cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.73n5tb2vg
title: Multivariate phenotypic divergence along an urbanization gradient

description: A growing body of evidence suggests that natural populations can evolve to
 better tolerate the novel environmental conditions associated with urban
 areas. Invariably, studies of adaptive divergence in urban areas examine
 only one or a few traits at a time from populations residing only at the
 most extreme urban and nonurban habitats. Thus, whether urbanization is
 driving divergence in many traits simultaneously in a manner that varies
 with the degree of urbanization remains unclear. To address this gap, we
 generated seed families of white clover (Trifolium repens) collected from
 27 populations along an urbanization gradient in Toronto, Canada, and grew
 them in a common garden to measure 14 phenotypic traits. Overall, families
 from urban sites had evolved later phenology and germination, larger
 flowers, thinner stolons, reduced cyanogenesis, greater biomass, and
 greater seed set. Pollinator observations revealed near complete turnover
 of pollinator morphological groups between urban and nonurban sites, which
 may explain some of the observed divergence in floral traits and
 phenology. Our results suggest that adaptation to urban environments
 involves multiple organismal traits.
description: We collected <em>Trifolium repens </em>plants from 27
 populations along an urban-rural gradient. We grew F1
 of these plants in a common garden, measured 14 phenotypic traits, and
 examined multivariate divergence in these traits across our urbanization
 transect. We additionally conducted pollinator
 observations in each population. 
description: Please See README.md file in the attached .zip folder.
 All datasets and code required to reproducibly generate the
 manuscript's results are provided in this repository. However, it is
 recommended that anyone wishing to reproduce this paper's results
 follow the instructions below using the code provided in the associated
 GitHub
 repository, which will additionally allow the code to be run
 using consistent package versions across platforms and R
 instances.
DOI: 10.5061/dryad.kd51c5b43
title: Online program metrics and evaluation for FMNP and NATA

description: Restrictions on public gatherings in early 2020 due to the COVID-19
 pandemic resulted in cancellation of in-person outreach programs offered
 by the Florida Master Naturalist Program and Natural Areas Training
 Academy, two successful University of Florida extension programs that
 provide natural history and resource management training to lay and
 professional audiences.  In response, both programs rapidly
 transitioned to blended or 100% online educational methods to continue
 offering courses and maintain program operations. To assess participant
 responses to these changes, we used surveys and course registry data to
 evaluate and compare course enrollment, satisfaction, and outcomes among
 courses with new online formats to courses offered prior to the COVID-19
 pandemic. We also examined logistical challenges and key programmatic
 elements that facilitated the transition of both programs to increased
 reliance on online education. Course participants responded favorably to
 classes offered online. Our results revealed an audience exists for online
 programming, that satisfaction with online courses was high and comparable
 to that measured for in-person courses, and that online approaches
 effectively transferred knowledge and promoted behavior change in
 participants. The transition to online programming required investments of
 time, energy, and in some cases, direct costs. However, this transition
 was greatly facilitated by the existence of well-defined program
 protocols, educational curricula, strong partnerships, and feedback
 mechanisms for both programs. Long-term investments in program structure,
 partnerships, and support systems enabled both programs to be resilient
 and adaptable and successfully implement online programming in response to
 the COVID-19 pandemic.
description: We used program surveys and course registry data to evaluate and
 compare course enrollment, satisfaction, and outcomes among FMNP and NATA
 course participants for courses offered prior to the COVID-19 pandemic
 (pre-COVID period, 2019 and earlier) and during the early COVID period
  (March 16 through June 30, 2020) when in-person events were prohibited
 (IRB protocols #202001365 and #201800987). Our questions of interest were
 whether there were differences between the pre-COVID and early COVID
 periods in (1) participants who enrolled in courses, (2) participant
 satisfaction with courses, and (3) outcomes of courses. We also evaluated
 our experiences related to logistical challenges and identified key
 programmatic elements we found helpful for adapting FMNP and NATA training
 courses to include increased levels of online delivery.
description: See README file
DOI: 10.5061/dryad.hhmgqnkf6
title: Microbial community structure across grazing treatments and environmental gradients in the Serengeti

