cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0zpc866zc
title: Simulated treatment effects on bird communities inform landscape‐scale dry conifer forest management

description: Human land use and climate change have increased forest density and
 wildfire risk in dry conifer forests of western North America, threatening
 various ecosystem services, including habitat for wildlife. Government
 policy supports active management to restore historical structure and
 ecological function. Information on potential contributions of restoration
 to wildlife habitat can allow assessment of tradeoffs with other
 ecological benefits when prioritizing treatments. We predicted avian
 responses to simulated treatments representing alternative scenarios to
 inform landscape‐scale forest management planning along the Colorado Front
 Range. We used data from the Integrated Monitoring in Bird Conservation
 Regions program to inform a hierarchical multispecies occupancy model
 relating species occupancy and richness with canopy cover at two spatial
 scales. We then simulated changes in canopy cover (remotely sensed in
 2018) under three alternative scenarios, (1) a “fuels reduction” scenario
 representing landscape‐wide 30% reduction in canopy cover, (2) a
 “restoration” scenario representing more nuanced, spatially variable
 treatments targeting historical conditions, and (3) a reference, no‐change
 scenario. Model predictions showed areas of potential gains and losses for
 species richness, richness of ponderosa pine forest habitat specialists,
 and the ratio of specialists to generalists at two (1 km2 and 250 m2)
 spatial scales. Under both fuels reduction and restoration scenarios, we
 projected greater gains than losses for species richness. Surprisingly,
 despite restoration more explicitly targeting ecologically relevant
 historical conditions, fuels reduction benefited bird species richness
 over a greater spatial extent than restoration, particularly in the lower
 montane life zone. These benefits reflected generally positive species
 associations with moderate canopy cover promoted more consistently under
 the fuels reduction scenario. In practice, contemporary forest management
 is likely to lie somewhere between the fuels reduction and restoration
 scenarios represented here. Therefore, our results inform where and how
 active forest management can best support avian diversity. Although our
 study raises questions regarding the value of including landscape‐scale
 heterogeneity as a management objective, we do not question the value of
 targeting finer-scale heterogeneity (i.e., stand and treatment level).
 Rather, our results combined with those from previous work clarify the
 scale at which targeting structural heterogeneity and historical reference
 conditions can promote particular ecosystem services.
description: All methods data collection and spatial analysis methods are
 described in the manuscript related to this dataset.
description: A readme file included in this data repository catalogs its
 contents. The data repository include a git repository containing all
 scripts necessary to reproduce research results using the data provided in
 the data repository.
DOI: 10.15468/dl.6t5gtr
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Happywhale - Polar bear in Arctic Ocean"
 ]
}

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002992-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bnzs7h4c7
title: Data from: Using metabolic theory to describe temperature and thermal acclimation effects on parasitic infection

description: Predicting temperature effects on species interactions can be challenging,
 especially for parasitism where it is difficult to experimentally separate
 host and parasite thermal performance curves. Prior authors proposed a
 possible solution based on the metabolic theory of ecology (MTE), using
 MTE-based equations to describe the thermal mismatch between host and
 parasite performance curves and account for thermal acclimation responses.
 Here we use published infection data, supplemented with experiments
 measuring metabolic responses to temperature in each species, to show that
 this modeling framework can successfully describe thermal acclimation
 effects on two different stages of infection in a tadpole-trematode
 system. All thermal acclimation effects on host performance manifested as
 changes in one key model parameter (activation energy), with measurements
 of host respiration generating similar MTE parameter estimates and
 acclimation effects compared to measurements of the host’s ability to
 clear encysted parasites. This result suggests that metabolic parameter
 estimates for whole-body metabolism can sometimes be used to estimate
 temperature effects on host and parasite performance curves. However, we
 found different thermal patterns for measurements of host prevention of
 initial parasite encystment emphasizing potential challenges when applying
 MTE-based models to complex parasite-host systems with multiple distinct
 stages of infection.
DOI: 10.25338/b8vp85
title: A hierarchical N-mixture model to estimate behavioral variation and a case study of Neotropical birds

