cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qd504d9
title: Data from: Maasai pastoralists kill lions in retaliation for depredation of livestock by lions

description: The borders of national parks in Kenya are hotspots for human–wildlife
 conflict. The deliberate killing of lions by Maasai pastoralists is
 illegal, but continues despite mitigation attempts. Currently, there is a
 somewhat pervasive opinion, within the human–wildlife conflict literature,
 that lions are killed by Maasai people either as cultural ceremony or
 indiscriminately in response to the loss of livestock. We reconsider the
 indiscriminate reputation of lion‐killing, using a combination of
 structured dialogue and quantitative analysis. Focus group discussions
 with Maasai pastoralists in three different pastoral regions, performed by
 in‐country experts, minimized the risk of cross‐cultural misinterpretation
 through a platform of shared Kenyan heritage. In our survey of 213 Maasai
 pastoralist communities, we found universal agreement that humans and
 lions should coexist in Kenya. Maasai communities distinguished among
 drought, disease, theft, loss and depredation as drivers of livestock
 losses. Maasai also distinguished among predatory species that take their
 livestock. The only cause of livestock loss that provoked increased
 killing of lions, was depredation by lions. Lion‐killing was not provoked
 by other predatory species. We found regional variation in the baseline
 probability of lion‐killing, and discuss the sources of this variation.
 The probability of lion‐killing increases as an act of retribution for
 predation of livestock that discriminates among species of carnivore.
 This, coupled with universal acceptance of coexistence between lions and
 Maasai pastoralists, should guide mitigation strategies for human–wildlife
 interactions in Kenya and beyond.
description: Ontiri et al 2018 Lion
 KillingQuantitative results of
 213 focus group discussions, describing: 1. Numeric identifier for focus
 group community; 2. Number of livestock lost to drought; 3. livestock lost
 to disease; 4. livestock lost to predators; 5. livestock lost to theft; 6.
 livestock lost in the wild (to unknown cause); 7. admission of number of
 lions speared; 8. admission of number of lions poisoned; 9. whether
 livestock taken by lion; 10. taken by cheetah; 11. taken by leopard; 12.
 taken by hyena; 13. taken by dog; 14. taken by jackal; 15 region of Kenya
 in which focus group took place.
DOI: 10.5061/dryad.7j0c8dm
title: Data from: Molecular diet analysis finds an insectivorous desert bat community dominated by resource sharing despite diverse echolocation and foraging strategies

description: Interspecific differences in traits can alter the relative niche use of
 species within the same environment. Bats provide an excellent model to
 study niche use because they have a wide variety of behavioural, acoustic
 and morphological traits that may lead to multi-species, functional
 groups. Predatory bats have been classified by their foraging location
 (edge, clutter, open space), ability to aerial hawk and/or substrate glean
 prey and echolocation call design and flexibility, all of which may
 dictate their diet. For example, high frequency, broadband calls do not
 travel far but offer high object resolution while high intensity, low
 frequency calls travel further but provide lower resolution. Because these
 behaviours can be flexible four behavioural categories have been proposed:
 (1) gleaning, (2) behaviourally flexible (gleaning and hawking), (3)
 clutter tolerant hawking, and (4) open space hawking. Recent studies of
 diet in bats use molecular tools to identify prey but mainly focus on one
 or two species in isolation and few studies provide evidence for
 substantial differences in prey use despite the many behavioural, acoustic
 and morphological differences. Here we analyse the diet of 17 sympatric
 species in the Chihuahuan desert and test the hypothesis that peak
 echolocation frequency and behavioural categories are linked to
 differences in diet. We find no significant correlation between dietary
 richness and echolocation frequency (though it spanned close to 100kHz
 across species). However, our data suggest that behaviourally flexible
 bats that use gleaning and aerial hawking have the broadest diets and are
 the most differentiated from clutter-tolerant aerial hawking species.
description: ALLAll sequence data
 analysed in this manuscript. Primers and adapters have been removed,
 sequences have been collapsed into haplotypes and singleton sequences have
 been removed. Sequences have been re-named to indicate species and
 individual bat from which the sample originated for exampe AP1 is
 Antrozous pallidus individual 1. To use this data please contact the
 corresponding author for additional details.
DOI: 10.5061/dryad.p6m33p3
title: Data from: Higher nest predation favors rapid fledging at the cost of plumage quality in nestling birds