description: Field-based observational research is the first step in understanding the
 factors that structure microbial communities and generate biogeography of
 soil microbes. As one of the last remaining naturally grazed ecosystems on
 Earth, the Serengeti National Park in Tanzania is an ideal location to
 study the influence of large migratory mammals on microbial communities.
 Also, active volcanoes generate strong environmental gradients due to ash
 deposition and a rain shadow. We used 16S rRNA amplicons to characterize
 bacterial and archaeal communities in soils from a 13-year herbivore
 removal experiment to study the influence of grazing and environmental
 gradients on the natural distribution of soil microbes. Removal of
 mammalian herbivores shifted microbial community structure, with 31
 amplicon sequence variants (ASVs) that were significant indicator taxa of
 the ungrazed treatment and only three ASVs that were significant
 indicators of the grazed treatment. The abundance of many ASVs were
 correlated with soil texture, phosphorus, iron, calcium and rainfall, and
 the evenness of taxa within samples increased with fine-textured soil.
 Bayesian general linear mixed effects  models that parse the
 relative importance of multiple, highly correlated predictors of beta
 diversity were consistent with a significant, but weak (2%), effect of
 grazing, and stronger effects of phosphorus (14%) and silt (14%) contents
 in soil. Beta diversity of microbial communities was greater in grazed
 than in ungrazed plots; consequently, our results suggest that the impacts
 of grazing on the community assembly of microbes results from
 deterministic environmental filtering caused by the influence of
 herbivores on plant communities and soil properties rather than stochastic
 dispersal via herds of large mammalian herbivores. These herbivore effects
 are superimposed on deterministic environmental filtering by natural soil
 and precipitation gradients across the Serengeti.
DOI: 10.5061/dryad.sf7m0cg44
title: The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population

description: Transmission ratio distortion (TRD) refers to a widespread phenomenon in
 which one allele is transmitted by heterozygotes more frequently to the
 progeny than the opposite allele. TRD is considered as a mark suggesting
 the presence of reproductive barrier. However, the genetic and molecular
 mechanisms underlying TRD in rice remain largely unknown. In the present
 study, a population of backcross inbred lines (BILs) derived from the
 cross of a japonica cultivar Nipponbare and an indica variety 9311 was
 utilized to study the genetic base of TRD. A total of eighteen genomic
 regions were identified for TRD in the BILs. Among them, twelve and six
 regions showed indica (9311) and japonica (Nipponbare) alleles with
 preferential transmission, respectively. A series of F2 populations were
 used to confirm the TRD effects, including six genomic regions that were
 confirmed by chromosome segment substitution line (CSSL)-derived F2
 populations from inter-subspecific allelic combinations. However, none of
 the regions was confirmed by the CSSL-derived populations from
 intra-subspecific allelic combination. Furthermore, significant epistatic
 interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could
 positively contribute to breaking inter-subspecific reproductive barriers.
 Our results have laid the foundation for identifying the TRD genes and
 provide an effective strategy to breakdown TRD for breeding
 wide-compatible lines, which will be further utilized in the
 inter-subspecific hybrid breeding programs.
description: The BILs were genotyped using a genotyping-by-sequencing (GBS)
 strategy.  Sequencing was
 performed on the selected tags using Illumina HiSeq with the paired-end
 mode and 150-bp read length.  The Burrows Wheeler Aligner software was
 used to map the clean reads for each sample on the reference genome
 (MSU7.0) (http://rice.plantbiology.msu.edu/index.shtml). 
 Single nucleotide polymorphism
 (SNP) calling was performed by Genome Analysis
 Toolkit.<br style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;white-space:normal;"> <br style="font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;white-space:normal;">
DOI: 10.5061/dryad.hdr7sqvg1
title: New insights into the patterns and drivers of avian altitudinal migration from a growing crowdsourcing data source

