cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d1zm33
title: Accounting for environmental stress in restoration of intertidal foundation species

description: 1. Restoration of foundation species in historical habitat may be
 difficult if adult facilitation is obligatory for survival of early life
 stages. 2. On intertidal Mediterranean coasts, large-scale loss of the
 dominant forest-forming macroalga Ericaria amentacea, have prompted
 restoration efforts using recruits. Yet, early life stages may be more
 susceptible to the abiotic stress that characterizes their habitat. 3. We
 tested strategies to enhance resilience of lab-cultured juveniles of E.
 amentacea to environmental stress in historical habitat lacking
 conspecifics. Juveniles were exposed in culture to fluctuations of the
 dominant physical stressors, irradiance and temperature, and then
 outplanted in upper and lower zones of their native intertidal range. 4.
 Without adult canopy, juvenile outplant survival was limited to the lower
 tidal range, with nearly complete mortality in the upper zone. Survival
 was also strongly determined by spatial clumping of recruits. Longer-term
 growth in the lower zone was enhanced by fluctuating mild stress in
 culture, with variable irradiance and concurrent heat pulses increasing
 post-outplant cover by 40-60% after 4 months. Clumping also promoted
 growth across experimental treatments. 5. Synthesis and applications:
 Reliance on self-faciliation feedbacks is a common barrier to foundation
 species restoration in high-stress habitats. Our results suggest that
 without adult habitat amelioration, environmental stress limits recruit
 survival in intertidal algal forest. Yet, exposure to transient, low
 environmental stress in culture and outplanting of clumped individuals may
 confer resilience and allow successful establishment of early life stages
 in zones of reduced abiotic stress, providing a source for gradual
 colonization of more high stress areas.
description: Percent cover and the degree of spatial aggregation of
 <em>Ericaria amentacea</em> individuals (i.e. clumping) on
 each tile were determined post-culture (week 0) by photo analysis (ImageJ
 v1.52, National Institute of Health, USA). Percent cover was measured by
 manual thresholding to select pixels in the correct color spectrum that
 corresponded to the area covered by <em>E. amentacea</em>
 juveniles. Clumping was assessed by the number and size distribution of
 polygons (larger than 2 mm<sup>2</sup>) resulting from
 aggregated individuals identified in the thresholding process. Length was
 determined visually. After outplant, tiles were
 monitored at 2–5 week intervals over 4 months (3, 6, 8, 12, 15 wks) as
 allowed by weather conditions. Survival (presence/absence) was determined
 by visual inspection in the field and change in percent cover was assessed
 by photographic analysis.
DOI: 10.5061/dryad.crjdfn37k
title: Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation

description: The group Anguimorpha represents one of the most unified squamate clades
 in terms of body plan, ecomorphology, ecophysiology and evolution. On the
 other hand, the anguimorphs vary between different habitats and ecological
 niches. Therefore, we focused on the group Anguimorpha to test a possible
 correlation between heart morphology and ecological niche with respect to
 phylogenetic position in Squamata with Sphenodon, Salvator, and Pogona as
 the outgroups. The chosen lepidosaurian species were investigated by
 microCT. Generally, all lepidosaurs had two well-developed atria with
 complete interatrial septum and one ventricle divided by ventricular septa
 to three different areas. The ventricles of all lepidosaurians had a
 compact layer and abundant trabeculae. The compact layer and trabeculae
 were developed in accordance with the particular ecological niche of the
 species; the trabeculae in nocturnal animals with low metabolism, such as
 Sphenodon, Heloderma or Lanthanotus, were more massive. On the other hand,
 athletic animals, such as varanids or Salvator, had ventricle
 compartmentalization divided by three incomplete septa. A difference
 between varanids and Salvator was found in compact layer thickness:
 thicker in monitor lizards and possibly linked to their mammalian-like
 high blood pressure, and the level of ventricular septation. In summary:
 heart morphology varied among clades in connection with the ecological
 niche of particular species and it reflects the phylogenetic position in
 the model clade Anguimorpha. In the absence of fossil evidence, this is
 the closest approach to understanding heart evolution and septation in
 clades with different cardiac compartmentalization levels.
DOI: 10.15468/dl.z6cp9x
title: Occurrence Download

description: A dataset containing 296 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Falcataria falcata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 296 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003320-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x95x69pnr
title: Data for: Male-specific nocturnal song functions similar to day song in a diurnal bird species

