cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dncjsxm46
title: Data from: The impact of predators and vegetation on shoaling in wild zebrafish

description: In their natural habitats, animals experience multiple ecological factors
 and regulate their social responses accordingly. To unravel the impact of
 two ecological factors on the immediate behavioral response of groups, we
 conducted experiments on wild zebrafish shoals in arenas with vegetation,
 predator cues, both factors simultaneously, or neither (control
 treatments). Analysis of 297 trials revealed that while shoals formed
 significantly larger subgroups in the presence of predator cues, their
 subgroup size was comparable to control treatments when they faced
 predator cues and vegetation. Shoals were highly polarized in open arenas,
 in the absence of either ecological factor and in the presence of predator
 cues (with/without vegetation). The presence of vegetation alone, however,
 significantly reduced shoal polarization. Furthermore, food intake was
 significantly reduced when predator cues and/or vegetation were present.
 Tracking individuals revealed that: (i)individuals within shoals receiving
 predator cues had a significantly higher probability to continue being in
 a group compared to control treatments, and (ii)individuals occupying the
 front positions deviated lesser from their median position within a shoal
 as compared to other individuals regardless of predator cues. The
 adaptability of animals depends on behavioural responses to changing
 environments, making this study significant in the context of
 environmental changes.
description: ## Data from: The impact of predators and vegetation on shoaling in wild
 zebrafish Shoaling in wild zebrafish is impacted by various ecological
 factors. Here, through a series of manipulative experiments, we examine
 the impact of vegetation or/and predator odors on shoaling tendencies in
 this cyprinid species. The given excel files contains data on: (1) the
 mean largest subgroup size, (2) mean polarisation score; (3)foraging
 behavior of shoals in terms of number of bites at bloodworms,
 (4)probability to switch states from solitary to solitary and group to
 group (5)mean position of individuals and the standard deviation
 corresponding to the mean position (6) The date of experimentation for
 each shoal The above data have been presented in a single sheet.
 Abbreviations used: PT stands for predator treatment, CT stands for
 control treatment, PVT stands for Predator Vegetation Treatment and VT
 stands for Vegetation Treatment. Data was derived from the following
 sources: Data was derived from video recordings of exeperimental
 observations. Code/Software: NA (1)(2)(3) were quantified manually from
 video recordings. (4)(5) were quantified manually from tracked video
 recordings (videos tracked using free software:idTracker).
DOI: 10.5061/dryad.zpc866tcq
title: Sand lizards (Lacerta agilis) decrease nymphal infection prevalence for tick-borne pathogens Borrelia burgdorferi sensu lato and Anaplasma phagocytophilum in a coastal dune ecosystem

description: 1. Understanding which factors determine tick-borne disease hazard can
 contribute to effective disease control. In Europe, the hazard of the
 pathogens Borrelia burgdorferi s.l. and Anaplasma phagocytophilum is
 determined by local tick densities (mainly Ixodes ricinus) and the
 reservoir competence of the host species community. Sand lizards (Lacerta
 agilis) are common hosts for larvae and nymphs of I. ricinus and
 non-competent reservoirs for both pathogens. Consequently, high relative
 abundance of L. agilis is hypothesized to be associated with lower
 infection prevalence in nymphs. Here, we aimed to test whether this
 effectively occurs in natural settings. 2. We sampled different habitat
 types within a heterogenous dune landscape at the Dutch coast and
 estimated 1) L. agilis densities, 2) host community competence, 3) the
 density and infection prevalence of questing I. ricinus ticks, and 4) the
 number and infection prevalence of ticks feeding on L. agilis. 3. Captured
 L. agilis had high tick burdens and contributed substantially to feeding
 I. ricinus larvae in their natural habitat. B. burgdorferi s.l. and A.
 phagocytophilum were virtually absent from feeding larvae and nymphs. 4.
 The nymphal infection prevalence of both pathogens in questing ticks was
 lower in habitat types where L. agilis was more abundant. Hence, L. agilis
 strongly reduced community competence. 5. The density of questing nymphs
 was higher in habitat types with denser vegetation and also varied more
 between habitat types than infection prevalence. As a result, nymphal
 density had a stronger effect on the density of infected ticks than did
 nymphal infection prevalence. 6. Synthesis and applications. Coastal dune
 habitats favourable for L. agilis have lower densities of questing nymphs,
 and a lower human infection hazard. These results might be applicable to
 similar ecosystems where L. agilis is present. From a public health
 perspective, this underlines the importance of preserving early
 successional habitat, as encroaching shrubs are associated with higher
 tick-borne disease hazard, and vegetation removal might be a solution to
 reduce hazard in coastal dunes. The high degree of spatial heterogeneity
 in the abundance of tick-borne pathogens also poses opportunities to
 manage recreational activities to limit human exposure to tick-borne
 diseases.
description: Please see the README document ("README.md") and the
 accompanying published article: Köhler, C.F., Sprong, H., Fonville, M.,
 Esser, H.J., De Boer, W.F., van der Spek, V., Spitzen - van der Sluijs,
 A., 2023. Data from: Sand lizards (<em>Lacerta</em>
 <em>agilis</em>) decrease nymphal infection prevalence for
 tick-borne pathogens <em>Borrelia</em>
 <em>burgdorferi</em> sensu lato and
 <em>Anaplasma</em> <em>phagocytophilum</em> in a
 coastal dune ecosystem. Journal of Applied Ecology. Accepted. DOI:
 10.1111/1365-2664.14379
DOI: 10.5061/dryad.0p2ngf25d
title: Multi‐marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird

description: Avian diet can be affected by site‐specific variables, such as habitat, as
 well as intrinsic factors such as sex. This can lead to dietary niche
 separation, which reduces competition between individuals, as well as
 impacting how well avian species can adapt to environmental variation.
 Estimating dietary niche separation is challenging, due largely to
 difficulties in accurately identifying food taxa consumed. Consequently,
 there is limited knowledge of the diets of woodland bird species, many of
 which are undergoing serious population declines. Here, we show the
 effectiveness of multi‐marker fecal metabarcoding to provide in‐depth
 dietary analysis of a declining passerine in the UK, the Hawfinch
 (Coccothraustes coccothraustes). We collected fecal samples from (n = 262)
 UK Hawfinches prior to, and during, the breeding seasons in 2016–2019. We
 detected 49 and 90 plant and invertebrate taxa, respectively. We found
 Hawfinch diet varied spatially, as well as between sexes, indicating broad
 dietary plasticity and the ability of Hawfinches to utilize multiple
 resources within their foraging environments.
description: This dataset is raw sequencing reads generated from an Illumina
 MiSeq run. The original samples the DNA was extracted from were Hawfinch
 faecal samples. This dataset also includes R scripts necessary for running
 the results within the manuscript.
description: MobaX term, R, and a server are required. FastP, Mothur, Unoise,
 and Blast are all recommended programs to run these data files.
DOI: 10.5061/dryad.37pvmcvq5
title: Development of microsatellite markers for colony delineation of the invasive Asian subterranean termite in South Florida and Taiwan

description: Delineating the colony identity of Coptotermes
 gestroi (Wasmann) is a core issue of colony elimination
 in the implementation of subterranean termite baiting
 systems. Invasion history is believed the possible cause of
 genetic variabilities among colonies. Haplotype network analysis of
 mitochondrial cytochrome c oxidase subunit II revealed
 the multiple origins of
 American C. gestroi from the
 Philippines and Southeast Asia and the Taiwan population only from the
 Philippines. We further developed 21 new microsatellite
 markers for the comparison of genetic variabilities on colony delineation
 of C. gestroi colonies from South
 Florida (invaded ~30 years; 3–7 generations) and Taiwan (~110
 years; 13–27 generations). The present microsatellite
 markers with 1–4 alleles per locus have validated the
 effectiveness of colony delineation for three incipient colonies reared in
 the laboratory and three field colonies from Taiwan. Genetic admixture of
 the Floridian C. gestroi probably caused by
 recent invasion history, multiple invasions, and anthropogenic activities
 among regions. A possible introduction event likely
 occurred through human-mediated activities between Fort Lauderdale and
 Miami. Overall, these new microsatellite markers provide suitable and
 efficient candidate genetic markers for colony
 delineation of C. gestroi to consolidate the
 effectiveness of the colony elimination system in termite
 management.
DOI: 10.5061/dryad.r4xgxd2j4
title: Tree community composition stabilizes ecosystem functions in response to drought