description: Altitudinal migration is a common and important but understudied behavior
 in birds. Difficulty in characterizing avian altitudinal migration has
 prevented a comprehensive understanding of this behavior. To address this,
 we investigated the altitudinal migration patterns and explored potential
 drivers for a major proportion (~70%) of the entire resident bird
 community along an almost 4,000 m elevational gradient on the main island
 of Taiwan. Based on the occurrence records collected by citizen
 scientists, we examined the seasonal shifts in the center and the upper
 and lower boundaries of elevational distributions for 104 individual
 species. We then built phylogeny-controlled regression models to
 investigate the associations between the birds’ seasonal distribution
 shifts and seven of their traits, and examined whether the observed shifts
 can be explained by three main hypotheses on potential drivers. Results
 showed that at least 60 species (58%) seasonally changed their
 distributions along elevations. While most of them (42 species) tended to
 move downhill in winter, a considerable number of species (14) tended to
 move uphill. While the species breeding at high or low elevations tended
 to move downhill in winter, those breeding at medium-low elevations tended
 to move or extend their distributions to higher elevations. Our regression
 models suggested that seasonal variations in climates and food
 availability could be major drivers of the behavior. However, the three
 hypotheses can only partially explain the observed downhill migration
 patterns and none of them can well explain the uphill patterns, indicating
 an important knowledge gap. This study investigated avian altitudinal
 migration from a new perspective with a novel and generalizable approach,
 and revealed interesting patterns that could be difficult to identify with
 conventional approaches. It demonstrated the power of citizen science data
 to provide new insights into this behavior by characterizing the general
 patterns and mechanisms across a large number of species.
description: The zip file contains one R script and one "data"
 folder. The "data" folder contains the eBird data
 (ebd_TW_relFeb-2019_ebirdp.txt), phylogenetic trees (phylogenytree.nex),
 trait data (Taiwan_Breeding_Bird_Trait.csv), a shapefile of the study area
 (Taiwan_diss_without_island), and dem data (in the folder of
 "twdtm_asterV2_30m). All results and major figures reported in the
 associated paper can be obtained by running the R script
 (almig_tw_202009.R).
DOI: 10.34740/kaggle/dsv/14644523
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.8w9ghx3k4
title: Data for: Temperature-mediated male condition shapes female fitness and oviposition preference in a butterfly

description: Habitat choice by ovipositing females critically shapes fitness in species
 lacking parental care. We aimed at manipulating female oviposition
 choosiness using the Glanville fritillary butterfly (Melitaea cinxia) as
 study species. We tested whether female choosiness is influenced by
 individual condition and/or that of the mating partner, which was
 manipulated experimentally by subjecting adults to night temperatures
 warmer than usual. Against our prediction, female life expectancy was not
 altered by the treatment and impacted her fitness only mildly. Males
 exposed to warm nights, on the other hand, lived shorter and females who
 mated with warm-exposed males sired larger clutches with higher hatching
 success, in line with the terminal investment hypothesis. We also tested
 whether females base their oviposition choices primarily on habitat type
 (open/shaded) or plant condition (dry/well-watered) under a semi-natural
 experimental set-up. We show that females choose primarily open habitats
 and within those habitats well-watered host plants. While female
 choosiness for oviposition was not affected by their own thermal
 treatment, mating with warm-exposed males also strengthened the female
 oviposition preference towards the generally preferred host plant species
 in this study (Plantago lanceolata). The present work brings new awareness
 on the often-neglected role of male condition in shaping female fitness
 and choice.
DOI: 10.5061/dryad.j3tx95xbq
title: Innate immunity promotes sleep through epidermal antimicrobial peptides