description: High predation risk can favor rapid offspring development at the expense
 of offspring quality. Impacts of rapid development on phenotypic quality
 should be most readily expressed in traits that minimize fitness costs. We
 hypothesize that ephemeral traits that are replaced or repaired over a
 short period of life might express trade-offs in quality as a result of
 rapid development more strongly than traits used for life. We explored
 this idea using plumage quality in nestling body feathers, an ephemeral
 trait. We found a strong trade-off whereby nestlings that spend less time
 in the nest produced lower quality plumage with less dense barbs relative
 to adults across 123 temperate and tropical species. Using a subset of
 these species (n=67), we found that variation in the risk of nest
 predation explained additional variation in plumage quality beyond
 development time. Ultimately, the fitness costs of a poor quality
 ephemeral trait, like nestling body feathers, may be outweighed by the
 fitness benefits of shorter development times that reduce predation risk.
 At the same time, reduced resource allocation to traits with small fitness
 costs, like ephemeral traits, may ameliorate resource constraints from
 rapid development on traits with larger fitness impacts.
description: Callan et al_data file
 with references
DOI: 10.5061/dryad.8g38172
title: Data from: Fighting in rounds: males of a Neotropical cricket switch assessment strategies during contests

description: How animals decide to withdraw from contests is central to understand the
 evolution of fighting behavior. Game theory models suggest two major types
 of decision criteria: 1) self-assessment, where individuals withdraw when
 they reach a cost-threshold determined by their own fighting ability that
 may or may not be affected by injuries, or 2) mutual assessment, where the
 decision is based on information about the relative fighting ability of
 the opponents. Many empirical studies have assumed that opponents use a
 single strategy throughout the whole fight. However, they often find
 partial support for a specific model. This might be due to individuals
 changing their strategy between phases of a contest. In this work, we
 addressed this issue by evaluating if males of the cricket Melanotes
 ornata switch their assessment strategy between phases. We used hind femur
 length as a proxy for fighting ability, as it was the attribute most
 strongly associated with contest outcome. Overall fight duration was
 positively associated with the loser’s femur length and negatively
 associated with the winner’s femur length, while the probability of
 escalation to physical aggression was negatively related to the difference
 in femur between opponents. However, such relationships held only at the
 first contest phase. During the escalated phase, fight duration was only
 correlated (although weakly) with femur length of losers. These results
 indicate that M. ornata males perform mutual assessment in the initial
 phase but switch their assessment strategy when fights escalate,
 suggesting a single strategy does not correctly explain how contests are
 settled.
description: 2019-Lobregatetal-SwitchassessMornataA RAR file containing seven files: (1) three *.txt files with processed data to be used in the statistical analysis, (2) one *.xls file containing raw data, (3) one editable *.Rnw file containing R and LaTeX code used to generate a pdf file of the analysis, (4) one *.pdf file describing all variables and analyses` steps, (5) one README file.2019-Lobregatetal.rar
DOI: 10.5061/dryad.h11125b
title: Data from: New records of very high nitrous oxide fluxes from rice cannot be generalized for water management and climate impacts

description: This supplement aims to substantiate and expand our comments made in the
 Letter to the Editor. This format as a separate document was necessary due
 to the complexity of the issues raised in our comments vis-à-vis the word
 limit of PNAS Letters (500 words). The text elaborates on individual
 concerns raised in the letter and also adds new aspects on the research
 quality that have not yet been discussed in the letter. Moreover, the
 supplement also includes an outlook on the implications for future
 mitigation projects at the end of this document.
description: Supplement to Letter on
 High N2O Emissions from RiceThis document comprises
 supplementary information to a Letter to the Editor published by
 Proceedings of the National Academy of Sciences of the United States of
 America (PNAS). The letter and the supplement have been written by 17
 authors from the International Rice Research Institute as well as other
 research institutes and academe. The rationale of the letter and this
 supplement is to clarify the author’s position on a recent PNAS article
 that reports very high emissions of nitrous oxide from rice fields.
 Collectively, these two documents elaborate on several concerns regarding
 some generalizations of this PNAS article that are deemed unfounded and
 speculative.Letter PNAS
 Editor_Supplement_High N2O_Jan2019.docx
DOI: 10.5061/dryad.19mn6vm
title: Data from: Modelling durophagous predation and mortality rates from the fossil record of gastropods