description: Historically, birdsong research has been biased towards song of male birds
 at dawn and during the day, even though some diurnal birds sing at night.
 To address this gap, we studied how song in the willie wagtail, Rhipidura
 leucophrys—a diurnal species with prolific male-specific nocturnal song
 during the breeding season—varies with time of day, breeding status, and
 simulated intrusions. We recorded male nocturnal and dawn song over three
 breeding seasons and examined how this related to fertile and non-fertile
 breeding stages of females. To test whether song functions for territory
 defence, we simulated territorial intrusion experimentally in both sexes
 with daytime and nighttime playback of male and female song. To test
 whether nocturnal song could function for mate guarding or post-pairing
 mate attraction, we describe the mating system of willie wagtails using
 molecular genetic methods. We showed that both nocturnal and daytime song
 of male willie wagtails has roles in mate attraction and territory
 defence, while daytime song by females functioned primarily for
 territorial defence. Males increased song behaviour during fertile periods
 of resident females, suggesting possible roles in mate stimulation and
 mate guarding. Males and females responded similarly to simulated daytime
 intrusions and no differences were seen in male responses dependent on the
 time of day. We found 10%-14% of offspring were fathered by extra-pair
 males, suggesting song may also function for mate guarding and
 post-pairing mate attraction. In a species with small repertoires and
 simple songs like the willie wagtail, differences between males in overall
 song output achieved through nocturnal singing may be important in mate
 attraction and territory defence.
description: Observational methods of breeding data in willie wagtails.
 Experimental results of playback experiments.
DOI: 10.5061/dryad.gf1vhhmt0
title: Contrasting soil- and canopy-nurse effects on dependent species in metalliferous systems may be explained by dominant plant functional strategies

description: Plant-plant interaction studies in metalliferous systems have focused
 either on the role of facilitation or on the negative effects of elemental
 allelopathy. However, no studies have investigated both of these effects
 in the same system, and their relationships with the functional strategy
 of the nurse species, although this is crucial for the ecological
 restoration of polluted sites. We assessed the effects of two dominant
 nurse species, with apparent contrasting strategies, on two target species
 on a slag heap in the Pyrenees (France). We quantified both long-term
 soil-engineering and short-term canopy effects on the growth of two target
 species. We also measured morphological traits and leaf metal
 concentration of the two nurse species and their effects on air moisture,
 temperature, and vapour pressure deficit. Nurse functional strategies, as
 inferred from morphological traits and leaf metal concentration seem to
 drive their long-term soil engineering effects on target species:
 Gypsophila repens, the relatively larger and more exploitative species
 with high leaf metal concentration, had negative long-term effects likely
 due to elemental allelopathy, whereas Minuartia verna, the relatively
 smaller and more conservative species with a lower amount of metals in
 leaves, had neutral long-term effects. Although Gypsophila repens had a
 slightly stronger positive effect on microclimate than Minuartia verna,
 this did not turn into higher short-term effects for the target species.
 Our study highlights the possible role of the nurse’s functional
 strategies in driving the relative importance of long and short-term
 effects on target species in metalliferous systems. This knowledge is key
 to increasing our understanding of plant-plant interaction outcomes in
 metalliferous systems and our ability to restore polluted environments.
DOI: 10.5061/dryad.41ns1rnj2
title: Seed dispersal by waterbirds: a mechanistic understanding by simulating avian digestion

description: Waterbirds disperse plant species via ingestion and egestion of seeds
 (endozoochory). However, our understanding about the regulating effects of
 seed traits, underlying mechanisms and possible (co)evolutionary processes
 is limited by our traditional reliance on data from feeding experiments
 with living waterbirds. Here, we overcome these limitations by developing
 and applying a new bioassay that realistically simulates digestive
 processes for Anseriformes waterbirds. We test three hypotheses: (1) seed
 survival and germination are most affected by mechanical digestion in the
 waterbird gizzard; (2) seed size, hardness, imbibition and shape regulate
 seed survival; and (3) plants growing in aquatic habitats benefit most
 from endozoochory by waterbirds. Experiments with 28,200 seeds of 48 plant
 species demonstrated species-specific seed survival that was entirely
 determined by digestion in the avian gizzard. Intestinal digestion did not
 affect seed survival but affected seed establishment (germinability and
 germination time) for 21% of the species. Large, hard seeds survived the
 simulations the best, in contrast to generally higher seed survival for
 smaller seeds during in vivo experiments. This mechanistically explains
 that small seeds escape digestive processes rather than being inherently
 more resistant (the ‘escape mechanism’), while large seeds are retained
 until fully digested or regurgitated (the ‘resistance and regurgitation
 mechanism’). Plants growing in wetter habitats had similar seed survival,
 but digestive processes stimulated their germinability and accelerated
 their germination more than for terrestrial plants. This indicates a
 relative advantage of endozoochory for plant species growing in wet
 habitats, possibly reflecting a co-evolutionary response related to
 dormancy breaking by gut passage. Simulating seed gut passage using a
 bioassay allowed establishing mechanisms and identifying relevant seed
 traits involved in seed dispersal by waterbirds. This information enhances
 our understanding of how animal species shape plant species distributions,
 which is extremely relevant now that current anthropogenic pressures
 already severely impact plant dispersal capacities.
description: We developed and applied a new bioassay that realistically
 simulates digestive processes for Anseriformes waterbirds. We tested the
 effects of different phases of simulated digestion on seed survival and
 germination in relation to seed traits (seed size, hardness, imbibition
 and shape). Experiments were performed with 28,200 seeds of 48 different
 plant species.
DOI: 10.5061/dryad.p2ngf1vv1
title: Data for: Direct and indirect effects of management and landscape on biological pest control and crop pest infestation in apple orchards