description: In summer 2018, Central Europe was hit by an extreme drought event that
 widely impacted ecosystems and markedly increased tree mortality in forest
 ecosystems across the continent. As climate models predict an increase in
 frequency and severity of such events, there is an urgent need to adapt
 forests in order to maintain the diverse benefits they provide. Soil
 processes play an essential role in this context and are key for a
 plethora of terrestrial ecosystem functions but are strongly dependent on
 water availability. Here we investigated how tree species richness,
 composition, and identity in a 13-year-old temperate tree diversity
 experiment influenced selected ecosystem functions (as important
 representatives of different ecosystem processes) during the 2018 summer
 drought. We focused on the stability of soil microbial biomass and
 standard litter decomposition, as well as tree species-specific mortality
 rates. Contrary to our expectations, tree species richness did not
 generally increase the resistance of soil functions and decrease tree
 mortality rates. However, the resistance of these functions was determined
 by tree species identity and community composition. For the resistance of
 both soil functions (microbial biomass and litter decomposition), we found
 that tree species richness effects depended on the presence of certain
 tree species. Moreover, we found that the performance of a specific tree
 species in monoculture, Norway Spruce, was a poor predictor of its
 response to drought in tree species mixtures. Taken together, the results
 of our study demonstrate that the species composition of tree stands
 determines tree mortality and the resistance of soil functions under
 drought. This indicates that enhancing multiple ecosystem functions under
 environmental disturbance requires maintaining diverse forests.
DOI: 10.5061/dryad.5qfttdz9s
title: Thermally controlled intein splicing of engineered DNA polymerases provides a robust and generalizable solution for accurate and sensitive molecular diagnostics

description: DNA polymerases are essential for nucleic acid synthesis, cloning,
 sequencing and molecular diagnostics technologies. Conditional intein
 splicing is a powerful tool for controlling enzyme reactions. We have
 engineered a thermal switch into thermostable DNA polymerases from two
 structurally distinct polymerase families by inserting a thermally
 activated intein domain into a surface loop that is integral to the
 polymerase active site, thereby blocking DNA or RNA template access. The
 fusion proteins are inactive but retain their structures such that the
 intein excises during a heat pulse delivered at 70–80°C to generate
 spliced, active polymerases. This straightforward thermal activation step
 provides a highly effective, one-component ‘hot-start’ control of PCR
 reactions that enables accurate target amplification by minimizing
 unwanted by-products generated by off-target reactions. In one engineered
 enzyme, derived from Thermus aquaticus DNA polymerase, both DNA polymerase
 and reverse transcriptase activities are controlled by the intein,
 enabling single-reagent amplification of DNA and RNA under hot-start
 conditions. This engineered polymerase provides high-sensitivity detection
 for molecular diagnostics applications, amplifying 5–6 copies of the
 tested DNA and RNA targets with &gt;95% certainty. The design
 principles used to engineer the inteins can be readily applied to
 construct other conditionally activated nucleic acid processing enzymes.
description: Proteins were separated by 8%
 SDS-PAGE. The gels were stained by Coomassie Blue. The gel bands were
 quantified using ImageJ. Fluorescence polarization was measured
 using SpectraMax M5e plate reader (Molecular Devices): 485 nm excitation
 (9 nm bandwidth), 525 nm emission (15 nm bandwidth). Real-time fluorescence signals were
 recorded using CFX96 thermocycler (Bio-Rad). Protein melting curves were recorded using
 CFX96 thermocycler (Bio-Rad). All data were outputs of
 the software of the instruments or ImageJ without further
 processing.  All images were untrimmed raw gel images
 captured by UVP Gel Studio.
description: The raw data were organized in one Microsoft Excel file, which
 can be opened using Microsoft Excel. The raw images
 were organized in one Microsoft Word file, which can be opened
 using Microsoft Word.
DOI: 10.5061/dryad.866t1g1vc
title: Data from: Dim light pollution prevents diapause induction in urban and rural moths

