cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dq0tt96
title: Data from: Computerized stimuli for studying oddity effects

description: Visually hunting predators must overcome the challenges that prey groups
 present. One such challenge is the confusion effect where an overburdened
 visual system means predators are unable to successfully target prey. A
 strategy to overcome confusion is the targeting of distinct, or odd,
 individuals (the oddity effect). In live prey experiments, manipulation of
 group member phenotypes can be challenging and prey may differ on more
 than the single feature one intends to define as odd. The use of highly
 controllable computerized stimuli to study predator-prey interactions is
 increasingly popular in the field of behavioral ecology. However, to our
 knowledge, the validity of computerized stimuli to study the oddity effect
 has not been established. Predator choice experiments were conducted using
 naive stickleback predators to ascertain whether the oddity effect could
 be demonstrated in the absence of live prey. We found evidence for both
 the oddity effect and preferential targeting of group edges and low
 density regions, as would be predicted if predators targeted prey
 individuals to minimize confusion. The oddity effect was evident at a low
 threshold, above which dots were no longer perceived as odd, and no longer
 attacked more often than expected by chance. We conclude that computerized
 stimuli are an improved, practical method for studying oddity effects
 while further validating the use of similar methods for studying other
 aspects of visual predation. In addition to higher control of ‘prey’
 appearance, the replacement of live prey animals with digital stimuli is
 ethically beneficial and reusing code improves experimental efficiency.
description: Dobbinson_AllPreydotCoordinatesData were generated in laboratory study that used three-spined stickleback preying on computerised targets. Each data point represents a prey-dot and gives information on whether the prey-dot was odd (isodd=1), whether it was the target of the first attack made towards the group (istarget=1), whether they were located in the group (centre/edge) and their distance to their nearest neighbours (nn).
DOI: 10.5061/dryad.1f4h58f
title: Data from: Seed dispersal effectiveness by a large-bodied invasive species in defaunated landscapes

description: Animal-dispersed plants are increasingly reliant on effective seed
 dispersal provided by small-bodied frugivores in defaunated habitats. In
 the Neotropical region the non-native wild pig (Sus scrofa) is expanding
 its distribution and we hypothesized that they can be a surrogate for seed
 dispersal services lost by defaunation. We performed a thorough analysis
 of their interaction patterns, interaction frequencies, seed viability and
 characteristics of the seed shadows they produce. We found 15,087 intact
 seeds in 56% of the stomachs and 5186 intact seeds in 90% of the scats
 analyzed, 95% of which were smaller than 10 mm in diameter. Wild pigs were
 the third most effective disperser among 21 extant frugivore species in a
 feeding trail experiment in terms of quantity of seeds removed and gut
 retention time was 70 ±23 h, indicating they can promote long distance
 seed dispersal. Seed survival after seed handling and gut passage by wild
 pigs was positively related with seed size, but large seeds were spat out
 and only smaller were defecated intact, for which we observed a positive
 or neutral effect on germination relative to manually de-pulped seeds.
 Finally, deposition of seeds were four times more frequent in unsuitable
 than suitable sites for seedling recruitment and establishment. Seed
 dispersal effectiveness by wild pigs is high in terms of the quantity of
 seeds dispersed but variable in terms of the quality of the service
 provided. Our study highlights that negative and positive effects
 delivered by non-native species should be examined in a case by case
 scenario.
description: Quantitative
 SDEThe following file
 contains the data used to analyze the Quantitative Component of Seed
 Dispersal Effectiveness.Germination_plant
 speciesThe following file
 contains the data on Germination of seeds of plant species ingested by
 wild pigs and seeds manually defleshed (Control). The values are the
 proportion of germinated seed in a given time period (lines) in relation
 to the total number of seeds set to germinate for the given treatment
 (ingested or control).
DOI: 10.5061/dryad.03g98h6
title: Data from: A Bayesian hierarchical approach to quantifying stakeholder attitudes toward conservation in the presence of reporting error

