cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tmpg4fbz
title: Landscape scale lake surveys of Algonquin Provincial Park

description: To better understand the status of Lake Trout and Brook Trout populations
 across the Algonquin Provincial Park landscape 192 index netting surveys
 were conducted on 161 lakes utilizing standardized multimesh benthic
 gillnets between the years 2009 and 2022. Index netting was conducted
 using a depth-stratified randomized site survey design and employed
 multi-pass sampling on a majority of the lakes to provide the opportunity
 for occupancy analysis. Two primary netting methods were employed; Summer
 Profundal Index Netting (SPIN) for Lake Trout populations sampled between
 2009-2012; and a modified Ontario Broadscale Monitoring (BsM) method we
 refer to as Short Duration Point Sampling (SDPS). The SDPS method uses the
 large mesh BsM nets (NA1) deployed for a one-hour duration within the same
 depth strata used in the BsM program with a sampling intensity in each
 stratum proportional to the surface area. The overall sampling intensity
 (nets/lake) is greater than that employed in the BsM program as we are
 interested in lake-specific analyses.  This data dryad provides
 general information on each lake sampled including lake characteristics,
 lake volumes, netting site locations, and spring water
 chemistry.  
description: This dataset was collected by field crews based on the Harkness
 Laboratory of Fisheries Research between the years 2009 - 2022. Field
 activities included spring water chemistry sampling, digital bathymetry
 surveys, and fisheries index netting.  Sample
 collection for spring water chemistry was conducted shortly after ice out
 and analyses were conducted by the Ministry of Environment, Conservation,
 and Parks, Dorset Lab.  Digital bathymetry data were
 collected in the spring on each lake using GPS depth sounders. Lake volume
 in 1m depth increments was calculated using ArcGIS from the resulting
 bathymetry rasters.  Index netting was conducted using
 a depth-stratified randomized site survey design and employed multi-pass
 sampling on a majority of the lakes to provide the opportunity for
 occupancy analysis. Two primary netting methods were employed; Summer Profundal Index Netting (SPIN) for Lake Trout populations sampled between 2009-2012; and a modified Ontario Broadscale Monitoring (BsM) method we refer to as Short Duration Point Sampling (SDPS). The SDPS method uses the large mesh BsM nets (NA1) deployed for a one-hour duration within the same depth strata used in the BsM program with a sampling intensity in each stratum proportional to the surface area. The overall sampling intensity (nets/lake) is greater than that employed in the BsM program as we are interested in lake-specific analyses. Many of the lakes surveyed using the SPDS method were conducted using multipass sampling where each site was sampled a minimum of three times over the course of the survey. 
description: All of the provided files are in csv format and should be
 readable by a variety of software.
DOI: 10.5061/dryad.mkkwh712c
title: Data from: Use of an exotic host plant shifts immunity, chemical defense, and viral burden in wild populations of a specialist insect herbivore

