cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7r61gp6
title: Data from: NDVI is not reliable as a surrogate of forage abundance for a large herbivore in tropical forest habitat

description: Remotely-sensed vegetation indices are increasingly being used in wildlife
 studies but field-based support for their utility as a measure of forage
 availability come largely from open-canopy habitats. We assessed whether
 normalized difference vegetation index (NDVI) represents forage
 availability for Asian elephants in a southern Indian tropical forest. We
 found that the number of food species was a small percentage of all plant
 species. NDVI was not a good measure of food abundance in any vegetation
 category partly because of (a) small to moderate proportional abundances
 of food species relative to the total abundance of all species in that
 category (herbs and shrubs), (b) abundant overstorey vegetation resulting
 in low correlations between NDVI and food abundance, despite a high
 proportional abundance of food species and a concordance between total
 abundance and food species abundance (graminoids), and (c) the relevant
 variables measured and important as food at the ground level (count and
 GBH) not being related to primary productivity (trees and recruits). NDVI
 had a negative relationship with the total abundance of graminoids, which
 represent a bulk of elephant and other herbivore diet, because of negative
 interaction with other vegetation and canopy cover that positively
 explained NDVI. Spatially interpolated total graminoid abundance modelled
 from field data outperformed NDVI in predicting total graminoid abundance,
 although interpolation models of food graminoid abundance were not
 satisfactory. Our results reject the utility of NDVI in mapping elephant
 forage abundance in tropical forests, a finding that has implications for
 studies of other herbivores also.
description: Archive_data_NDVI_paper
DOI: 10.5061/dryad.4b866r7
title: Data from: Predator co-evolution and prey trait variability determine species coexistence

description: Predation is one of the key ecological mechanisms allowing species
 coexistence and influencing biological diversity. However, ecological
 processes are subject to contemporary evolutionary change, and the degree
 to which predation affects diversity ultimately depends on the interplay
 between evolution and ecology. Furthermore, ecological interactions that
 influence species co-existence can be altered by reciprocal co-evolution
 especially in the case of antagonistic interactions such as predation or
 parasitism. Here we used an experimental evolution approach to test for
 the role of initial trait variation in the prey population and
 co-evolutionary history of the predator in the ecological dynamics of a
 two-species bacterial community predated by a ciliate. We found that
 initial trait variation both at the bacterial and ciliate level enhanced
 species coexistence, and that subsequent trait evolutionary trajectories
 depended on the initial genetic diversity present in the population. Our
 findings provide further support to the notion that the ecology-centric
 view of diversity maintenance must be reinvestigated in light of recent
 findings in the field of eco-evolutionary dynamics.
description: Data from: Evolutionary
 contribution to coexistence of competitors in microbial food
 websScheuerl
 data.zip
DOI: 10.5061/dryad.gc7qf50
title: Data from: The role of partial incubation and egg repositioning within the clutch in hatching asynchrony and subsequent effects on breeding success

description: The main mechanism to achieve hatching asynchrony (HA) for incubating
 birds is to start heating the eggs before clutch completion. This might be
 achieved through partial incubation and/or early incubation. Even in the
 absence of incubation behaviour during the laying phase, clutches still
 experience a certain degree of asynchrony. Recent studies have shown that
 eggs located in the centre of the nest receive more heat than peripheral
 ones during incubation. Since eggs receiving more heat would develop
 faster, we hypothesised that HA should be shorter in nests where eggs were
 moved homogeneously along the centre-periphery space during incubation
 compared to those nests where eggs repeatedly remained in the same
 locations, either centrally or peripherally. We explored the relative
 roles of egg repositioning and partial incubation in determining HA in
 wild birds by (1) removing eggs from 20 Great Tit Parus major nests on day
 of laying and replacing them with fake eggs to avoid partial incubation,
 and returning them when full incubation began; (2) monitoring twice a day
 the position of each individually marked egg relative to the clutch centre
 during incubation, and estimating the coefficient of variation of the
 distances (CVdistance); (3) determining HA in each nest. Preventing
 partial incubation reduced HA by 51% days in experimental nests. It also
 caused negative effects for the incubating females (lengthening the full
 incubation period) and positive effects for the brood (increasing fledging
 success). However, our hypothesis about the role of egg repositioning on
 HA was not supported: all the females moved the eggs with remarkable
 consistency, generally attaining a CVdistance around 33%, and it was not
 related to the HA experienced. We therefore conclude that partial
 incubation is an important factor regulating HA, and females compensate
 for the potential effects of differential heating by moving the eggs
 homogeneously within the clutch.
description: Breeding parameters and
 egg positions1. Breed Data tab, 2.
 Nestling Data tab, 3. Egg Data tab, 4. Egg distances
 tabEggrepositioning.xlsx
DOI: 10.5061/dryad.0cb693v
title: Data from: Stage- and thermal-specific genetic architecture for preadult viability in natural populations of Drosophila melanogaster

