water potential,
 photosystem II heat tolerance, and thermal safety margin data for the
 Australian desert plant species <em>Myoporum montanum</em>
 under experimental well-watered and water-stressed conditions during the
 summer month December. All temperatures are in degrees
 celsius.
DOI: 10.5061/dryad.12jm63xz3
title: Data from: Temporal and spatial comparisons of angiosperm diversity between eastern Asia and North America

description: Eastern Asia (EA) and North America north of Mexico (NA) have comparable
 latitude, land area, and climate, but the overall plant diversity is much
 higher in EA than in NA. Despite intensive studies on disjunct taxa of the
 two regions, the temporal and spatial diversity patterns between the two
 floras remain unclear. Here we explore the floristic differences between
 EA and NA using the well-studied floras of China and the United States of
 America (USA) as exemplars, while also employing a newly generated dated
 phylogeny covering ~90% of the angiosperm genera of the two countries and
 comprehensive spatial distribution data. We find that China possesses both
 higher richness and phylogenetic diversity (PD) for angiosperm genera than
 the USA. Notably, most lineages contribute to the PD anomaly between the
 two floras, with 46 of 58 lineages having higher PD in China. Temporally,
 China has a higher proportion of genera that originated before the Miocene
 than are found in the USA (29.9% vs 23.2%). The eastern USA has more
 genera that originated during the Paleogene than does the western USA, but
 the reverse pattern is observed after the middle Miocene, with more genera
 originating in the west. Spatially, China shows a more distinct east-west
 deviation in diversity than the USA with eastern China possessing much
 higher generic richness and PD and more ancient lineages than western
 China. However, the eastern USA possesses lower generic richness, but
 higher PD and more ancient lineages than the western USA. Both the floras
 in China and the USA share a signature of an older east and a younger
 west, and this pattern may be largely driven by regional orogenic
 activities and climatic changes in the west of the two regions. Finally,
 our study indicates that more efforts are needed to enhance biodiversity
 conservation in southern China and the eastern USA by identifying and
 protecting phylogenetic diversity hotspots.
description: The dataset contains:<br>(1) The genus-level richness, PD,
 and standardized PD of each grid cell with the top 5% PD (in blue) and
 standardized PD (in red)
 highlighted;<br>grid_richness_pd_standarized_PD.xlsx
 (2) The five-gene matrix of 9035
 species;<br>matrix_five_gene_9035sp.phy (3) The
 best ML tree of 9035 species with support values from 1000 bootstrap
 replicates;<br>best_ML_tree_9035sp.tre (4) The
 time tree of 9035 species estimated using
 treePL;<br>time_tree_9035sp.tre (5) Ten
 complete-species trees of 41410 species generated by randomly inserting
 species without sequence data using “scenario 2” in “V.PhyloMaker” package
 of R;<br>10_species_tree_41410sp.tre (6) Gridded
 distribution information for the Chinese and the USA angiosperms (not
 including non-native species). As we do not have copyright for maps of
 China and the USA, please contact us for further information about the
 grid numbers.<br>spatial_distribution_data.csv
DOI: 10.5061/dryad.j0zpc86f5
title: Data from: Slow and fast evolutionary rates in the history of lepidosaurs

description: Biodiversity today is uneven, with equally ancient sister groups
 containing few or many species. It has often been assumed that high
 biodiversity indicates fast evolution, and yet in a classic work in 1944
 George Simpson suggested that fast evolution might generate instability
 and extinction, and that slow evolution led to high biodiversity. Here we
 show that evolutionary rates can vary substantially through the history of
 a clade and find evidence for Simpson’s claim. In a comparative
 phylogenetic study deploying Bayesian methods, we find that Squamata,
 comprising today over 10,000 species of lizards and snakes, showed slow
 rates of evolution in the first two-thirds of their history, whereas their
 sister clade, Rhynchocephalia, comprising just one living species, showed
 high rates of evolution in the past. Slow and steady won the race for the
 Mesozoic squamates, and the high-rate boom and bust existence of
 rhynchocephalians at that time leaves them with a single survivor. We need
 to explore other cases where fast evolution can lead to short-term high
 diversification, but in the end long-term low biodiversity.
DOI: 10.5061/dryad.prr4xgxmg
title: Light condition experienced by parent plants influences the response of offspring to light via both parental effects and soil legacy effects

