cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dfn2z355r
title: Data from: Soil phosphorus drawdown by perennial bioenergy cropping systems in the Midwestern US

description: Without fertilization, harvest of perennial bioenergy cropping systems
 diminishes soil nutrient stocks, yet the time course of nutrient drawdown
 has not often been investigated. We analyzed phosphorus (P) inputs
 (fertilization and atmospheric deposition) and outputs (harvest and
 leaching losses) over seven years in three representative biomass
 crops—switchgrass (Panicum virga­tum L.), miscanthus (Miscanthus X
 giganteus) and hybrid poplar trees (Populus nigra X P. maximowiczii) – as
 well as in no-till corn (maize; Zea mays L.) for comparison, all planted
 on former cropland in SW Michigan, USA. Only corn received P fertilizer.
 Corn (grain and stover), switchgrass, and miscanthus were harvested
 annually, while poplar was harvested after six years. Soil test P (STP;
 Bray-1 method) was measured in the upper 25 cm of soil annually. Harvest P
 removal was calculated from tissue P concentration and harvest yield (or
 annual woody biomass accrual in poplar). Leaching was estimated as total
 dissolved P concentration in soil solutions sampled beneath the rooting
 depth (1.25 m), combined with hydrological modeling. Fertilization and
 harvest were by far the dominant P budget terms for corn, and harvest P
 removal dominated the P budgets in switchgrass, miscanthus, and poplar,
 while atmospheric deposition and leaching losses were comparatively
 insignificant. Because of significant P removal by harvest, the P balances
 of switchgrass, miscanthus, and poplar were negative and corresponded with
 decreasing STP, whereas P fertilization compensated for the harvest P
 removal in corn, resulting in a positive P balance. Results indicate that
 perennial crop harvest without P fertilization removed legacy P from
 soils, and continued harvest will soon draw P down to limiting levels,
 even in soils once heavily P-fertilized. Widespread cultivation of
 bioenergy crops may therefore alter P balances in agricultural landscapes,
 eventually requiring P fertilization, which could be supplied by P
 recovery from harvested biomass.
DOI: 10.5061/dryad.rv15dv4bf
title: Data for: Long-term clade-wide shifts in trilobite segment number and allocation during the Palaeozoic

description: Arthropods are characterized by having an exoskeleton, paired jointed
 appendages, and segmented body. The number and shape of those segments
 varies dramatically and unravelling the evolution of segmentation is
 fundamental to our understanding of arthropod diversification. Because
 trilobites added segments to the body post-hatching which were expressed
 and preserved in biomineralized exoskeletal sclerites, their fossil record
 provides an excellent system for understanding the early evolution of
 segmentation in arthropods. Over the last 200 years, palaeontologists have
 hypothesized trends in segment number and allocation in the trilobite
 body, but they have never been rigorously tested. We tabulated the number
 of segments in the post-cephalic body for over 1500 species, selected to
 maximize taxonomic, geographic, and temporal representation. Analysis
 reveals long-term shifts in segment number and allocation over the
 250-million-year evolutionary history of the clade. For most of the
 Palaeozoic, the median number of segments in the body did not change
 significantly. Instead, the total range decreased over time and there was
 long-term increase in the proportion of segments allocated to the fused
 terminal sclerite relative to the articulated thoracic region. There was
 also increased conservation of thoracic segment number within families.
 Neither taxonomic turnover nor trends in functionally-relevant defensive
 behaviour sufficiently explain these patterns.
DOI: 10.15468/dl.tuyzsy
title: Occurrence Download

description: A dataset containing 1125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus molleri"
 ]
}

 The dataset includes 1125 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003377-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tb2rbp046
title: The first African record of Isothecium algarvicum in Kroumiria (Tunisia), a relictual element of the Neogene flora?