description: Stakeholder support is vital for achieving conservation success, yet there
 are few reliable mechanisms to monitor stakeholder attitudes towards
 conservation. Importantly, few approaches account for bias arising from
 reporting errors; that is, reporting a positive attitude towards
 conservation when the respondent actually does not have one (a false
 positive error), or not reporting a positive attitude when the respondent
 is positive towards conservation (a false negative error). We borrow from
 developments in applied conservation science to use a Bayesian
 hierarchical model to quantify stakeholder attitudes as the probability of
 having a positive attitude towards wildlife, notionally (or in abstract
 terms) and at localized scales. The model allows us to assess stakeholder
 attitudes, and factors influencing these attitudes, while accounting for
 false negative and false positive reporting errors. We show through
 simulations that this method has lower bias than naïve estimates of the
 proportion of respondents who are positive towards wildlife, or
 Likert‐scores. We demonstrate the utility of the model by applying it to
 questionnaire surveys on Asian elephants Elephas maximus in the
 Kaziranga–Karbi Anglong landscape, Northeast India. After accounting for
 reporting errors, we estimated the probability of being positive towards
 elephants notionally as 0.85; at a localized scale, however, the
 proportion of respondents that were positive towards elephants was 50%. In
 comparison, without accounting for reporting errors, the proportion of
 respondents professing positive attitudes towards elephants in at least
 one of the certain questions, was 0.69 and 0.23, notionally and at local
 scales, respectively. False (positive and negative) reporting
 probabilities were consistently non‐zero (0.22–0.68). We submit that
 regular and reliable assessment of stakeholder attitudes––combined with an
 understanding of factors contributing to variation in attitudes––can feed
 into participatory conservation monitoring programs, help assess the
 success of initiatives aimed at facilitating human behavioral change, and
 inform conservation decision‐making.
description: Data and script for
 Bayesian hierarchical modelData are from
 questionnaire surveys conducted across tea estates in the landscape
 surrounding Kaziranga, Assam, Northeast India, on stakeholder attitudes
 towards the Asian elephant and its conservation. Script file is for
 assessing stakeholder attitudes while accounting for reporting error,
 using a Bayesian hierarchical model implemented in R and RStudio.
 Associated information is provided in Conservation Biology article titled
 'A Bayesian hierarchical approach to quantifying stakeholder
 attitudes toward conservation in the presence of reporting error',
 authored by Divya Vasudev and Varun Goswami.Vasudev and Goswami_Bayesian
 Latent_Data and Script_ConBio.zip
DOI: 10.5061/dryad.22mq8g2
title: Data from: Movement ecology of Afrotropical birds: Functional traits provide complementary insights to species identity

description: Effects of anthropogenic activities on habitats and species communities
 and populations are complex and vary across species depending on their
 ecological traits. Movement ecology may provide important insights into
 species´ responses to habitat structures and quality. We investigated how
 movement behavior across a human-modified landscape depends on species
 identity and species traits, with particular focus on habitat
 specialization, feeding guilds and dispersal behavior. We tracked 34
 individuals of nine Afrotropical bird species during three years in an
 anthropogenic riparian landscape of East Africa. We investigated whether
 species’ functional traits predicted their habitat use and movement
 behavior better than species´ identities. Our results indicate that
 habitat specialists mainly occur in dense riparian thickets, while habitat
 generalists do occur in agricultural land. Home-ranges of omnivorous
 habitat generalists are larger than of frugivorous and insectivorous
 generalists and omnivorous and insectivorous specialists. Movement speed
 was highest in settlement areas for all species, with activity peaks
 during morning and afternoon for habitat specialists. Our results reveal
 that functional traits and species identity provide complementary insights
 into responses of organisms to habitat structures and habitat quality.
description: Habitat use and movement
 behavior of Afrotropical birdsThe data include
 movement data collected by radio tracking of nine Afrotropical bird
 species differing in habitat specialization, feeding preference and
 dispersal ability. The first spreadsheet includes data concerning
 birds' habitat use, the second spreadsheet includes home-range sizes
 and the third spreadsheet includes movement speed within the different
 habitats and for the different times of the day.Habitat use and movement
 behavior.xlsx
DOI: 10.5061/dryad.f0kr74v
title: Data from: Plumage redness signals mitochondrial function in the house finch