description: Understanding how and why animals use the environments where they occur is
 both foundational to behavioral ecology and essential to identify critical
 habitats for species conservation. However, some behaviors are more
 difficult to observe than others, which can bias analyses of raw
 observational data. To our knowledge, no method currently exists to model
 how animals use different environments while accounting for imperfect
 behavior-specific detection probability. We developed an extension of a
 binomial N-mixture model (hereafter the behavior N-mixture model) to
 estimate the probability of a given behavior occurring in a particular
 environment while accounting for imperfect detection. We then conducted a
 simulation to validate the model’s ability to estimate the effects of
 environmental covariates on the probabilities of individuals performing
 different behaviors. We compared our model to a naïve model that does not
 account for imperfect detection, as well as a traditional N-mixture model.
 Finally, we applied the model to a bird observation dataset in Northwest
 Costa Rica to quantify how three species behave in forests and farms.
 Simulations and sensitivity analyses demonstrated that the behavior
 N-mixture model produced unbiased estimates of behaviors and their
 relationships with predictor variables (e.g., forest cover, habitat type).
 Importantly, the behavior N-mixture model accurately characterized
 uncertainty, unlike the naïve model which often suggested erroneous
 effects of covariates on behaviors. When applied to field data, the
 behavior N-mixture model suggested that Hoffmann’s woodpecker (Melanerpes
 hoffmanii) and Inca dove (Columbina inca) behaved differently in forested
 versus agricultural habitats, while turquoise-browed motmot (Eumomota
 superciliosa) did not. Thus, the behavior N-mixture model can help
 identify habitats that are essential to a species’ life cycle (e.g., where
 individuals nest, forage) that non-behavioral models would miss. Our model
 can greatly improve the appropriate use of behavioral survey data and
 conclusions drawn from them. In doing so, it provides a valuable path
 forward for assessing the conservation value of alternative habitat types.
  
description: The datasets uploaded here were collected
 through avian point-count surveys in Northwest Costa Rica. Read the
 methods section in the publication and the supplementary information for
 more details.
description: We are uploading eight data sets that refer to the ecological
 data and basic physical parameters of the study area, and one file
 containing the code used for our simulation study. Read the README file
 for a complete description of each file.
DOI: 10.5061/dryad.q573n5tjw
title: Data from: Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon

description: After a half a century of salmon farming, we have yet to understand how
 the influx of genes from farmed escapees affects the full life history of
 Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over
 6900 wild adult salmon from 105 rivers, we document that increased farmed
 genetic ancestry is associated with increased growth throughout life and a
 younger age at both seaward migration and sexual maturity. There was large
 among-population variation in the effects of introgression. Most
 saliently, the increased growth at sea following introgression declined
 with the population’s average growth potential. Variation at two
 major-effect loci previously shown to be associated with age at maturity
 was little affected by farmed genetic ancestry and could not explain the
 observed phenotypic effects of introgression. Our study provides knowledge
 crucial for redicting the ecological and evolutionary consequences of
 increased aquaculture production worldwide.
description: Column names: organismID = unique
 identifier of organism inhouseID = label of each
 individual used at NINA (not necessarily unique)
 random_sample = value of 0 means that the individual is
 considered for the wild population with regards to phenotype expressed in
 freshwater, but not for phenotypes expressed at sea
 riverName = name of the river rivID =
 Unique code for Norwegian watercourse outlets issued by The Norwegian
 Water Resource and Energ y Directorate (NVE) dataType
 = collection method yearCapture = the year the fish
 was captured dateCapture = the date the fish was
 captured (format: dd.mm.yyyy) sex = sex of the fish,
 where F denotes female, and M denotes male VGLL3_TOP
 = genotype at the VGLL3_TOP marker (format: 0,1,2, where 1 is the
 heterozygous genotype, while 0 and 2 are homozygores)
 SIX6_TOP = genotype at the SIX6_TOP marker (same format as for
 VGLL3_TOP) seaAgeMaiden = sea age at first return to
 freshwater (years) seaAgeCapture = sea age when
 captured (years) smoltAge = age at outmigration
 (years) length_mm = length from tip of snout to end
 of tail (mm) mass_g = mass of fish at capture
 (g) Lsmolt_mm = back calculated length at
 outmigration (mm) L1sea_mm = back calculated length
 after first winter at sea (mm) L2sea_mm = back
 calculated length after second winter at sea (mm)
 L3sea_mm = back calculated length after third winter at sea
 (mm) L4sea_mm = back calculated length after fourth
 winter at sea (mm) Pind = the proportional ancestry
 for each individual to the domesticated reference populations
 I = farmed genetic ancestry Julian = the
 Julian date (ordinal date) Note that most
 of the data published in “Bolstad, Geir H. et al. (2018), Data from: Gene
 flow from domesticated escapes alters the life history of wild Atlantic
 salmon, Dryad, Dataset, https://doi.org/10.5061/dryad.gh721” is a subset of the data published here.
DOI: 10.5061/dryad.4b8gthtdr
title: Using genomics to guide seed-sourcing at the right taxonomical level for ecological restoration projects: the complex case of Carex bigelowii s.lat. in Norway