description: Isothecium algarvicum W. E. Nicholson & Dixon, was discovered in
 Tunisia, which constitutes the first report of this Macaronesianoceanic
 species in Africa. Three distinct populations were observed in ravines in
 the humid Meso-Mediterranean vegetation belt of Kroumiria. The Tunisian
 material is fully described, with particular attention to alar and
 supra-alar cells, prorate cells and other morphological characteristics.
 The density and size of the prorate cells appear to be a robust diagnostic
 characteristic for the separation of Isothecium algarvicum, I.
 alopecuroides and I. myosuroides. Detailed analysis of the forest habitat
 reveals a uniquely rich environment. The origin of a possibly relict
 species with Macaronesian-oceanic affinities is discussed.
description: To measure density and size of the prorate cells, we studied
 three species of <em>Isothecium</em>:<em> I.
 algarvicum</em>, <em>I. alopecuroides</em> and
 <em>I. myosuroides</em> (Table 1). Five leaves were dissected
 from each of five randomly chosen stems of each specimen, and measurements
 were made at 100 μm from the leaf apex in an area of ca 78 × 78 μm. For
 <em>I</em>. <em>myosuroides</em>, given the length
 of the leaf acumen, we took measurements where an area of 78 × 78 μm was
 reached. Table 1. Provenance of the specimens used for
 the measurements of density and size of prorate cells. <strong>Species</strong> <strong>Country of origin</strong> <strong>Localities</strong> <em>Isothecium algarvicum</em> Tunisia Canary Islands Spain Kroumiria: Waterfall Aïn Jmel; Oued Ellil; O. Zen La Palma, Barranco de San Juan Màlaga Benahavís; without location <em>Isothecium alopecuroides</em> France Pontgibaud, Puy de Dôme Auvergne:Haute Loire Polignac Orne, Bellême forest <em>Isothecium myosuroides</em> France Auvergne: Cantal, Vezels Roussy, les Bories<br>Pays de Loire Sarthe Perseigne forest
description: Excel
DOI: 10.5061/dryad.5qfttdz98
title: Spatiotemporal predictions of the alternative prey hypothesis: Predator habitat use during decreasing prey abundance

description: The alternative prey hypothesis supposes that predators supported by a
 primary prey species will shift to consume alternative prey during a
 decrease in primary prey abundance. The hypothesis implies that during
 declines of one prey species, a predator modifies their behavior to
 exploit a secondary, or alternative, species. Despite occurring in many
 systems, the behavioral mechanisms (e.g., habitat selection) allowing
 predators to shift toward alternative prey during declines in the
 abundance of their primary prey are poorly understood. We evaluated
 habitat selection and use by a generalist predator with respect to two
 prey species during a dramatic decrease in the abundance of primary prey.
 Further, we evaluated how spatial variation in access to primary prey
 affected habitat selection and assessed similarity and overlap between
 habitats used by each prey species. Coyotes (Canis latrans) exhibited
 decreasing selection for cottontail rabbits (Sylvilagus spp.; primary
 prey) during population decreases but did not shift habitat selection
 toward neonate mule deer (Odocoileus hemionus; alternative prey). Use of
 rabbit habitat remained high even during historically low rabbit
 abundance, while mule deer habitat was used in proportion to its
 availability. Coyotes seemingly do not make large shifts in habitat
 selection toward alternative prey following spatial and temporal decreases
 in the abundance of primary prey, but instead, take advantage of habitat
 overlap to facilitate prey-switching behavior. Our work extends previous
 research conducted under the alternative prey hypothesis by explicitly
 evaluating the influence of habitat overlap between prey species and
 variation in access to prey habitat as factors affecting prey-switching
 behaviors in predators.
DOI: 10.5061/dryad.h44j0zpps
title: Data for: Social learning in a nocturnal marsupial: Is it a possum-ability?

description: Social learning can reduce the costs associated with trial-and-error
 learning. There is speculation that social learning could contribute to
 trap and bait avoidance in invasive species like the Common Brushtail
 Possum (Trichosurus vulpecula) – a marsupial for which social learning has
 not previously been investigated. In large outdoor pens, we presented
 wild-caught ‘demonstrator’ possums with puzzle devices containing an
 attractive food reward; 2 of 8 demonstrators accessed the reward the first
 night the puzzle was presented and another 3 succeeded on later nights.
 Meanwhile, ‘observer’ possums in adjacent pens watched the demonstrators
 for five nights and then were given the opportunity to solve the puzzle
 themselves; 15 of 15 succeeded on their first night (a highly significant
 improvement). This experiment thus provides strong evidence of social
 learning by common brushtail possums. Future research should investigate
 whether information about aversive stimuli (such as traps and toxic baits)
 can similarly be transmitted between possums by social learning; if so,
 this could have important implications for possum pest control.
DOI: 10.5061/dryad.ffbg79czt
title: Misaligned plastic and evolutionary responses of lifespan to novel carbohydrate diets

