cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6078/d1tt5w
title: Parallel and non-parallel phenotypic responses to environmental variation across Lesser Antillean anoles

description: Species whose ranges encompass substantial environmental variation should
 experience heterogeneous selection, potentially resulting in local
 adaptation. Repeated covariation between phenotype and environment across
 ecologically similar species inhabiting similar environments provides
 strong evidence for adaptation. Lesser Antillean anoles present an
 excellent system in which to study repeated local adaptation because most
 species are widespread generalists occurring throughout environmentally
 heterogenous island landscapes. We leveraged this natural replication to
 test the hypothesis that intraspecific variation in phenotype (coloration
 and morphology) is consistently associated with environment across nine
 species of bimaculatus series anoles. We measured dorsal coloration from
 173 individuals from six species and 16 morphological traits from 883
 individuals from nine species, spanning their island ranges. We identified
 striking, but incomplete, parallelism in dorsal coloration associated with
 annual precipitation in our study species. By contrast, we observed
 significant patterns of morphological isolation-by-environment in only two
 species and no signal of parallel morphological evolution. Collectively,
 our results reveal strong divergent natural selection by environment on
 dorsal coloration but not morphology.
description: No specialized software should be required to open files (.txt
 and .csv).
DOI: 10.5281/zenodo.18390319
title: More tropical cyclones striking continental coasts at peak intensity

description: This repository provides the data and Python scripts used in Wu and Fu's study, 'More tropical cyclones striking continental coasts at peak intensity.' Key datasets include IBTrACS-derived annual variability of landfall intensification and tropical cyclones striking coasts at peak intensity. It also features ERA5-calculated environmental parameters (humidity, shear, MPI, vorticity, and GPI) and CMIP6 climate model simulations across various forcing scenarios. Users can run the provided scripts to reproduce the figures presented in the manuscript.
DOI: 10.5061/dryad.qfttdz0n2
title: Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation

description: Almost nothing is known about the diets of bathypelagic fishes, but
 functional morphology can provide useful tools to infer ecological
 processes. Here we quantify variation in jaw and tooth morphologies across
 anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea
 habitats. Deep-sea ceratioid anglerfishes are believed to be dietary
 generalists due to the presumed necessity of opportunistic feeding in the
 food-limited bathypelagic zone. However, we found unexpected diversity in
 the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a
 functional continuum ranging from species with numerous stout teeth, a
 relatively slow but forceful bite, and high jaw protrusibility at one
 extreme (characteristics shared with benthic anglerfishes), to species
 with large fang-like teeth, a fast but weak bite, and low jaw
 protrusibility at the other (including a unique “wolftrap” phenotype). Our
 finding of high morphological diversity seems to be at odds with
 ecological generality, reminiscent of Liem’s paradox (morphological
 specialization allows organisms to have broader niches). Another possible
 explanation is that diverse ceratioid morphologies may yield similar
 trophic success (many-to-one mapping of morphology to diet), allowing
 diversity to arise through neutral evolutionary processes. Our results
 highlight that there are many ways to be a successful predator in the deep
 sea.
description: Measurements were taken directly from CT scans of anglerfishes
 using the program 3D Slicer. R scripts describe data transformations,
 analyses, and figures. Phylogenetic trees were constructed as described in
 the Methods section of the associated article.
description: Scripts are written in the programming language R.
DOI: 10.5061/dryad.63xsj3v6j
title: Exploring the behaviors and social preferences of a large, multi-generational herd of zoo-housed southern white rhinoceros (Ceratotherium simum simum), 2020–2021

description: The zoo-housed southern white rhinoceros (SWR) population is of special
 concern due to their lack of consistent breeding success. An enhanced
 understanding of SWR social preferences could better inform management
 planning by promoting natural social relationships, which can positively
 affect their well-being. The large, multigeneration herd housed at the
 North Carolina Zoo provides an ideal opportunity to examine rhino
 sociality across different ages, kin types, and social groupings. Eight
 female rhinos' social and nonsocial behaviors were recorded from
 November 2020 through June 2021 across 242 hours. Activity budget analyses
 revealed strong seasonal and temporal variations in grazing and resting
 behaviors, with no stereotypic behaviors recorded. Bond strength
 calculations suggested that each female maintained strong social bonds
 with one to two partners. Beyond mother-nursing calf bonds, we found that
 the strongest social ties were maintained between calf-less adults and
 subadults in these dyads. Considering these findings, we recommend that
 management plans attempt to house immature females with calf-less adult
 females, as they may be necessary to the social landscape of immature
 females and, ultimately, improve their welfare.
description: Please see README.md file as well as the accompanying manuscript:
 Williams, B, et al. (2023) Exploring the behaviors and social preferences
 of a large, multi-generational herd of zoo-housed southern white
 rhinoceros (<em>Ceratotherium simum simum</em>). Zoo Biology
 Journal.
DOI: 10.5061/dryad.hqbzkh1md
title: Data for: Predicting age and mass at maturity from feeding behavior and diet in M. sexta: An empirical test of a life history model

