cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7783vg
title: Data from: Intercropping of marine finfish in shrimp ponds: a maiden feasibility study

description: Diversification of shrimp farming with marine finfish in a farmer
 participatory research model was attempted. The study is intended to find
 an economically viable finfish culture during the fallow period of shrimp
 farms. The Silver pompano, Trachinotus blochii intercropped with Pacific
 white shrimp, Litopenaeus vannamei culture in coastal shrimp ponds was
 assessed for growth, survival, and economic viability. During the grow-out
 period of 100 days; fishes grew from 40.23 ± 1.40 g to 256.56 ± 1.08 g in
 weight and 12.83 ± 0.19 cm to 25.11 ± 0.09 cm in length. The daily weight
 gain (DWG) and daily length gain (DLG) were 2.16 g/day and 0.12 cm/day,
 respectively. Relative growth rate (RGR) and specific growth rate (SGR)
 recorded for weight was 537.80% in 100 days and 1.85% per day,
 respectively. Pompano has exhibited its sturdiness and adaptability to the
 land-based culture system as evident by an overall survival percentage of
 89.8% including nursery and grow-out phases. The realized feed conversion
 ratio was 1.94. The culture period of 100 days is found to be enough to
 attain a desirable harvest size of 250 g. The projected production
 potential of the experimental demonstration farm of 4500 m2 water spread
 area for culture was 16.2 tonnes/cycle with a benefit-cost ratio (BCR) of
 1.34 over operational cost. The present participatory trial empirically
 proved the viability of Silver pompano as an intercrop in coastal shrimp
 ponds. Thus, the introduction of Pompano in shrimp ponds is recommended
 and can be promoted for sustainable intercropping with shrimp farming
 along the Indian coast for improving people’s livelihoods.
description: Pompano data sheets
 csvcontains length and
 weight progression data, condition factor, water quality parameter,
 harvest and survival and length-weight key for length weight
 relationship
DOI: 10.5061/dryad.813nj25
title: Data from: Test collections for EHR-based clinical information retrieval

description: Objectives: To create test collections for evaluating clinical Information
 Retrieval (IR) systems and advancing clinical IR research. Materials and
 Methods: Electronic Health Records (EHR) data, including structured and
 free text data, from 45,000 patients who are a part of the Mayo Clinic
 Biobank cohort was retrieved from the clinical data warehouse. The
 clinical IR system indexed 42 million free-text EHR documents. The search
 queries consisted of 56 topics developed through a collaboration between
 Mayo Clinic and Oregon Health & Science University. We described
 the creation of test collections, including a to-be-evaluated document
 pool using five retrieval models, and human assessment guidelines. We
 analyzed the relevance judgment results in terms of human agreement and
 time spent, and results of three levels of relevance, and reported
 performance of five retrieval models. Results: The two judges had a
 moderate overall agreement with a Kappa value of 0.49, spent a consistent
 amount of time judging the relevance, and were able to identify easy and
 difficult topics. The conventional retrieval model performed best overall
 on most topics while a concept-based retrieval model had better
 performance on the topics requiring conceptual level retrieval.
 Discussion: Information Retrieval can provide an alternate approach to
 leveraging clinical narratives for patient information discovery as it is
 less dependent on semantics. Our study showed the feasibility of test
 collections as well as challenges. Conclusion: The conventional test
 collections for evaluating the IR system show potential for successfully
 evaluating clinical IR systems with a few challenges to be investigated.
description: Patient Cohort Topics
 for Clinical Information RetrievalThis file contains the
 topics in plain text for evaluating clinical information retrieval
 systems. A total of 56 topics, each illustrating a patient cohort, were
 developed through a collaboration between Mayo Clinic and Oregon Health
 & Science University (OHSU). Initially there were 29 topics generated
 from OHSU and 30 from Mayo Clinic. Three topics with similar
 characteristics from both sides were merged during topic development to
 avoid redundancy. Clinical study data requests, as submitted by
 researchers to the Oregon Clinical and Translational Research Institute
 (OCTRI), OHSU’s Research Data Warehouse (RDW), provided the basis for 26
 topics at OHSU. The 30 topics from Mayo Clinic were modeled after cohorts
 from the Phenotype KnowledgeBase (PheKB) (7 topics), Rochester
 Epidemiology Project (REP) (9 topics), National Quality Forum (NQF) (12
 topics), and Mayo RDW (2 topics).Topics_JAMIAOpen.docx
DOI: 10.5061/dryad.b554m44
title: Data from: Macroevolution of Arboreality in Salamanders

