cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.98sf7m0mx
title: Increasing efficiency and reducing bias in the detection of seed-dispersal interactions based on mist-netted birds

description: Efficient and unbiased sampling of ecological interactions is essential to
 our understanding of the functions they mediate. Seed dispersal by
 frugivorous birds is a key mutualism for plant regeneration and community
 dynamics. Mist-netting is one of the most widely used methods to sample
 avian seed dispersal through the identification of seeds in droppings of
 captured birds kept inside cloth bags. However, birds may drop seeds on
 the ground before being extracted from the net, leading to a fraction of
 missing information due to ineffective sampling. Worryingly, this fraction
 could be unevenly distributed across bird and plant species, leading to
 sampling biases. Here, we assess the effectiveness of using a 1- m wide
 mesh below mist nets to sample seeds dropped by entangled birds. We used
 data from birds mist-netted during one-year-round. We sampled nearly 50%
 of interaction events and 75% of dispersed seeds on the mesh band below
 the mist nets (i.e. lost information without this optimization). The
 proportion of seeds sampled on the mesh bands was not evenly distributed
 among bird species but strongly related to bird size, ranging from 57-63%
 in warblers to 84-94% in thrushes. Moreover, the proportion of seeds
 sampled on the mesh was negatively related to seed size, although this
 relationship was weaker. We also evaluated accumulation curves of species
 and pairwise interactions with increasing sampling effort, both with and
 without using the mesh bands. The number of seed species sampled increased
 by 21% when using the mesh bands and the number of pairwise interactions
 by 36%. Our findings provide strong evidence on how inefficient and biased
 traditional mist-netting can be for sampling community-wide seed-dispersal
 interactions. We thus urge the use of mesh bands in future studies to
 increase sampling effectiveness and avoid biases, which will ultimately
 improve our understanding of the seed dispersal function.
DOI: 10.5061/dryad.b8gtht7gc
title: Data corresponding to: Evaluation of sequencing and PCR-based methods for the quantification of the viral genome formula

description: Viruses show great diversity in their genome organisation. Multipartite
 viruses package their genome segments into separate particles, most or all
 of which are required to initiate infection in the host cell. The benefits
 of such seemingly inefficient genome organization are not well understood.
 One hypothesised benefit of multipartition is that it allows for flexible
 changes in gene expression by altering the frequency of each genome
 segment in different environments, such as encountering different host
 species. The ratio of the frequency of  segments is termed the
 genome formula (GF). Thus far, formal studies quantifying the GF have been
 performed for well-characterised virus-host systems in experimental
 settings using RT-qPCR. However, to understand GF variation in natural
 populations or novel virus-host systems, a comparison of several methods
 for GF estimation including high-throughput sequencing (HTS) based methods
 is needed. Currently, it is unclear how HTS-methods compare a golden
 standard, such as RT-qPCR. Here we show a comparison of multiple GF
 quantification methods (RT-qPCR, RT-digital PCR, Illumina RNAseq and
 Nanopore direct RNA sequencing) using three host plants (Nicotiana
 tabacum, Nicotiana benthamiana, and Chenopodium quinoa) infected with
 cucumber mosaic virus (CMV), a tripartite RNA virus. Our results show that
 all methods give roughly similar results, though there is a significant
 method effect on genome formula estimates. While the RT-qPCR and RT-dPCR
 GF estimates are congruent, the GF estimates from HTS methods deviate from
 those found with PCR. Our findings emphasise the need to tailor the GF
 quantification method to the experimental aim, and highlight that it may
 not be possible to compare HTS and PCR-based methods directly. The
 difference in results between PCR-based methods and HTS highlights that
 the choice of quantification technique is not trivial.
DOI: 10.5061/dryad.fxpnvx0w4
title: Data for: Fast adjustment of POLS to food quality