description: Feeding for most animals involves bouts of active ingestion alternating
 with bouts of no ingestion. In insects, the temporal patterning of bouts
 varies widely with resource quality and is known to affect growth,
 development time, and fitness. However, the precise impacts of resource
 quality and feeding behavior on insect life history traits is poorly
 understood. To explore and better understand the connections between
 feeding behavior, resource quality and insect life history traits, we
 combined laboratory experiments with a recently proposed mechanistic model
 of insect growth and development for a larval herbivore, Manduca sexta. We
 ran feeding trials for 4th and 5th instar larvae across different diet
 types (two hostplants and artificial diet) and used these data to
 parameterize a joint model of age and mass at maturity that incorporates
 both insect feeding behavior and hormonal activity. We found that the
 estimated durations of both feeding and non-feeding bouts were
 significantly shorter on low- than on high-quality diets. We then explored
 how well the fitted model predicted historical out-of-sample data on age
 and mass of M. sexta. We found that the model accurately described
 qualitative outcomes for the out-of-sample data, notably that a
 low-quality diet results in reduced mass and later age at maturity
 compared to high-quality diets. Our results clearly demonstrate the
 importance of diet quality on multiple components of insect feeding
 behavior (feeding and non-feeding), and partially validate a joint model
 of insect life history. We discuss the implications of these findings with
 respect to insect herbivory and discuss ways in which our model could be
 improved or extended to other systems.
DOI: 10.5061/dryad.x3ffbg7pp
title: Data from: Can the soil seed bank of Rumex obtusifolius in productive grasslands be explained by management and soil properties?

description: Rumex obtusifolius is a problematic weed in temperate grasslands worldwide
 as it decreases yield and nutritional value of forage. Because the species
 can recruit from the seed bank, we determined the effect of management and
 soil properties on the soil seed bank of R. obtusifolius in intensively
 managed, permanent grasslands in Switzerland (CH), Slovenia (SI), and
 United Kingdom (UK). Following a paired case-control design, soil cores
 were taken from the topsoil of grassland with a high density of R.
 obtusifolius plants (cases) and from nearby parcels with very low R.
 obtusifolius density (controls). Data on grassland management, soil
 nutrients, pH, soil texture, and density of R. obtusifolius plants were
 also collected. Seeds in the soil were germinated under optimal conditions
 in a glasshouse. The number of germinated seeds of R. obtusifolius in case
 parcels was 866 ±152 m-2 (CH, mean ±SE), 628 ±183 m-2 (SI), and 752 ±183
 m-2 (UK), with no significant difference among countries. Densities in
 individual case parcels ranged from 0 up to approximately 3000 seeds m-2
 (each country). Control parcels had significantly fewer seeds, with a mean
 of 51 ±18, 75 ±52, and 98 ±52 seeds m-2 in CH, SI, and UK, respectively,
 and a range between 0 and up to 1000 seeds m-2. Across countries,
 variables explaining variation in the soil seed bank of R. obtusifolius in
 case parcels were soil pH (negative relation), silt content (negative),
 land-use intensity (negative), and aboveground R. obtusifolius plant
 density (positive). Because a large soil seed bank can sustain grassland
 infestation with R. obtusifolius, management strategies to control the
 species should target the reduction in the density of mature plants,
 prevention of the species’ seed production and dispersal, as well as the
 regulation of the soil pH to a range optimal for forage production.
description: Data were acquired from managed grasslands with and without
 <em>Rumex obusifolius</em> in the three countries Switzerland,
 Slovenia and UK following a common protocol. The selection of parcels was
 restricted to intensively managed, permanent grasslands relevant for
 forage production and established since at least five years. A paired
 case-control design was implemented: field parcels with high density of
 <em>R. obtusifolius</em> plants (cases) were identified and
 compared with nearby parcels with no or very few <em>R.
 obtusifolius</em> plants (controls). Measured variables include data
 on management type and intensity, grassland disturbance, regulation of
 <em>R. obtusifolius</em>, soil properties, and seeds of
 <em>R. obtusifolius</em> in the topsoil. Seeds of <em>R.
 obtusifolius</em> from the parcels' topsoil (0-10 cm) were
 germinated under optimal conditions in a glasshouse to determine the soil
 seed bank of the species.
DOI: 10.5061/dryad.63xsj3v6k
title: Data from: Heteroaggregation of virions with microplastics reduces the number of active bacteriophages in aqueous environments