description: Evolutionary theory predicts that selection in distinct microhabitats
 generates correlations between morphological and ecological traits, and
 may increase both phenotypic and taxonomic diversity. However, some
 microhabitats exert unique selective pressures that act as a restraining
 force on macroevolutionary patterns of diversification. In this study, we
 use phylogenetic comparative methods to investigate the evolutionary
 outcomes of inhabiting the arboreal microhabitat in salamanders. We find
 that arboreality has independently evolved at least five times in Caudata,
 and has arisen primarily from terrestrial ancestors. However, the rate of
 transition from arboreality back to terrestriality is 24 times higher than
 the converse. This suggests that macroevolutionary trends in microhabitat
 use tend towards terrestriality over arboreality, which influences the
 extent to which use of the arboreal microhabitat proliferates.
 Morphologically, we find no evidence for an arboreal phenotype in overall
 body proportions or in foot shape, as variation in both traits overlaps
 broadly with species that utilize different microhabitats. However, both
 body shape and foot shape display reduced rates of phenotypic evolution in
 arboreal taxa, and evidence of morphological convergence among arboreal
 lineages is observed. Taken together, these patterns suggest that
 arboreality has played a unique role in the evolution of this family,
 providing neither an evolutionary opportunity, nor an evolutionary dead
 end.
description: AllSpecimensList of all species and specimens used in this study, including all microhabitat classifications as well as museum collections and specimen IDs from which morphological data were obtained.Bonett_and_Blair_PhyloPruned consensus phylogeny used in all main analysesMicrohabitatsMicrohabitat designation for each species across different classification schemes.LinMeas.SpeciesSummariesSpecies summaries of 7 linear measurements used in body shape analyses.FootLandmarks.BB.SpeciesSummarySpecies summaries of foot shape after generalized procrustes.FootLandmarks.SpeciesSummary.CsizeSpecies mean centroid sizes for foot shape analyses. Used in tests of allometric convergence.MainAnalysesR Script containing all main analyses.
DOI: 10.5061/dryad.8rq9465
title: Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

description: Selection on spore dispersal mechanisms in mosses is thought to shape the
 transformation of the sporophyte. The majority of extant mosses develop a
 sporangium that dehisces through the loss of an operculum, and regulates
 spore release through the movement of articulate teeth, the peristome,
 lining the capsule mouth. Such complexity was acquired by the Mesozoic
 Era, but was lost in some groups during subsequent diversification events,
 challenging the resolution of the affinities for taxa with reduced
 architectures. The Funariaceae are a cosmopolitan and diverse lineage of
 mostly annual mosses, and exhibit variable sporophyte complexities,
 spanning from long, exerted, operculate capsules with two rings of
 well-developed teeth, to capsules immersed among maternal leaves, lacking
 a differentiated line of dehiscence (i.e., inoperculate) and without
 peristomes. The family underwent a rapid diversification, and the
 relationships of taxa with reduced sporophytes remain ambiguous. Here we
 infer the relationships of five taxa with highly reduced sporophytes based
 on 648 nuclear loci (exons complemented by their flanking regions), based
 on inferences from concatenated data and concordance analysis of single
 gene trees. Physcomitrellopsis is resolved as nested within one clade of
 Entosthodon. Physcomitrella s. lat., is resolved as a polyphyletic
 assemblage and, along with its putative relative Aphanorrhegma, nested
 within Physcomitrium. We propose a new monophyletic delineation of
 Physcomitrium, which accommodates species of Physcomitrella and
 Aphanorrhegma. The monophyly of Physcomitrium s. lat. is supported by a
 small plurality of exons, but a majority of trees inferred from exons and
 their adjacent non-coding regions.
description: Physcomitrium-Entosthodon datasetThis archive contains nucleotide alignments, gene trees, bipartition analysis for the reduced dataset consisting only of Physcomitrium and Entosthodon. More details in the readme filephyscoent_dataset.tar.gzFunariaceae single gene alignmentsAligned matrices for for the individual loci of the whole Funariaceae datasetfunariaceae.single_gene_alignments.tar.gzFunariaceae gene trees collapsed bt70Gene trees of the full Funariaceae dataset with nodes collapsed when support value drops below 70% bootstrapfunariaceae.genetrees.collapsed70.rerooted.tar.gzFunariaceae gene trees collapsed bt33Gene trees of the full Funariaceae dataset with nodes collapsed when support value drops below 33% bootstrapfunariaceae.genetrees.collapsed30.rerooted.tar.gzNuclear baitsBaits used for the targeted enrichmentnubaits-120-60.fas
DOI: 10.5061/dryad.3j46s79
title: Data from: Thermal landscape change as a driver of ectotherm responses to plant invasions