description: 1. Environmental conditions experienced by parent plants can influence
 offspring performance through parental effects induced by DNA methylation.
 The offspring can also be influenced by environmental conditions
 experienced by their parents via soil legacy effects due to plant-mediated
 changes in the composition of soil microbes. These two effects are likely
 to act simultaneously, but empirical evidence for combined effects is
 limited. 2. We conducted a two-phase experiment with five genotypes of a
 clonal plant Hydrocotyle vulgaris. In the first phase, we grew parent
 plants of each genotype under two light conditions (ambient vs. shade) and
 two DNA demethylation treatments (treated with water vs. 5-azacytidine).
 We then collected soils and clonal offspring for each genotype from each
 of these four treatments and measured soil (a)biotic properties. In the
 second phase, we grew the offspring from each of the four treatments in
 the four different soils, under the two light conditions. 3. When grown
 under ambient light condition and in soil from ambient parents, offspring
 produced by ambient parents grew larger than offspring produced by shaded
 parents when the parents were treated with water. This difference was
 smaller when the parents were treated with 5-azacytidine, and disappeared
 when the offspring were grown in soil from shaded parents. The growth
 difference was also observed when the offspring were grown under shaded
 condition and in soil from shaded parents. However, this difference was
 greater when the parents were treated with 5-azacytidine, and disappeared
 when the offspring were grown in soil from ambient parents. Moreover,
 offspring growth was associated with fungal composition and total
 phosphorus of the soil in which the parents had grown. 4. Our results
 show, for the first time, that light condition experienced by parents can
 influence offspring responses to light through both parental effects and
 soil legacies. The parental effects were mediated by changes in DNA
 methylation and the soil legacies were due to plant-mediated changes in a
 combination of soil biotic and abiotic properties. These impacts may
 eventually influence the ecological and evolutionary trajectories of
 clonal plant populations.
description: See main text for details.
description: Microsoft excel can be used to open the data files.
DOI: 10.5061/dryad.jwstqjq8v
title: Diversity of response and effect traits provides complementary information about avian community dynamics linked to ecological function

description: Functional diversity metrics based on species traits are widely used to
 investigate ecosystem functioning. In theory, such metrics have different
 implications depending on whether they are calculated from traits
 mediating responses to environmental change (response traits) or those
 regulating function (effect traits), yet trait choice in diversity metrics
 is rarely scrutinized. Here, we compile effect and response traits for
 British bird species supplying two key ecological services – seed
 dispersal and insect predation – to assess the relationship between
 functional diversity and both mean and stability of community abundance
 over time. As predicted, functional diversity correlates with stability in
 community abundance of seed dispersers when calculated using response
 traits. However, we found a negative relationship between functional
 diversity and mean community abundance of seed dispersers when calculated
 using effect traits. Subsequently, when combining all traits together, we
 found inconsistent results with functional diversity correlating with
 reduced stability in insectivores, but greater stability in seed
 dispersers. Our findings suggest that trait choice should be considered
 more carefully when applying such metrics in ecosystem management.
description: Please find information on methodology and a description of the
 data in the ReadMe file.
DOI: 10.5061/dryad.cc2fqz667
title: Data from: Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa

