cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7d7wm37zc
title: Data from: Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird

description: Parental age can have considerable effects on offspring phenotypes and
 health. However, intergenerational effects may also have longer-term
 effects on offspring fitness. Few studies have investigated parental age
 effects on offspring fitness in natural populations while also testing for
 sex- and environment-specific effects. Further, longitudinal parental age
 effects may be masked by population-level processes such as the selective
 disappearance of poor-quality individuals. Here, we used
 multi-generational data collected on individually marked Seychelles
 warblers (Acrocephalus sechellensis) to investigate the impact of maternal
 and paternal age on offspring lifespan and lifetime reproductive success.
 We found negative effects of maternal age on female offspring lifespan and
 lifetime reproductive success, which were driven by within-mother effects.
 There was no difference in annual reproductive output of females born to
 older versus younger mothers, suggesting that the differences in offspring
 lifetime reproductive success were driven by effects on offspring
 lifespan. In contrast, there was no association between paternal age and
 female offspring lifespan or either maternal or paternal age and male
 offspring lifespan. Lifetime reproductive success, but not annual
 reproductive success, of male offspring increased with maternal age, but
 this was driven by between-mother effects. No paternal age effects were
 found on female offspring's lifetime reproductive success but there
 was a positive between-father effect on male offspring's lifetime
 reproductive success. We did not find strong evidence for
 environment-dependent parental age effects. Our study provides evidence
 for parental age effects on the lifetime fitness of offspring and shows
 that such effects can be sex-dependent. These results add to the growing
 literature indicating the importance of intergenerational effects on
 long-term offspring performance and highlight that these effects can be an
 important driver of variation in longevity and fitness in the wild.
description: These datasets are related to the manuscript (accepted for
 publication in Evolution Letters): Sex-dependent
 effects of parental age on offspring fitness in a cooperatively breeding
 bird A. M. Sparks, M. Hammers, J. Komdeur, T. Burke, D.
 S. Richardson, H. L. Dugdale
description: Please see the README files for descriptions of the columns in
 the datasets. Full details of the methods can be found in the journal
 article.  R scripts for analyses can be found at
 https://github.com/Seychelle-Warbler-Project/Sparks_2022_EvolLett These datasets were collected as part of the long-term individual-based study of Seychelles warblers on Cousin Island in the Seychelles. For questions related specifically to these datasets please contact Alexandra Sparks or Hannah Dugdale
DOI: 10.57707/fmi-b2share.6dkkr-f5c41
title: CO2, CH4 and N2O fluxes in a Nordic agricultural field growing barley intercropped with undersown species

description: This package contains data from an experimental site in southern Finland, where barley was cultivated either as a monoculture or intercropped with 1 to 8 undersown species. After the barley harvest, the undersown species remained in the field and served as a cover crop until tillage in the following spring. The field, located in Helsinki (60°13'29.4"N, 25°01'12.7"E), is classified as coarse mineral soil. Manual chamber flux measurements included NEE, TER, N₂O, and CH₄, and were conducted over a two-year period from May 2020 to May 2022.
DOI: 10.57707/fmi-b2share.dsr9d-3ev26
title: CO2, CH4 and N2O fluxes in a Nordic agricultural field growing barley intercropped with undersown species

description: This package contains data from an experimental site in southern Finland, where barley was cultivated either as a monoculture or intercropped with 1 to 8 undersown species. After the barley harvest, the undersown species remained in the field and served as a cover crop until tillage in the following spring. The field, located in Helsinki (60°13'29.4"N, 25°01'12.7"E), is classified as coarse mineral soil. Manual chamber flux measurements included NEE, TER, N₂O, and CH₄, and were conducted over a two-year period from May 2020 to May 2022.
DOI: 10.5061/dryad.prr4xgxqj
title: T cell deficiency precipitates antibody evasion and emergence of neurovirulent polyomavirus