description: Gastropods often show signs of unsuccessful attacks by durophagous
 predators in the form of healed scars in their shells. As such, fossil
 gastropods can be taken as providing a record of predation through
 geological time. However, interpreting the number of such scars has proved
 to be problematic - would a low number of scars mean a low rate of attack,
 or a high rate of success, for example? Here we develop a model of
 population dynamics amongst individuals exposed to predation, including
 both lethal and non-lethal attacks. Using this model we calculate the
 equilibrium distributions of ages and healed scars in the population and
 amongst fossilised specimens, based on the assumption that predation is
 independent of age or scar number. Based on these results we formally show
 that the rates of attack and success cannot be disambiguated without
 further information about population structure. Nevertheless, by making
 the assumptions that the non-durophagous predatory death rate is both
 constant and low, we show that it is possible to use relatively small
 assemblages of gastropods to produce accurate estimates of both attack and
 success rates, if the overall death rate can be estimated. We consider
 likely violations of the assumptions in our model and what sort of
 information would be required to solve this problem in these more general
 cases. However, it is not easy to extract the relevant information easily
 from the fossil record: a variety of important biases are likely to
 intervene to obscure the data that gastropod assemblages may yield.
description: Code for simulating
 snail populations and performing analysesR code for simulating
 scar distribution and inferring predation parameters.budd_mann_SI.R
DOI: 10.5061/dryad.7mg3d80
title: Data from: Digital gene expression analyses of mammary glands from meat ewes naturally infected with clinical mastitis

description: Clinical mastitis in sheep has gravely restrained production performance
 for a long time. Knowledge of mechanisms of its pathogenesis and
 resistance in meat sheep mammary gland with clinical mastitis are not yet
 understood, especially for clinical mastitis caused by natural infection.
 In this work, RNA-seq was firstly used to screen differentially expressed
 genes (DEGs) in clinical mastitic mammary tissues (CMMTs) as compared to
 healthy mammary tissues (HMTs) from meat sheep flocks. We identified 420
 DEGs including 316 up-regulated and 104 down-regulated genes in CMMTs.
 Gene Ontology annotation revealed these DEGs were mainly engaged in immune
 response, inflammation response, etc. Pathway enrichment showed they were
 primarily enriched in pathways relevant to inflammation, immune response
 and metabolism. Alternative splicing analysis showed most common
 differential splicing genes (DSGs) in CMMTs and HMTs were implicated in
 immune response. Immunostaining for two immune response-related proteins
 encoded by DEGs were mainly observed in mammary epithelium between CMMTs
 and HMTs, and their positive signals were more intensive in CMMTs. These
 findings provide experimental basis and reference for further researching
 the molecular genetic mechanisms particularly immune defense mechanisms of
 mammary gland in clinical ovine mastitis.
description: transcript
DOI: 10.5061/dryad.72d1v26
title: Data from: Frequency and characteristics of MODY 1 (HNF4A mutation) and MODY 5 (HNF1B mutation) - Analysis from the DPV database