description: Wounding and infection trigger a protective innate immune response that
 includes the production of antimicrobial peptides in the affected tissue
 as well as increased sleep. Little is known, however, how peripheral
 wounds or innate immunity signal to the nervous system to increase sleep.
 We found that during C. elegans larval molting, an epidermal
 tolloid/BMP-1-like protein called NAS-38 promotes sleep. NAS-38 is
 negatively regulated by its thrombospondin domain and acts through its
 astacin protease domain to activate p38 MAP/PMK-1 kinase and
 TGF-β-SMAD/SMA-3-dependent innate immune pathways in the epidermis that
 cause STAT/STA-2 and SLC6 (solute carrier)/SNF-12-dependent expression of
 antimicrobial peptide (AMP) genes. We show that more than a dozen
 epidermal AMPs act as somnogens, signaling across tissues to promote sleep
 through the sleep-active RIS neuron. In the adult, epidermal injury
 activates innate immunity and turns up AMP production to trigger sleep, a
 process that requires EGFR signaling that is known to promote sleep
 following cellular stress. We show for one AMP, NLP-29, that it acts
 through the neuropeptide receptor NPR-12 in locomotion-controlling neurons
 that are presynaptic to RIS and that depolarize this neuron to induce
 sleep. Sleep in turn increases the chance of surviving injury. Thus, we
 found a novel mechanism by which peripheral wounds signal to the nervous
 system to increase protective sleep. Such a cross-tissue somnogen
 signaling function of AMPs might also boost sleep in other animals
 including humans.
DOI: 10.5061/dryad.h70rxwdgs
title: Data from: Dietary constraints of phytosaurian reptiles revealed by dental microwear textural analysis

description: Phytosaurs are a group of large, semi-aquatic archosaurian reptiles from
 the Middle–Late Triassic. They have often been interpreted as carnivorous
 or piscivorous due to their large size, morphological similarity to extant
 crocodilians and preservation in fluvial, lacustrine and coastal deposits.
 However, these dietary hypotheses are difficult to test, meaning that
 phytosaur ecologies and their roles in Triassic food webs remain
 incompletely constrained. Here, we apply dental microwear textural
 analysis to the three-dimensional sub-micrometre scale tooth surface
 textures that form during food consumption to provide the first
 quantitative dietary constraints for five species of phytosaur. We
 furthermore explore the impacts of tooth position and cranial robusticity
 on phytosaur microwear textures. We find subtle systematic texture
 differences between teeth from different positions along phytosaur tooth
 rows, which we interpret to be the result of different loading pressures
 experienced during food consumption, rather than functional partitioning
 of food processing along tooth rows. We find rougher microwear textures in
 morphologically robust taxa. This may be the result of seizing and
 processing larger prey items compared to those captured by gracile taxa,
 rather than dietary differences per se. We reveal relatively low dietary
 diversity between our study phytosaurs and that individual species show a
 lack of dietary specialisation. Species are predominantly carnivorous
 and/or piscivorous, with two taxa exhibiting slight preferences for
 ‘harder’ invertebrates. Our results provide strong evidence for higher
 degrees of ecological convergence between phytosaurs and extant
 crocodilians than previously appreciated, furthering our understanding of
 the functioning and evolution of Triassic ecosystems.
DOI: 10.5061/dryad.573n5tb5h
title: Data From: Genetic structure of recently fragmented suburban populations of European stag beetle

