cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ttdz08m0f
title: Discovery of thermostable fluorescently responsive glucose biosensors by structure-assisted function extrapolation

description: Accurate assignment of protein function from sequence remains a
 fascinating and difficult challenge.   The periplasmic
 binding protein (PBP) superfamily present an interesting case of function
 prediction, because they are both ubiquitous in prokaryotes, and they tend
 to diversify through gene duplication “explosions” that can lead to large
 numbers of paralogs in a genome.  An engineered version of the
 moderately thermostable glucose-binding PBP from Escherichia coli has been
 used successfully as a reagentless fluorescent biosensor both in vitro and
 in vivo.  To develop more robust sensors that meet the challenges
 of real-world applications, we report the discovery of thermostable
 homologs that retain a glucose-mediated conformationally coupled
 fluorescence response.  Accurately identifying a glucose-binding
 PBP homolog among closely related paralogs is challenging.  We
 demonstrate that a structure-based method that filters sequences by
 residues that bind glucose in an archetype structure is highly
 effective.  Using fully sequenced bacterial genomes we found that
 this filter reduced high paralog numbers to single hits in a genome,
 consistent with accurate separation of glucose binding from other
 functions.  We expressed engineered proteins for eight homologs,
 chosen to represent different degrees of sequence identity and tested
 their glucose-mediated fluorescence responses.  We accurately
 predicted the presence of glucose binding down to 31% sequence
 identity.  We also have successfully identified suitable
 candidates for next-generation robust, fluorescent glucose sensors.
description: Bioinformatics: the NCBI database of fully sequenced bacterial
 genomes was searched for sequence of homologs of the E. coli periplasmic
 glucose-binding protein (ecGBP).  True glucose-binding homologs were
 selected by applying sequence filters derived from analysis of the 3D
 structure of ecGBP.  The deposited information includes the results from
 these searches, the software package that was developed to carry out this
 type of search, and the scripts used for this project.
 Protein Chemistry: synthetic genes for glucose-binding proteins
 homologs were built, and proteins produced by over-expression.  The
 glucose-binding properties and glucose-dependent thermostabilities of
 their fluorescent conjugates were determined experimentally.  The
 deposited information comprises the raw data sets, and the software used
 to analyze these.
DOI: 10.5061/dryad.3ffbg79jw
title: Data from: Does pollen limitation limit plant ranges? Evidence and implications

description: Sexual reproduction often declines towards range edges, reducing fitness,
 dispersal, and adaptive potential at range edges. For plants, sexual
 reproduction is frequently limited by inadequate pollination. While case
 studies show that pollen limitation can limit plant distributions, the
 extent to which pollination commonly declines toward plant range edges is
 unknown. Here, we leverage global databases of pollen-supplementation
 experiments and plant occurrence data to test whether pollen limitation
 increases toward plant range edges, using a phylogenetically controlled
 meta-analysis. While there was significant pollen limitation across
 studies, we found little evidence that pollen limitation increases toward
 plant range edges. Pollen limitation was not stronger toward the tropics,
 nor at species’ equatorward vs poleward range limits. Meta-analysis
 results are consistent with results from targeted experiments, in which
 pollen limitation increased significantly toward only 14% of 14 plant
 range edges, suggesting that pollination contributes to range limits less
 often than do other interactions. Together, these results suggest
 pollination is one of the rich variety of potential ecological factors
 that can contribute to range limits, rather than a generally important
 constraint on plant distributions.
description: Here, we present all of the R scripts used in the processing and
 analysis of data for "Does pollen limitation limit plant ranges?
 Evidence and implications." We also provide a list of species for
 which GBIF occurrence data was originally downloaded, the list of species
 deemed to have sufficient GBIF coverage upon initial review, and a final
 list of species with occurrence cleaning instructions. In data, NA values
 indicate data not available. The readme file contains information on the R
 scripts and a description of the variables in each species list. All
 details of how to derive our final dataset are provided in the processing
 and analysis scripts. Information on data cleaning protocols and analysis
 methods can be found in the associated manuscript referenced above. GloPL
 and GBIF data (which are used in our data generation and analysis) should
 be downloaded directly from those data repositories.
DOI: 10.5061/dryad.tb2rbp021
title: Rates of dispersal of cane toads during their global invasion