description: JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy
 (PML), a life-threatening brain disease in immunocompromised patients.
 Inherited and acquired T cell deficiencies are associated with PML. The
 incidence of PML is increasing with the introduction of new
 immunomodulatory agents, several of which target T cells or B cells. PML
 patients often carry mutations in the JCPyV VP1 capsid protein, which
 confer resistance to neutralizing VP1 antibodies (Ab). Polyomaviruses
 (PyV) are tightly species-specific; the absence of tractable animal models
 has handicapped understanding of PyV pathogenesis. Using mouse
 polyomavirus (MuPyV), we found that T cell deficiency during persistent
 infection, in the setting of monospecific VP1 Ab, was required for
 outgrowth of VP1 Ab-escape viral variants. CD4 T cells were primarily
 responsible for limiting polyomavirus infection in the kidney, a major
 reservoir of persistent infection by both JCPyV and MuPyV, and checking
 emergence of these mutant viruses. T cells also provided a second line of
 defense by controlling the outgrowth of VP1 mutant viruses that evaded Ab
 neutralization. A virus with two capsid mutations, one conferring
 Ab-escape yet impaired infectivity and a second compensatory mutation,
 yielded a highly neurovirulent variant. These findings link T cell
 deficiency and evolution of Ab-escape polyomavirus VP1 variants with
 neuropathogenicity.
description: The data files were generated on a Leica DM4000 fluorescence
 microscope.
description: Leica Application Suite X (LAS X) or Fiji/ImageJ with the
 Bio-Formats plugin is required to open the .lif files.
DOI: 10.5061/dryad.rxwdbrvcr
title: Luna 20 spinel-bearing lithic fragments

description: The Luna 20 mission returned samples from the Hilly and Furrowed Terrain
 of the Moon that is associated with the impact event that formed the
 Crisium Basin. This event potentially excavated deep crustal and upper
 mantle lithologies. Spinel is commonly considered to be a mineralogical
 indicator of rocks of high-pressure origin, and orbital data indicate the
 presence of spinel-bearing lithologies exterior to the basin. We have
 examined 166 Luna 20 particles in the 250-500 µm size range and found 31
 spinel-bearing fragments. Of these 10 are igneous plutonic Mg-suite rocks,
 most of which are troctolitic, and 16 are impact melt rocks. The other
 five are fused soil or devitrified glass fragments. The spinel-bearing
 lithic fragments are plagioclase-rich and do not have the high modal
 abundances of Mg-Al spinel previously identified in the region through
 remote sensing analyses. The textures, compositions, and inferred
 crystallization sequences of the present magmatic spinel-bearing samples
 are most consistent with a relatively shallow crustal (rather than a deep
 crustal) origin, with a petrogenesis involving the assimilation of ferroan
 anorthosite crust by Mg-rich, mantle-derived magmas. Both relict and
 newly-formed spinels are found in impact melt rocks and are also inferred
 to have formed at relatively low pressures. Thus, the presence of spinel
 is not an unambiguous indicator of mantle or deep crustal material. The
 insights gained from this study show that studies of a small, robotically
 collected sample can improve our understanding of regional lithologies and
 petrologic processes.
description: - Backscattered electron images obtained with a scanning electron
 microscope. - Quantitative analyses obtained by
 energy-dispersive spectroscopy. - Quantitative analyses
 obtained by wavelength-dispersive spectroscopy.
description: Excel, TextEdit, image viewer for TIFF files
DOI: 10.5061/dryad.j6q573nhq
title: Data for: Invasion history of Lycium ferocissimum in Australia – the impact of admixture on genetic diversity and differentiation