description: The pace-of-life syndrome hypothesis provides a framework for the adaptive
 integration of behaviour, physiology and life history at between and
 within species. It suggests that behaviours involving a risk of death or
 injury should co-vary with a higher allocation to fast reproduction.
 Empirical support for this hypothesis is mixed, presumably because
 important influencing factors such as environmental variation, are usually
 neglected. By experimentally manipulating the food quality of wild mice
 living under semi-natural conditions for three generations, we show that
 individuals adjust their life history strategies and risk-taking
 behaviours as well as trait covariation (Nindividuals = 1442). These
 phenotypic differences are correlated to differences in transcriptomic
 gene expression of primarily metabolic processes in the liver while no
 changes in gene frequencies occurred. Our discussion emphasizes the need
 to integrate the role of environmental conditions and phenotypic
 plasticity in shaping relationships among behaviour, physiology and
 life-history in response to changing environmental conditions.
description: The dataset contains behavioural data (Open Field and Novel
 Environment) for house mice caught and tested across four generations.
 Four semi-natural enclosures were run in parallel, each two receiving
 high-quality food (HQ) and two receiving standard mouse diet
 (SQ). In addition, the data contain life history data
 of individual fecundity rates and generations times for all mice being
 born within these four generations. Lastly, the data
 contain an overview and individual reports for transcriptomic data
 obtained from each 5 males and 5 females per enclosure per
 generation.
DOI: 10.5061/dryad.mkkwh713f
title: Gray wolf packs and human-caused wolf mortality

description: Gray wolves (Canis lupus) are group-living carnivores that travel over
 large areas and are one of the most controversial species in North
 America. Gray wolf management over the last century has ranged
 from eradication by nearly any means to preservation under the Endangered
 Species Act to state-managed which often includes limited hunting and, in
 some areas, population reduction. Management decisions are complicated by
 transboundary movements of wildlife, especially when the bordering
 agencies have disparate goals or mandates. This data is specific
 to gray wolves and packs using five National Park Service (NPS) units
 (years of data): Denali National Park and Preserve (33 years), Grand Teton
 National Park (23 years), Voyageurs National Park (12 years), Yellowstone
 National Park (27 years), and Yukon-Charley Rivers National Preserve (23
 years). This dataset features two measures of gray wolf
 biological processes, pack persistence and reproduction, and was used to
 determine the impacts of anthropogenic mortality on the pack. We
 examined persistence and reproduction at the pack level given known wolf
 mortalities and pack sizes.
description: All data were collected by NPS staff and partners by deploying
 radio collars on each wolf pack using the National Park unit. Wolf packs
 were tracked aerially several times per month to determine persistence
 through time. Pack size was recorded during tracking. For each biological
 year a pack persisted, they were given a pack-year entry. Reproduction was
 determined through localization around a den or visual of at least one pup
 during the biological year. Human-caused mortalities were recorded and
 confirmed with necropsies and other wildlife official reports and then
 assigned to a specific pack-year.
DOI: 10.5061/dryad.73n5tb30z
title: Data: Sex-specific effects of capital resources on reproductive timing and success in red squirrels

description: Reproduction is an energetically expensive activity for both sexes.
 However, if males and females differ in their annual timing of
 reproduction, such that peak investment for one sex occurs during a more
 resource-limited period, there is an opportunity for sex-specific
 selection to act on the acquisition of energetic resources. Both male and
 female North American red squirrels (Tamiasciurus hudsonicus) cache
 conifer cones, although males typically have larger caches than females.
 Peak energetic investment in reproduction occurs for males during the
 mating season in winter and early spring (when squirrels rely almost
 exclusively on cached resources) and for females during lactation (which
 can align with fresh food availability). We provide evidence that suggests
 sex differences in cache size are likely driven by a stronger positive
 connection between cached resources and components of fitness for males
 than for females. Specifically, males with larger caches have greater
 siring success than males with smaller caches, whereas for females, only
 early breeding females experience a positive effect of cache size on the
 number of recruits produced. We also show that males sire pups and females
 give birth earlier in the year if they have larger caches compared with
 squirrels of the same sex with smaller caches. Sexual selection can thus
 extend beyond traits directly connected to mating behavior, and can act on
 traits related to acquiring resources needed to fuel reproduction that are
 expressed months or years in advance of breeding efforts.
description: See detailed methods in Haines et al. Behavioral Ecology and
 Sociobiology. Data were collected in conjunction with the Kluane Red
 Squirrel Project (KRSP) in the southwest Yukon, Canada.
description: Data files are in .csv format and README files are in rich text
 format.
DOI: 10.5061/dryad.vt4b8gtvs
title: Data from: Foraging history of individual elephants using DNA metabarcoding