description: Defense against natural enemies constitutes an important driver of
 herbivore host range evolution in the wild. Populations of the Baltimore
 checkerspot butterfly, Euphydryas phaeton (Nymphalidae),
 have recently incorporated an exotic plant, Plantago
 lanceolata (Plantaginaceae), into their dietary range. To
 understand the tritrophic consequences of utilizing this exotic host
 plant, we examined immune performance, chemical defense, and interactions
 with a natural entomopathogen (Junonia coenia
 densovirus, Parvoviridae) across wild populations of this
 specialist herbivore. We measured three immune parameters, sequestration
 of defensive iridoid glycosides (IGs), and viral infection load in
 field-collected caterpillars using either P.
 lanceolata or a native plant, Chelone
 glabra (Plantaginaceae). We found that larvae using the exotic
 plant exhibited reduced immunocompetence, compositional differences in IG
 sequestration, and higher in situ viral burdens compared
 to those using the native plant. On both host plants, high IG
 sequestration was associated with reduced hemocyte concentration in the
 larval hemolymph, providing the first evidence of incompatibility between
 sequestered chemical defenses and the immune response (i.e., the
 “vulnerable host” hypothesis) from a field-based study. However, despite
 this negative relationship between IG sequestration and cellular immunity,
 caterpillars with greater sequestration harbored lower viral loads. While
 survival of virus-infected individuals decreased with increasing viral
 burden, it ultimately did not differ between the exotic and native plants.
 These results provide evidence that (1) phytochemical sequestration may
 contribute to defense against pathogens even when immunity is compromised,
 and (2) herbivore persistence on exotic plant species may be facilitated
 by sequestration and its role in defense against natural enemies.
description: Methodological details pertaining to this dataset are described
 in: Muchoney, N.D., Bowers, M.D., Carper, A.L., Mason, P.A., Teglas, M.B.,
 Smilanich, A.M. Accepted. Use of an exotic host plant shifts immunity,
 chemical defense, and viral burden in wild populations of a specialist
 insect herbivore. Ecology and Evolution. 
description: Muchoney_et_al_2022: This file contains the dataset presented in
 our publication. Descriptions of all column headings are provided in an
 additional metadata tab.
DOI: 10.5061/dryad.612jm6455
title: Traits of soil bacteria predict plant responses to soil moisture

description: Microbes can promote beneficial plant and animal responses to abiotic
 environments, but the ecological drivers of this benefit remain elusive.
 Here we investigated byproduct benefits, which occur when traits that
 increase the fitness of one species provide incidental benefits to another
 species with no direct cost to the provider species. In experimental
 mesocosms, microbial traits predicted plant responses to soil moisture
 such that bacteria with self-beneficial traits in drought increased plant
 early growth, size at reproduction, and chlorophyll concentration under
 drought, while bacteria with self-beneficial traits in well-watered
 environments increased these same plant traits in well-watered
 environments. Thus, microbial traits that promote microbial success in
 different soil moisture environments also promote plant success in these
 same environments. Our results show that the concept of byproduct
 benefits, originally conceived to explain the evolution of cooperation in
 pairwise mutualisms, also applies to interactions between plants and
 non-symbiotic soil microbes.
description: Descriptions of the data can be found in the
 README_Bolin_Lennon_Lau_2022.txt file.
DOI: 10.5061/dryad.1rn8pk0w8
title: Wyoming hummingbird breath d13C

description: Here, we present data from two experiments conducted n the Rocky
 Mountains of Wyoming, USA to assess the relative use of
 feeder and flower nectar by Broad-tailed and Rufous hummingbirds using two
 distinct methods to measure the δ13C values of exhaled CO2 – manual sample
 collection (2010) and automated analysis (2018).
DOI: 10.5061/dryad.cfxpnvx73
title: Integrating fossil flowers into the angiosperm phylogeny using molecular and morphological evidence

description: Fossils are essential to infer past evolutionary processes. The assignment
 of fossils to extant clades has traditionally relied on morphological
 similarity and on apomorphies shared with extant taxa. The use of explicit
 phylogenetic analyses to establish fossil affinities has so far remained
 limited. In this study, we built a comprehensive framework to investigate
 the phylogenetic placement of 24 exceptionally preserved fossil flowers.
 For this, we assembled a new species-level dataset of 30 floral traits for
 1,201 extant species that were sampled to capture the stem and crown nodes
 of all angiosperm families. We explored multiple analytical approaches to
 integrate the fossils into the phylogeny, including different phylogenetic
 estimation methods, topological-constrained analyses, and combining
 molecular and morphological data of extant and fossil species. Our results
 were widely consistent across approaches and showed minor differences in
 the support of fossils at different phylogenetic positions. The placement
 of some fossils agrees with previously suggested relationships, but for
 others, a new placement is indicated. We also identified fossils that are
 well supported within particular extant families, whereas others showed
 high phylogenetic uncertainty. Finally, we present recommendations for
 future analyses combining molecular and morphological evidence, regarding
 the selection of fossils and appropriate methodologies, and provide some
 perspectives on how to integrate fossils into the investigation of
 divergence times and the temporal evolution of morphological traits.
DOI: 10.5061/dryad.w3r2280sn
title: Data from: Temporal dissonance between group size and its benefits requires whole-of-lifecycle measurements