description: Studying the processes affecting variation for preadult viability is
 essential to understand the evolutionary trajectories followed by natural
 populations. This task requires focusing on the complex nature of the
 phenotype-genotype relationship by taking into account usually neglected
 aspects of the phenotype and recognizing the modularity between different
 ontogenetic stages. Here we describe phenotypic variability for viability
 during the larval and pupal stages in lines derived from three natural
 populations of Drosophila melanogaster, as well as the variability for
 phenotypic plasticity and canalization at two different rearing
 temperatures. The observed phenotypic differences between populations can
 be attributed both to adaptation to environmental conditions and lack of
 gene flow between them. According to our results, different aspects of the
 phenotype (means, plasticity, canalization, plasticity of canalization)
 are affected by different genetic bases underlying changes in viability in
 a stage- and environment-specific manner. These findings explain the
 generalized maintenance of genetic variability for this fitness trait.
description: Preadult viability
 dataSheet 1. Means by Line
 and Temperature for the three populations, Sheet 2. Means by replicate,
 Sheet 3. Variance components, Sheet 4. Phenotypic
 plasticitymeansbyline.xls
DOI: 10.5061/dryad.4sm0dq1
title: Data from: Distracted decision-makers: ship noise and predation risk change shell choice in hermit crabs

description: Human induced rapid environmental change such as noise pollution alters
 the ability of animals to integrate information cues. Many studies focus
 on how noise impacts single sensory channels but in reality animals rely
 on multi-modal sources of information. In this study, we investigated the
 effect of anthropogenic noise and the visual presence of a predator on
 tactile information gathering during gastropod shell assessment in the
 European hermit crab Pagurus bernhardus. For hermit crabs, empty gastropod
 shells are a crucial resource affecting growth, reproduction and survival.
 We measured shell assessment behavior and manipulated (i) the shell size
 (50% or 80% of the optimal), (ii) sound condition (ship or ambient) and
 (iii) visual predator cue (absence/ presence). Overall we found that crabs
 were less likely to accept an optimal shell in the presence of ship noise,
 suggesting that exposure to ship noise disrupted the information gathering
 ability of the crabs. We also found a significant interaction between
 noise, predator presence and shell size on the mean duration for the final
 decision to accept or reject the optimal shell. Hermit crabs in 50% shells
 took less time for their final decision when exposed to both ship noise
 and predator cue while crabs in 80% shells showed shorter decision time
 only when the predator cue was absent. Our results indicate that
 anthropogenic noise can interact with predation threat and resource
 quality to change resource acquisition, suggesting that noise pollution
 can disrupt behavior in a non-additive way, by disrupting information use
 across multiple sensory channels.
description: Hermit crab shell
 assessment under noiseshell_noise.xlsx
DOI: 10.5061/dryad.g2t6204
title: Data from: Impacts of dead-wood manipulation on the biodiversity of temperate and boreal forests - A systematic review

description: Dead wood (DW) provides critical habitat for thousands of species in
 forests, but its amount, quality and diversity have been heavily reduced
 by forestry. Therefore, interventions aiming to increase DW might be
 necessary to support its associated biodiversity, even in protected
 forests, which may be former production forests. Our aim was to synthesise
 the current state of knowledge drawn from replicated experimental studies
 into solid quantitative evidence of the effects of DW manipulation on
 forest biodiversity, with a focus on protected forests. We conducted a
 full systematic review of effects of DW manipulation on forest
 biodiversity in boreal and temperate regions. We included three
 intervention types: creation of DW from live trees at the site, addition
 of DW from outside the site, and prescribed burning. Outcomes included
 abundance and species richness of saproxylic insects, ground insects,
 wood‐inhabiting fungi, lichens, reptiles and cavity‐nesting birds. In
 total, we included 91 studies, 37 of which were used in meta‐analyses.
 Although meta‐analysis outcomes were heterogeneous, they showed that
 increasing the amount of DW (“DW enrichment”) has positive effects on the
 abundance and richness of saproxylic insects and fungi. The positive
 effect on saproxylic pest insect abundance tended to be less than that on
 saproxylic insects in general. No significant effects were found for
 ground insects or cavity‐nesting birds. Although reviewed studies were
 mainly short‐term, our results support that management that increases DW
 amounts has the potential to increase the abundance of DW‐dependent
 species and, in most cases, also their species richness. Studies of
 burning showed positive effects on the abundance of saproxylic insects
 similar to those of other interventions, even though burning on average
 resulted in a smaller enrichment of DW amounts. Policy implications. The
 findings of the review suggest that manipulating dead wood can be an
 effective part of conservation management to support biodiversity in
 protected areas. The findings also indicate that the diversity of
 dead‐wood types is important, a mix of dead‐wood qualities should be
 favoured. Burning seems to be an effective method to increase biodiversity
 but to benefit cavity‐nesting birds, snag losses need to be minimised.
description: A narrative description
 of all included studies_Appendix ST6Here is meta data and
 information on all included studies summarised. Examples of available
 information are: experimental set-up, time elapsed since intervention,
 geopgraphical information, scale of study, focal species or relevant
 species Groups, change of dead Wood amounts and effetcs of
 intervention.Extracted data_Appendix
 ST2JPESandstromST2.xlsx
DOI: 10.5061/dryad.360b25r
title: Data from: The chemical basis of a signal of individual identity: Shell pigment concentrations track the unique appearance of Common Murre eggs

