cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr7bk
title: Data from: Cohabitation with farm animals rather than breeding effort increases the infection with feather-associated bacteria in the barn swallow Hirundo rustica

description: Feather-associated bacteria are widespread inhabitants of avian plumage.
 However, the determinants of the between-individual variation in plumage
 bacterial loads are less well understood. Infection intensities can be
 determined by ecological factors, such as breeding habitat, and can be
 actively regulated by hosts via preening. Preening, yet, is a resource
 intensive activity, and thus might be traded-off against reproductive
 investment in breeding birds. Here, we studied barn swallows Hirundo
 rustica to assess the bacterial cost of reproduction in relation to
 nesting site micro-habitats. Barn swallows prefer to breed in the company
 of large-sized farm animals, although the presence of mammalian livestock
 in barns assures a warm and humid micro-climate that favours bacterial
 proliferation. Thus, we experimentally manipulated brood sizes of birds
 breeding in barns with, or without, farm animals and measured total
 cultivable bacteria (TCB) and feather-degrading bacteria (FDB) from the
 plumage. We found that the abundance of feather-associated bacteria (i.e.
 both TCB and FDB) in females, but not males, breeding in barns with
 livestock were significantly higher than in conspecifics breeding in empty
 barns. Plumage bacterial loads, however, were not affected by brood size
 manipulations in either sex. In addition, we report a negative
 relationship between both TCB and FDB and hatching date in females, and
 several sex and seasonal differences in plumage bacterial abundances. Our
 study is the first to show that breeding micro-habitat (i.e. livestock
 co-tenancy) has consequences for the abundance of feather-associated
 bacteria.
description: Barn swallow data for
 Fulop et al. 2017 Journal of Avian BiologyData file containing:
 (i) data of adult Barn swallows involved in the study; (ii) body mass an
 tarsus length data of 319 Barn swallow individuals used to calculate SMA
 slope for scaled-mass index; and (iii) data of Barn swallow nests involved
 in the study.Fulop_et_al_2017_JAVBIO_DATA.xlsx
DOI: 10.5061/dryad.51vs3
title: Data from: What factors influence where researchers deposit their data? A survey of researchers submitting to data repositories

description: In order to better understand the factors that most influence where
 researchers deposit their data when they have a choice, we collected
 survey data from researchers who deposited phylogenetic data in either the
 TreeBASE or Dryad data repositories. Respondents were asked to rank the
 relative importance of eight possible factors. We found that factors
 differed in importance for both TreeBASE and Dryad, and that the rankings
 differed subtly but significantly between TreeBASE and Dryad users. On
 average, TreeBASE users ranked the domain specialization of the repository
 highest, while Dryad users ranked as equal highest their trust in the
 persistence of the repository and the ease of its data submission process.
 Interestingly, respondents (particularly Dryad users) were strongly
 divided as to whether being directed to choose a particular repository by
 a journal policy or funding agency was among the most or least important
 factors. Some users reported depositing their data in multiple
 repositories and archiving their data voluntarily.
description: Combined Survey
 ResponsesThis spreadsheet shows
 the combined survey responses from Dryad Digital Repository, Figshare and
 TreeBASE survey populations.combined_survey_responses.csv
DOI: 10.5281/zenodo.18383738
title: COVID-19-Hospitalisierungen in Deutschland

description: Im Datensatz "COVID-19-Hospitalisierungen in Deutschland" des Robert Koch-Institutswerden täglich aktualisierte Informationen zu Hospitalisierungen im Zusammenhang mit COVID-19 basierend auf den Meldungen nach dem Infektionsschutzgesetz (IfSG) bereitgestellt. Neben tagesaktuellen Fallzahlen und Inzidenzen auf Bundes- und Länderebene enthält der Datensatz auch modellgestützte Schätzungen verzögert gemeldeter Hospitalisierungen mittels Nowcasting. Ziel ist es, die tatsächliche Belastung des Gesundheitssystems durch COVID-19 besser abzubilden, insbesondere durch die Berechnung adjustierter 7-Tage-Hospitalisierungsinzidenzen.
DOI: 10.5061/dryad.h8t3v
title: Data from: Testing alternative hypotheses for evolutionary diversification in an African songbird: rainforest refugia versus ecological gradients