description: The benefits of living in groups drive the evolution of sociality, and
 these benefits could vary across a life-cycle. However, there may be
 experimental problems in linking group size at one time in a life-cycle to
 benefits that only become apparent later on when group size has changed,
 leading to what we call ‘temporal dissonance’. In the only known social
 colletid bee, Amphylaeus morosus, parasite pressures arise at various
 times throughout the life-cycle from different parasitoid species.
 Amphylaeus morosus is impacted by eight different parasitoid species
 operating at different host-colony phenology phases, including five
 species of Gasteruption wasps, a bombyliid fly and two mutillid wasp
 species. We found that, as the reproductive season progressed, the number
 of host adults in a nest declined, often to zero, but the presence of even
 one adult host female during late brood-rearing stages appeared to offer
 substantial brood protection against mutillids. We propose that the
 apparent benefits of colony size at one point in time may not reflect the
 benefits that become apparent at a later point in the season, leading to a
 temporal dissonance between group size and its later fitness benefits. We
 also show that A. morosus is strongly protogynous, with variation in
 parasitoid pressure across the reproductive phenology distorting
 operational sex ratios away from initial investment ratios. Combined, our
 data suggest that seasonal variation in parasitoid pressure may have major
 consequences for understanding social evolution, but these kinds of
 consequences are largely unexplored in current studies of insect social
 evolution. 
description: Please refer to README file.
DOI: 10.5061/dryad.2547d7ws8
title: Area of habitat maps for amphibians and reptiles of Italy

description: Area of Habitat (AOH) maps reveal the distribution of the habitat
 available to the species within their geographic range. Information on the
 distribution of species’ habitats can help identify sites where viable
 populations of a species are found. We produced high resolution (100 m),
 freely accessible global area of habitat maps for 60 species of reptiles
 and amphibians distributed in Italy, which represent 60% of all Italian
 amphibian and reptile species. AOH maps can be used as a reference for
 conservation planning and can help monitoring habitat loss, which is known
 to be a major threat to many reptile and amphibian species in Europe.
description: Area of habitat (AOH) maps were produced
 based on a set of global distribution ranges obtained from the IUCN Red
 List database. We retrieved a total of 25 amphibian and 34 reptile
 distribution ranges of species occurring in Italy. Species were linked to
 their natural habitat using Copernicus Global Land Service Land Cover
 (CGLS-LC100) 2019 classes as a habitat surrogate. Species-Habitat
 associations and altitude limits were based on monographs on the biology
 of target species. A binary classification was compiled to link species
 habitat  to land cover classes. Furthermore, altitude limits (minimum and
 maximum) were compiled for each species. The CGLS-LC100 map was combined
 with altitude information to produce a base map. Each raster cell in the
 base map holds information on the land cover class and altitude data. We
 used IUCN species ranges to mask the area of the base map which is found
 out of the species range. Then, the base map was filtered according to
 species habitat requirements to produce the area of habitat
 maps.
DOI: 10.5061/dryad.2280gb5tw
title: Biotic filtering by species’ interactions constrains food-web variability across spatial and abiotic gradients