description: There is a growing demand for ecological restoration using suitable seeds
 following international standards or national legal demands for local
 seed-sourcing. However, before selecting the appropriate geographic origin
 of seeds, it is vital to explore taxonomic complexity related to the focal
 taxa. We used ddRAD-seq to screen genomic diversity within Carex bigelowii
 s.lat. focussing on Norway. This species complex is considered a candidate
 for seeding, but presents considerable morphological, ecological, and
 genetic variation. The genetic structure of 132 individuals of C.
 bigelowii s.lat., including C. nigra as an outgroup, was explored using
 ordinations, clustering analyses, and a genetic barrier algorithm. Two
 highly divergent clusters were evident, supporting the recognition of two
 taxonomic units ‘C. dacica’ and ‘subsp. bigelowii’. Previously defined
 seed-sourcing regions for C. bigelowii s.lat. did not consider the known
 taxonomic complexity, and therefore interpreted the overall genetic
 structure as seed-sourcing regions, not taxa. We estimated genetic
 neighbourhood sizes within each taxon to be 100-150 km and 300 km,
 respectively, indicating species-specific delimitations of local
 seed-sourcing regions. Frequent hybrids, local genetic distinctiveness,
 and suggested ecotypes add complexity to the discussed seed-sourcing
 regions. Our results show how genomic screening of diversity and structure
 in a species complex can alleviate the taxonomic impediment, inform
 practical questions and legal requirements related to seed-sourcing, and
 together with traditional taxonomic work provide necessary information for
 a sound management of biodiversity.
description: Leaf samples from 139 individuals of Carex bigelowii s.lat.
 collected from 33 sites across its Norwegian distribution and 16 sites
 outside Norway. Information on collection sites, lat and long, collectors
 and voucher IDs are all given in Table 1 (uploaded to DRYAD).
 Preparation of ddRAD-seq libraries, de novo assembly of loci,
 variant calling and filtering (including MAF sensitivity analyses) are
 described in the publication.   Two
 datasets are uploaded:
 dataset_A_all_het0.8_r90_maf0.01.vcf includes all SNPs for
 ordinations (15,095 SNPs, including linked markers from the same
 locus) dataset_B_all_het0.8_r90_maf0.01_single_snp.stru
 includes only one SNP per locus (5,134 SNPs, approximating unlinked
 markers)
description: Uploaded file "Pop_vs_Sample_vs_CollectorsID" lists the
 pop_ID, Sample_ID_vcf and the Voucher_ID for all samples.
 pop_ID is the site number as listed in Table 1 in the
 publication. Sample_ID_vcf is the individual sample ID
 as used in the dataset files A and B Voucher_ID is the
 individual herbarium/DNA-collection identification for each samples, also
 listed in Table 1 (uploaded to DRYAD). Uploaded file
 "Table 1" lists all sample collection information.
DOI: 10.5061/dryad.9p8cz8whg
title: Inverse design of soft materials via a deep-learning-based evolutionary strategy

description: Colloidal self-assembly -- the spontaneous organization of colloids into
 ordered structures -- has been considered key to producing next-generation
 materials. However, the present-day staggering variety of colloidal
 building blocks and the limitless number of thermodynamic conditions make
 a systematic exploration intractable. The true challenge in this field is
 to turn this logic around and to develop a robust, versatile algorithm to
 inverse design colloids that self-assemble into a target structure. Here,
 we introduce a generic inverse design method to efficiently
 reverse-engineer crystals, quasicrystals, and liquid crystals by targeting
 their diffraction patterns. Our algorithm relies on the synergetic use of
 an evolutionary strategy for parameter optimization, and a convolutional
 neural network as an order parameter, and provides a new way forward for
 the inverse design of experimentally feasible colloidal interactions,
 specifically optimized to stabilize the desired structure.
description: # Inverse design of soft materials via a deep-learning-based evolutionary
 strategy
 [https://doi.org/10.5061/dryad.9p8cz8whg](https://doi.org/10.5061/dryad.9p8cz8whg) ## Description of the data and file structure All the codes and data used in "Inverse design of soft materials via a deep-learning-based evolutionary strategy", by G. M. Coli, E. Boattini, L. Filion, and M. Dijkstra. Because of size limits, some files have been zipped. ### Files and variables #### Folders: CodesTraining2D CodesTraining3D Trajectories ##### Each subfolder contains a README.
DOI: 10.5061/dryad.pc866t1px
title: Dcp2 C-terminal cis-binding elements control selective targeting of the decapping enzyme by forming distinct decapping complexes