description: Background Secondary endosymbionts of aphids provide benefits to their
 hosts, but also impose costs such as reduced lifespan and reproductive
 output. The aphid Aphis fabae is host to different
 strains of the secondary endosymbiont Hamiltonella defensa, which
 encode different putative toxins. These strains have very different
 phenotypes: They reach different densities in the host, and the costs and
 benefits (protection against parasitoid wasps) they confer to the host
 vary strongly. Results We used RNA-Seq to generate hypotheses on why four
 of these strains inflict such different costs to A. fabae. We
 found different H. defensa strains to cause
 strain-specific changes in aphid gene expression, but little effect
 of H. defensa on gene expression of the primary
 endosymbiont, Buchnera aphidicola. The highly costly and
 over-replicating H. defensa strain H85, was
 associated with strongly reduced aphid expression of hemocytin, a marker
 of hemocytes in Drosophila. The closely related strain H15 was
 associated with downregulation of ubiquitin-related modifier 1, which is
 related to nutrient-sensing and oxidative stress in other organisms.
 Strain H402 was associated with strong differential regulation of a set of
 hypothetical proteins, the majority of which were only differentially
 regulated in presence of H402. Conclusions Overall, our results suggest
 that costs of different strains of H. defensa are likely
 caused by different mechanisms, and that these costs are imposed by
 interacting with the host rather than the host’s obligatory
 endosymbiont B. aphidicola.
DOI: 10.5061/dryad.zw3r22880
title: Simulation code for: The role of phenotypic plasticity in the establishment of range margins

description: It has been argued that adaptive phenotypic plasticity may facilitate
 range expansions over spatially and temporally variable environments.
 However, plasticity may induce fitness costs. This may hinder the
 evolution of plasticity. Earlier modelling studies examined the role of
 plasticity during range expansions of populations with fixed genetic
 variance. However, genetic variance evolves in natural populations. This
 may critically alter model outcomes. We ask: How does the capacity for
 plasticity in populations with evolving genetic variance alter range
 margins that populations without the capacity for plas- ticity are
 expected to attain? We answered this question using computer simulations
 and analytical approximations. We found a critical plasticity cost above
 which the capacity for plasticity has no impact on the expected range of
 the population. Below the critical cost, by contrast, plasticity
 facilitates range expansion, extending the range in comparison to that
 expected for populations without plasticity. We further found that
 populations may evolve plasticity to buffer temporal environmental
 fluctuations, but only when the plasticity cost is below the critical
 cost. Thus, the cost of plasticity is a key factor involved in range
 expansions of populations with the potential to express plastic response
 in the adaptive trait. This article is part of the theme
 issue ‘Species ranges in the face of changing environments (Part
 I)’.
description: Custom-made Matlab simulation.
DOI: 10.5061/dryad.931zcrjkc
title: Temocillin susceptibility in Enterobacterales with an ESBL/AmpC phenotype

description: Carbapenems are considered the drugs of choice for first-line treatment of
 severe infections caused by carbapenem-susceptible, extended-spectrum
 β-lactamases (ESBL)-producing Enterobacterales, while
 piperacillin-tazobactam has been recommended as an alternative for
 treatment of non-severe infections. Temocillin is stable to ESBL and AmpC
 enzymes and may thus represent another treatment option. This study
 assessed the in vitro activity of piperacillin-tazobactam and temocillin
 against third-generation cephalosporin (3GC)-resistant
 Escherichia coli and Klebsiella pneumoniae, as compared
 to 3GC-susceptible isolates of either species. One hundred and nine
 isolates from hospitalised patients with bloodstream and urinary tract
 infections were tested. All isolates were collected during the resistance
 surveillance study of the Paul-Ehrlich-Society for Chemotherapy in
 2016/17. Minimum inhibitory concentrations (MICs) were determined by broth
 microdilution according to the standard ISO 20776-1 and interpreted using
 EUCAST clinical breakpoints (version 11.0). Seventy-nine isolates (E.
 coli, n = 58; K. pneumoniae, n = 21) were 3GC-resistant and 30 (E. coli, n
 = 15; K. pneumoniae, n = 15) were 3GC-susceptible. Susceptibility
 to piperacillin-tazobactam was detected in 93.7 % of 3GC-susceptible
 isolates (for both E. coli and K. pneumoniae) and in 79.3 % and 57.1 % of
 the 3GC-resistant E. coli and K. pneumoniae, respectively. In contrast,
 3GC-susceptible isolates were 100% susceptible to temocillin as were 94.8%
 and 90.5% of the 3GC-resistant E. coli and K. pneumoniae, respectively. In
 conclusion, temocillin demonstrated potent in vitro activity against
 carbapenem-susceptible, 3GC-resistant E. coli and K. pneumoniae from
 bloodstream and urinary tract infection samples, with susceptibility rates
 exceeding those of piperacillin-tazobactam.
description: See publication for details.