description: In group-living species with parental care, the accurate recognition of
 one’s own young is critical to fitness. Because discriminating offspring
 within a large colonial group may be challenging, progeny of colonial
 breeders often display familial or individual identity signals to elicit
 and receive costly parental provisions from their own parents. For
 instance, the Common Murre (or Common Guillemot: Uria aalge) is a
 colonially breeding seabird that does not build a nest and lays and
 incubates an egg with an individually unique appearance. How the shell’s
 physical and chemical properties generate this individual variability in
 coloration and maculation has not been studied in detail. Here, we
 quantified two characteristics of the avian-visible appearance of murre
 eggshells collected from the wild: background coloration spectra and
 maculation density. As predicted by the individual identity hypothesis,
 there was no statistical relationship between avian-perceivable shell
 background coloration and maculation density within the same eggs. In
 turn, variation in both sets of traits was statistically related to some
 of their physico-chemical properties, including shell thickness and
 concentrations of the eggshell pigments biliverdin and protoporphyrin IX.
 These results illustrate how individually unique eggshell appearances,
 suitable for identity signaling, can be generated by a small number of
 structural mechanisms.
description: HauberetalDataJRSI
 copyPigment Concentration
 and Reflectance Data of Murre Eggshells
DOI: 10.5061/dryad.5501rv4
title: Data from: No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods

description: Loss of sex and recombination is generally assumed to impede the
 effectiveness of purifying selection and to result in the accumulation of
 slightly deleterious mutations. Empirical evidence for this has come from
 several studies investigating mutational load in a small number of
 individual genes. However, recent whole transcriptome based studies have
 yielded inconsistent results, hence questioning the validity of the
 assumption of mutational meltdown in asexual populations. Here, we study
 the effectiveness of purifying selection in eight asexual hexapod lineages
 and their sexual relatives, as present in the 1K Insect Transcriptome
 Evolution (1KITE) project, covering eight hexapod groups. We analyse the
 accumulation of slightly deleterious nonsynonymous and synonymous point
 mutations in 99 single copy orthologue protein-coding loci shared among
 the investigated taxa. While accumulation rates of nonsynonymous mutations
 differed between genes and hexapod groups, we found no effect of
 reproductive mode on the effectiveness of purifying selection acting at
 nonsynonymous and synonymous sites. Although the setup of this study does
 not fully rule out nondetection of subtle effects, our data does not
 support the established consensus of asexual lineages undergoing
 ‘mutational meltdown’.
description: Supplementary_Archives
DOI: 10.5061/dryad.j482vf7
title: Data from: Life-history differences across latitude in common side blotched lizards (Uta stansburiana)

description: Life‐history strategies are known to shift with latitude in many species.
 While life‐history variation related to body size, reproductive
 investment, and behavior has been studied for years, another crucial
 life‐history component is the immune system, which can influence an
 animal's survival. We measured selected life‐history traits in
 side‐blotched lizards in southern Utah and Oregon in the field for two
 consecutive years and conducted a common‐garden experiment in the
 laboratory to determine how organisms from different latitudes optimize
 either immunity or reproduction. We observed lizards from southern
 populations, which are known to be shorter‐lived, had lower immune
 function during reproduction when compared to northern lizards in 2012,
 but the relationship reversed in the following year. Our laboratory study
 revealed that southern lizards healed cutaneous wounds faster and had
 higher microbiocidal ability when compared to their northern counterparts,
 but lost mass doing so. The northern lizards ate more than the southern
 ones and maintained their body mass. It is possible that northern lizards
 are better adapted to taking advantage of available food resources.
 Alternatively, southern lizards may have exhibited sickness behavior in
 response to an immune challenge or reacted more strongly to the stress of
 captivity. We found differences in life‐history strategies used by animals
 from different latitudes, and that these changes can shift within a
 population depending on the weather conditions of the year. Furthermore,
 when taken from the field and placed into a common‐garden environment,
 some of these differences in strategy appear to be intrinsic to the
 animals (i.e., whether they came from southern or northern populations).
description: latitude_dryad_dataLizard data used to compare latitudes
DOI: 10.4119/unibi/3013296
title: Data for Article "Expertise-dependent mental representation in chess: Evaluation and comparisons based on structural dimensional analysis-motoric"

