cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.57680/asep.0645286
title: Multidisciplinary study of lime and gypsum plasters from the Paphian region – comprehensive dataset

description: The present dataset is the result of a research project concerning plaster production in southwestern Cyprus (Paphos region) over an extensive time period, spanning from the Late Bronze to the Roman age. This dataset includes results obtained from a multi-analytical approach to material analysis, including methods such as petrography, scanning electron microscopy, thermogravimetry, x-ray diffractometry, Raman and infra-red spectroscopy, and proteomics. The aim of this publication is to create a reliable database for future researchers interested in the same topic, in order to create similar classifications and uniform terminology.
DOI: 10.5061/dryad.xsj3tx9kz
title: Association of Wolbachia with gene expression in Drosophila testes

description: Wolbachia is a genus of intracellular symbiotic bacteria that are widely
 distributed in arthropods and nematodes. These maternally inherited
 bacteria regulate host reproductive systems in various ways to facilitate
 their vertical transmission. Since the identification of
 Wolbachia in many insects, the relationship between Wolbachia and the host
 has attracted great interest. Numerous studies have indicated
 that Wolbachia modifies a variety of biological processes in the host.
 Previous studies in Drosophila melanogaster (D. melanogaster)
 have demonstrated that Wolbachia can affect spermatid differentiation,
 chromosome deposition, and sperm activity in the early stages of
 spermatogenesis, leading to sperm dysfunction. Here, we explored
 the putative effect of Wolbachia in sperm maturation using
 transcriptomic approaches to compare gene expression in
 Wolbachia-infected and Wolbachia-free D. melanogaster adult
 testes. Our findings show that Wolbachia affects many biological
 processes in D. melanogaster adult testes, and most of the
 differentially expressed genes involved in carbohydrate metabolism,
 lysosomal degradation, proteolysis, lipid metabolism, and immune
 response were upregulated in the presence of Wolbachia. In
 contrast, some genes that are putatively associated with cutin
 and wax biosynthesis and peroxisome pathways were downregulated.
 We did not find any differentially expressed genes that are
 predicted to be related to spermatogenesis in the datasets. This
 work provides additional information for understanding the
 Wolbachia-host intracellular relationships.
description: This is the raw RNA-seq data, and sequenced by the BGISEQ500
 platform (BGI, Shenzhen, China) to obtain PE150 bp paired-end
 transcriptome data in the size of 6 Gb.
DOI: 10.5061/dryad.p8cz8w9vx
title: CocciEnv qPCR data and accompanying metadata from soil and settled dust in the San Joaquin Valley

description: Coccidioidomycosis is a typically respiratory fungal disease that, in the
 United States, occurs primarily in Arizona and California. In California,
 most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily
 agricultural region where the disease poses a risk for outdoor workers. We
 collected 710 soil samples and 265 settled dust samples from nine sites in
 the San Joaquin Valley and examined how Coccidioides detection
 varied by month, site, and the presence and abundance of other fungal
 species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil
 samples at five undeveloped sites and were unable to detect Coccidioides
 in any of 472 surface and subsurface soil samples at four agricultural
 sites. In what is the largest sampling effort undertaken on agricultural
 land, our results provide no evidence that agricultural soils in the San
 Joaquin Valley harbor Coccidioides. We found no clear association between
 Coccidioides and the greater soil fungal community, but we identified 19
 fungal indicator species that were significantly associated with
 Coccidioides detection in burrows. We also did not find a seasonal pattern
 in Coccidioides detection in the rodent burrow soils we sampled. These
 findings suggest both the presence of a spore bank and that
 coccidioidomycosis incidence may be more strongly associated with
 Coccidioides dispersal than Coccidioides growth. Finally, we were able to
 detect Coccidioides in only five of our 265 near-surface settled dust
 samples, one from agricultural land, where Coccidioides was undetected in
 soils, and four from undeveloped land, where Coccidioides was common in
 the rodent burrow soils we sampled. Our ability to detect Coccidioides in
 few settled dust samples indicates that improved methods are likely needed
 moving forward, though raises questions regarding aerial dispersal in
 Coccidioides, whose key transmission event likely occurs over short
 distances in rodent burrows from soil to naïve rodent lungs.
DOI: 10.6084/m9.figshare.31169518
title: Raw data of selective chiral multistate switching.