description: Invasions often accelerate through time, as dispersal-enhancing traits
 accumulate at the expanding range edge. How does the dispersal behaviour
 of individual organisms shift to increase rates of population spread? We
 collate data from 44 radio-tracking studies (in total, of 650 animals) of
 cane toads (Rhinella marina) to quantify distances moved per day, and the
 frequency of displacement in their native range (French Guiana) and two
 invaded areas (Hawai’i and Australia). Here we show that toads in their
 native-range, Hawai’i and eastern Australia are relatively sedentary,
 while toads dispersing across tropical Australia increased their daily
 distances travelled from 20 to 200 m per day. That increase reflects an
 increasing propensity to change diurnal retreat sites every day, as well
 as to move further during each nocturnal displacement. Daily changes in
 retreat site evolved earlier than did changes in distances moved per
 night, indicating a breakdown in philopatry before other movement
 behaviours were optimised to maximise dispersal.
description: Cane toads were radio-tracked using waistbelts holding small
 transmitters. Locations were recorded daily for 5 days, providing
 information on distances moved between successive diurnal retreat-sites,
 and the proportion of nights on which taods changed shelter-sites. For
 this paper, data were colelcted fro mmany such studies over a wide area,
 to explore changes in dispersal-related traits during the toad's
 invasion history.
DOI: 10.5061/dryad.7m0cfxpvw
title: Data from: Impact of squid predation on juvenile fish survival

description: Predation is a major source of mortality during the early life stages of
 marine fishes; however, few studies have demonstrated its
 impact—especially that of squid predation—on survival processes. Here, we
 examined the feeding habits and predation impacts of swordtip squid on a
 major prey fish, juveniles of jack mackerel, in the East China Sea.
 Otoliths of the juveniles extracted from the squid stomach were used to
 reconstruct the age–length relationship and the growth trajectory of the
 consumed juveniles, and they were compared to those of juveniles collected
 with a net using a newly developed statistical framework. The juveniles
 consumed by squid had significantly shorter body lengths and smaller body
 sizes during the late larval and early juvenile stages than the netted
 juveniles, suggesting that smaller juveniles with slower growth rates have
 a higher probability to be selected. The body mass ratio of the predator
 squid to prey juveniles (predator-prey mass ratio, PPMR) ranged from 7 to
 700, which was remarkably lower than the PPMR reported in various marine
 ecosystems based on analyses of fishes. Our findings demonstrate that
 squid predation can significantly impact the early life survival of fish
 and the trophodynamics in marine ecosystems.
description: These datasets were collected in the predator-prey relationships
 between the swordtip squid and the juvenile jack mackerel.
DOI: 10.5061/dryad.r7sqv9sd1
title: Costs of territoriality: A review of hypotheses, meta-analysis, and field study

description: The evolution of territoriality reflects the balance between the benefit
 and cost of monopolising a resource. While the benefit of territoriality
 is generally intuitive (improved access to resources), our understanding
 of its cost is less clear. This paper combines: 1. a review of hypotheses
 and meta-analytic benchmarking of costs across diverse taxa; and 2. a new
 empirical test of hypotheses using a longitudinal study of free-living
 male territorial lizards. The cost of territoriality was best described as
 a culmination of multiple factors, but especially costs resulting from the
 time required to maintain a territory (identified by the meta-analysis) or
 those exacerbated by a territory that is large in size (identified by the
 empirical test). The meta-analysis showed that physiological costs such as
 energetic expenditure or stress were largely negligible in impact on
 territory holders. Species that used territories to monopolise access to
 mates appeared to incur the greatest costs, whereas those defending food
 resources experienced the least. The single largest gap in our current
 understanding revealed by the literature review is the potential cost
 associated with increased predation. There is also a clear need for
 multiple costs to be evaluated concurrently in a single species. The
 empirical component of this study showcases a powerful analytical
 framework for evaluating a range of hypotheses using correlational data
 obtained in the field. More broadly, this paper highlights key factors
 that should be considered in any investigation that attempts to account
 for the evolutionary origin or ecological variation in territorial
 behaviour within and between species.
description: Details are provided in the README file.
DOI: 10.15468/dl.nhc4g5
title: Occurrence Download

description: A dataset containing 6004 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Papilio paris"
 ]
}

 The dataset includes 6004 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002978-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dbrv15f2c
title: Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus

description: Microbiome constitutes and important axis of individual variation that,
 together with genes and the environment, influences an individual’s
 physiology and fitness. Microbiomes are dependent not only on an
 individual’s body condition but also on external factors, such as diet or
 stress levels, and as such can be involved into feedbacks between the
 external ecological factors and internal physiology. In our study we used
 a wild population of blue tits (Cyanistes caeruleus) to investigate the
 impact of external habitat composition on the microbiome of adult birds.
 We hypothesized, that – through differences in plant composition,
 potentially affecting diet complexity – habitat type may impact the
 diversity and structure of the gut microbiome. Blue tits breeding in dense
 deciduous forests tended to have more diverse microbiomes, and
 significantly different in terms of microbiome composition from birds
 breeding in open, sparsely forested hay meadows. Distinct study plots also
 tended to differ in a number of parameters describing microbiome
 diversity. We observed no microbiome differentiation according to
 individual characteristics such as sex or age. The study emphasizes, that
 external environment is one of the important modulators of microbiome
 diversity and calls for more such studies in wild animal populations.
description: Fields in data: sample-id: unique identifier
 of each sample isNegative: Sample = bird sample, Neg =
 contamination control samples sex: F = female, M =
 male repl: R = samples in duplicate (see MS for how
 they were treated) plotTop: ID of the study
 plot habitat: type of forest habitat
 ambiguous: A = box assignment to habitat may be ambiguous, see MS
 for how it was treated year: study year
 age: bird age, 3+ = adult, 20 = juvenile
 bird_id: id of each studied individual
DOI: 10.5061/dryad.k98sf7m6w
title: Path-finding algorithm as a dispersal assessment method for invasive species with human-vectored long-distance dispersal event