description: Despite intensive research on species dissimilarity patterns across
 communities (i.e. beta-diversity), we still know little about their
 implications for variation in food-web structures. Our analyses of 50 lake
 and 48 forest soil communities show that, while species dissimilarity
 depends on environmental and spatial gradients, these effects are only
 weakly propagated to the networks. Moreover, our results show that species
 and food-web dissimilarities are consistently correlated, but that much of
 the variation in food-web structure across spatial, environmental, and
 species gradients remains unexplained. Novel food-web assembly models
 demonstrate the importance of biotic filtering during community assembly
 by (1) the availability of resources, and (2) limiting similarity in
 species’ interactions to avoid strong niche overlap and thus competitive
 exclusion. This reveals a strong signature of biotic filtering processes
 during local community assembly, which constrains the variability in
 structural food-web patterns across local communities despite substantial
 turnover in species composition.
description: This archive contains the data and scripts necessary to reproduce
 the statistical analyses of the study <em>Biotic filtering by
 species’ interactions constrains food-web variability across spatial and
 abiotic gradients</em>. Food-web and
 environmental data were obtained from the GATEWAy (1.0) database: https://idata.idiv.de/ddm/Data/ShowData/283?version=3. Food-web topolgical metrics were calculated using the script <em>allMetBB.R</em>.  Jaccard dissimilarity was calculated using the R package <em>vegan</em>. Structural Equation Models (SEMs) were performed using the R package <em>lavaan</em>. This archive contains also the script <em>src/sampling-error.R</em>, which reproduce potential sampling errors in species composition through a Monte Carlo approach. The data file <em>data/samling-error.csv</em> contains the raw data generated from the Monte Carlo and can be loaded to reproduce the sensitivity analyses. The script <em>SEM_bootstrap.R</em> reproduces the bootstrap analyses for the SEMs.
description: Data files have <em>.csv</em> extensions or
 <em>.RData</em> extension. All R scripts
 have <em>.R</em> extension. To save all
 plots, first create the subfolder <em>plots</em> in this
 directory. The script
 <em>simulations.R</em> is very resource
 intensive and requires a long time to complete; to skip this, simply load
 the results already saved in
 <em>simluations.csv</em>.
DOI: 10.5061/dryad.3j9kd51m0
title: Data in support of Patterns of parental care and movement in divided broods of Golden-winged Warblers

description: This dataset contains observations of parental care and movement for
 divided broods of Golden-winged Warblers tracked from fledging until
 indpendence at three sites in Minnesota and Manitoba. Movement data
 consists of minimum daily distance (i.e., the linear distance between
 daily locations) and daily change in azimuth (i.e., the daily change in
 direction traveled relative to the previous day). Parental care data
 includes, parental attendance, provisioning rate, unattended begging rate
 (i.e., fledgling begging without a parent present), and total begging
 rate. We also include spatial data in the form of distance between
 sub-broods and within sub-broods. These data can be used to replicate the
 findings of the publication "Patterns of Parental Care and Movement
 in Divided Broods of Golden-winged Warblers", published in the
 Journal of Avian Biology. Detailed methodology may be found in that
 manuscript.
description: These data were gathered using radio telemetry to track the daily
 locations of Golden-winged Warbler fledglings. When fledglings were
 located, we observed fledgling and adult behavior for five minutes to
 assess begging, provisioning, and sex of primary care parent.
DOI: 10.5061/dryad.kkwh70s6k
title: Floral shape predicts bee-parasite transmission potential