description: Geographic isolation in rainforest refugia and local adaptation to
 ecological gradients may both be important drivers of evolutionary
 diversification. However, their relative importance and the underlying
 mechanisms of these processes remain poorly understood because few
 empirical studies address both putative processes in a single system. A
 key question is to what extent is divergence in signals that are important
 in mate and species recognition driven by isolation in rainforest refugia
 or by divergent selection across ecological gradients? We studied the
 little greenbul, Andropadus virens, an African songbird, in Cameroon and
 Uganda, to determine whether refugial isolation or ecological gradients
 better explain existing song variation. We then tested whether song
 variation attributable to refugial or ecological divergence was
 biologically meaningful using reciprocal playback experiments to
 territorial males. We found that much of the existing song variation can
 be explained by both geographic isolation and ecological gradients, but
 that divergence across the gradient, and not geographic isolation, affects
 male response levels. These data suggest that ecologically divergent
 traits, independent of historical isolation during glacial cycles, can
 promote reproductive isolation. Our study provides further support for the
 importance of ecology in explaining patterns of evolutionary
 diversification in ecologically diverse regions of the planet.
description: Measurements of little
 greenbul songEvolution_datafile1_songs.csvResponses to playback experimentsEvolution_datafile2_playbacks.csv
DOI: 10.5061/dryad.5h6c1
title: Data from: Ecological outsourcing: a pitcher plant benefits from transferring pre-digestion of prey to a bat mutualist

description: Mutualisms are interspecific interactions where each of the species
 involved gains net benefits from the other(s). The exchange of resources
 and/or services between mutualistic partners often involves tasks that
 species originally accomplished themselves but which have been taken over
 by or transferred to the more efficient partner during the evolution of
 the mutualism. Such ‘ecological outsourcing’ can be seen, for example, in
 several carnivorous plants that have transferred prey capture and
 digestion to animal partners. However, the outcome of this transfer and
 its fitness relevance has rarely been quantified. Using a digestive
 mutualism between a carnivorous pitcher plant (Nepenthes hemsleyana) and a
 bat (Kerivoula hardwickii) as a model, we tested the hypothesis that
 ecological outsourcing is a profitable strategy for the outsourcing
 partner. To evaluate the value of this mutualism, we conducted a series of
 field and glasshouse experiments. We measured the benefits of ecological
 outsourcing by comparing survival, growth, photosynthesis and nutrient
 content of N. hemsleyana plants fed with bat faeces to those fed with
 arthropods. To investigate the costs of such outsourcing processes, we
 repeated the experiment with the closest relative (Nepenthes rafflesiana)
 that is not adapted to digest bat faeces. We found that N. hemsleyana
 plants fed with faeces had increased survival, growth and photosynthesis
 compared to plants fed with arthropods only. On average, plants covered
 95% of their nitrogen demand from faeces under strong nutrient
 deprivation. Despite N. rafflesiana's higher arthropod capture rate,
 faeces covered a large part of this species’ nutrient demand as well,
 suggesting low costs for outsourcing. Synthesis. Outsourcing prey capture
 and digestion to the mutualism partner seems to be a beneficial strategy
 for N. hemsleyana. It may explain the evolutionary trend of several
 carnivorous plants to lose their carnivorous traits while increasing their
 attractiveness to mutualistic partners. On a much broader scale, we
 propose that ecological outsourcing could be one of the major drivers for
 the evolution and maintenance of mutualisms.
description: Schöner et al. (2016) J.
 Ecol. DataSchöner et
 al._Data.xlsx
DOI: 10.5061/dryad.cr17v
title: Data from: Sharp genetic discontinuity across a unimodal Heliconius hybrid zone