description: The objective of this study is to explore the effects of microplastics on
 the viability of the bacteriophages in an aqueous environment.
 Bacteriophages (phages), i.e., viruses of bacteria, are essential in
 homeostasis. It is estimated that phages cause up to 40% of the death of
 all bacteria daily. Any factor affecting phage activity is vital for the
 whole food chain and the ecology of numerous niches. We hypothesize that
 the number of active phages decreases due to the virions’ adsorption on
 microplastic particles or by the released leachables from additives used
 in the production of plastic, e.g., stabilizers, plasticizers, colorants,
 and reinforcements. We exposed three diverse phages, namely T4 (tailed),
 MS2 (icosahedral), and M13 (filamentous), to 1 mg/mL suspension of twelve
 industrial-grade plastics [acrylonitrile butadiene styrene (ABS),
 high-impact polystyrene (HIPS), poly-ε-caproamide (PA6), polycarbonate
 (PC), polyethylene (PE), polyethylene terephthalate (PET), poly(methyl
 methacrylate) (PMMA), polypropylene (PP), polystyrene (PS),
 polytetrafluoroethylene (PTFE), polyurethane (PUR), polyvinyl chloride
 (PVC)] shredded to obtain microparticles of radius ranging from 2 to 50
 µm. The effect of leachables was measured upon exposure of phages not to
 particles themselves but to the buffer pre-incubated with microplastics. A
 double-overlay plaque counting method was used to assess phage titers. We
 employed a classical linear regression model to verify which
 physicochemical parameters (65 variables were tested) govern the decrease
 of phage titers. The key finding is that adsorption mechanisms result in
 up to complete scavenging of virions, whereas leachables deactivate up to
 50% of phages. This study reveals microplastic pollution’s plausible and
 unforeseen ecotoxicological effect causing phage deactivation. Also, phage
 transmission through adsorption can alter the balance of the food chain in
 the new environment. The effect depends mainly on the zeta potentials of
 the polymers and the phage type.
description: We built a database of the physicochemical variables based on the
 literature (i.e., density, zeta potential, contact angle) and our
 experimental data (i.e., BET measurements, wetting angle). We also
 modified them by considering their functions (i.e., tanh x,
 x<sup>2</sup>), binary representations (i.e.,
 hydrophobic/hydrophilic), or synergy effects (interactions between the
 variables). For all the details, see the Database file. Supporting
 information contains detailed descriptions of the variable selection,
 construction of the model, and diagnoses of the selected models.
description: Microsoft Office - Excel program (or alternatives) is
 required.
DOI: 10.5061/dryad.31zcrjdqs
title: How woodcocks produce the most brilliant white plumage patches among the birds

description: Until recently, and when compared with diurnal birds that use contrasting
 plumage patches and complex feather structures to convey visual
 information, communication in nocturnal and
 crepuscular species was considered to follow acoustic and
 chemical channels. However, many birds that are active
 in low-light environments have evolved intensely white plumage
 patches within otherwise inconspicuous plumages. We used
 spectrophotometry, electron microscopy, and optical modelling to explain
 the mechanisms producing bright white tail feather tips of the Eurasian
 woodcock Scolopax rusticola. Their diffuse reflectance was ~30%
 higher than any previously measured feather. This intense reflectance is
 the result of incoherent light scattering from a disordered nanostructure
 composed of keratin and air within the barb rami. In addition, the
 flattening, thickening, and arrangement of those barbs create a
 Venetian-blind-like macrostructure that enhances the surface area for
 light reflection. We suggest that the woodcocks have evolved these bright
 white feather patches for long-range visual communication in dimly lit
 environments.
description: Wider comparisons taken from: Igic, B., L.
 D’Alba and M. D. Shawkey. 2018. Fifty shades of white: how white feather
 brightness differs among species. Sci. Nat. 105(18): 3-4. doi.org/10.1007/s00114-018-1543-3.
description: All data processed in R.
DOI: 10.5061/dryad.m37pvmd6d
title: Effects of environmental factors on the ecology and survival of a widespread, endemic Cerrado frog