description: All raw data supporting the selective chiral multistate switching.
DOI: 10.25349/d9vs54
title: Data used in: The causes and consequences of seed size variation in the California-native annual species, Nemophila menziesii

description: I.  Seed size is a critical factor in determining various aspects
 of a plant’s life cycle, such as germination rate, seedling size, and
 survival. The sources of variation in the trait are essential to
 understand its adaptive potential to changing environments. This study
 evaluates the genetic and environmental influences on seed size variation
 within and among four wild populations of Nemophila menziesii, a
 widespread California annual herb. By leveraging a greenhouse breeding
 experiment with a nested half-sibling mating design, this study examines
 the magnitude of additive genetic variance and heritability of seed size
 within populations, the concordance between different heritability
 estimation methods, and the contribution of the maternal and paternal
 parents to seed size. Mean seed size differed significantly among
 populations, regardless of growing location, while the magnitude of
 plasticity in response to environmental conditions was similar among
 populations. The study revealed a disparity between the two methods used
 to estimate heritability – parent-offspring regression and the nested
 half-sibling analysis. We found evidence for maternal variance in seed
 size in all four populations, but significant additive genetic variance
 was only present in two populations.   II. Seed size is also a
 critical trait that affects life-history attributes, reproductive output,
 and overall fitness of adult plants. Despite the competitive advantages of
 larger seeds, seed size variation persists within and among plant
 populations due to additive genetic effects, non-additive genetic effects,
 environmental influences, and differential seed provisioning by the
 maternal sporophyte. This study investigates the factors contributing to
 seed size variation and its fitness consequences in the California-native
 annual species, Nemophila menziesii, across multiple conspecific
 populations that were reintroduced to their home environments following a
 one-generation greenhouse breeding experiment. Seeds produced in
 greenhouse conditions were generally larger than those produced in the
 field, and environmental factors were significant determinants of
 offspring seed size across populations. Parental genotype and phenotype
 effects on seed size were population-specific, with maternal influences
 tending to exceed paternal effects. The impact of maternal seed size on
 reproductive traits and fitness was also population-specific, with larger
 maternal seed size associated with increased fruit production in three of
 the four populations, and increased fecundity and reproductive yield in
 two of the four populations. Tradeoffs between seed mass and the number of
 seeds produced per fruit by a reproductive individual were detected in two
 of the four populations.
DOI: 10.6084/m9.figshare.31169518.v3
title: Raw data of selective chiral multistate switching.

description: All raw data supporting the selective chiral multistate switching.
DOI: 10.6084/m9.figshare.31169518.v2
title: Raw data of selective chiral multistate switching.

description: All raw data supporting the selective chiral multistate switching.
DOI: 10.5061/dryad.2rbnzs7sr
title: Climate or diet? The importance of biotic interactions in determining species range size

description: Aim: Species geographical range sizes play a crucial role in determining
 species vulnerability to extinction. Although several mechanisms affect
 range sizes, the number of biotic interactions and species climatic
 tolerance are often thought to play discernible roles, defining two
 dimensions of the Hutchinsonian niche. Yet, the relative importance of the
 trophic and the climatic niche for determining species range sizes is
 largely unknown.Location: Central and Northern EuropeTime period:
 PresentMajor taxa studied: Gall-inducing sawflies and their
 parasitoidsMethods: We use data documenting the spatial distributions and
 biotic interactions of 96 herbivore species, and their 125 parasitoids,
 across Europe and analyse the relationship between species range size and
 the climatic and trophic dimensions of the niche. We then compare the
 observed relationships with null expectations based on species occupancy
 to understand whether the relationships observed are an inevitable
 consequence of species range size or if they contain information about the
 importance of each dimension of the niche on species range size.Results:
 We find that both niche dimensions are positively correlated with species
 range size, with larger ranges being associated with wider climatic
 tolerances and larger numbers of interactions. However, diet breadth
 appears to more strongly limit species range size. Species with larger
 ranges have more interactions locally and they are also able to interact
 with a larger diversity of species across sites (i.e. higher
 beta-diversity), resulting in a larger number of interactions at
 continental scales.Main conclusions: We show for the first time how
 different aspects of species diet niche are related to their range size.
 Our study offers new insight into the importance of biotic interactions in
 determining species spatial distributions, which is critical for improving
 understanding and predictions of species vulnerability to extinction under
 the current rates of global environmental change.
DOI: 10.5061/dryad.tb2rbp053
title: Parasitoid development and superparasitism in invasive versus native widow spider host egg sacs