description: Biological pest control, relying on naturally occurring predator-prey
 dynamics, is considered a key element to achieve more sustainable farming
 systems. However, the combined effects of local management and landscape
 factors on communities of natural enemies as well as the cascading effects
 on pest infestations are rarely addressed, especially in perennial crops.
 Here, we used Piecewise Structural Equation Modelling (PSEM) to test
 direct and indirect effects of landscape composition, landscape
 configuration and local management practices on natural enemy communities,
 the pest control services they provide and ultimately on pest infestation
 and pest-related yield damage in apple crops. To this end, we surveyed 12
 organic and 12 Integrated Pest Management (IPM) orchards during three
 consecutive years, and we also established a semi-natural benchmark to
 quantify the extent to which predator communities in the orchards were
 degraded. Natural enemies had a different community composition and were
 more abundant in organic orchards compared to IPM orchards. This had a
 small and positive effect on sentinel egg predation rates in organic
 orchards, but overall had very little impact on actual apple pest
 infestation. On the contrary, apple pest infestation levels were directly
 and positively affected by organic management practices and by increasing
 semi-natural habitat cover and landscape edge density. Compared to a
 semi-natural benchmark, both agricultural management systems showed
 degraded predator communities, which translated into an impaired delivery
 of biological control services. Synthesis and applications. Our results
 indicate that organic management and habitat conservation can enhance
 natural enemies and stimulate pest control, but also show that these
 factors can enhance pest infestations and can even lead to an overall
 increase in pest-related crop damage. Our study thus highlights the
 complex interplay of ecosystem services and disservices provided by
 biodiversity, which should be taken into account when advising farmers,
 policy makers and land managers on effective and sustainable strategies to
 control pest species and safeguard crop production.
description: All information concerning the data is included in the first
 excel sheet. Cells with N/A indicate that no data could be collected or
 calculated for a specific variable (columns) at a study site
 (rows).
DOI: 10.5061/dryad.hqbzkh1kk
title: Filtered survey data for: AOS professional ethics committee

description: In response to a growing need to foster ethical behavior within scientific
 societies, the American Ornithological Society’s (AOS) professional ethics
 committee conduct a survey of members in spring 2021 to identify the
 primary challenges and ethical conduct concerns. The survey indicated that
 the AOS has a strong culture of professional ethics and highlighted areas
 needing improvement. Participants identified discrimination and lack of
 inclusivity (44%), scientific fraud and abuse in data and publications
 (35%), and sexual harassment (31%) as the highest potential risks for
 unethical behavior in our organization. Moreover, approximately one-third
 of respondents (34%) had personally witnessed or experienced unethical
 behavior as an AOS member. A smaller proportion (16%) felt pressure to
 compromise their work standards in ornithology. These findings are likely
 representative of broader patterns that professional, scientific societies
 face as they seek to provide safe, welcoming, and thoughtful environments
 for researchers to share their work, gain valuable feedback, and develop
 collaborations. The survey results also create a framework for workshops,
 training opportunities, and disseminating information within the AOS and,
 ideally, with the broader, international community of ornithologists.
description: The survey consisted of 13 questions, six of which were designed
 to collect demographic data from survey respondents. The online survey was
 open from March 4 to April 4, 2021, and weekly reminders and requests for
 survey participation were sent to our general membership via email for the
 duration of the survey period. In total, 479 individuals participated
 (approximately 19% of our current membership). Based on these results, we
 estimate that our response rate is a large enough sample size to put us
 within a 5% margin of error
 (https://www.surveymonkey.com/curiosity/how-many-people-do-i-need-to-take-my-survey/).  Raw survey data were filtered to remove missing responses separately for each question. For open-ended questions, we categorized responses to facilitate interpretation. The data shared here are for filtered, close-ended questions only. We have removed demographic data, as well as detailed open-ended responses to preserve the anonymity of the respondents. While the responses were already anonymous, we wanted to be extra vigilant about filtering out any information that could possibly be traced back to an individual.
DOI: 10.5061/dryad.n5tb2rc04
title: Automated and manual pooled sample testing with panther fusion and aptima SARS-CoV-2 assays