description: 1. Light pollution is increasingly affecting biodiversity and may also
 disrupt seasonal adaptations. Even dim artificial light, such as
 skyglow—which can spread far beyond urban areas—can interfere with using
 photoperiod as a seasonal cue. 2. Here, we test how light pollution
 impacts diapause induction and whether urban evolution counteracts it, by
 using common-garden experiments with a common, widespread geometrid moth
 (Chiasmia clathrata). We raised offspring from urban and rural populations
 from North- and Mid-European countries in treatments with and without dim
 light at night. 3. The dim light treatment strongly increased direct
 development overall—with no evidence for urban adaptation to it—but
 distinctly more so in Mid- than in North-European populations. 4. Because
 diapause induction is critical for surviving winter, these results
 indicate that dim but widespread light pollution may have detrimental
 effects on insect populations, especially so at mid-latitudes, and may
 hence explain part of the ongoing, large-scale insect declines globally.
 5. Synthesis and applications: Latitudinal variation in sensitivity to
 light pollution means that its contribution to insect declines—and its
 conservation importance—should likewise vary among regions. In
 mid-latitude regions, where populations seem more sensitive to light
 pollution, mitigating light pollution should be a high priority for insect
 conservation Reducing skyglow from cities should benefit both urban
 populations—which were just as susceptible as rural populations in our
 study—and rural populations—because skyglow extends far beyond the
 geographic boundaries of cities.
DOI: 10.5061/dryad.05qfttf72
title: Data for: Experimental test of the influence of light availability on the evolution of eye size and behavior in Daphnia

description: There exists extensive variation in eye size. Much work has provided a
 connection between light availability and differences in eye size across
 taxa. Experimental tests of the role of the light environment on the
 evolution of eye size are lacking. Here we performed a selection
 experiment that examined the influence of light availability on shifts in
 eye size and the connection between eye size and phototactic
 (anti-predator) behavior in Daphnia. We set up replicate experimental
 populations of Daphnia, repeatedly evaluated phenotypic shifts in eye size
 during the ~50-day experiment and performed a common garden experiment at
 the end of the experiment to test for evolutionary shifts in eye size and
 behavior. Our phenotypic analyses showed that eye size rapidly diverged
 between the light treatments; relative eye size was consistently larger in
 the low versus high light treatments. Selection on eye size was also
 modified by variation in density as increases in Daphnia density favored a
 larger eye. However, we did not observe differences in eye size between
 the light treatments following two generations of common garden rearing at
 the end of the experiment. We instead observed strong shifts in
 anti-predator behavior. Daphnia from the low light treatment exhibited
 decreased phototactic responses to light. Our results show that decreased
 light relaxes selection on anti-predator behavior. Such trends provide new
 insights into selection on eye size and behavior.
DOI: 10.5061/dryad.vx0k6djx5
title: Data from: Temporary thinning shock in previously shaded red spruce

description: Silvicultural thinning can lead to rapid microclimatic changes for
 residual trees. Despite the benefits of decreased competition, thinning
 may induce “thinning shock” – temporary negative physiological responses
 as trees acclimate to new conditions. We examined the impact of thinning
 on the microclimate and physiology of residual, previously shaded red
 spruce (Picea rubens Sarg.) trees relative to non-thinned controls. Both
 daily maximum temperature and vapor pressure deficit increased
 post-thinning, with larger increases observed on hotter and drier days. In
 response to these environmental changes, we found clear evidence of
 physiological declines. At 1.7 weeks post thinning, we found a 0.59-MPa
 reduction in average midday water potential relative to control trees,
 which lasted for an additional 1.4 weeks. Thus, the trees in the thinning
 treatment were at or beyond published estimates of needle turgor loss.
 Thinning decreased photosynthetic efficiency of current-year needles by
 3.8% after two weeks, and it declined by 1.3% per week for the remainder
 of the growing season. These results suggest that thinning shock occurs in
 red spruce, a shade-adapted, climate-sensitive species. Thinning shock may
 contribute to the lagged growth responses commonly observed post-thinning,
 and these effects may be more extreme in novel future climates.
description: The data were collected in the summer of 2020 at the University
 of Maine. Details on data collection are included in the full publication.
 The data reported here are the processed data used to generate all the
 graphs and calculate statistics reported in the manuscript.
DOI: 10.5061/dryad.fj6q57400
title: 3D dataset of tissue cleared MADM mouse brain