description: Aim: An assessment method that can precisely represent human-vectored
 long-distance dispersals (HVLDD) is currently in need for effective
 management of invasive species. Here, we focused on HVLDD happening along
 roads and proposed a path-finding algorithm as a more precise dispersal
 assessment tool than the most widely used Euclidean distance method by
 using pine wilt disease (PWD) as a case study. Location: Busan
 Metropolitan City, Republic of Korea Methods: A path-finding algorithm,
 which calculates distances by considering spatial distribution of road
 networks, was tested for its effectiveness in estimating dispersal
 distances of HVLDD events. To this end, annual HVLDD cases were classified
 from entire PWD occurrence data from 2016 to 2019 and their dispersal
 distances were calculated using the path-finding algorithm and the
 Euclidean distance method. We constructed potential dispersal ranges based
 on the occurrence points in 2016, 2017, and 2018 using the respective
 year's mean dispersal distance for both methods, and their
 performances in accounting for each subsequent year's HVLDD cases
 were compared to determine which method calculated more precise distances.
 The information on which road class contributed more to dispersal
 occurrences and distances was analysed as well using the proposed
 algorithm. Results: The potential dispersal ranges of the path-finding
 algorithm accounted for more future anthropogenic infection cases than the
 ones that used the Euclidean distance method, validating its higher
 functionality. It also revealed that most HVLDDs started and ended on
 small roads, and large roads constituted the majority of the total
 dispersal length. Main Conclusions: The path-finding algorithm has proven
 to be a more effective dispersal assessment method for HVLDD events. It
 can help design effective control strategies. Thus, we encourage using the
 path-finding algorithm for dispersal assessment of invasive species that
 move along road networks, as well as for the development of more powerful
 HVLDD prediction models.a
DOI: 10.5061/dryad.xksn02vh4
title: Improving citizen science data for long-term monitoring of plant species

description: In 2012, a new volunteer-based recording scheme for vascular plants was
 launched in the Netherlands. Its purpose is to track the changes in the
 number of occupied 1-km grid cells for as many native plant species as
 possible between survey rounds of 8 years. We did not prescribe a strict
 field protocol to minimize variation in observer effort, but instead chose
 to statistically correct for this variation with occupancy models. These
 models require replicated visits to a grid cell per season, which was
 implemented by having two independent observers survey grid cells and
 record all plant species observed. Now that a first survey round has ended
 (2012–2019), we evaluate our approach, i.e. we tested whether the scheme
 has the potential to produce proper trend estimates. The number of
 occupied grid cells in the first round was estimated per species, using an
 occupancy model with day of year, visit duration and observer experience
 as covariates for detection. The detection probability, which was 0.43 on
 average, strongly depended on visit duration and day of year. It was
 possible to estimate the number of occupied grid cells quite precisely for
 several hundreds of species, such that the statistical power is expected
 to be high enough to detect changes of 10% between survey rounds. For rare
 species, however, the power to detect changes is expected to be quite low.
 We conclude that the approach works well, but further improvements are
 suggested.
description: A total of 2851 sites (1 x 1 square km grid cells) were visited
 by (groups of) observers between 2012 and 2019. During a visit, the
 observers recorded all vascular plant species that they detected, as well
 as some basic information about the visit.
DOI: 10.5061/dryad.nvx0k6dth
title: Performance and microbiota of Lupinus polyphyllus for Plant and Soil