description: Objective. To characterize initial presentation and clinical course of
 patients with hepatocyte nuclear factor (HNF) 4A- and HNF1B-MODY in a
 multinational registry. Design, setting and participants. Within the
 Diabetes Patienten Verlaufsdokumentation (DPV) registry, 44 patients with
 HNF4A- and 35 patients with HNF1B-MODY were characterized and compared
 with patients &lt; 20years old with type 1 diabetes (T1D)/type 2
 diabetes (T2D). Main outcome measure. Clinical and laboratory parameters,
 therapy, metabolic control, and extrapancreatic symptoms in patients with
 HNF1B-MODY. Results. Patients with both MODY types were significantly
 older than T1D patients at diagnosis (HNF4A, 13.8 years and HNF1B, 13.5
 years, vs. T1D, 8.8 years, P&lt;0.0001). Mean C-peptide at diagnosis
 was higher for HNF4A-MODY than for T1D (1.8 vs. 0.9 ng/ml, P
 &lt;0.01). 36.4% of patients with HNF4A-MODY and 65.7% of patients
 with HNF1B-MODY were treated with insulin, 20.5% and 8.6% received oral
 antidiabetics only (p&lt;0.05 and p&lt;0.01 vs. T2D). At the most
 recent visit, glycated hemoglobin levels were lower in HNF4A- and
 HNF1B-MODY compared to T1D (mean, 6.5% and 6.1%) than in T1D. In 40% of
 patients with HNF1B-MODY, extrapancreatic symptoms were reported. Several
 clinical predictors previously described to differentiate between MODY and
 T1D or T2D could be revalidated by logistic regression analyses in this
 cohort.Conclusion The DPV registry enabled us to precisely characterize
 phenotype and treatment in these two rare MODY types. Although phenotype
 of HNF4A-and HNF1B-MODY shows distinct differences to T1D and T2D, 38% of
 patients were initially misclassified as having T1D or T2D.
description: Warncke et al. Features
 of MODY 1 and 5. suppl. informationList of centers which
 contributed patients to this analysis.Warncke et al. Features
 of MODY 1 and 5. suppl. table 1Recalls and validation
 of disease-causing mutations.Warncke et al. Features
 of MODY 1 and 5. suppl. table 2Logistic regression
 analysis, given as odds ratio (OR) in favor of the respective MODY subtype
 vs. T1D/T2D for each variable at the most recent visit.
DOI: 10.5061/dryad.rm5c4qr
title: Data from: Rapid evolution in response to warming does not affect the toxicity of a pollutant: insights from experimental evolution in heated mesocosms

description: While human-induced stressors such as warming and pollutants may co-occur
 and interact, evolutionary studies typically focus on single stressors.
 Rapid thermal evolution may help organisms better deal with warming, yet
 it remains an open question whether thermal evolution changes the toxicity
 of pollutants under warming. We investigated the effects of exposure to a
 novel pollutant (zinc oxide nanoparticles, nZnO) and 4°C warming (20°C vs
 24°C) on key life history and physiological traits of the water flea
 Daphnia magna, a keystone species in aquatic ecosystems. To address the
 role of thermal evolution, we compared these effects between clones from
 an experimental evolution trial where animals were kept for two years in
 outdoor mesocosms at ambient temperatures or ambient +4°C. The nZnO was
 more toxic at 20°C than at 24°C: only at 20°C it caused reductions in
 early fecundity, intrinsic growth rate, and metabolic activity. This was
 due to a higher accumulated zinc burden at 20°C than at 24°C, which was
 associated with an upregulation of a metallothionein gene at 20°C but not
 at 24°C. Clones from the heated mesocosms better dealt with warming than
 clones from the ambient mesocosms, indicating rapid thermal evolution.
 Notably, rapid thermal evolution did not change the toxicity of nZnO,
 neither at 20°C nor at 24°C, suggesting no pleiotropy or metabolic
 trade-offs were at work under the current experimental design. Evaluating
 whether thermal evolution influences the toxicity of pollutants is
 important for ecological risk assessment. It provides key information to
 extrapolate laboratory-derived toxicity estimates of pollutants both in
 space to warmer regions and in time under future global warming scenarios.
 In general, studying how the evolution of tolerance to one anthropogenic
 stressor influence tolerance to other anthropogenic stressors should get
 more attention in a rapidly changing world where animals increasingly face
 combinations of stressors.
description: Life history and
 physiology of Daphnia magna to nano Zinc and warmingThese are the data for
 the paper "Rapid evolution in response to warming does not affect the
 toxicity of a pollutant: insights from experimental evolution in heated
 mesocosms".Data
 archive.csv
DOI: 10.5061/dryad.jd1kn44
title: Data from: Ultra-Conserved Element phylogenomics of new world Ponera (Hymenoptera: Formicidae) illuminates the origin and phylogeographic history of the endemic exotic ant Ponera exotica