description: Combining diagnostic specimens into pools has been considered as a
 strategy to augment throughput, decrease turnaround time, and leverage
 resources. This study utilized a multi-parametric approach to assess
 optimum pool size, impact of automation, and effect of nucleic acid
 amplification chemistries on the detection of SARS-CoV-2 RNA in pooled
 samples for surveillance testing on the Hologic Panther Fusion® System.
 Dorfman pooled testing was conducted with previously tested SARS-CoV-2
 nasopharyngeal samples using Hologic’s Aptima® and Panther Fusion®
 SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used
 to generate pool sizes of 5:1 (five samples: one positive, four negative)
 and 10:1. An automated workflow was used to generate pool sizes of 3:1,
 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay
 chemistry on sensitivity, specificity, and lower limit of detection (LLOD)
 was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2
 assays demonstrated &gt;85% positive percent agreement between neat
 testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant
 results between neat and pooled testing were more frequent for positive
 samples with CT&gt;35. Fusion® CT (cycle threshold) values for pooled
 samples increased as expected for pool sizes of 5:1 (CT increase of 1.92 -
 2.41) and 10:1 (CT increase of 3.03 - 3.29). The Fusion® assay
 demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs
 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the
 Aptima® assay from 560 kRLU (manufacturer’s setting) to 350 kRLU improved
 the assay sensitivity to that of the Fusion® assay for pooled testing.
 Both Hologic’s SARS-CoV-2 assays met the FDA recommended guidelines for
 percent positive agreement (&gt;85%) for pool sizes ≤5:1. Automated
 pooling increased test throughput and enabled automated sample tracking
 while requiring less labor. The Fusion® SARS-CoV-2 assay, which
 demonstrated a lower LLOD, may be more appropriate for surveillance
 testing.
description: 1. Data was copied from .csv files from the Panther Fusion system
 into an .xlsx file 2. Data for both the Manual and
 Automated pooling studies have been combined into one file
 3. Data that was previously collected by testing sites such as
 CDC and TaqPath (Manual) and cobas (Automated) results are also included
 in the spreadsheet
description: Microsoft Excel Alternative: LibreOffice
DOI: 10.5061/dryad.dfn2z355g
title: Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

description: The influence of genetic drift on population dynamics during Pleistocene
 glacial cycles is well understood, but the role of selection in shaping
 patterns of genomic variation during these events is less explored. We
 used resequenced whole genomes to investigate how demography and natural
 selection interact to generate the genomic landscapes of Downy and Hairy
 Woodpeckers, species co-distributed in previously glaciated North America.
 First, we explored the spatial and temporal patterns of genomic diversity
 produced by neutral evolution. Next, we tested (1) whether levels of
 nucleotide diversity along the genome are correlated with intrinsic
 genomic properties, such as recombination rate and gene density, and (2)
 whether different demographic trajectories impacted the efficacy of
 selection. Our results revealed cycles of bottleneck and expansion and
 genetic structure associated with glacial refugia. Nucleotide diversity
 varied widely along the genome, but this variation was highly correlated
 between the species, suggesting the presence of conserved genomic
 features. In both taxa, nucleotide diversity was positively correlated
 with recombination rate and negatively correlated with gene density,
 suggesting that linked selection played a role in reducing diversity.
 Despite strong fluctuations in effective population size, the maintenance
 of relatively large populations during glaciations may have facilitated
 selection. Under these conditions, we found evidence that the individual
 demographic trajectory of populations modulated linked selection, with
 purifying selection being more efficient in removing deleterious alleles
 in large populations. These results highlight that while genome-wide
 variation reflects the expected signature of demographic change during
 climatic perturbations, the interaction of multiple processes produces a
 predictable and highly heterogeneous genomic landscape.
description: Whole genome sequencing of 140 samples of Downy
 (<em>Dryobates pubescens</em>) and Hairy (<em>D.
 villosus</em>) Woodpecker from seven (<em>n</em> per
 population = 10) North American populations.