cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hhmgqnkmj
title: Resurrection of Tectaria cadieri from T. ingens (Tectariaceae, Pteridophyta) based on morphological and molecular data

description: We demonstrate that Tectaria cadieri (Tectariaceae) is a
 distinct species in Vietnam after long being placed under the synonymy
 of T. ingens. Morphologically, T. cadieri is
 similar to T. ingens, T. setulosa, T.
 trichotoma in their large fronds (up to 0.8–2 m long), 3-pinnate
 laminae, fully free veins, and sori in two rows on ultimate segments.
 However, T. cadieri differs from these species in the presence of
 linear, membranaceous stipe scales. The analyses of five plastid regions
 (atpB, ndhF plus ndhF-trnN, rbcL, rps16-matK plus matK, and trnL-trnF) also show that T. cadieri is neither closely related to T. ingens, T. setulosa, or T. trichotoma. Rather, T. cadieri is closely related to T. multicaudata, a morphologically distinct species with anastomosing veins. Along with a detailed description and illustrations for T. cadieri, we provided morphological comparisons and comments on the relationships between T. cadieri and morphologically similar species.
DOI: 10.25338/b89h1t
title: Data and code for: Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist and stimulatory G protein

description: G protein-coupled receptors (GPCRs) belong to the largest group of
 membrane receptors for transmembrane signal transduction. Ligand-induced
 activation of GPCRs triggers G protein activation followed by various
 signaling cascades. The uploaded data set help to understand structural
 and energetic determinants of ligand binding to GPCRs and GPCRs to G
 proteins.  In this dataset we presented the way how we
 performed molecular dynamics (MD) simulations by using both Anton 2
 supercomputer and Gaussian accelerated MD method for production runs.
 Before the production runs, we run 90 ns equilibration with gradually
 reducing protein restraints in the first 40 ns using NAMD. We simulated
 two systems, beta-2 adrenergic receptor with norepinephrine bound
 (β2AR-only) and the NE bound β2AR further bound with stimulatory G protein
 (Gs) (β2AR-Gs). For the β2AR-only system, one Anton simulation and three
 repeat GaMD simulations were performed. For the β2AR-Gs systems, four
 Anton simulations and three repeat GaMD simulations were performed. The
 repeat runs for the same system are identical except the starting
 velocities. The needed restraint files used in equilibration, the
 simulation input files, forcefield parameters and structure files for both
 Anton 2 and GaMD simulations were provided. Short trajectories for each
 run of each system were uploaded as well. For each system, we analyzed the
 binding poses of NE, interaction energies between NE and β2AR,
  the conformational changes of the Gs protein, and the 2D
 potential of mean force (PMF). The original data related to the analyses
 and the codes for performing the analyses were provided as well. The codes
 proved in this data set can be reused free of charge. This data set
 corresponds to the paper "Elucidation of a dynamic interplay between
 a beta-2 adrenergic receptor, its agonist and stimulatory G
 protein"  (https://doi.org/10.1073/pnas.2215916120)
description: The dataset was collected based on our simulation setup files which were used by us to do conventional Equilibration, Production runs on Anton 2 supercomputer, and Gaussian accelerated molecular dynamics simulations (GaMD). The dataset also includes analyses and codes used for the analyses.
DOI: 10.5061/dryad.gqnk98st0
title: Data for: Cooperative partnerships of the azure-winged magpie shift from kin to non-kin during colonization of the Tibetan Plateau