description: Aim: We investigated the invasion history of Lycium ferocissimum, a
 spine-covered shrub native to South Africa that has developed into a
 damaging invasive plant of undisturbed landscapes and pastures across
 southern and eastern Australia. In addition to identifying the provenance
 of the Australian plants, we tested for evidence of admixture, and
 contrasted genetic diversity and structuring across the native and
 introduced ranges. Location: Samples were collected across South Africa
 (24 localities) and Australia (26 localities). Methods: We used
 genotyping-by-sequencing (3,130 SNPs across 381 individuals) to assess
 population genetic structuring in L. ferocissimum across Australia and
 South Africa. Coalescent analyses were used to explicitly test contrasting
 invasion scenarios. Results: Clear geographic genetic structuring was
 detected across South Africa, with distinct clusters in the Eastern and
 Western Cape provinces. The L. ferocissimum plants in Australia form their
 own genetic cluster, with a similar level of genetic diversity as plants
 in South Africa. Coalescent analyses demonstrated that the lineage in
 Australia was formed by admixture between Eastern Cape and Western Cape
 plants, with analyses suggesting that plants from both African regions
 were originally introduced to South Australia. We detected little evidence
 of geographic genetic structure across Australia, although many of the
 populations were genetically distinct from one another. Main conclusions:
 Our results illustrate how admixture can result in genetically diverse and
 distinct invasive populations. The complex invasion history of L.
 ferocissimum in Australia poses particular challenges for biological
 control. We suggest potential biological control agents should be screened
 against admixed plants (in addition to plants from the Eastern and Western
 Cape) to test whether they provide effective control of the genetically
 distinct invasive lineage.
description: Genotyping-by-sequencing dataset for African boxthorn
 (<em>Lycium ferocissimum</em>) samples from Australia and
 South Africa.
description: Tassel, STACKS, any R package that can process vcf files (e.g.
 adgenet, vcftools).
DOI: 10.5061/dryad.zkh1893cz
title: Dataset for: Numerical simulations of sheared granular materials by 3D DEM for analyzing formation of internal structures and relationship between it and frictional behavior

description: We conducted numerical simulations of sheared granular materials under
 normal stress by using 3D DEM method in order to analyze internal
 structures and relationship between their formation and frictional
 behavior. This dataset includes raw data for plotting figures in our
 article and run scripts and CAD files for simulations.
DOI: 10.5061/dryad.m37pvmd5n
title: Data from: Grooming time predicts survival in American kestrels

description: Animals have evolved a variety of adaptations to care for the body
 surface, such as grooming behavior, which keeps the integument clean,
 parasite-free, and properly arranged.  Despite extensive research
 on the grooming of mammals, birds, and arthropods, the survival value of
 grooming has never been measured directly in natural
 populations.  We monitored grooming and survival in a population
 of marked American kestrels (Falco sparverius) on San Salvador Island,
 Bahamas. We found a strong association between time spent grooming and
 survival over a two-year period.  The quadratic relationship we
 show is consistent with stabilizing natural selection on grooming
 time.  To our knowledge, this is the first evidence for a
 correlation between grooming time and survival in a natural
 population.  Grooming time may predict the survival of many
 animal taxa, but additional studies are needed to determine the shape and
 strength of the relationship among birds, mammals and arthropods.
description: Data from this field study are availble here as csv files.  See
 publication for more information about data collection methods.
DOI: 10.25338/b8jh10
title: Discovery and genetic characterization of single cohort adult colonies with male aggregations, and preliminary evidence for lekking in a Malagasy kite spider (Isoxya, Gasteracanthinae)

description: Spiders are notoriously solitary and cannibalistic, with instances of
 colonial or social lifestyles in only about 50-60, or ~0.1% of 50,000
 described species. Population analyses indicate that most colonies consist
 of multiple cohorts formed by close relatives. Territorial social spiders
 facultatively form colonies by interlinking individual webs, but further
 cooperation is infrequent, and only among juveniles or (rarely) females.
 In spiders, therefore, aggregations of males outside of the male-male
 competition context have been unknown. Here, we report on a discovery of a
 kite spider from Madagascar that exhibits unique colonies. We found
 colonies of the newly described araneid Isoxya manangona n. sp. formed by
 up to 41 interconnected, single-cohort adult female webs with up to 38
 adult males aggregating on a central, single, non-sticky line. With males
 resting tightly together, we found no evidence of male-male aggression.
 Genetic analyses from RAD sequencing suggest that most colonies consist of
 unrelated individuals. Furthermore, the genetic variability of males was
 somewhat less than that of females. Single cohort colonies made up purely
 of adults, and peaceful male aggregations, have not previously been
 observed in spiders. Although direct behavioral observations are
 preliminary, we speculate based on the available evidence that these
 colonies may represent a novel and first case of lekking in spiders.
description: Genomic DNA was isolated from 80 individuals representing nine
 web colonies using the Qiagen DNeasy Blood and Tissue kit (Qiagen). SNP
 data was generated using the 3RAD technique detailed in Bayona-Vásquez et
 al. (2019). We used enzymes EcoRI, MspI, and ClaI following Petersen et
 al. (2012) and Burns et al. (2017), and adapters provided by the
 University of Georgia (BadDNA@UGA). Paired-end 150 base pair reads were
 generated for the 3RAD library with Nextseq at the University of
 California, Davis DNA Technologies Core. Further detail regarding our 3RAD
 procedure is given in Newton et al. (2020). Read demultiplexing,
 filtering, and clustering were performed with ipyrad (Eaton and Overcast,
 2020). For each end of each locus, maxima of six uncalled bases, ten
 heterozygous sites, 25 SNPs, and ten indels were allowed. The clustering
 threshold was set to 0.9, and locus occupancy was set to a minimum of
 50%.
DOI: 10.5061/dryad.n5tb2rc00
title: Data from: Fertilization mode covaries with body size