description: Habitat loss and fragmentation due to urbanisation can negatively affect
 metapopulation persistence when gene flow among populations is reduced and
 population sizes decrease. Inference of patterns and processes of
 population connectivity derived from spatial genetic analysis has proven
 invaluable for conservation and management. However, a more complete
 account of population dynamics may be obtained by combining spatial and
 temporal sampling. We, therefore, performed a genetic study on European
 stag beetle (Lucanus cervus L.) populations in a suburban context using
 samples collected in three locations and during the period 2002-2016. The
 sampling area has seen recent landscape changes which resulted in
 population declines. Through the use of a suite of FST, clustering
 analysis, individual assignment, and relatedness analysis we assessed fine
 scale spatiotemporal genetic variation within and among habitat patches
 using 283 individuals successfully genotyped at 17 microsatellites. Our
 findings suggested the three locations to hold demographically independent
 populations, at least over time scales of relevance to conservation,
 though with higher levels of gene flow in the past. Contrary to
 expectation from tagging studies, dispersal appeared to be mainly
 female-biased. Although the life cycle of stag beetle suggests its
 generations to be discrete, no clear temporal structure was identified,
 which could be attributed to the varying duration of larval development.
 Since population bottlenecks were detected and estimates of effective
 number of breeders were low, conservation actions are eminent which should
 include the establishment of suitable dead wood for oviposition on both
 local and regional scales to increase (re)colonisation success and
 connectivity among current populations.
description: Genotypes European stag beetle The csv file
 shows the microsatellite genotypes of European stag beetle with in the
 first column the sample codes, in the second the year when the individual
 was sampled, in the third the municipality, in the fourth the sex, and in
 the fifth and sixth column the X and Y coordinates, respectively
 (Lambert-72 coordinates). The next 17 columns represent the different
 microsatellite markers. Alleles are separated by a forward slash. Missing
 genotypes and individuals of unknown sex are indicated with
 'NA'.
DOI: 10.5061/dryad.zw3r2286j
title: Experimentally induced intrasexual mating competition and sex-specific evolution in female and male nematodes

description: Sexual dimorphism in life history traits and their trade-offs is
 widespread among sexually reproducing animals, and is strongly influenced
 by the differences in reproductive strategies between the sexes. We
 investigated how intrasexual competition (pre- and postcopulatory) acted
 on specific life history traits, important to fitness, and their
 trade-offs in the outcrossing nematode Caenorhabditis remanei. Here, we
 imposed strong sex-specific selection through experimental evolution with
 increased potential for intrasexual competition by skewing the adult sex
 ratio towards either males or females (1:10 or 10:1) over 30 generations,
 and subsequently measured the phenotypic response to selection in three
 traits related to fitness; body size, fecundity and tolerance to heat
 stress. We observed a stronger response to selection in females for body
 size and peak fitness, suggesting that females may experience stronger net
 selection and potentially harbour higher amounts of standing genetic
 variance compared to males. Our study highlights the importance of
 investigating direct and indirect effects of intrasexual competition in
 both sexes in order to capture sex-specific responses and understand the
 evolution of sexual dimorphism in traits expressed by both sexes.
DOI: 10.5061/dryad.95x69p8hr
title: Evaluation of a microplate spectrophotometer for soil organic carbon determination in south central Idaho

description: Determination of soil organic carbon (SOC) is highly desirable for
 assessing fertility and carbon sequestration; however, numerous methods of
 determination warrant study of method agreement. Recently, a novel method
 was developed following dichromate oxidation using a microplate
 spectrophotometer. This novel method was compared with (i) total C by dry
 combustion - soil inorganic carbon (DCw/o pretreatment - Pcal); (ii)
 traditional Walkley-Black titration (WBTIT) and (iii) loss on ignition
 (LOI360°C) in calcareous soils of south central Idaho (n=75) in
 conjunction with North American Proficiency Testing program soils (n=10).
 A two-way ANOVA was fit with soils as a blocking factor to identify any
 difference between methods, means were separated using Tukey’s HSD
 (α=0.05). Additional comparisons were made for all soils (n=85) and for
 soils in the lower 75th percentile of SOC determined by WBTIT (n=56) using
 regression analysis. Only the WBTIT and LOI360°C methods were
 statistically equivalent nevertheless there was high agreement (Lin’s
 concordance coefficients &gt;0.90) between all methods (n=85). Under
 low SOC soils (n=56) the agreement between all methods decreased, but the
 WBSPEC method fit other methods comparatively well r2= 0.71, 0.74, and
 0.78 for LOI360°C, DCw/o pretreatment - Pcal, and WBTIT respectively. The
 WBSPEC method provided estimates of SOC between the methods currently used
 in the region while reducing hazardous waste generation over traditional
 WBTIT and sample handling over LOI360°C and DCw/o pretreatment - Pcal
 methods, positioning it as a sensible option for SOC determination in low
 SOC calcareous soils of south central Idaho.