description: Diet elicits varied effects on longevity across a wide range of animal
 species. For example, diets low in protein and high in
 carbohydrate typically extend lifespan while diets high in protein tend to
 reduce it. Although studies have also shown that diet-induced lifespan
 changes can persist through transgenerational plasticity, whether such
 changes lead to evolutionary shifts in lifespan remains unclear. In this
 study we combine experimental evolution and phenotypic plasticity assays
 to address this gap. Using Drosophila serrata, we investigated the
 evolutionary potential of lifespan in response to four novel diets
 spanning a carbohydrate-protein gradient. We also examined developmental
 plasticity effects using a set of control populations that were raised on
 the four novel environments. Our results show that although lifespan
 evolved in response to changes in dietary carbohydrate concentration, the
 plastic responses for lifespan differed from the evolved responses. The
 direction of the evolved response (increased lifespan) observed on low
 carbohydrate diets was in the opposite direction to the plastic response
 (decreased lifespan). Our results imply that plastic responses to low
 carbohydrates can be maladaptive for lifespan and misaligned with the
 evolved responses, laying the groundwork for future investigations of
 carbohydrate contributions to evolved and plastic effects on lifespan.
description: # Title of Dataset: Misaligned plastic and evolutionary responses of
 lifespan to novel carbohydrate diets ## Description of the Data and file
 structure The data are from an assay measuring the effects of diet on
 lifespan in D.serrata The data set is saved as a excel file. Each row
 corresponds to observations for one individual. The data set has the
 following columns: 1. id - A unique identification code assigned to each
 fly. 2. vial - A vial number nested within diet that records which vial
 adult flies were reared in. 3. sex - The sex of the flies 4. spop - Each
 alphabet (A-D) corresponds to one of the four replicates for each dietary
 treatment. 5. ediet - Evolutionary diet treatments 6. tdiet -
 Developmental diet treatments 7. days - Lifespan of flies 8. censored 1 if
 flies were included in the analysis, or zero if flies escaped during the
 lifespan assay and were excluded from the analysis N.B Diets 1, 2, 3, 4,
 and 5 correspond to 0.5, 1.0, 1.5, 2.0, and 2.5 S:Y respectively.
DOI: 10.5061/dryad.4tmpg4ff4
title: Data from: Season and herbivore defence trait mediate tri-trophic interactions in tropical rainforest

description: Bottom-up effects from host plants and top-down effects from predators on
 herbivore abundance and distribution vary with physical environment, plant
 chemistry, predator and herbivore trait and diversity. Tri-trophic
 interactions in tropical ecosystems may follow different patterns from
 temperate ecosystems due to differences in above abiotic and biotic
 conditions. We sampled leaf-chewing larvae of Lepidoptera (caterpillars)
 from a dominant host tree species in a seasonal rainforest in Southwest
 China. We reared out parasitoids and grouped herbivores based on their
 diet preferences, feeding habits, and defence mechanisms. We compared
 caterpillar abundance with leaf numbers (‘bottom-up’ effects) and
 parasitoid abundance (‘top-down’ effects) between different seasons and
 herbivore traits. We found bottom-up effects were stronger than top-down
 effects. Both bottom-up and top-down effects were stronger in the dry
 season than in the wet season, which were driven by polyphagous rare
 species and host plant phenology. Contrary to our predictions, herbivore
 traits did not influence differences in the bottom-up or top-down effects
 except for stronger top-down effects for shelter-builders. Our study shows
 season is the main predictor of the bottom-up and top-down effects in the
 tropics and highlights the complexity of these interactions.
description: Lepidopteran herbivore data for <em>Parashorea
 chinensis</em> saplings were collected by visual in late October to
 November 2019 (cool season) and late April to May 2020 (hot season). Each
 sampling was carried out in three close sub-sites (WTS, BB, CTFS).
 Sampling was carried out and recorded in "sampling units" (an
 area within ~2 m radius of the person sampling at a given sampling point).
 During each sampling, caterpillars were collected and reared in the lab to
 adults or parasitoids, and the number of leaves in the sampling units was
 also recorded. More details about sampling design and methodology can be
 found in the associated study. 
description: Microsoft Excel
DOI: 10.5061/dryad.vhhmgqnxt
title: Data from: Bedrock geological map predictions for Phanerozoic fossil occurrences