description: The brown widow spider, Latrodectus geometricus, is a hazardous and highly
 invasive species globally. One of the suggested mechanisms enhancing this
 spider’s invasiveness is lower susceptibility to natural enemies compared
 to other widow species. The parasitoid wasp, Philolema latrodecti, is
 known to attack egg sacs of L. geometricus, as well as those of other
 species of Latrodectus. Despite its potential importance as a natural
 enemy of L. geometricus, little is known about the development of this
 wasp and factors mediating its parasitism success. We investigated the
 development of this parasitoid in two widow spider host species, one
 native to Israel, the white widow, L. pallidus, and the invasive brown
 widow, L. geometricus. We compared wasp developmental success in egg sacs
 exposed to increasing wasp densities. We found increased wasp emergence
 and brood size, and smaller emerging wasp body size, with increasing wasp
 density. Across all wasp densities, more and larger parasitoids developed
 in the egg sacs of the native host species, L. pallidus, compared to the
 invasive host species, L. geometricus. Parasitoid sex ratio was highly
 female-biased and the proportion of males increased with wasp density,
 suggesting local mate competition. Overall, our results suggest that L.
 pallidus is a better host for the egg sac parasitoid P. latrodecti, which
 could give a competitive advantage to the less-affected invasive brown
 widow spider.
description: These data were collected at Ben-Gurion University in the Mitrani
 Department of Desert Ecology. Parasitism of egg sacs was done by MAM and
 VA. Wasp counting, body length measurement, egg sac diameter measurement,
 and sex ratio were done by MAM and ADJ. 
description: Microsoft Excel or Numbers
DOI: 10.34740/kaggle/dsv/14652515
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.brv15dvdp
title: Data from: Population divergence in heat and drought responses of a coastal plant: from metabolic phenotypes to plant morphology and growth

description: This dataset supports the article "Population divergence in heat and
 drought responses of a coastal plant: from metabolic phenotypes to plant
 morphology and growth", which is under minor revision in Journal of
 Experimental Botany. The study addresses the combined effects of and plant
 population origin, drought and heat stress on plant growth, plant
 morphology and the leaf metabolome. The data were assessed in Northern and
 Southern European individuals of Cakile maritma (See Rocket).  An
 R-script containing all statistical analyses that have been implemented
 with these data is also provided.
description: A detailed description of the experimental setup and data
 acquisition can be found in the associated manuscript.
description: txt editor alternatively excel /r-studio
DOI: 10.5061/dryad.63xsj3v70
title: Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history