description: Cooperative breeding (CB) has recently become hot research topic in the
 field of evolution of animal behavior. However, while CB-related factors
 have been identified at the species and individual level separately, few
 studies have used both large- and fine-scale effects to demonstrate
 CB-related tradeoffs. Here, we propose a “resource gain-fitness loss”
 model that addresses this question and applied it to the Tibetan
 azure-winged magpie during their colonization of a high-altitude (i.e.,
 harsh) habitat. We found that CB occurrence decreased with time after
 colonization and during the breeding season. The decrease coincided with
 increasing nest security as the threat of predation decreased. Along the
 same timeline, the relatedness of helpers to the opposite-sexed breeder
 shifted from kin to non-kin. Cooperative breeders allocated parentage
 among their social mate, helpers, and outgroup extra-pair mates, with
 extra-pair mates obtaining larger reproductive shares over time during
 colonization, indicating that CB facilitated genetic polygamy in the
 Tibetan population. Male breeders provisioned less with increased female
 reproductive skew, whereas female breeders’ provisioning rates did not
 change with male reproductive skew. It appeared that CB occurrence at the
 population and individual levels were both driven by the same selective
 force, nest predation, which decreased when other strategies of ensuring
 nest security were manifested, such as cooperative neighborhoods due to
 extra-pair copulations. Moreover, our findings suggested the reproductive
 skew strategy is not a fixed characteristic of the population, but a
 condition-dependent characteristic of individuals.
description: We collected the life history data of the azure-winged magpie the
 field on the Tibetan Plateau. The data about parentage analysis were
 collected in the labotory. All the data have been processed according to
 their characteristics.
DOI: 10.5061/dryad.9ghx3ffnc
title: Data from: Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria

description: Prosocial behavior is ubiquitous despite the relative fitness costs
 carried by cooperative individuals. However, the stability of cooperation
 in populations is fragile, and often maintained through enforcement. We
 propose that homologous recombination provides such a mechanism in
 bacteria. Using an agent-based model of recombination in a population of
 bacteria playing a public goods game, we demonstrate how changes in
 recombination rate affect the proportion of cooperating cells. In our
 model, recombination converts cells to a different strategy, either
 freeloading (cheaters) or cooperation, based on the strategies of
 neighboring cells and the recombination rate. Increasing the recombination
 rate expands the parameter space in which cooperators dominate
 freeloaders. However, increasing the recombination rate alone is neither
 sufficient nor necessary. Intermediate benefits of cooperation, lower
 population viscosity, and higher population size can promote cooperation
 in a population of cheater strains. Our findings demonstrate how
 recombination influences the persistence of cooperative behavior in
 bacteria. 
description: This is the NetLogo code used for running our agent-based model
 of bacterial cooperation and recombination. Also
 attached are data generated from this model.
description: Application and version used for the software file: NetLogo
 v.6.1.1
DOI: 10.5061/dryad.2ngf1vht5
title: Data from: Reassessment of morphological species delimitations in the Cyperus margaritaceus-niveus complex using morphometrics

description: Background and aims – The Cyperus margaritaceus-niveus complex is a group
 of ten tropical species from sub-Saharan Africa and Madagascar: C.
 karlschumanii, C. kibweanus, C. ledermannii, C. margaritaceus, C. niveus,
 C. nduru, C. obtusiflorus, C. somaliensis, C. sphaerocephalus, and C.
 tisserantii. They are characterised by a capitate head of white-yellow
 spikelets and modified culm bases and recent molecular analysis puts them
 in as a distinct clade. The group lacks a modern taxonomic revision, and
 the taxa described in the Flora treatments of the past 50 years differ
 considerably in their circumscription. In this study, morphometric
 analyses are used to test species limits to establish more stable
 morphological delimitations of the taxa. Material and methods – An
 examination of 15 morphological characters on 489 herbarium specimens was
 carried out and the data was analysed using Principal Component Analysis
 (PCA), Linear Discriminant Analysis (LDA) with cross-validation, and
 Classification and Regression Tree (CART) analysis. Cyperus kibweanus was
 not further considered due to lack of material. Key results – Both PCA and
 LDA showed varying degrees of overlap in the nine remaining taxa, with no
 single group clearly separating in multivariate space. However,
 cross-validation clearly showed C. margaritaceus as a distinct entity
 despite its overwhelming presence in the PCA. Both LDA and CART failed to
 separate C. niveus as a distinct group as its specimens were dispersed
 among the other groups. Differing results were obtained for other taxa
 depending on the type of analysis. C. margaritaceus, C. nduru, and C.
 sphaerocephalus were divided into two groups by CART but re-examination of
 the specimens does not definitively support the idea that these
 infraspecific groups represent separate taxa. Conclusions – The results
 show that eight morphospecies are recognised by LDA and six morphospecies
 by CART. Characters used to separate the taxa in Flora treatments scored
 high loadings in the analysis showing their high taxonomic utility value.
 The methods used can be applied to resolving other complexes in the
 Cyperaceae.
description: Please see the README document and the accompanying published
 article: Xanthos, M., Mayo, S.J. & Larridon (2022) Reassessment of
 morphological species delimitations in the Cyperus margaritaceus-niveus
 complex using morphometrics. Plant Ecology and Evolution. 156 (1):
 112-127.
description: The programs and software required to open the data files are as
 follows: R Studio 2022.07.02
 Mozilla/5.0 (Windows NT 10.0; Win64; x64), AppleWebKit/537.36
 (KHTML, like Gecko), QtWebEngine/5.12.8, Chrome/69.0.3497.128,
 Safari/537.36
DOI: 10.5061/dryad.dbrv15f5c
title: MALDI-MS dataset for use with open-source untargeted metabolomic workflow for complex biological samples