description: Understanding the mechanisms that affect habitat use by vertebrates is
 critical for understanding how species are distributed across landscapes
 and how they cope with habitat change. The Brazilian Savanna (the Cerrado)
 has vegetation ranging from grassland to woodland savannas and harbors a
 rich and diverse amphibian fauna impacted by accelerated habitat loss.
 Here, we test the influence of vegetation type (from grassy scrubland to
 woodland) and distance from breeding sites (ephemeral water bodies) on
 body size, abundance, and survival of the frog Physalaemus nattereri in a
 natural metapopulation system of south-central Brazil. We also test
 whether body size is a significant predictor of population abundance. We
 found that the abundance of P. nattereri varies according to the mean
 snout-vent length of each metapopulation (sampling unit), as well as a
 higher estimated mortality rate in woodlands compared to typical Cerrado.
 Furthermore, we found no difference in estimated mortality among sampling
 units located far or close to ephemeral water bodies. Thus, our results
 highlight variable responses of P. nattereri metapopulations to
 environmental factors, despite the observed high heterogeneity among
 sampled habitats and the importance of ephemeral water bodies for
 reproduction. These findings highlight that land cover and availability of
 breeding sites might not always interact to explain population persistence
 of Cerrado frogs. 
description: Sampling was performed monthly
 for 10 days, from August 2016 to July 2018, for a total of 24 field trips
 and 240 days of fieldwork. At each sampled vegetation type
 (<em>campo cerrado, campo sujo, cerrado sensu stricto</em>,
 and <em>cerradão</em>), three units of pitfall traps with
 drift fences were installed. Each unit corresponded to two 40-m trap
 lines, 60 m apart. Each trap line had four 100-L plastic buckets every 10
 m, connected by a plastic drift fence 60 cm tall. Dorsal
 marks of individual frogs were recorded using digital cameras. Then, we
 performed a computer-assisted matching method, using the Wild-ID program.
 This software detects recaptures based on an algorithm of Scale Invariant
 Feature Transform, which extracts and combines the distinctive features in
 the image, regardless of size and orientation.
description: Microsoft Excel R
DOI: 10.5281/zenodo.18366081
title: Have protein-ligand cofolding methods moved beyond memorisation?

description: This repository accompanies the paper: "Have protein-ligand cofolding prediction methods moved beyond memorisation?"

 

Changes from v4:

- posebusters_results.tar.gz - PoseBusters checks were run in "redock" mode, instead of "dock" mode, which added additional checks and thus changed overall PB valid counts. Additionally some missing systems for AF3 were added.

- prediction_files.tar.gz - Missing system from AF3 were added
DOI: 10.5281/zenodo.14794785
title: Have protein-ligand cofolding methods moved beyond memorisation?

description: This repository accompanies the paper: "Have protein-ligand cofolding prediction methods moved beyond memorisation?"

 

Changes from v4:

- posebusters_results.tar.gz - PoseBusters checks were run in "redock" mode, instead of "dock" mode, which added additional checks and thus changed overall PB valid counts. Additionally some missing systems for AF3 were added.

- prediction_files.tar.gz - Missing system from AF3 were added
DOI: 10.5061/dryad.5qfttdz9p
title: Data from: Local and landscape scale woodland cover and diversification of agroecological practices shape butterfly communities in tropical smallholder landscapes

description: The conversion of biodiversity-rich woodland to farmland and subsequent
 management has strong, often negative, impacts on biodiversity. In
 tropical smallholder agricultural landscapes, the impacts of agriculture
 on insect communities, both through habitat change and subsequent farmland
 management, is understudied. The use of agroecological practices has
 social and agronomic benefits for smallholders. Although ecological
 co-benefits of agroecological practices are assumed, systematic empirical
 assessments of biodiversity effects of agroecological practices are
 missing, particularly in Africa. In Malawi, we assessed butterfly
 abundance, species richness, species assemblages and community
 life-history traits on 24 paired woodland and smallholder-managed farmland
 sites located across a gradient of woodland cover within a 1 km radius. We
 tested whether habitat type (woodland vs. farmland) and woodland cover at
 the landscape scale interactively shaped butterfly communities. Farms
 varied in the implementation of agroecological pest and soil management
 practices and flowering plant species richness. Farmland had lower
 butterfly abundances and approximately half the species richness than
 woodland. Farmland butterfly communities had, on average, a larger
 wingspan than woodland site communities. Surprisingly, higher woodland
 cover in the landscape had no effect on butterfly abundance in both
 habitats. In contrast, species richness was higher with higher woodland
 cover. Butterfly species assemblages were distinct between wood- and
 farmland and shifted across the woodland cover gradient. Farmland
 butterfly abundance, but not species richness, was higher with higher
 flowering plant species richness on farms. Farms with a higher number of
 agroecological pest management practices had a lower abundance of the
 dominant butterfly species, but not of rarer species. However, a larger
 number of agroecological soil management practices was associated with a
 higher abundance of rarer species.  Synthesis and applications:
 We show that diversified agroecological soil practices and flowering plant
 richness enhanced butterfly abundance on farms. However, our results
 suggest that on-farm measures cannot compensate for the negative effects
 of continued woodland conversion. Therefore, we call for more active
 protection of remaining African woodlands in tandem with promoting
 agroecological soil management practices and on-farm flowering plant
 richness to conserve butterflies whilst benefiting smallholders.
DOI: 10.7910/dvn/bdkmoq
title: TechEthos

description: This excel sheet contains the transcripts of the conducted workshops, including the coded values and the value categories.