description: This is the supplementary data repository of the Paleobiology paper
 titled Bedrock Geological Map Predictions for Phanerozoic Fossil
 Occurrences. Geographically-explicit, taxonomically resolved fossil
 occurrences are necessary for reconstructing macroevolutionary patterns
 and for testing a wide range of hypotheses in the Earth and life sciences.
 Heterogeneity in the spatial and temporal distribution of fossil
 occurrences in the Paleobiology Database (PBDB) is attributable to several
 different factors, including turnover among biological communities,
 socioeconomic disparities in the intensity of paleontological research,
 and geological controls on the distribution and fossil yield of
 sedimentary deposits. Here we use the intersection of global geologic map
 data from Macrostrat and fossil collections in the PBDB to assess the
 extent to which the potentially fossil-bearing, surface-expressed
 sedimentary record has yielded fossil occurrences. We find a significant
 and moderately strong positive correlation between geologic map area and
 the number of fossil occurrences. This correlation is consistent
 regardless of map unit age and binning protocol, except at period level;
 the Neogene and Quaternary have non-marine map units covering large areas
 and yielding fewer occurrences than expected. The sedimentary record of
 North America and Europe yields significantly more fossil occurrences per
 sedimentary area than similarly-aged deposits in most of the rest of the
 world. However, geographic differences in area and age of sedimentary
 deposits lead to regionally different expectations for fossil occurrences.
 Using the sampling of surface-expressed sedimentary units in North America
 and Europe as a predictor for what might be recoverable from the
 surface-expressed sedimentary deposits of other regions, we find that the
 rest of the globe is approximately 45% as well sampled in the PBDB. Using
 age and area of bedrock and sampling in North America and Europe as a
 basis for prediction, we estimate that over 639 thousand occurrences from
 outside of these regions would need to be added to the PBDB to achieve
 global geological parity in sampling. In general, new terrestrial fossil
 occurrences are expected to have the greatest impact on macroevolutionary
 patterns.
DOI: 10.5061/dryad.0gb5mkm53
title: Data from: Surface Acoustic Wave-based Lab-On-a-Chip for the fast detection of Legionella pneumophila in water

description: Surface acoustic wave (SAW) -based immuno-biosensors are used for several
 applications, thanks to their versatility and faster response than
 conventional analytical methods. SAW immuno-biosensors can be usefully
 applied to promptly detect bacteria and prevent bacterial infections that
 can lead to severe diseases. Here, we present a SAW immuno-biosensor to
 detect Legionella pneumophila in water. Our device, working at ultra-high
 frequency (740 MHz), is functionalized with an anti-L. pneumophila
 antibody to maximize the specificity. We report the characteristic curve
 of the sensor, calculated measuring bacterial samples at known densities,
 and its related parameters. We also measure L. pneumophila samples
 contaminated with different Gram-positive and Gram-negative bacterial
 species (Escherichia coli and Enterococcus faecium) and samples diluted in
 mains waters. The proposed device is able to detect L. pneumophila in the
 range from 1×106 to 1×108 CFU/mL, with a limit of blank of 1.22×106 CFU/mL
 and a limit of detection of 2.01×106 CFU/mL. The nonspecific signal due to
 contaminant bacteria is very limited and measurements of L. pneumophila
 are not affected by contamination. We obtain a good detection also in
 mains water, representing a realistic matrix for L. pneumophila. Our
 results are encouraging and pave the way to the use of fast, easy-to-use,
 reliable and precise sensors to prevent bacterial infections in human
 activities.
description: Optical densities in the ELISA assay were acquired with a plate
 reader (ThermoFisher) at 450 nm. SAW-LoC data were
 acquired with a vectorial network analyzer E5071C (Agilent Technologies)
 connected to an RF switch 34980A (Agilent Technologies); an in-house
 software based on LabView® is used to pilot the RF-switch and the
 vectorial network analyzer.
description: Data files are uploaded as plain text.
DOI: 10.5061/dryad.wstqjq2qs
title: Data from: Morphological integration during postnatal ontogeny: Implications for evolutionary biology