description: Untargeted metabolomics is a powerful tool for measuring and understanding
 complex biological chemistries. However, employment, bioinformatics and
 downstream analysis of mass spectrometry (MS) data can be daunting for
 inexperienced users. Numerous open-source and free to-use data processing
 and analysis tools exist for various untargeted MS approaches, but
 choosing the ‘correct’ pipeline isn’t straight-forward. This data set can
 be used in conjunction with a user-friendly online guide which presents a
 workflow for connecting these tools to process, analyse and annotate
 various untargeted MS datasets. The workflow is intended to guide
 exploratory analysis in order to inform decision-making regarding costly
 and time-consuming downstream targeted MS approaches. The workflow
 provides practical advice concerning experimental design, organisation of
 data and downstream analysis, and offers details on sharing and storing
 valuable MS data for posterity. The workflow is editable and modular,
 allowing flexibility for updated/ changing methodologies and increased
 clarity and detail as user participation becomes more common allowing
 contributions and improvements to the workflow via the online
 repository. 
description: The dataset was collected from soil analysis by MALDI-TOF-MS.
 Three types of soil were collected from the field – arable, orchard and
 forest soil. The samples were extracted into chloroform, methanol and
 water and the aqueous fraction (methanol:water) was mixed 1:1 with 5mg/ml
 CHCA and 1ul was spotted onto a MALDI target plate. Each sample was
 analysed using MALDI-TOF-MS over a scan range of 50-800m/z with a 1-minute
 scan time and data was collected for 1min. Each sample was run 3 times for
 technical replication and 3 biological replicates per soil type were
 run.
description: The raw data files are available to download but need to be
 converted using Proteowizard to the universal mzML format. Proteowizard is
 an open-source tool for Windows users. https://proteowizard.sourceforge.io/download.html The mzML files are also available to download which can be used directly with the processing workflow. The workflow for processing the untargeted metabolomics data can be accessed from the following link. The workflow is based on open-source tools. https://untargeted-metabolomics-workflow.netlify.app/
DOI: 10.5061/dryad.q83bk3jnk
title: Data and code for: Optimal clutch size revisited: separating individual quality from the costs of reproduction

description: Life-history theory, central to our understanding of diversity in
 morphology, behaviour and senescence, describes how traits evolve through
 the optimisation of trade-offs in investment. Despite considerable study,
 there is only minimal support for trade-offs within species between the
 two traits most closely linked to fitness – reproduction and survival –
 questioning the theory’s general validity. We used a meta-analysis to
 separate quality effects from the costs of reproduction using studies of
 parental investment and survival in birds. Experimental enlargement of
 broods caused reduced parental survival. However, the effect of
 experimental enlargements was small and opposite to the effect of
 phenotypic quality, where individuals that naturally produced larger
 clutches also survived better. The opposite effects on survival in
 experimental and observational studies of parental care provide the first
 meta-analytic evidence for theory suggesting that quality differences mask
 trade-offs. Fitness projections using the overall effect size revealed
 that reproduction presented negligible costs, except when reproductive
 effort was forced beyond the level observed within species, to that seen
 between species. We conclude that there is little support for the most
 fundamental life-history trade-off, between reproduction and longevity,
 operating within a population. We suggest that within species, the fitness
 landscape of the reproduction–survival trade-off is flat until it reaches
 the boundaries of the between-species fast-slow life-history continuum.
 Our interpretation explains why the costs of reproduction are not apparent
 and why variation in reproductive output persists within species.
DOI: 10.17617/3.e9chbx
title: Friction Measurements with Picoliter Droplets Using Scanning Probe Microscopy