description: Carotenoid coloration is widely recognized as a signal of individual
 condition in various animals, but despite decades of study, the mechanisms
 that link carotenoid coloration to condition remain unresolved. Most birds
 with red feathers convert yellow dietary carotenoids to red carotenoids in
 an oxidation process requiring the gene encoding the putative cytochrome
 P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of
 carotenoid oxidation and feather pigmentation is functionally linked to
 mitochondrial performance. Consistent with this hypothesis, we observed
 high levels of red ketolated carotenoids associated with the hepatic
 mitochondria of molting wild house finches (Haemorhous mexicanus), and
 upon fractionation, we found the highest concentration of ketolated
 carotenoids in the inner mitochondrial membrane. We further found that the
 redness of growing feathers was positively related to the performance of
 liver mitochondria. Structural modeling of CYP2J19 supports a direct role
 of this protein in carotenoid ketolation that may be functionally linked
 to cellular respiration. These observations suggest that feather
 coloration serves as a signal of core functionality through inexorable
 links to cellular respiration in the mitochondria.
description: Hill et al finch
 coloration study Proceedings BData from the
 mitochondrial fractionation and mitochondrial physiology
 measurementsHill_procb_ESM_coordinates.pseA Pymol session file containing the molecular models for CYP2J19 model generated using robetta (obj. name = robetta) and ITASSER (obj. name = model1), the tunnels predicted in these structures using Caver (obj. name plus tunnel number designation), the structures of P450s solved with substrates (named corresponding to PDB ID) used to determine likely substrate binding sites and the structure of 3’-hydroxyechinenone.
DOI: 10.5061/dryad.rc76f30
title: Data from: Nature and significance of intraspecific variation in the early Cambrian oryctocephalid trilobite Oryctocephalites palmeri Sundberg and McCollum, 1997

description: Oryctocephalid trilobites are seldom abundant and often tectonically
 deformed, creating problems for robust species delimitation and
 compromising their utility in biostratigraphic and evolutionary studies.
 By studying more than 140 specimens recovered from the upper portion of
 the Combined Metals Member (Pioche Formation, Nevada; Cambrian Stage 4,
 Series 2), we exploit a rare opportunity to explore how morphological
 variation among oryctocephalid specimens is partitioned into intraspecific
 variation versus interspecific disparity. Qualitative and quantitative
 analyses reveal that two species are represented: Oryctocephalites palmeri
 Sundberg and McCollum, 1997 and Oryctocephalites sp. A, the latter known
 from a single cranidium stratigraphically below all occurrences of the
 former. In contrast to the conclusions of a previous study, there is no
 evidence of cranidial dimorphism in O. palmeri. However, that species
 exhibits considerable variation in cranidial shape and pygidial spine
 arrangement and number. Cranidial shape variation within O. palmeri is
 approximately one-half of the among-species disparity within the genus.
 Comparison of cranidial shape between noncompacted and compacted samples
 reveals that compaction causes significant change in mean shape and an
 increase in shape variation; such changes are interpretable in terms of
 observed fracture patterns. Nontaphonomic variation is partitioned into
 ontogenetic and nonallometric components. Those components share similar
 structure with each other and with interspecific disparity, suggesting
 that ontogenetic shape change might be an important source of variation
 available for selection. This highlights the importance of ontogenetic and
 taphonomic sources of variation with respect to species delimitation,
 morphospace occupation, and investigation of evolutionary patterns and
 processes.
description: OryctoDataTraditional morphometric data for oryctocephalids of the Combined Metals Member. Morphometric variables as illustrated in Figure 9. Values shaded in yellow were estimated; see text for details.OryctoEx_k137_n16_tpsLandmark data (tps format) for species exemplars.OryctoEx_k137_ProtocolProtocol file for sliding semi landmarks for exemplar dataset. For use with SemiLand IMP software.Opalmeri_k137_n36_tpsLandmark data (tps format) for Oryctocephalites palmeri specimens. Use same Protocol file as for exemplar analyses to generate sliding semilandmarks.
DOI: 10.5061/dryad.rd736bd
title: Data from: Out in the cold and sick: low temperatures and fungal infections impair a frog's skin defenses