description: A growing body of research demonstrates the impacts of invasive alien
 plants on native animals, but few studies consider thermal effects as a
 driver of the responses of native organisms. As invasive alien plants
 establish and alter the composition and arrangement of plant communities,
 the thermal landscapes available to ectotherms also change. Our study
 reviews the research undertaken to date on the thermal effects of alien
 plant invasions on native reptiles, amphibians, insects and arachnids. The
 37 studies published between 1970 and early 2019 portray an overall
 detrimental effect of invasive plants on thermal landscapes, ectothermic
 individuals' performance and species abundance, diversity and
 composition. With a case study of a lizard species, we illustrate the use
 of thermal ecology tools in plant invasion research and test the
 generality of alien plant effects: changes in thermoregulation behaviour
 in invaded landscapes varied depending on the level of invasion and lizard
 traits. Together, the literature review and case study show that thermal
 effects of alien plants on ectotherms can be substantial albeit
 context-dependent. Further research should cover multiple combinations of
 native/invasive plant growth forms, invasion stages and ectotherm traits.
 More attention is also needed to test causality along the chain of effects
 from thermal landscapes to individuals, populations and communities.
description: Garcia_Clusella-Trullas_Data_File_S1_Literature_review_datasetDataset for literature review of the thermal effects of alien plants on thermal landscapes and native ectothermsGarcia_Clusella-Trullas_Data_File_S2Operative temperature data collected in native, mildly invaded and highly invaded sites in renosterveld habitat. These files are 3-dimensional arrays created as R objects and can be accessed using the following code: get(load("path/file_name")).Garcia_Clusella-Trullas_Data_File_S3_Case_Study_Simulation_R_codeR code for individual-based model simulations of body temperature of thermoregulating and thermoconforming lizards moving across thermal landscapes
DOI: 10.15468/dl.8y58nx
title: Occurrence Download

description: A dataset containing 745 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Arachnofauna of the tropical dry forest in the Cerro Blanco Protected Forest, Ecuador"
 ]
}

 The dataset includes 745 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001684-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.278330p
title: Data from: High background risk induces risk allocation rather than generalized neophobia in the fathead minnow

description: To cope with the heterogeneous nature of predation and the trade-off
 between predator avoidance and foraging, prey animals have evolved several
 cognitive rules. One of these is the risk allocation hypothesis, which
 predicts that in environments with long periods of sustained high risk,
 individuals should decrease their antipredator effort to satisfy their
 metabolic requirements. The neophobia hypothesis, in turn, predicts
 increased avoidance of novel cues in high-risk habitats. Despite the
 recent interest in predator-induced neophobia across different sensory
 channels, tests of such generalized neophobia are restricted to a single
 fish taxon, the Cichlidae. Hence, we re-tested the generalized neophobia
 hypothesis in fathead minnows Pimephales promelas, a small schooling North
 American cyprinid fish. From hatching onwards, minnows were exposed to
 conspecific alarm cues, which indicate predation risk, or distilled water
 in a split-clutch design. After one month, shoaling behavior was examined
 prior and subsequent to a mechanical predator disturbance. Fish previously
 exposed to elevated background risk formed compact shoals for a shorter
 time interval following the stimulus compared to controls. These results
 contrast previous studies of generalized neophobia, but match the risk
 allocation hypothesis. Consequently, risk allocation and generalized
 neophobia are not ubiquitous cognitive rules but instead evolved
 adaptations of different taxa to their respective environments.
description: Shoaling behavior and
 body sizes of alarm cue-exposed and control Pimephales
 promelasThis data originates
 from a laboratory study on Pimephales promelas. In a split-clutch design,
 fish were raised under different levels of perceived predation risk (alarm
 cues or distilled water). The shoaling and body size data contained in
 this document was obtained during shoaling assays at 39 days age. Column
 headings contain both the variable name and the unit (after the last dot)
 where applicable. Detailed information on how this data was obtained is
 contained in the corresponding manuscript.Dataset_BehEcol_final.xlsx
DOI: 10.5061/dryad.h15c4sp
title: Data from: Effects of undergrowth removal and edge proximity on ground beetles and vascular plants in urban boreal forests