description: Topographical and chemical defects on solid surfaces tend to pin three-phase contact lines of moving liquid drops. Our quantitative understanding of the pinning process is, however, still poor. Here we use an atomic force microscope to slide ≈100  pL
droplets of water-glycerol mixtures over hydrophobic surfaces and measure friction forces. By using picoliter droplets, the sensitivity for detecting processes at the contact line is enhanced. We have found that only a region &lt;200  nm
around the contact line contributes to friction. By imaging isolated nanospherical defects, we could quantify the force and energy dissipation when the front and rear of the droplet passes the defect and compare it to theory.
description: Jupyter Notebook
DOI: 10.5061/dryad.95x69p8pv
title: Data from: Disruptive selection and the evolution of discrete color morphs in Timema stick insects

description: A major unresolved issue in biology is why phenotypic and genetic
 variation is sometimes continuous, yet other times packaged into discrete
 units of diversity, such as morphs, ecotypes, and species. In theory,
 ecological discontinuities can impose strong disruptive selection that
 promotes the evolution of discrete forms, but direct tests of this
 hypothesis are lacking. Here we show that Timema stick insects exhibit
 genetically-determined color morphs that range from weakly to strongly
 discontinuous. Color data from nature and a manipulative field experiment
 demonstrate that greater morph differentiation is associated with shifts
 from host plants exhibiting more continuous color variation to those
 exhibiting greater coloration distance between green leaves and brown
 stems, the latter of which generates strong disruptive selection. Our
 results show how ecological factors can promote discrete variation, and we
 further present results on how this can have variable effects on the
 genetic differentiation that promotes speciation.
description: These data were generated to investigate how color variation in
 host-plants is selecting for the evolution of discrete morphs in
 <em>Timema</em> stick insects. To do so, we measured
 <em>Timema</em> and host-plants reflectance and coloration. To
 estimate the strength and shape of selection we respectively transplanted
 60 and 60 <em>Timema</em> individuals onto two host-plant
 treatments (first treatment: combination of <em>Ceanothus
 sp.</em> and <em>Adenostoma sp.</em>, AC treatment;
 second treatment: <em>Cercocarpus sp.</em>, MM treatment).
 Within each treatment, we released 20 individuals with green coloration,
 20 individuals with a melanistic coloration (grey, red, or brown), and 20
 individuals with a coloration intermediate between green and melanistic.
 We marked all individuals on the ventral side using a Sharpie pen to
 recognize them from naturally occurring insects. We collected the
 surviving individuals two days after their release and counted them,
 allowing us to estimate survival of the different color categories in the
 different treatments.
description: none
DOI: 10.5061/dryad.d7wm37q58
title: Data for: The influence of vegetation structure on secondary diaspore dispersal by wind

description: The role of vegetation structure in relation to wind speed and diaspore
 attributes on secondary diaspore dispersal by wind has not been
 empirically studied. Here, we investigated secondary dispersal by wind of
 diaspores placed in 12 different kinds of vegetation and bare land. The
 experiments were conducted in a wind tunnel using a range of wind speeds
 and diaspores that differed in mass and kind of appendages. The
 explanations of wind speed, diaspore attributes, vegetation coverage,
 life-form, vertical pattern and horizontal pattern for diaspore dispersal
 capacity were 6.67~10.40%, 16.13~20.53%, 6.227~24.64%, 0.10%, 0.74%, and
 0.10%, respectively. Compared with wind speed and diaspore attributes,
 vegetation coverage contributed the most to diaspore dispersal capacity
 when vegetation coverage was low (&lt;10% in our study). However, but
 with a high (10-30%) coverage, vegetation coverage was the least
 influential factor in secondary diaspore dispersal by wind. Vegetation
 coverage significantly interacted with vegetation life-form, horizontal
 pattern and vertical pattern on affecting diaspore dispersal capacity.
 Thus, the most influential factor determining secondary diaspore dispersal
 by wind is vegetation coverage.
DOI: 10.5061/dryad.fn2z34v04
title: Data for: Large-scale long-term passive-acoustic monitoring reveals spatiotemporal activity patterns of boreal bats