description: Individual animals should adjust diets according to food availability. We
 used DNA metabarcoding to construct individual-level dietary timeseries
 for elephants from two family groups in
 Kenya varying in habitat use, social position, and
 reproductive status. We detected at least 367 dietary plant taxa,
 with up to 137 unique plant sequences in one fecal sample. Results matched
 well-established trends: elephants tended to eat more grass when it rained
 and other plants when dry. Nested within these switches from ‘grazing’ to
 ‘browsing’ strategies, dietary DNA revealed seasonal
 shifts in food richness, composition, and overlap
 between individuals. Elephants of both families converged on relatively
 cohesive diets in dry seasons but varied in their maintenance of cohesion
 during wet seasons. Dietary cohesion throughout the
 timeseries of the
 subdominant ‘Artists’ family was stronger and
 more consistently positive compared to
 the dominant ‘Royals’ family. The greater degree of
 individuality within the dominant family’s timeseries could reflect more
 divergent nutritional requirements associated with calf-dependency and/or
 priority access to preferred habitats. Whereas theory predicts
 that individuals should specialize on different foods under resource
 scarcity, our data suggest family bonds may promote cohesion and foster
 the emergence of diverse feeding cultures reflecting links between social
 behavior and nutrition.
DOI: 10.5281/zenodo.18375340
title: Experimental investigation of a highly-loaded half-journal bearing

description: Dataset from experimental rig is presented for a half-journal bearing operating under highly loaded, well-controlled hydrodynamic lubrication conditions relevant to turbomachinery. The apparatus combines pressure measurement in the film, distributed temperature measurement in the shaft and bush, and ultrasonic film thickness measurements that map the circumferential film height profile across the lubrication region. Experiments are reported for normal loads of 5–20 kN and shaft speeds of 1000–4000 rpm with controlled oil supply conditions.
DOI: 10.5281/zenodo.18375341
title: Experimental investigation of a highly-loaded half-journal bearing

description: Dataset from experimental rig is presented for a half-journal bearing operating under highly loaded, well-controlled hydrodynamic lubrication conditions relevant to turbomachinery. The apparatus combines pressure measurement in the film, distributed temperature measurement in the shaft and bush, and ultrasonic film thickness measurements that map the circumferential film height profile across the lubrication region. Experiments are reported for normal loads of 5–20 kN and shaft speeds of 1000–4000 rpm with controlled oil supply conditions.
DOI: 10.5061/dryad.931zcrjp9
title: Allocation of Salamandra auriculata Holbrook, 1838, with a new species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Atlantic Coastal Plain

description: Most swamp-dwelling dusky salamanders of the genus Desmognathus from the
 Coastal Plain were long treated as a single species (Desmognathus
 auriculatus) ranging from east Texas to southeastern Virginia. This taxon
 concept was based on the name Salamandra auriculata Holbrook, 1838 with
 type locality Riceboro, Liberty County, Georgia and a type series that
 could not be located by later authors. Recent workers have been unable to
 locate or verify swamp-dwelling populations from east Texas and western
 Louisiana, which appear to be extirpated and may not have represented a
 distinct taxon from co-occurring lineages of D. conanti. Recent molecular
 phylogenies have supported at least four distinct species-level taxa
 within D. auriculatus. Populations from the Gulf Coastal Plain in eastern
 Louisiana, Mississippi, and southwestern Alabama were recently described
 as D. valentinei Means, Lamb, and Bernardo, 2017 and D. pascagoula Pyron,
 O’Connell, Lamb, and Beamer, 2022. This leaves two remaining species-level
 lineages with uncertain taxonomy and nomenclature: D. auriculatus A
 (Alabama, Florida, and Georgia), and D. auriculatus B/C (Georgia, South
 Carolina, and North Carolina), both of which occur near the type locality.
 We recently located a specimen at the Muséum national d’Histoire naturelle
 in Paris (MNHN 0.4675) that we concluded is one of Holbrook’s syntypes and
 designated it as the lectotype, but without allocation. Here, we use
 linear morphometrics to confidently allocate it to D. auriculatus A,
 bolstered by examination of three historical topotypic collections. This
 requires a new name for D. auriculatus B/C, which we describe as D. valtos
 sp. nov. (suggested common name: Carolina Swamp Dusky Salamander) from
 Otter Creek, Craven County, North Carolina. Other related and sympatric
 species of Desmognathus remain to be described from the Atlantic Coastal
 Plain and adjacent Piedmont of the southeastern United States.  
description: Specimen measurements for all morphometric analyses to 0.01mm
 precision (log-transformed), with species assignment and locality
 data.
description: CSV
DOI: 10.5061/dryad.s1rn8pkc2
title: Data from: Comparative assessment of a novel fan box trap for collecting Anopheles farauti and culicine mosquitoes alive in tropical north Queensland, Australia