description: Amphibians worldwide continue to battle an emerging infectious disease,
 chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd). Southern
 leopard frogs, Rana sphenocephala, are known to become infected with this
 pathogen, yet they are considered 'of least concern' for
 declines due to chytridiomycosis. Previous studies have shown that R.
 sphenocephala secretes four antimicrobial peptides (AMPs) onto their skin
 which may play an important role in limiting susceptibility to
 chytridiomycosis. Here we examined the (1) effects of temperature and AMP
 depletion on infections with Bd and (2) effects of temperature and Bd
 infection on the capacity to secrete AMPs in juvenile leopard frogs.
 Pathogen burden and mortality were greater in frogs exposed to Bd at low
 temperature but did not increase following monthly AMP depletion. Both low
 temperature and Bd exposure reduced the capacity of juvenile frogs to
 restore peptides after monthly depletions. Frogs held at 14°C were poorly
 able to restore peptides in comparison with those at 26°C. Frogs held at
 26°C were better able to restore their peptides, but when exposed to Bd,
 this capacity was significantly reduced. These results strongly support
 the hypothesis that both colder temperatures and Bd infections impair the
 capacity of juvenile frogs to produce and secrete AMPs, an important
 component of their innate defense against chytrid fungi and other
 pathogens. Thus, in the face of unpredictable climate changes and enzootic
 pathogens, assessments of disease risk should consider the potential for
 effects of environmental variation and pathogen exposure on the quality of
 host defenses.
description: Robak_et_al_data The Robak_et_al_data.xlsx file contains data on survival, <em>Bd</em> load and antimicrobial peptide detection/relative intensity on separate tabs. On each tab, data are arranged by frogID and the treatment group of each frog (i.e., temperature, peptide treatment and pathogen exposure treatment combination) is indicated by three additional columns. For <em>Bd</em> load, only Bd<em>-</em>exposed frogs were assayed. For antimicrobial peptides, grayed rows indicate times when peptides were not collected (only mass was recorded).
DOI: 10.5061/dryad.f9n98b5
title: Data from: Do lianas shape ant communities in an early successional tropical forest?

description: Almost half of lowland tropical forests are at various stages of
 regeneration following deforestation or fragmentation. Changes in tree
 communities along successional gradients have predictable bottom-up
 effects on consumers. Liana (woody vine) assemblages also change with
 succession, but their effects on animal succession remain unexplored. Here
 we used a large-scale liana removal experiment across a forest
 successional chronosequence (7-31 years) to determine the importance of
 lianas to ant community structure. We conducted 1088 surveys of ants
 foraging on and living in trees using tree trunk baiting and hand
 collecting techniques at 34 paired forest plots, half of which had all
 lianas removed. Ant species composition, β-diversity, and species richness
 were not affected by liana removal; however, ant species co-occurrence
 (the coexistence of two or more species in a single tree) was more
 frequent in control plots, where lianas were present, vs. removal plots.
 Forest stand age had a larger effect on ant community structure than the
 presence of lianas. Mean ant species richness in a forest plot increased
 by ca. 10% with increasing forest age across the 31-year chronosequence.
 Ant surveys from forest &gt;20 years old included more canopy
 specialists and fewer ground-nesting ant species vs. those from forests
 &lt;20 years old. Consequently, lianas had a minimal effect on
 arboreal ant communities in this early-successional forest, where rapidly
 changing tree community structure was more important to ant species
 richness and composition.
description: Ant survey
 dataSummarizes
 presence/absence of ant species among plots, subplots, and
 years.Ant
 Community Data.xlsxPlot Biomass and Basal
 AreaAge, tree biomass, and
 tree basal area for the focal plots.Biomass and Basal
 Area.xlsxAnt Distribution Data
 for Co-occurrence AnalysisPresence/absence data
 for each ant species on each tree.Co Occurrence
 Data.xlsxData for Indicator
 Species AnalysisMatrix providing the
 number of trees in each subplot occupied by each ant
 species.Indicator Species
 Data.xlsx
DOI: 10.5061/dryad.v6m6454
title: Data from: Changing ecological communities along an elevation gradient in seasonally dry tropical forest on Hispaniola (Sierra Martín García, Dominican Republic)