description: Tissue clearing renders entire organs transparent to enable combination
 with light sheet fluorescence microscopy to accelerate whole tissue
 imaging. Yet, challenges remain in analyzing the large resulting 3D
 datasets that consist of terabytes of images and information on millions
 of labeled cells. Previous work has established pipelines for automated
 analysis of tissue cleared mouse brains, but focus there was on single
 color channels and/or detection of nuclear localized signals in
 low-resolution images. Here, we present an automated workflow (COMBINe,
 Cell detectiOn in Mouse BraIN) to map sparsely labeled neurons and
 astrocytes in genetically distinct mouse forebrains using Mosaic Analysis
 with Double Markers (MADM). COMBINe blends modules from multiple pipelines
 with RetinaNet at its core. We quantitatively analyzed the regional and
 subregional effects of MADM-based deletion of the Epidermal Growth Factor
 Receptor (EGFR) on neuronal and astrocyte populations in the mouse
 forebrain. 
description: Left brain hemisphere of a male P30
 <em>Emx1<sup>cre</sup>:MADM11<sup>TG/GT</sup>:Egfr<sup>+/+</sup></em> (wildtype) mouse was collected, cleared and stained using iDISCO+ protocol. The cleared mouse brain hemisphere was imaged using a custom-built light sheet fluorescence microscope by illumination of 561 nm (RFP-Cy3) and 640 nm (GFP-AF647) respectively, with a voxel size of 0.65 × 0.65 × 10 μm<sup>3</sup>. 
description: This is an example dataset for running the COMBINe
 workflow. The dataset contains tiff images which can be opened with image
 tools (e.g. ImageJ) that support tiff format.
DOI: 10.5061/dryad.mcvdnck4x
title: Hetaerina SNPs data for: Genomic differentiation and niche divergence in the Hetaerina americana (Odonata) cryptic species complex

description: The evolution of reproductive barriers, that is, the speciation process,
 implies the limitation of gene flow between populations. Different
 patterns of genomic differentiation throughout the speciation continuum
 may provide insights into the causal evolutionary forces of species
 divergence. In this study, we analyzed a cryptic species complex of the
 genus Hetaerina (Odonata). This complex includes H. americana and H.
 calverti; however, in H. americana, two highly differentiated genetic
 groups have been previously detected, which, we hypothesize, may
 correspond to different species with low morphological variation. We
 obtained single nucleotide polymorphism (SNP) data for 90 individuals
 belonging to the different taxa in the complex and carried out
 differentiation tests to identify genetic isolation. The results from
 STRUCTURE and discriminant analysis of principal components (DAPC), based
 on almost 5,000 SNPs, confirmed the presence of three highly
 differentiated taxa. Also, we found FST values above 0.5 in pairwise
 comparisons, which indicates a considerable degree of genetic isolation
 among the suggested species. We also found low climatic niche overlap
 among all taxa, suggesting that each group occurs at specific conditions
 of temperature, precipitation and elevation. We propose that H. americana
 comprises two cryptic species, which may be reproductively isolated by
 ecological barriers related to niche divergence, since the morphological
 variation is minimal and, therefore, mechanical barriers are probably less
 effective compared to other related species such as H. calverti.
description: # Hetaerina SNPs data Data for the article: Genomic differentiation and
 niche divergence in the Hetaerina americana (Odonata) cryptic species
 complex ## Description of the data and file structure The data includes
 different SNP sets used for population genomics of the damselfly complex
 *Hetaerina americana.* The different datasets included vcf files with the
 SNPs called by STACKS software. Dataset 1 included all individuals (n =
 90) belonging to *H. calverti*, *H. americana* North and *H.
 americana*South. Secondly, Dataset 2 included only individuals of *H.
 calverti* (n = 31), Dataset 3 included individuals of *H. americana* North
 (n = 24) and Dataset 4 included individuals of *H. americana* South (n =
 35). Finally, to compare taxa by pairs, we performed three more SNP
 callings: Dataset 5 included individuals of *H. calverti* and *H.
 americana* North (n = 55), Dataset 6 included individuals of *H. calverti*
 and *H. americana* South (n = 66) and Dataset 7 included individuals of
 *H. americana* North and South (n = 59).