description: The evolution of internal fertilization has occurred repeatedly and
 independently across the tree of life.  As it has evolved,
 internal fertilization has reshaped sexual selection and the covariances
 among sexual traits such as testes size and gamete traits. But it is
 unclear whether fertilization mode also shows evolutionary associations
 with traits other than primary sex traits. Theory predicts that
 fertilization mode and body size should covary, but formal tests with
 phylogenetic control are lacking. We used a phylogenetically-controlled
 approach to test the covariance between fertilization mode and adult body
 size (while accounting for latitude, offspring size, and offspring
 developmental mode) among 1,232 species of marine invertebrates from 3
 phyla. Within all phyla, external fertilizers are consistently larger than
 internal fertilizers: the consequences of fertilization mode extend to
 traits that are only indirectly related to reproduction. We suspect that
 other traits may also coevolve with fertilization mode in ways that remain
 unexplored.  
description: We compiled data for adult size, fertilization mode,
 developmental mode, and latitude for 1,232 species of marine annelids,
 echinoderms, and molluscs, and for a subset of the species for which it
 was available, we compiled additional data for offspring size. Most of the
 species in our dataset came from previously published meta-analyses on
 various marine invertebrate life-history traits (Marshall et al. 2012;
 Monro and Marshall 2015), supplemented with additional data for the adult
 size from the literature. Data were compiled in Microsoft Excel and
 analyzed in RStudio v. 4.2.2 (RStudio Team 2022).
 <em><strong>Literature
 cited</strong></em> Marshall,
 D. J., P. J. Krug, E. K. Kupriyanova, M. Byrne, and R. B. Emlet. 2012. The
 biogeography of marine invertebrate life histories. Annual Review of
 Ecology, Evolution, and Systematics 43:97–114. Monro,
 K., and D. J. Marshall. 2015. The biogeography of fertilization mode in
 the sea. Global Ecology and Biogeography 24:1499–1509.
 RStudio Team. 2022. RStudio: Integrated Development Environment
 for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
description: Programs/software required to
 open/analyze the data files: Microsoft Excel (view raw data and
 metadata, .csv files for analyses) Adobe
 Reader (view PDF's of phylogenetic trees) RStudio
 (open files, manipulate and analyze data)
DOI: 10.5061/dryad.x3ffbg7nv
title: Data and codes for: A link model approach to identify congestion hotspots

description: Congestion emerges when high demand peaks put transportation systems under
 stress. Understanding the interplay between the spatial organization of
 demand, the route choices of citizens, and the underlying infrastructures
 is thus crucial to locate congestion hotspots and mitigate the delay. Here
 we develop a model where links are responsible for the processing of
 vehicles, which can be solved analytically before and after the onset of
 congestion, and provide insights into the global and local congestion. We
 apply our method to synthetic and real transportation networks, observing
 a strong agreement between the analytical solutions and the Monte Carlo
 simulations, and a reasonable agreement with the travel times observed in
 12 cities under congested phase. Our framework can incorporate any type of
 routing extracted from real trajectory data to provide a more detailed
 description of congestion phenomena and could be used to dynamically adapt
 the capacity of road segments according to the flow of vehicles, or reduce
 congestion through hotspot pricing.
description: Synthetic and real network data used in the paper together with
 the code to perform the simulations.
description: Networks are provided in .csv format.
DOI: 10.5061/dryad.f1vhhmh14
title: NO2 gas sensing properties of hydrothermally synthesized WO3.nH2O nanostructures