description: Hybrid zones are powerful natural systems to study evolutionary processes
 to gain an understanding of adaptation and speciation. In the Cauca Valley
 (Colombia), two butterfly races, Heliconius cydno cydnides and Heliconius
 cydno weymeri, meet and hybridize. We characterized this hybrid zone using
 a combination of mitochondrial DNA (mtDNA) sequences, Amplified Fragment
 Length Polymorphisms (AFLPs), microsatellites, and sequences for nuclear
 loci within and outside of the genomic regions that cause differences in
 wing color pattern. The hybrid zone is largely composed of individuals of
 mixed ancestry. However, there is strong genetic discontinuity between the
 hybridizing races in mtDNA and, to a lesser extent, in all nuclear markers
 surveyed. The mtDNA clustering of H. c. cydnides with the H. cydno race
 from the Magdalena Valley and H. c. weymeri with the H. cydno race from
 the pacific coast suggests that H. c. cydnides colonized the Cauca Valley
 from the north, whereas H. c. weymeri did so by crossing the Andes in the
 southern part, implying a secondary contact origin. Colonization of the
 valley by H. cydno was accompanied by mimicry shift. Strong ecological
 isolation, driven by locally adaptive differences in mimetic wing
 patterns, is playing an important role in maintaining the hybrid zone.
 However, selection on wing pattern alone is not sufficient to explain the
 genetic discontinuity observed. There is evidence for differences in male
 mating preference, but the contribution of additional barriers need
 further investigation. Overall our results support the idea that
 speciation is a cumulative process, where the combination of multiple
 isolation barriers, combined with major phenotypic differences, facilitate
 population divergence in face of gene flow.
description: Squenence
 Aligments-Sequence Aligment for
 mtDNA (2261bp) region: spanning the COI, tRNA-Leu and COII genes,
 including the ‘barcode’ region. -Sequence Aligments for 7 color pattern
 candidate loci [Trehalase1B (665 bp), Trehalase1A (798bp bp), BmSuc2 (Inv
 612 bp), RecQ (716 bp), Hm0021 (554bp), Lrr (540 pb), and Unkempt (667
 bp)] within HmYb interval (Baxter et al. 2010). -Sequenced Aligments for 3
 loci [suzy (466 bp), cat (1004 bp) and sae1 (719 bp)] that are not linked
 to each other or to any known color pattern gene (Counterman et al. 2010;
 Salazar et al. 2010).HZCydnosequencesAligments.zipMicrosatellite, AFLP and Hybrid index data-Table with individual genotypification for 3 Color pattern (Sb,Kw,Yb) loci and 14 Microsatellite Loci. For a total 14 populations and 478 individuals. -Table with individual genotypification for 562 AFLP loci. For a total of 14 populations and 169 individuals. -Genoypic and Phenotypic Hybrid Index. For 107 individualas from the contact zone.
DOI: 10.5061/dryad.q1b24
title: Data from: Two new species of Limbodessus diving beetles from New Guinea - short verbal descriptions flanked by online content (digital photography, μCT scans, drawings and DNA sequence data)

description: Background: To date only one species of Limbodessus diving beetles has
 been reported from the Island of New Guinea, L. compactus (Clark, 1862),
 which is widerspread in the Australian region. New information: We
 describe two new species of microendemic New Guinea Limbodessus and use a
 compact descriptive format flanked by enriched online content in wiki
 powered species pages. Limbodessus baliem sp.n. is described from ca.
 1,600 m altitude in the Baliem Valley of Papua and Limbodessus alexanderi
 sp.n. from &gt;3,000 m altitude north of Sugapa, Papua. Based on our
 analysis, we also transfer three species from other genera to Limbodessus
 Guignot, 1939, with the following changes: Limbodessus deflectus (Ordish,
 1966), new combination; Limbodessus leveri (J. Balfour-Browne, 1944), new
 combination; and Limbodessus plicatus (Sharp, 1882), new combination.
description: Limbodessus cox1 BDJ
 PaperA 3' cox1 sequence
 dataset for New Guinea Limbodessus species
DOI: 10.5061/dryad.905j6
title: Data from: Exercise changes behaviour