description: How covariance patterns of phenotypes change during development is
 fundamental for a broader understanding of evolution. There is compelling
 evidence that mammalian cranium covariance patterns change during
 ontogeny. However, it is unclear to what extent variation in covariance
 patterns during ontogeny can impact the response to selection. To tackle
 this question we explored: i) the extent to which covariance patterns
 change during postnatal ontogeny; ii) in which ontogenetic stages
 covariance patterns differ the most, and iii) the extent to which the
 phenotypic covariance pattern at different ontogenetic stages can be
 explained by the same processes determining additive genetic covariance.
 We sampled postnatal ontogenetic series for both marsupials, and
 placentals. Within each ontogenetic series, we compared covariance
 matrices (P-matrices) at different ontogenetic stages. Furthermore, we
 compared these P-matrices to two target matrices [adult P-matrix and an
 additive genetic covariance matrix (G-matrix)]. Our results show that for
 all ontogenetic series, covariance patterns from weaning onward are
 conserved and probably shaped by the same processes determining the
 G-matrix. We conclude that irrespective of eventual differences in how
 selection operates during most of postnatal ontogeny, the net response to
 such pressures will probably not be affected by ontogenetic differences in
 the covariance pattern.
description: The traits are 35 linear distances derived from the 3D
 coordinates of 32 homologous landmarks measured on all specimens using a
 3D digitizer. All specimens were measured with the same instrument
 (Microscribe MX; Immersion Corporation, San Jose, California) with the
 exception of adult <em>Sapajus</em> that were measured with a
 3Draw digitizer (Polhemus Inc., Colchester, Vermont).
DOI: 10.5061/dryad.1g1jwsv14
title: Phenotypic plasticity in desiccation physiology of closely related, range restricted and broadly distributed fruit fly species

description: 1. Variation in geographic range size among closely related species may
 result from differences in physiological traits, such as desiccation
 tolerance, that enable these species to interact with their environment or
 adapt to new surroundings. 2. We tested the hypothesis that insect species
 with a broader geographic range have either a higher basal desiccation
 tolerance or mount a more plastic response than more narrowly distributed
 species by exposing four fruit fly species (Ceratitis capitata, Ceratitis
 rosa, Ceratitis cosyra and Ceratitis podocarpi) to one of three
 acclimation treatments (control: standard relative humidity and
 temperature; desiccation: standard temperature and low humidity; and
 temperature: low relative humidity and high temperature) and measuring
 metabolic rate, activity, water loss rates and survival. 3. The targeted
 physiological responses differed between species and acclimation
 treatments. Survival of the widely distributed C.
 capitata improved by up to 43% after short term exposure to high
 temperature and desiccation (35°C; 0% RH) treatment, while survival in the
 more narrowly distributed species only improved by 4-30% after a
 desiccation treatment (25°C; 0% RH). 4. Less water was lost by broadly
 distributed C. capitata through excretion after both
 high temperature and desiccation treatments, but only activity and
 respiratory water loss were reduced after the temperature treatment, and
 total water loss and cuticular water loss declined after the desiccation
 treatment. The narrowly distributed C. rosa also lost
 less water through excretion after both acclimation treatments but showed
 reduced cuticular and respiratory water loss only after desiccation. While
 basal tolerance in C. cosyra was high, acclimation
 responses in this species and C. podocarpi were
 insignificant in that they did not produce a measurable survival benefit.
 5. Broadly distributed species successfully employed unique combinations
 of physiological strategies, with some having highly flexible responses to
 stressful environmental conditions, which ultimately results in beneficial
 acclimation to enhance survival during dry conditions. By contrast, range
 restricted species showed limited responses to desiccation stress.
 Flexible desiccation responses likely contribute to species geographic
 ranges in changing climate conditions.