description: During preliminary mosquito surveys at Cowley Beach Training Area in north
 Queensland, Australia, it was found that the utility of the standard
 encephalitis virus surveillance (EVS) trap for collecting the malaria
 vector Anopheles farauti (Laveran) adults was compromised by the
 harsh tropical conditions. With the aim of increasing the survival rate of
 mosquitoes, we designed a downdraft fan box trap (FBT) that incorporated a
 screened fan at the bottom of the trap, so mosquitoes did not have to pass
 through a fan. The FBT was tested against the EVS and Centers for Disease
 Control (CDC) light traps, where mosquitoes do pass through a fan, and a
 nonpowered passive box trap (PBT). We conducted four trials to compare the
 quantity and survival of An. farauti and culicine mosquitoes were
 collected in these traps. Although not significant, the FBT collected more
 An. farauti than the EVS trap and PBT and significantly less An. farauti
 than the CDC light trap. However, the FBT improved on the CDC light trap
 in terms of the survival of An. farauti adults collected, with a
 significantly higher percentage alive in the FBT (74.6%) than in the CDC
 light trap (27.5%). Thus, although the FBT did not collect as many
 anophelines as the CDC, it proved to be superior to current trap systems
 for collecting large numbers of live and relatively undamaged mosquitoes.
 Therefore, it is recommended that FBTs be used for collecting An. farauti
 adults in northern Australia, especially when high survival and sample
 quality are important.
description: Mosquito trapping experiments at Cowly Beach north
 Queensland.
description: # Comparative assessment of a novel fan box trap for collecting Anopheles
 farauti and culicine mosquitoes alive in tropical north Queensland,
 Australia ## Description
 of the data and file structure File contains an Excel spreadsheet with the
 raw data for the mosquito trap comparisons at the Cowley Beach Training
 Area (CBTA) in Queensland Australia
 (17° 41' 35" S, 146° 6' 40" E) in 2015 Data includes
 mosquito trap collection comparisons for anophelines and culicines. Dates
 and collection numbers of the trapping experiment trials are presented.
 Traps included the Passive Box Trap (PBT), the Fan Box Trap (FBT) and the
 Encephalitis Virus Surveillance trap (EVS). Mosquito collection data are
 provided in three Excel sheets detailed below.  Mosquito collection
 comparison:   1\. Sheet 1: Mosquito trap collection comparisons. Trial 1
 is EVS vs PBT and Trial 2 is EVS vs FBT 2\. Sheet 2: Mosquito trap
 collection comparisons for FBT, EVS and CDC traps over multiple sites 3\.
 Sheet 3: Mosquito trap collection quality comparisons FBT, EVS and CDC
 traps.
DOI: 10.5061/dryad.rr4xgxdc2
title: 2021 Soil and nutrient loss monitoring data of Sunjiagou sub-watershed

description: This dataset observes soil and nutrient loss from runoff plots at a
 monitoring station in the black soil area in 2021. The details of the
 runoff plots are as follows: A1: 3°, smooth monopoly, planted with
 soybeans; A2: 3°, cross monopoly, planted with soybeans; A3: 3°, bare
 ground; B1: 5°, smooth monopoly, planted with soybeans; B2: 5°, cross
 monopoly, planted with soybeans and planted with purple acacia as a plant
 hedge; B3: 5°, bare ground.
DOI: 10.5061/dryad.70rxwdc1v
title: Urbanisation impacts plumage colouration in a songbird across Europe: evidence from a correlational, experimental, and meta-analytical approach