description: Urban forests are regularly managed for human safety and aesthetic
 reasons, but they are crucial habitat for many species. Removals of
 undergrowth occur commonly in these forests, yet the ecological
 consequences of these operations are poorly understood. We sampled ground
 beetles (Coleoptera, Carabidae) and vascular plants along 20-m edge
 gradients in Finnish urban forests, in five stands treated 0.5−2.5 years
 earlier with undergrowth removal and in five untreated stands. We
 hypothesized that undergrowth removal and edge proximity would benefit
 opportunistic and open-habitat species, whereas shady-habitat species
 would be affected negatively. (1) Regarding carabids, diversity and
 evenness indices, open-habitat species and Carabus nemoralis responded
 positively, and forest species, Leistus terminatus and Pterostichus
 oblongopunctatus responded negatively, to the undergrowth removal.
 Regarding plants, generalists, Maianthemum bifolium, Rubus saxatilis and
 Sorbus aucuparia responded positively, and forest species, Geranium
 sylvaticum, Oxalis acetocella and Vaccinium myrtillus responded
 negatively, to the undergrowth removal. (2) Edge proximity had little
 effect on both plants and carabids. However, open-habitat carabids were
 less abundant and less speciose, and the plants Oxalis acetocella,
 Trientalis europaea and Rubus saxatilis had higher cover, 10−20 m from
 than right at the edge. (3) Plant (but not carabid) community responded to
 the undergrowth removal but not to the edge proximity. While managing
 urban forests, we recommend an avoidance of undergrowth removals at sites
 that host rare or threatened forest-associated flora and fauna.
description: Koivula et al. Urban
 forest fragment carabids and plantsData contain ground
 beetle and vascular plant data collected from 10 urban forest stands, at
 three edge distances in each stand: 0, 10 and 20 m from the edge toward
 interior. Half of the stands had been treated with undergrowth removal.
 Beetle data are numbers of individuals, and plants are average percent
 covers, per distance x stand. Data contain numbers of individuals and
 numbers of species of forest, open-habitat and generalist species, and
 species-level numbers; column names show species with 4+4 letter
 abbreviations of their scientific names. Please consult Appendix and
 Readme file for details.Koivula_JUE-2019_data.csv
DOI: 10.5061/dryad.t7pd371
title: Data from: Reconstructing hyperdiverse food webs: gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs

description: 1. Anthropogenic stressors have strong impacts on ecosystems. To
 understand their influence, detailed knowledge about trophic relationships
 among species is critical. However, this requires both exceptional
 resolution in dietary assessments and sampling breadth within communities,
 especially for highly-diverse, tropical ecosystems. 2. We used gut content
 metabarcoding across a broad range of coral reef fishes (8 families, 22
 species) in Mo’orea, French Polynesia to test whether this technique has
 the potential to capture the structure of a hyperdiverse marine food web.
 Moreover, we explored whether taxonomic groups (families) and traditional,
 broad-scale trophic assignments explained fish diet across four different
 metrics of quantifying predator-prey interactions. 3. Metabarcoding
 yielded a large number (4,341) of unique operational taxonomic units (i.e.
 prey) with high-resolution taxonomic assignments (i.e. often to the level
 of genus or species). We demonstrate that across multiple metrics,
 taxonomic group at the family level is a consistently better, albeit still
 weak, predictor of empirical trophic relationships than frequently-used,
 broad-scale functional assignments. Our method also reveals a complex
 trophic network with fine-scale partitioning among species, further
 emphasizing the importance of examining fish diets beyond broad trophic
 categories. 4. We demonstrate the capacity of metabarcoding to reconstruct
 diverse and complex food webs with exceptional resolution, a significant
 advancement from traditional food web reconstruction. Further, this method
 allows us to pinpoint the trophic niche of species with niche-based
 modelling, even across hyperdiverse species assemblages such as coral
 reefs. In conjunction with complementary techniques such as stable isotope
 analysis, applying metabarcoding to whole communities will provide
 unparalleled information about energy and nutrient fluxes and inform their
 susceptibility to disturbances even in the world’s most diverse
 ecosystems.
description: otu_tableOTU table excluding host sequences, including OTU representative sequences and taxonomymapping_filesMapping files for FASTA files, formatted as oligos files for input to Mothurraw_fastqRaw FASTA files
DOI: 10.5061/dryad.s31v04d
title: Data from: Honeybees possess a structurally diverse and functionally redundant set of queen pheromones