description: Nitrogen dioxide (NO2) has been identified as a serious air
 pollutant that threats to our environment, human life
 and world ecosystems. Therefore, detection of this air pollutant is
 crucial. Metal oxide semiconductor (MOS) is one of the best approaches
 frequently used to detect NO2 at relatively low temperatures. Hydrated
 tungsten trioxide (WO3•nH2O), an n-type semiconductor, is regarded to be a
 promising material for fabricating gas sensors, which are widely utilized
 in environmental and safety monitoring. In this work, WO3•nH2O
 nanoparticles have been synthesized using a polyfunctional
 surfactant-mediated hydrothermal approach in the addition of H2C2O4 and
 K2SO4 at a molar ratio of 1:1. This paper has also reported the effect of
 reaction temperature (120°C to 200°C) on morphological changes and gas
 sensing performance. The characterization of these synthesized
 nanostructures was carried out by UV–Vis absorption spectroscopy (UV-Vis),
 X-ray diffraction (XRD) and field emission scanning electron microscopy
 (FESEM). The UV absorption peak was obtained around 300 nm. FESEM analysis
 showed sheet-like structures come together to form flower-type morphology.
 The synthesized WO3•nH2O flower-like structures was then used for NO2 gas
 sensing application. The prepared sensors showed considerably better
 sensor response (Rg/Ra=17.48) at 185°C for 25 ppm NO2.
DOI: 10.5061/dryad.x0k6djhp6
title: Data for: Positive legacies of severe droughts in the Inner Mongolia grassland

description: Global change-induced extreme droughts are increasing in grasslands
 worldwide, and drought legacies may greatly affect the responses
 of grassland ecosystems to these changes. However, it remains poorly
 understood whether and how severe droughts have a positive legacy effect
 on grassland productivity. By combining a 4-year precipitation
 manipulation experiment with a 40-year observational study in a semiarid
 grassland, we showed that extreme droughts could create strong positive
 legacies on community productivity, and that such legacies could last for
 multiple years. The mechanism behind this was the coupled effect of the
 drought-induced increase in annuals and the favorable precipitation
 pattern that facilitated the flourishing of annuals in subsequent years.
 This study provides experimental and observational evidence for novel
 positive drought legacies and reveals their underlying mechanisms. Our
 findings suggest that positive drought legacies should be incorporated
 into Earth system models to better predict the impact of extreme droughts
 on grassland ecosystems.
DOI: 10.5061/dryad.8cz8w9gvb
title: Human activities favour prolific life histories in both traded and introduced vertebrates

description: Species’ life histories determine population demographics and thus the
 probability that introduced populations establish and spread. Life
 histories also influence which species are most likely to be introduced,
 but how such ‘introduction biases’ arise remains unclear. Here, we
 investigate how life histories affect the probability of trade and
 introduction in phylogenetic comparative analyses across three vertebrate
 classes: mammals, reptiles and amphibians. We find that traded species
 have relatively high reproductive rates and long reproductive lifespans.
 Within traded species, introduced species have a more extreme version of
 this same life history profile. Species in the pet trade also have long
 reproductive lifespans but lack ‘fast’ traits, likely reflecting demand
 for rare species which tend to have slow life histories. We identify
 multiple species not yet traded or introduced but with life histories
 indicative of high risk of future trade, introduction and potentially
 invasion. Our findings suggest that species with high invasion potential
 are favoured in the wildlife trade and therefore that trade regulation is
 crucial for preventing future invasions.
description: Please see Methods section of associated article.
description: Please see README file.