description: Species that exhibit very peculiar ecological traits combined with limited
 dispersal ability pose a challenge to our understanding of ecological and
 evolutionary mechanisms. This is especially true when they have managed to
 spread over long distances, overcome physical barriers and colonise large
 areas. Climate and landscape changes, trophic web relations as well as
 life history all interact to shape migration routes and present-day
 species distributions and their population genetic structures. Here we
 analysed the post-glacial colonization of northern Europe by the gall
 midge Contarinia vincetoxici, which is a monophagous parasite on the
 perennial herb White swallowwort (Vincetoxicum hirundinaria). This insect
 not only has a narrow feeding niche but also limited dispersal ability and
 an exceptionally long dormancy. Gall midge larvae (n = 329) were collected
 from 16 sites along its distribution range in Denmark, Sweden, and
 Finland. Using microsatellite loci and knowledge of the species and the
 regions’ history, we investigated the role of landscape change, host plant
 distribution, insect population dynamics, and life history in shaping the
 population genetic structure of the insect. We devoted particular interest
 to the role of the insect’s presumed poor dispersal capacity in
 combination with its exceptionally extended diapause. We found significant
 levels of local inbreeding (95% highest posterior density interval =
 0.42–0.47), low level within-population heterozygosity (mean HE = 0.45,
 range 0.20–0.61) with private alleles in all populations except two. We
 also found significant (p &lt; 0.001) regional isolation-by-distance
 patterns, suggesting regularly recurring mainly short-distance dispersal.
 According to approximate Bayesian computations, C. vincetoxici appears to
 have colonized the study area via wind-aided flights from remote areas
 approximately 4600 to 700 years before present when the land has gradually
 risen above the sea level. Extremely long dormancy periods have allowed
 the species to “disperse in time”, thereby aiding population persistence
 despite generally low census population sizes.
DOI: 10.5061/dryad.fn2z34v0h
title: New soft-bodied panarthropods from diverse Spence Shale (Cambrian; Miaolingian; Wuliuan) depositional environments

description: The Cambrian (Miaolingian; Wuliuan) Spence Shale Lagerstätte of northern
 Utah and southern Idaho is one of the most diverse Burgess Shale-type
 deposits of Laurentia. It yields a diverse fauna consisting of abundant
 biomineralized and locally abundant soft-bodied fossils, along a range of
 environments from shallow water carbonates to deep shelf dark shales.
 Panarthropods are the dominant component throughout the deposit, both in
 time and space, but while the trilobites and agnostoids are abundant, most
 of the soft-bodied taxa are only known from very few specimens.
 Additionally, the knowledge of the soft-bodied panarthropods is currently
 largely limited to locations in the Wellsville Mountains of northeastern
 Utah. This contribution describes 21 new soft-bodied panarthropods from
 six locations, including the first occurrences of soft-bodied
 panarthropods in the High-Creek, Smithfield Creek, Spence Gulch, and
 Two-Mile Canyon localities. Additionally, we report the presence of
 bradoriids, Branchiocaris pretiosa, Perspicaris? dilatus, Naraoia? sp.,
 Thelxiope cf. T. palaeothalassia, and Tuzoia guntheri for the first time
 from the Spence Shale Lagerstätte, the first occurrence reported outside
 of the Burgess Shale for Thelxiope cf. T. palaeothalassia and the first
 Wuliuan occurrence of Tuzoia guntheri. We also report on a new hurdiid
 carapace element and additional specimens of Buccaspinea cooperi?,
 Dioxycaris argenta, Hurdia sp., and Tuzoia retifera. This new material
 improves our understanding of the panarthropod fauna of the Spence Shale
 Lagerstätte and substantially increases our understanding of the
 distribution of the described taxa in time and space.
DOI: 10.5061/dryad.cfxpnvx9q
title: Data from: Ready to detect a reversal of time’s arrow: a psychophysical study using short video clips in daily scenes

description: It is generally believed that time flows in one direction and that a
 reversal of time’s arrow would render the external world nonsensical. We
 evaluated our ability to tell the direction of time’s arrow in a wide
 range of dynamic scenes in our daily life by presenting 360 video clips in
 the correct or incorrect direction. Participants, who judged the direction
 in a speeded manner, erred in 39% of trials when a video was played in
 reverse, but in only 9% when it was played normally. Due to the bias
 favouring the “forward” judgement, reaction was generally faster for the
 forward response. However, the reaction became paradoxically faster and
 more synchronous for the detection of reversal in some critical occasions
 such as forward motion, free fall, diffusion, division, and addition of
 materials by hand. Another experiment with a fraction of the video clips
 revealed that reversal replay of these videos provided instantaneous
 evidence strong enough to overtake the forward judgment bias. We suggest
 that our brain is equipped with a system that predicts how the external
 organisms behave or move in these critical occasions and that the
 prediction error of the system contributes to the fast “reversal”
 detection.
DOI: 10.5061/dryad.7pvmcvdzg
title: Data from: Global variations and controlling factors of anammox rates