description: The genus Ponera is a lineage of leaf litter ants, with a center of
 diversity in the Indo-Australian region. Two species occur in the New
 World; however, uncertainty exists with regard to their biogeographic
 origins and species limits, especially for isolated cloud forest
 populations in Middle America. We investigate the geographic distribution,
 phylogeny, and phylogeography of these two species to better characterize
 the American ant fauna and to gain insight into the biogeography of taxa
 that span hemispheres. Sequencing of Ultra-Conserved Element (UCE) loci
 was used to infer phylogenetic relationships, estimate divergence dates,
 and test species boundaries. The widespread native species P. exotica and
 P. pennsylvanica are each more closely related to Old World relatives than
 they are to each other, implying two independent colonizations of the New
 World. Ponera pennsylvanica is most closely related to the European
 species P. coarctata, while P. exotica is related to a clade of
 Indo-Australian species. Ponera pennsylvanica is abundant throughout the
 eastern USA, with scattered occurrences further west. Ponera exotica
 occurs from the southern USA to Nicaragua. Both species have alate and
 ergatoid queens. Sequenced specimens from multiple populations of P.
 exotica reveal a pectinate phylogeographic structure, from north to south,
 with the potential for multiple cryptic species. The southern USA to
 Middle America distribution pattern of P. exotica mirrors that of many
 plant and animal species and may be the result of climatic cooling in the
 Pliocene followed by repeated glacial cycles in the Pleistocene, which
 condensed and fragmented mesic forest habitat.
description: tree-filesAll of the main result tree files and the gene tree files used for the ASTRAL and TR2 analyses. Trees in newick or nexus formats.dna-matrices-and-analysis-filesAll concatenated and aligned DNA matrices analyzed for this study. Includes UCE, COI, and BEAST2 matrices. The BEAST2 xml file includes all analysis settings. The package also includes the IQ-Tree partition files for the SWSC-EN-partitioned analysis of the UCE data and the COI data.trinity-uce-contigsThe bulk set of Trinity v2013-02-25 assemblies in FASTA format for all samples included in this study. Includes all UCE and non-UCE contigs.
DOI: 10.5061/dryad.db8853f
title: Data from: Incidence of multiple paternity and inbreeding in high-density brown bear populations on the Shiretoko Peninsula, Hokkaido, Japan

description: Understanding the breeding ecology of a species is essential for the
 appropriate conservation and management of wildlife. In brown bears,
 females occasionally copulate with multiple males in one breeding season,
 which may lead to multiple paternity in a single litter. In contrast,
 inbreeding, a potential factor in the reduction of genetic diversity, may
 occur, particularly in threatened populations. However, few studies have
 reported the frequency of these phenomena in brown bear populations. Here,
 we investigated the incidence of multiple paternity and inbreeding in a
 high-density brown bear population on the Shiretoko Peninsula in Hokkaido,
 Japan. A total of 837 individuals collected from 1998 to 2017 were
 genotyped at 21 microsatellite loci, and parentage analysis was performed.
 Out of 70–82 litters with ≥2 offspring, 14.6–17.1% of litters were sired
 by multiple males. This was comparable to the rate reported in a
 Scandinavian population, although population density and litter size,
 factors that potentially affect the incidence of multiple paternity,
 differed between the two populations. Out of 222 mother-father mating
 pairs, six litters (2.7%) resulted from matings between fathers and
 daughters. Additionally, one (0.5%) and four (1.8%) cases of mating
 between maternal half-siblings and between paternal half-siblings,
 respectively, were observed; however, no cases of mating between mothers
 and sons or between full-siblings were observed. Our results suggest that
 male-biased natal dispersal effectively limits mating between closely
 related individuals (aside from fathers and daughters) in brown bears.
description: GenotypeMicrosatellite genotyping data for 837 brown bears.