description: Urbanisation is increasing rapidly across the globe, transforming
 landscapes, presenting organisms with novel challenges, shaping
 phenotypes, and impacting fitness. Urban individuals are claimed to have
 duller tones in carotenoid-based traits, the so-called ″urban dullness″
 phenomenon. However, at the intra-specific level, this generalisation is
 surprisingly inconsistent and often based on examples from few populations
 or a limited geographic area. Here, combining correlational, experimental,
 and meta-analytical results from a common songbird, the great tit (Parus
 major), we investigated carotenoid-based plumage coloration in urban and
 forest populations across Europe. We find that, as predicted, urban
 individuals are paler than forest individuals, although there are large
 population-specific differences in the magnitude of the urban-forest
 contrast in colouration. Our meta-analysis indicates a non-significant
 effect of environmental pollution on carotenoid-based plumage for the
 species, suggesting that the observed differences across urban populations
 are not only driven by pollution. Finally, using one region as an example
 (Malmö, Sweden), we reveal population-specific processes behind plumage
 colouration differences, which are likely the result of variation in the
 spatial and temporal distribution of carotenoid-rich resources in
 anthropogenic environments. Our results provide convincing evidence for
 consistency on the “urban dullness” phenomenon but highlight that its
 magnitude depends on local urban characteristics.
description: Great tit plumage carotenoid colouration (chroma and brightness)
 measurements from 5 urban/forest population pairs, in addition to
 cross-sectional data, a cross-fostering experiment for one urban/forest
 population and a meta-analysis on the effects of anthropogenic stressors
 (urbanisation and pollution) on great tit plumage colouration.
DOI: 10.5061/dryad.ksn02v77n
title: Developmental bias in the evolution and plasticity of beetle horn shape

description: The degree to which developmental systems bias the phenotypic effects of
 environmental and genetic variation, and how these biases affect
 evolution, is subject to much debate. Here, we assess whether
 developmental variability in horn shape aligns with the phenotypic effects
 of plasticity and evolutionary divergence, yielding three salient results.
 First, we find that most pathways previously shown to regulate horn length
 also affect shape. Second, we find that the phenotypic effects of
 manipulating divergent developmental pathways are correlated with each
 other as well as multivariate fluctuating asymmetry – a measure of
 developmental variability. Third, these effects further aligned with
 thermal plasticity, population differences, and macroevolutionary
 divergence between sister taxa and more distantly related species.
 Collectively, our results support the hypothesis that changes in horn
 shape —whether brought about by environmentally plastic responses,
 functional manipulations, or evolutionary divergences— converge along
 ‘developmental lines of least resistance’, i.e., are biased by the
 developmental system underpinning horn shape.
description: To investigate the evolution
 and development of horn shape, we used a two-dimensional geometric
 morphometric approach. For each of the data sets described below
 (fluctuating asymmetry, functional genetic manipulations, environmental
 plasticity, and evolutionary divergence), we took pictures of beetle head
 horns using a digital camera (Scion) mounted on a Leica MZ-16
 stereomicroscope. The final data set included measurements for several
 wild-caught and laboratory-reared populations of
 <em>Onthophagus</em> <em>taurus</em>, one
 wild-caught population of the closely related <em>Onthophagus
 illyricus</em>, as well as laboratory-reared individuals of the more
 distantly related <em>Digitonthophagus</em>
 <em>gazella</em>. TpsDig2 was used to quantify horn shape using 4
 landmarks and 26 semi-landmarks. The landmarks of all 1,044 specimens were
 subjected simultaneously to a Procrustes analysis in the R-package
 geomorph. The position of
 semi-landmarks was optimized by minimizing bending energy. Centroid size
 was extracted as a shape-independent measure of overall structural
 size. See Rohner et al.
 (doi: 10.1098/rspb.2022.1441) for furhter
 information.
description: Raw data is supplied as .txt file. Code is
 supplied as an R script. The packages necessary to run the code and the
 respecive versions are indicated in the script.
DOI: 10.15468/dl.6jdt4k
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eligmocarpus cynometroides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 87 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003271-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.