description: The spread of parasites is one of the primary drivers of population
 decline of both managed and wild bees. Several bee parasites are
 transmitted by the shared use of flowers, turning floral resources into
 potential disease hotspots. However, we know little about how floral
 morphology and floral species identity affect different steps of the
 transmission process. Here, we used the gut parasite Crithidia bombi and
 its primary host, bumble bees (Bombus spp.), to examine whether floral
 traits or species identity better predict three basic steps of parasite
 transmission on flowers: feces deposition on flowers, survival of the
 parasite on flowers, and acquisition by a new host. We also identified
 which traits and/or species were most strongly associated with each step
 in the transmission process. We found that both trait- and species-based
 models fit the data on deposition of feces and survival of C. bombi on
 flowers, but that species-based models provided a better fit than
 trait-based ones. However, trait-based models were better at predicting
 the acquisition of C. bombi on flowers. While different species tended to
 support higher fecal deposition or parasite survival, we found that floral
 shape provided explanatory power for each of the transmission steps. When
 we assessed overall transmission potential, floral shape had the largest
 explanatory effect, with wider, shorter flowers promoting higher
 transmission. Taken together, our results highlight the importance of
 flower species identity and floral traits in disease transmission dynamics
 of bee parasites, and floral shape as an important predictor of overall
 transmission potential. Identifying traits associated with transmission
 potential may help us create seed mix that presents lower parasite
 transmission risk for bees for use in pollinator habitat.
description: Data involved field cage experiments to measure parasite
 deposition, survival, and acquisition on flowers. Data were analyzed using
 R.
description: Because these are experimental data, we recommend reading the
 manuscript associated with these data to understand and interpret the
 data.
DOI: 10.5281/zenodo.18398159
title: The data for the article "Strain-induced magnetic order in RuO2 from first pricinples calculations"

description: The files give the data in the article "Strain-induced magnetic order in RuO2 from first pricinples calculations".

The file name corresponds to the figure in the article. 

The file layout1-2.opju corresponds to Figure1 and Figure2 in the article.

 The file layout3.opju corresponds to Figure3 in the article.

The file layout4.opju corresponds to Figure4 in the article.

The file layout5.opju corresponds to Figure5 in the article.

The file layout6.opju corresponds to Figure6 in the article.

The file layoutS1.opju corresponds to FigureS1 in the supplymental material.

The file layoutS2.opju corresponds to FigureS2 in the supplymental material.

The file layoutS3.opju corresponds to FigureS3 in the supplymental material.
DOI: 10.5281/zenodo.18398160
title: The data for the article "Strain-induced magnetic order in RuO2 from first pricinples calculations"

description: The files give the data in the article "Strain-induced magnetic order in RuO2 from first pricinples calculations".

The file name corresponds to the figure in the article. 

The file layout1-2.opju corresponds to Figure1 and Figure2 in the article.

 The file layout3.opju corresponds to Figure3 in the article.

The file layout4.opju corresponds to Figure4 in the article.

The file layout5.opju corresponds to Figure5 in the article.

The file layout6.opju corresponds to Figure6 in the article.

The file layoutS1.opju corresponds to FigureS1 in the supplymental material.

The file layoutS2.opju corresponds to FigureS2 in the supplymental material.

The file layoutS3.opju corresponds to FigureS3 in the supplymental material.
DOI: 10.5061/dryad.xgxd254j6
title: Evolution of binding preferences among whole-genome duplicated transcription factors

description: Throughout evolution, new transcription factors (TFs) emerge by gene
 duplication, promoting growth and rewiring of transcriptional networks.
 How TF duplicates diverge is known for only a few studied cases. To
 provide a genome-scale view, we considered the 35% of budding yeast TFs,
 classified as whole-genome duplication (WGD)-retained paralogs. Using
 high-resolution profiling, we find that ~60% of paralogs evolved
 differential binding preferences. We show that this divergence results
 primarily from variations outside the DNA binding domains (DBDs), while
 DBD preferences remain largely conserved. Analysis of non-WGD orthologs
 revealed that ancestral preferences are unevenly split between duplicates,
 while new targets are acquired preferentially by the least conserved
 paralog (biased sub/neo-functionalization). Dimer-forming paralogs evolved
 mostly one-sided dependency, while other paralogs interacted through
 low-magnitude DNA-binding competition that minimized paralog interference.
 We discuss the implications of our findings for the evolutionary design of
 transcriptional networks.
description: Next-generation Sequencing (NGS) data processed with MATLAB.
description: This dataset is meant to be used with the scripts provided in the
 associated GitHub
 repo:<br>https://github.com/barkailab/Gera2021