description: Purpose: In cold climates, glyphosate residues may linger in
 soils, with effects on plant-microbe interactions and, consequently, plant
 performance. Here, we explore the influence of glyphosate residues on the
 endophytic microbiota (bacteria and fungi) and performance of the
 perennial nitrogen-fixing weed Lupinus polyphyllus. Methods: In a common
 garden, we grew plants from six populations of L. polyphyllus in
 glyphosate-treated or untreated control soils, with or without additional
 phosphorus. We sampled plant microbiota (leaves, roots, nodules) and
 assessed plant performance based on six traits: height, retrogression
 probability (i.e. shrinkage), biomass, root:shoot ratio, nodule number,
 and nodule viability. Results: The richness of plant endophytic microbial
 communities was determined by soil phosphorus level rather than by
 glyphosate treatment. However, for bacteria, the composition of these
 communities differed between glyphosate-treated and control soils across
 plant tissue types; no difference was observed for fungi. The plant
 bacterial communities in both soil types were dominated by potential
 nitrogen-fixing bacteria belonging to family Bradyrhizobiaceae, and
 particularly so in glyphosate-treated soils. Overall, though, these
 changes in plant bacterial communities had a minor effect on plant
 performance: the only difference we detected was that the probability of
 retrogression was occasionally higher in glyphosate-treated soils than in
 control soils. Conclusion: Our findings indicate that glyphosate-based
 herbicides, when applied at the recommended frequency and concentration,
 may not have critical effects on the growth of short-lived weeds after the
 safety period has passed; however, the endophytic microbiota of such weeds
 may experience longer-lasting shifts in community structure.
description: Individuals of Lupinus polyphyllus were grown from
 seed in a greenhouse and seedlings were planted in the common garden to
 observe the effects of glyphosate residues on plant performance during
 June-August 2019 (in two different experiments). Plant endophytic
 microbiota were sampled (roots, nodules and leaves) in July 2019 to
 identify fungal and bacterial OTUs.
description: Empty fields indicate missing data.
DOI: 10.5061/dryad.5x69p8d43
title: The Phanerozoic aftermath of the Cambrian information revolution: sensory and cognitive complexity in marine faunas

description: The Cambrian information revolution describes how biotically-driven
 increases in signals, sensory abilities, behavioral interactions, and
 landscape spatial complexity drove a rapid increase in animal cognition
 concurrent with the Cambrian radiation. Here, we compare cognitive
 complexity in Cambrian and post-Cambrian marine ecosystems, documenting
 changes in animal cognition after the initial Cambrian increase. In a
 comparison of Cambrian and post-Cambrian Lagerstätten, we find no strong
 trend in the proportion of genera possessing two types of macroscopic
 sense organs (eyes and chemoreceptive organs such as antennae, feelers or
 nostrils). There is also no trend in general nervous system complexity.
 These results suggest that sophisticated information processing was
 already common in early Phanerozoic ecosystems, comparable with behavioral
 evidence from the trace fossil record. Most taxa capable of complex
 information processing in Cambrian ecosystems were panarthropods, whereas
 mollusks and chordates made up larger proportions afterward. In both the
 Cambrian and present day, ecological occupation of diverse habitat tiers
 and feeding modes are possible with even simple nervous systems, but
 ecological lifestyles requiring rapid, regular movement are almost
 exclusively associated with brain-bearing taxa, suggesting a connection
 with fast information processing abilities and bodily responses. The
 overall rise in cognitive sophistication in the Cambrian was likely a
 unique event in the history of life, although some lineages subsequently
 developed more elaborate sensory systems and/or larger brains.
description: The cells within the data that contain "?" represent
 uncertain anatomical coding or taxonomic assignment.
DOI: 10.5061/dryad.9ghx3ffj9
title: An experimental test of the impact of avian diversity on attentional benefits and enjoyment of people experiencing urban green-space

description: Biodiversity may play a key role in generating the well-being benefits of
 visiting green-spaces. The ability of people to accurately perceive
 variation in biodiversity is, however, unclear and evidence supporting
 links between biodiversity exposure and well-being outcomes remains
 equivocal. In part, this is due to the paucity of controlled experimental
 studies that deal adequately with confounding factors that covary with
 biodiversity. Attention restoration theory (ART) proposes that natural
 environments contain many softly fascinating stimuli that provide visitors
 with a sense of separation from their normal settings and routines,
 switching off direct attention and allowing recovery from attention
 fatigue. Increased biodiversity could increase these stimuli, and ART
 therefore potentially provides a mediating effect linking biodiversity to
 well-being. Here, we conduct a controlled experiment in which participants
 virtually experience urban green-space containing high and low levels of
 avian biodiversity (altered by manipulating bird song). Respondents
 accurately identified the contrast in biodiversity and reported greater
 enjoyment of the high biodiversity treatment than the low diversity
 control. Higher biodiversity did not, however, elicit greater
 self-reported stimulation or restoration, and did not increase perceived
 restorativeness scores or attentional capacity (quantified using the Digit
 Span Backwards attention test). Respondents that were more connected to
 nature, however, had greater attentional capacity following exposure to
 green-space. Our study provides rare experimental evidence that people can
 accurately detect variation in biodiversity, that high avian diversity
 boosts visitor perceptions of urban green-space quality, and that people
 with increased nature connectedness show enhanced attentional capacity.