description: 1. Exercise, which may be defined as bodily movement produced by the
 contraction of skeletal muscle and which increases energy expenditure
 above basal levels, is essential for fitness-related activities such as
 foraging, migration, and dispersal. The frequency with which individuals
 engage in exercise depends on a range of intrinsic and environmental
 factors. Exercise itself can modify behaviour by inducing endocrine
 changes and by a training effect that increases physiological capacities.
 2. Here we test the hypothesis that exercise changes behaviour, and that
 there is positive feedback so that performing exercise increases the
 likelihood of performing exercise-related behaviours. 3. We show that
 there was a training effect that improved sustained swimming performance
 of mosquitofish (Gambusia holbrooki) exposed to chronic exercise in
 flowing water for four weeks compared to sedentary controls. Exercised
 fish also became bolder and were quicker to leave a refuge, showed an
 increasing tendency to explore unfamiliar environments, and were more
 aggressive than sedentary fish. These physiological and behavioural
 changes reverted back to control levels when exercised fish assumed a
 sedentary lifestyle again. 4. We used the calcium channel blocker
 nifedipine to decrease swimming performance of exercised fish to control
 levels, which allowed us to determine whether increased locomotor capacity
 per se influences behaviour. We show that reducing the swimming
 performance of exercised fish also reduced exploration and aggression, but
 it did not affect the latency to leave a refuge (boldness). 5. Our data
 show that behavioural phenotypes are not fixed. Exercise changes behaviour
 and may thereby alter interactions between individuals and dispersal.
 Environmental changes that demand increased levels of exercise induce
 behavioural responses that are likely to increase the success of
 individuals under these changed conditions.
description: Sinclair et al_all
 data
DOI: 10.5061/dryad.vm32c
title: Data from: The effects of supplementary food on the breeding performance of Eurasian reed warblers Acrocephalus scirpaceus; implications for climate change impacts

description: Understanding the mechanisms by which climate variation can drive
 population changes requires information linking climate, local conditions,
 trophic resources, behaviour and demography. Climate change alters the
 seasonal pattern of emergence and abundance of invertebrate populations,
 which may have important consequences for the breeding performance and
 population change of insectivorous birds. In this study, we examine the
 role of food availability in driving behavioural changes in an
 insectivorous migratory songbird; the Eurasian reed warbler Acrocephalus
 scirpaceus. We use a feeding experiment to examine the effect of increased
 food supply on different components of breeding behaviour and first-brood
 productivity, over three breeding seasons (2012–2014). Reed warblers
 respond to food-supplementation by advancing their laying date by up to
 5.6 days. Incubation periods are shorter in supplemented groups during the
 warmest mean spring temperatures. Nestling growth rates are increased in
 nests provisioned by supplemented parents. In addition, nest predation is
 reduced, possibly because supplemented adults spend more time at the nest
 and faster nestling growth reduces the period of vulnerability of eggs and
 nestlings to predators (and brood parasites). The net effect of these
 changes is to advance the fledging completion date and to increase the
 overall productivity of the first brood for supplemented birds. European
 populations of reed warblers are currently increasing; our results suggest
 that advancing spring phenology, leading to increased food availability
 early in the breeding season, could account for this change by
 facilitating higher productivity. Furthermore, the earlier brood
 completion potentially allows multiple breeding attempts. This study
 identifies the likely trophic and behavioural mechanisms by which
 climate-driven changes in invertebrate phenology and abundance may lead to
 changes in breeding phenology, nest survival and net reproductive
 performance of insectivorous birds.
description: Laying date
 dataData
 file 1.csvNestling
 massdata
 file 3 nestling mass.csv
DOI: 10.5061/dryad.r2b26
title: Data from: Sex-specific maternal effects in a viviparous fish

description: Mothers vary in their effects on their offspring, but studies of variation
 in maternal effects rarely ask whether differences between mothers are
 consistent for sons and daughters. Here, we analysed maternal effects in
 the mosquitofish Gambusia holbrooki for development time and adult size of
 sons and daughters, and a primary male sexual character (gonopodium
 length). We found substantial maternal effects on all traits, most notably
 for gonopodium length. There were significant correlations within each sex
 for maternal effects on different traits, indicative of trade-offs between
 development rate and adult size. By contrast, there was no evidence of any
 consistency in maternal effects on sons and daughters. This suggests that
 the evolution of maternal effects will follow independent trajectories
 dependent on sex-specific selection on offspring. Importantly, failure to
 recognize the sex-specific nature of maternal effects in this population
 would have substantially underestimated the extent of their variation
 between mothers.
description: Kruuk BiolLetters
 GambusiaPlease see ReadMe
 file.
DOI: 10.5061/dryad.s04h8
title: Data from: Genetic sampling for estimating density of common species