description: A single Dcp1-Dcp2 decapping enzyme targets diverse classes of yeast mRNAs
 for decapping-dependent 5’ to 3’ decay, but the molecular mechanisms
 controlling selective mRNA targeting by the enzyme remain elusive. Through
 extensive genetic analyses we uncover cis-regulatory elements in the Dcp2
 C-terminal domain that control selective targeting of the decapping enzyme
 by forming distinct decapping complexes. Two Upf1-binding motifs target
 the decapping enzyme to NMD substrates, and a single Edc3-binding motif
 targets both Edc3 and Dhh1 substrates. Pat1-binding leucine-rich motifs
 target Edc3 and Dhh1 substrates under selective conditions. Although it
 functions as a unique targeting component of specific complexes, Edc3 is a
 common component of multiple complexes. Xrn1 also has a specific Dcp2
 binding site, allowing it to be directly recruited to decapping complexes.
 Collectively, our results demonstrate that Upf1, Edc3, and Pat1 function
 as regulatory subunits of the holo-decapping enzyme, controlling both its
 targeting specificity and enzymatic activation
description: Data were generated by northern blotting and hybridization.
 Transcript-specific hybridization signals on the membrane were detected
 and imaged with a FUJI BAS-2500 analyzer.
description: Each source data file has two different file types.  An
 illustrator file contains the images used for the corresponding figure and
 their associated original image file names. The image files are the raw
 data generate by the FUJI BAS-2500 analyzer. Files can
 also be viewed using Fiji (ImageJ).
DOI: 10.5061/dryad.3j9kd51k5
title: Evolution of vocal performance and song complexity in island birds

description: Oceanic islands share distinctive characteristics thought to underlie a
 set of parallel evolutionary trends across islands and taxonomic groups –
 including life history traits, morphology and visual signals. To which
 extent acoustic signals also change in parallel on islands is less clear.
 Some important processes associated with insularity, such as founder
 effects and reduced sexual selection, could lead to a decrease in vocal
 performance and song complexity on islands. In a field-based study, we
 recorded 11 insular species and their closest mainland relatives. Out of
 the 11 species pairs, 6 live in the tropics (São Tomé / Mount Cameroon),
 and 5 in the temperate region (Madeira / southern France). For each
 species we measured two proxies of vocal performance (song duration and
 syllable rate) and one proxy of song complexity (syllable diversity). This
 study did not recover a clear relationship between the island environment
 and song traits. If as expected, syllable rate was lower in island species
 than in their mainland counterparts, the two other proxies showed no clear
 island-mainland pattern of divergence. Several factors may explain the
 absence of reduction for song duration and syllable diversity. Among
 those, relaxation of interspecific competition on islands may have led to
 an increase in syllable diversity, or correlations between song variables
 may have constrained song evolution. More studies on island species are
 needed to draw a better picture of divergence patterns and go beyond the
 confounding ecological factors that could explain peculiar song
 characteristics in islands.
description: Field based study. Song recordings.
DOI: 10.5061/dryad.1g1jwstxv
title: Motivational crowding in PES: experiment results

description: Nature is perceived and valued in many different ways. Often, the types of
 values that are the most important to people depend on how they
 cognitively frame desirable human-nature relations. For instance, the
 value of nature can be seen through a utilitarian lens, e.g., as providing
 ecosystem services for humans. Alternatively, it can also be considered
 valuable for non-instrumental reasons, e.g., for its sacred or spiritual
 significance. In this paper, we use a framed field experiment to test how
 people belonging to three distinct communities in Colombia (Indigenous,
 Afro-Colombian, and Campesino) respond to different ways of framing
 payments for ecosystem services (PES) schemes, so as to assess potential
 motivational crowding effects of pro-social/intrinsic motivations for
 forest conservation. The experimental results indicate that crowding-in of
 intrinsic motivations for forest conservation occurred in participants
 from the Indigenous community when the PES scheme was framed in a way that
 highlighted relational values of the forest. By contrast, motivational
 crowding-in took place for participants in the framed field experiment
 from the Campesino community when the PES scheme was introduced in a way
 that highlighted instrumental values instead. Participants from the
 Afro-Colombian community did not show evidence of motivational crowding
 under either framing. Together, these results suggest that PES schemes
 that are framed in a way that harmonizes with locally salient human-nature
 relational models and associated values are more likely to cause
 motivational crowding-in, and thus encourage higher rates of environmental
 conservation, even after payments are discontinued.
description: Data represents the results of a framed field experiment which
 simulated conservation decisions before, during, and after the
 implementation of a PES program.  Data additionally
 includes the responses from the survey that was implemented following the
 framed field experiment.
DOI: 10.5061/dryad.x0k6djhkn
title: No evidence for future planning in Canada Jays (Perisoreus canadensis)

description: In the past 20 years, research in animal cognition has challenged the
 belief that complex cognitive processes are uniquely human. At the
 forefront of these challenges has been research on mental time travel and
 future planning in jays. We tested whether Canada Jays (Perisoreus
 canadensis) demonstrated future planning, using a procedure that had
 previously produced evidence of future planning in California Scrub-Jays
 (Aphelocoma californica). Future planning in this procedure is caching in
 locations where the bird will predictably experience a lack of food in the
 future. Canada Jays showed no evidence of future planning in this sense
 and instead placed caches in a location where food was usually available,
 the opposite of the behaviour described for California Scrub-Jays. We
 provide potential explanations for these differing results and suggest a
 re-evaluation of “complex cognition” as an explanation of caching
 behaviour in jays.