description: Soil anammox is an environmentally-friendly way to eliminate reactive
 nitrogen (N) without generating nitrous oxide. Nevertheless, the current
 earth system models have not incorporated the anammox due to the lack of
 parameters in anammox rates on a global scale, limiting the accurate
 projection for N cycling. A global synthesis with 1212 observations from
 89 peer-reviewed papers showed that the average anammox rate was 1.60 ±
 0.17 nmol N g-1 h-1 in terrestrial ecosystems, with significant variations
 across different ecosystems. Wetlands exhibited the highest rate (2.17 ±
 0.31 nmol N g-1 h-1), followed by croplands at 1.02 ± 0.09 nmol N g-1 h-1.
 The lowest anammox rates were observed in forests and grasslands. The
 anammox rates were positively correlated with the mean annual temperature,
 mean annual precipitation, soil moisture, organic carbon (C), total N, as
 well as nitrite and ammonium concentrations, but negatively with the soil
 C:N ratio. Structural equation models revealed that the geographical
 variations in anammox rates were primarily influenced by the N contents
 (such as nitrite and ammonium) and abundance of anammox bacteria, which
 collectively accounted for 42% of the observed variance. Furthermore, the
 abundance of anammox bacteria was well simulated by the mean annual
 precipitation, soil moisture, and ammonium concentrations, and 51%
 variance of the anammox bacteria was accounted for. The key controlling
 factors for soil anammox rates diﬀered from ecosystem type, e.g., organic
 C, total N, and ammonium contents in croplands, versus soil C:N ratio and
 nitrite concentrations in wetlands. The controlling factors in soil
 anammox rate identified by this study are useful to construct an accurate
 anammox module for N cycling in earth system models.
DOI: 10.5061/dryad.t1g1jwt6s
title: Data from: Remodeling male coercion and the evolution of sexual autonomy by mate choice

description: Models of sexual conflict over mating, including conflict over indirect
 benefits of mate choice, have generally presumed that female resistance to
 male coercion must involve direct confrontation, which can lead to
 sexually antagonistic co-evolutionary arms-races. We built a quantitative
 model examining the largely ignored possibility that females may evolve
 new, additional mate preferences for new male traits that undermine male
 capacity to coerce. Thus, females may “remodel” the coercive capacity of
 the male phenotype in order to enhance their own sexual autonomy – a novel
 alternative mechanism by which females may avoid arms-races. We
 demonstrate that evolutionary “remodeling” is possible, in spite of costs
 to males, because females that prefer males with protective,
 autonomy-enhancing traits (traits correlated with lower coercion
 effectiveness) are likelier to gain indirect benefits of having attractive
 mates. Our analysis reveals new possibilities for the evolution of systems
 of sexual conflict over indirect benefits, showing that autonomy-enhancing
 male traits can act as a “public good,” benefiting all females regardless
 of mating preferences, leading to oscillatory dynamics; and that
 preferences for more protective male traits will often be favored relative
 to preferences for less protective traits, potentially leading to an
 evolutionary “snowball” of expanding sexual autonomy.
description: Mathematica code for the dynamic evolutionary model and analyses
 presented in the main text, supplementary appendices and figures, and raw
 data from simulations underlying parameter-sweep figures.
description: Wolfram Mathematica software version 10 or higher is necessary to
 run the code contained in the Mathematica notebooks.
DOI: 10.5066/p1veaiho
title: Estimates of United States bird trends and bird group relative abundance trajectories, 1970 - 2022

description: This dataset consists of estimates of population trends for 236 species and species complexes of North American birds, and bird taxonomic, primary habitat biome, or conservation status group relative abundance trajectories. Both sets of estimates cover the period 1970 - 2022. Sources of data include the North American Breeding Bird Survey (BBS), Christmas Bird Count (CBC), Waterfowl Breeding Population and Habitat Survey (WBPHS), and the American Woodcock Singing-ground Survey (SGS). The groups with collective relative abundance trajectories are Aridland, Dabbling and Diving Ducks, Eastern Forest, Geese and Swans, Grassland, Sea Ducks, Tipping Point, Waterbirds, and Western Forest.