description: Understanding population dynamics requires reliable estimates of
 population density, yet this basic information is often surprisingly
 difficult to obtain. With rare or difficult-to-capture species, genetic
 surveys from noninvasive collection of hair or scat has proved
 cost-efficient for estimating densities. Here, we explored whether
 noninvasive genetic sampling (NGS) also offers promise for sampling a
 relatively common species, the snowshoe hare (Lepus americanus Erxleben,
 1777), in comparison with traditional live trapping. We optimized a
 protocol for single-session NGS sampling of hares. We compared spatial
 capture–recapture population estimates from live trapping to estimates
 derived from NGS, and assessed NGS costs. NGS provided population
 estimates similar to those derived from live trapping, but a higher
 density of sampling plots was required for NGS. The optimal NGS protocol
 for our study entailed deploying 160 sampling plots for 4 days and
 genotyping one pellet per plot. NGS laboratory costs ranged from
 approximately $670 to $3000 USD per field site. While live trapping does
 not incur laboratory costs, its field costs can be considerably higher
 than for NGS, especially when study sites are difficult to access. We
 conclude that NGS can work for common species, but that it will require
 field and laboratory pilot testing to develop cost-effective sampling
 protocols.
description: Cheng et al 2017_Ecol
 Evol_DRYADMicrosatellite genotypes
 (8 loci) for 114 snowshoe hares, representing all unique genotypes
 confirmed from hare tissue or fecal pellet samples collected at 5 study
 sites.
DOI: 10.5061/dryad.31s59
title: Data from: Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

description: Background: The New Zealand collembolan genus Holacanthella contains the
 largest species of springtails (Collembola) in the world. Using Illumina
 technology we have sequenced and assembled a draft genome and
 transcriptome from Holacanthella duospinosa (Salmon). We have used this
 annotated assembly to investigate the genetic basis of a range of traits
 critical to the evolution of the Hexapoda, the phylogenetic position of H.
 duospinosa and potential horizontal gene transfer events. Results: Our
 genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and
 sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and
 LINEs formed the largest components and SINEs were very rare.
 Phylogenomics (370,877 amino acids) placed H. duospinosa within the
 Neanuridae. We recovered orthologs of the conserved sex determination
 genes thought to play a role in sex determination. Analysis of CpG content
 suggested the absence of DNA methylation, and consistent with this we were
 unable to detect orthologs of the DNA methyltransferase enzymes. The small
 subunit rRNA gene contained a possible retrotransposon. The Hox gene
 complex was broken over two scaffolds. For chemosensory ability, at least
 15 and 18 ionotropic glutamate and gustatory receptors were identified,
 respectively. However, we were unable to identify any odorant receptors or
 their obligate co-receptor Orco. Twenty-three chitinase-like genes were
 identified from the assembly. Members of this multigene family may play
 roles in the digestion of fungal cell walls, a common food source for
 these saproxylic organisms. We also detected 59 and 96 genes that blasted
 to bacteria and fungi, respectively, but were located on scaffolds that
 otherwise contained arthropod genes. Conclusions: The genome of H.
 duospinosa contains some unusual features including a Hox complex broken
 over two scaffolds, in a different manner to other arthropod species, a
 lack of odorant receptor genes and an apparent lack of environmentally
 responsive DNA methylation, unlike many other arthropods. Our detection of
 candidate horizontal gene transfer candidates confirms that this
 phenomenon is occurring across Collembola. These findings allow us to
 narrow down the regions of the arthropod phylogeny where key innovations
 have occurred that have facilitated the evolutionary success of Hexapoda.
description: Alignment of dsx
 proteinsAlignment of dsx
 proteinsDsx_AlignBlosum45.fastaDsx maximum likelihood phylogenyDsx maximum likelihood phylogenyDsx_AlignBlosum45_consensus Tree.newickSxl protein alignmentSxl protein alignmentSxl_AlignBlosum45.fastaSxl_AlignBlosum45_consensusTreeSxl maximum likelihood phylogeny