description: The distribution ranges and spatio-temporal patterns in the occurrence and
 activity of boreal bats are yet largely unknown due to their cryptic
 lifestyle and lack of suitable and efficient study methods. We approached
 the issue by establishing a permanent passive-acoustic sampling setup
 spanning the area of Finland to gain an understanding on how latitude
 affects bat species composition and activity patterns in northern Europe.
 The recorded bat calls were semi-automatically identified for three target
 taxa; Myotis spp., Eptesicus nilssonii or Pipistrellus nathusii and the
 seasonal activity patterns were modeled for each taxa across the seven
 sampling years (2015–2021). We found an increase in activity since 2015
 for E. nilssonii and Myotis spp. For E. nilssonii and Myotis spp. we found
 significant latitude -dependent seasonal activity patterns, where seasonal
 variation in patterns appeared stronger in the north. Over the years,
 activity of P. nathusii increased during activity peak in June and late
 season but decreased in mid season. We found the passive-acoustic
 monitoring network to be an effective and cost-efficient method for
 gathering bat activity data to analyze spatio-temporal patterns. Long-term
 data on the composition and dynamics of bat communities facilitates better
 estimates of abundances and population trend directions for conservation
 purposes and predicting the effects of climate change.
DOI: 10.5061/dryad.7h44j0zzk
title: A global data set of realized treelines sampled from Google Earth aerial images

description: We sampled Google Earth aerial images to get a representative and globally
 distributed dataset of treeline locations. Google Earth images are
 available to everyone, but may not be automatically downloaded and
 processed according to Google's license terms. Since we only wanted
 to detect tree individuals, we evaluated the aerial images manually by
 hand.   Doing so, we scaled Google Earth’s GUI interface to a
 buffer size of approximately 6000 m from a perspective of 100 m (+/- 20 m)
 above Earth’s surface. Within this buffer zone, we took coordinates and
 elevation of the highest realized treeline locations. In some remote areas
 of Russia and Canada, individual trees were not identifiable due to
 insufficient image resolution. If this was the case, no treeline was
 sampled, unless we detected another visible treeline within the 6,000 m
 buffer and took this next highest treeline. We did not apply an automated
 image processing approach. We calculated mass elevation effect as the
 distance to the nearest mountain chain limits. Continentality was assessed
 by the distance to the nearest coastline. Isolation was calculated by the
 nearest distance of a mountain chain to another mountain chain within a
 comparable elevational band. 
description: The file global-treeline-data.csv contains the
 whole data set. Please find further information about the data set in the
 README.md. Please download both files and load the .csv file into your
 stats software, e.g. R.<br>
description: The global-treeline-data.csv file can
 be opened with several software options, e.g. R, LibreOffice or any simple
 editor.
DOI: 10.5061/dryad.12jm63z2j
title: Data for: Sex-biased infections scale to population impacts for an emerging wildlife disease

description: Demographic factors are fundamental in shaping infectious disease
 dynamics. Aspects of populations that create structure, like age and sex,
 can affect patterns of transmission, infection intensity and population
 outcomes. However, studies rarely link these processes from individual to
 population-scale effects. Moreover, the mechanisms underlying demographic
 differences in disease are frequently unclear. Here, we explore sex-biased
 infections for a multi-host fungal disease of bats, white-nose syndrome,
 and link disease-associated mortality between sexes, the distortion of sex
 ratios, and the potential mechanisms underlying sex differences in
 infection. We collected data on host traits, infection intensity, and
 survival of five bat species at 42 sites across seven years. We found
 females were more infected than males for all five species. Females also
 had lower apparent survival over winter and accounted for a smaller
 proportion of populations over time. Notably, female-biased infections
 were evident by early hibernation and likely driven by sex-based
 differences in autumn mating behavior. Male bats were more active during
 autumn which likely reduced replication of the cool-growing fungus. Higher
 disease impacts in female bats may have cascading effects on bat
 populations beyond the hibernation season by limiting recruitment and
 increasing the risk of Allee effects.