description: Queen pheromones, which signal the presence of a fertile queen and induce
 workers to remain sterile, play a key role in regulating reproductive
 division of labour in insect societies. In the honeybee, volatiles
 produced by the queen’s mandibular glands have been argued to act as the
 primary sterility-inducing pheromones. This contrasts with evidence from
 other groups of social insects, where specific queen-characteristic
 hydrocarbons present on the cuticle act as conserved queen signals. This
 led us to hypothesise that honeybee queens might also employ cuticular
 pheromones to stop workers from reproducing. Here we support this
 hypothesis with the results of bioassays with synthetic blends of
 queen-characteristic alkenes, esters, and carboxylic acids. We show that
 all these compound classes suppress worker ovary development, and that one
 of the blends of esters that we used was as effective as the queen
 mandibular pheromone (QMP) mix. Furthermore, we demonstrate that the two
 main QMP compounds 9-ODA and 9-HDA tested individually were as effective
 as the blend of all four major QMP compounds, suggesting considerable
 signal redundancy. Possible adaptive reasons for the observed complexity
 of the honeybee queen signal mix are discussed.
description: Princen_etal_datafig1CSV-file with raw peak areas of cuticular compounds on A. mellifera queens, virgin queens and workers, including compound ID and class..R-Script-Princen_etal_Fig1Princen_etal_datafig2Bioassay data. CSV fileR-Script_Princen_etal_Fig2
DOI: 10.5061/dryad.c270ft8
title: Data from: Abundance drives broad patterns of generalisation in plant-hummingbird pollination networks

description: Abundant pollinators are often more generalised than rare pollinators.
 This could be because abundant species have more chance encounters with
 potential interaction partners. On the other hand, generalised species
 could have a competitive advantage over specialists, leading to higher
 abundance. Determining the direction of the abundance-generalisation
 relationship is therefore a ‘chicken-and-egg’ dilemma. Here we determine
 the direction of the relationship between abundance and generalisation in
 plant-hummingbird pollination networks across the Americas. We find
 evidence that hummingbird pollinators are generalised because they are
 abundant, and little evidence that hummingbirds are abundant because they
 are generalised. Additionally, most patterns of species-level abundance
 and generalisation were well explained by a null model that assumed
 interaction neutrality (interaction probabilities defined by species
 relative abundances). These results suggest that neutral processes play a
 key role in driving broad patterns of generalisation in animal pollinators
 across large spatial scales.
description: Plant-hummingbird
 interaction networks19 plant-hummingbird
 interaction networks. If used, please ensure taxonomy is up-to-date and
 cite Simmons, B. I., Vizentin‐Bugoni, J. , Maruyama, P. K., Cotton, P. A.,
 Marín‐Gómez, O. H., Lara, C. , Rosero‐Lasprilla, L. , Maglianesi, M. A.,
 Ortiz‐Pulido, R. , Rocca, M. A., Rodrigues, L. C., Tinoco, B. ,
 Vasconcelos, M. F., Sazima, M. , González, A. M., Sonne, J. , Rahbek, C. ,
 Dicks, L. V., Dalsgaard, B. and Sutherland, W. J. (2019), Abundance drives
 broad patterns of generalisation in plant–hummingbird pollination
 networks. Oikos. doi:10.1111/oik.06104networks.zipSpecies abundances from each of the 19 plant-hummingbird pollination networksIf used, please ensure taxonomy is up-to-date and cite Simmons, B. I., Vizentin‐Bugoni, J. , Maruyama, P. K., Cotton, P. A., Marín‐Gómez, O. H., Lara, C. , Rosero‐Lasprilla, L. , Maglianesi, M. A., Ortiz‐Pulido, R. , Rocca, M. A., Rodrigues, L. C., Tinoco, B. , Vasconcelos, M. F., Sazima, M. , González, A. M., Sonne, J. , Rahbek, C. , Dicks, L. V., Dalsgaard, B. and Sutherland, W. J. (2019), Abundance drives broad patterns of generalisation in plant–hummingbird pollination networks. Oikos. doi:10.1111/oik.06104abundance.txt