description: We report the results of systematic vascular plant and bird surveys in
 Seasonally Dry Tropical Forest (SDTF) across leeward and windward
 elevation gradients (31– 884 masl) in the Sierra Martín García (SMG),
 Dominican Republic. We expected to see gradual, systematic changes in
 plant distributions with elevation owing to the strong effect of
 topoclimate. In contrast, we predicted bird community composition to be
 related only weakly to elevation, because we expected bird distributions
 to be more strongly related to vegetation structure than composition.
 Based on 48 vegetation transects, we identified seven groups that differed
 in their species composition, which was correlated with elevation and
 precipitation. The most distinctive vegetation community occurs in dry,
 warm, low elevations on the leeward slope, featuring large numbers of
 non-woody indicator species (those species found frequently within one
 group but not in other groups) even though most of its trees and shrubs
 represent species that are widespread. Low rainfall and shale bedrock
 (rather than limestone) may be the primary drivers of distinctiveness in
 the low elevation leeward plots. On the leeward slope, where we also
 surveyed the birds, the vegetation community changes gradually with
 elevation at mid- to high elevations. The most distinctive bird community
 also was associated with the low-elevation forest on shale bedrock and was
 dominated by widespread species. At higher elevations, but still within
 leeward SDTF, the bird communities had a stronger component of species
 endemic either to Hispaniola or to Caribbean islands, and species turnover
 did not correspond to the elevation gradient.
description: Bird point counts and
 plant species presence/absence for plotsa single csv file has
 the plant occurrences (present=1, absent=0) for species/taxa (columns) in
 plots (rows), followed by bird point counts (integers) for species
 (columns) in points (rows). Plot/point locations are included (decimal
 lon/lat). There is a line of description ahead of the header line of each
 dataset. Bird species and plant species lists can be found in the
 Supporting Information of the article (Tables S2 and
 S3).SGMvegplot_birdplot_data_archive.csv
DOI: 10.5061/dryad.c7g6573
title: Data from: Density-dependent fitness effects stabilize parasitic hitchhiking within a mutualism

description: 1. Mutualisms are often subject to perturbations by parasitism arising
 from third-party interactions. How third-party perturbations are dampened
 is a fundamental question pertaining to mutualism stability. Phoretic
 organisms that turn parasitic within a mutualism may destabilise it. If
 the fitness cost of such phoresy is high, then density-dependent effects
 could be one mechanism to stabilize these interactions. 2. We
 experimentally examined the fitness effects of a phoretic nematode
 community on a brood-site pollination mutualism involving a pollinating
 fig wasp (the vehicle) and its associated fig species (the host for wasp
 and nematode development). 3. We comprehensively investigated fitness
 impacts of phoresy on wasp lifespan, lifetime reproductive success,
 dispersal ability and predation risk as well as on host brood-site volume
 and seed number. We employed a range of hitchhiker densities that
 encompassed natural and overloading levels for two nematode taxa (one
 plant- and one animal-parasitic type). 4. None of the plant host and
 vehicle fitness parameters were affected by wasps with low nematode
 transportation loads for either type of nematode. Furthermore, wasps
 arriving at their destinations carried lower densities of both animal- and
 plant-parasitic nematodes compared to dispersing wasps suggesting that
 there is selection on hitchhiker numbers during the dispersal process, and
 that wasps loaded with a greater density of nematodes do not successfully
 disperse. Overloaded wasps had shorter flight durations, suggesting
 limited dispersal ability; on arrival at their destination they suffered
 greater predation risk. Such overloaded wasps delivered impaired
 pollination services and produced fewer offspring resulting in lower
 lifetime fitness. Therefore, the direct and indirect effects of nematodes
 on their vehicles are strong. These effects also translated into impacts
 on host plant fitness, with the overloaded pollinators promoting the
 development of smaller brood-sites with fewer seeds, thus reducing fig
 tree reproductive success. The effects of the animal parasites were
 greater than that of the plant parasite in this study. 5. The third-party
 interaction is therefore self-limited and exhibits density dependence. The
 strong negative effects of overloading likely explain the low number of
 nematodes found in nature on dispersing and arriving fig wasps.
 Consequently, parasitic hitchhikers do not destabilise the mutualism.
description: Gupta_Borges_rawdata_FuncEcol2019This file contains data for all experiments, and for all statistical measurements.
DOI: 10.48331/scielodata.vhrsgc/g7txph
title: Supplemental Material.docx