description: All relevant data, a data dictionary to facilitate interpretation, the task code, and all instructions to participants for the Article "Expertise-dependent mental representation in chess: Evaluation and comparisons based on structural dimensional analysis-motoric".
DOI: 10.5061/dryad.hm6q64h
title: Data from: Predictors of nephrolithiasis, osteoporosis and mortality in primary hyperparathyroidism

description: Context: Primary Hyperparathyroidism (PHPT) has a prevalence of 0.86% and
 is associated with increased risk of nephrolithiasis and osteoporosis.
 PHPT may also be associated with an increased risk of cardiovascular
 disease and mortality. Objective: To identify risk factors for
 nephrolithiasis, osteoporosis and mortality in PHPT. Design: Retrospective
 cohort study. Setting: University teaching hospital. Patients: PHPT
 presenting between 2006 – 2014 (n = 611). Main outcome measures:
 Assessment of nephrolithiasis, osteoporosis and mortality. Results: 13.9%
 of PHPT patients had nephrolithiasis. Most had already documented stone
 disease and only 4.7% of asymptomatic patients screened for renal stones
 had calculi identified, not very dissimilar to the rate in the non-PHPT
 population. Younger age (P &lt; 0.001) and male gender (P = 0.003)
 were the only independent predictors of nephrolithiasis. 48.4% of patients
 with DXA data had osteoporosis (223/461). Older age (P &lt; 0.001),
 lower BMI (P = 0.002) and lower creatinine (P = 0.006) were independently
 associated with a diagnosis of osteoporosis. Higher PTH was independently
 associated with lower Z-score at the hip (P = 0.009), but otherwise
 calcium and PTH were not associated with lower Z-score. Mortality in PHPT
 was associated with older age (P &lt; 0.008), social deprivation (P =
 0.028) and adjusted calcium (P = 0.009) but not independently with PTH at
 diagnosis. Conclusions: Screening for nephrolithiasis has a low yield,
 particularly in lower risk patients. Osteoporosis is only minimally
 associated with biochemical indices of PHPT. Mortality is associated with
 higher calcium (and possibly vitamin D deficiency) but not PTH.
description: Supplementary
 materials
DOI: 10.5061/dryad.s027503
title: Data from: Genome-wide inference of somatic translocation events during potato dihaploid production

description: Potato (Solanum tuberosum L.) breeders often use dihaploids, which are 2×
 progeny derived from 4× autotetraploid parents. Dihaploids can be used in
 diploid crosses to introduce new genetic material into breeding germplasm
 that can be integrated into tetraploid breeding through the use of
 unreduced gametes in 4× by 2× crosses. Dihaploid potatoes are usually
 produced via pollination by haploid inducer lines known as in vitro
 pollinators (IVP). In vitro pollinator chromosomes are selectively
 degraded from initially full hybrid embryos, resulting in 2× seed. During
 this process, somatic translocation of IVP DNA may occur. In this study, a
 genome-wide approach was used to identify such events and other
 chromosome-scale abnormalities in a population of 95 dihaploids derived
 from a cross between potato cultivar Superior and the haploid inducing
 line IVP101. Most Superior dihaploids showed translocation rates of
 &lt;1% at 16,947,718 assayable sites, yet two dihaploids showed
 translocation rates of 1.86 and 1.60%. Allelic ratios at translocation
 sites suggested that most translocations occurred in individual cell
 lineages and were thus not present in all cells of the adult plants.
 Translocations were enriched in sites associated with high gene expression
 and H3K4 dimethylation and H4K5 acetylation, suggesting that they tend to
 occur in regions of open chromatin. The translocations likely result as a
 consequence of double-stranded break repair in the dihaploid genomes via
 homologous recombination during which IVP chromosomes are used as
 templates. Additionally, primary trisomy was observed in eight
 individuals. As the trisomic chromosomes were derived from Superior,
 meiotic nondisjunction may be common in potato.
description: vt_sup_all_introgressions.txtThis file contains somatic translocation positions inferred from a population of 95 dihaploid potato (Solanum tuberosum) lines derived from a cross between the cultivar Superior and the haploid inducer line IVP101. The columns contain the following information: CHROM: chromosome, POS: physical position, REF: reference allele, ALT: alternate allele, QUAL: SNP quality, superior_gdna.AD: Superior allele counts, ivp_101.AD: IVP101 allele counts, line: Superior dihaploid line, alleles: Superior dihaploid alleles