cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7h44j0zs5
title: Built to change: dominance strategy changes with life stage in a primitively eusocial bee

description: Access to reproduction is determined by an individual’s dominance rank in
 many species and is achieved through aggression and/or dominance
 signalling. In eusocial insects one or several dominant females (queens)
 monopolize reproduction but to what extent queens rely on aggression and
 signalling remains obscure. Aggression is costly and its efficiency
 depends on the group size, whereas signalling may reduce the risks and
 costs of aggression. Both strategies are used to regulate reproduction in
 social taxa, with aggression being more common in small social groups,
 compared to signalling in larger societies. Here, we examine the use of
 aggression and chemical signalling in a social species (Bombus impatiens)
 where the dominant queen interacts with increasing numbers of workers as
 she ages. We found that the queen’s strategy to monopolize reproduction
 changes with life stage, shifting from overt aggression to chemical
 signalling as the queen gets older. Particularly, old queens exhibited a
 higher ratio of short to long cuticular hydrocarbons compared to young
 queens, an endogenous shift that was attributed to age, as all egg-laying
 queens were fecund and kept with the same number of workers. Our findings
 contribute to the understanding of reproductive dominance in the context
 of an individual’s life history.
description: Methods are described in the manuscript.
DOI: 10.5061/dryad.vhhmgqnrj
title: More than just meat: Carcass decomposition shapes trophic identities in a terrestrial vertebrate

description: Most food web models fail to account for the full complexity of
 interactions within a community, particularly where microbes are involved.
 Carcasses are microbe-rich resources and may represent a common nexus for
 the macro- and microbiome, effectively uniting autotrophs, consumers,
 predators, and microbiota. We evaluated the role of carcasses as
 multitrophic resources and explored dietary partitioning for a sexually
 dimorphic obligate scavenger known for its hierarchical social system.
 This study was set in a well-studied community of camelids (Vicugna
 vicugna, Lama guanicoe), pumas (Puma concolor), and Andean condors (Vultur
 gryphus) in the Andes. We hypothesized that condors, by feeding on
 trophically distinct dietary substrates within any given carcass, would
 have highly variable trophic position (TP) values. Further, we expected
 that the microbial consumers within the carcass would inflate TP values in
 both, the carrion and the condors. Thus, we expected that the trophic
 heterogeneity within a carcass could facilitate sex-based dietary
 partitioning in condors. We used a multifaceted approach to assess the
 foraging of Andean condors, using regurgitated pellet and, bulk isotopic
 analyses, and also quantified the TP of the entire community of
 graminoids, camelids, camelid carrion, pumas, and female and male condors
 employing compound-specific stable isotopes analysis of amino-acids. Our
 analysis of condor pellets and bulk isotopes revealed non-trivial plant
 consumption, close to 10% of condor diet. Isotope analysis of amino-acids
 revealed that condors had highly variable TPs (2.9±0.3) compared to pumas
 (3.0±0.0) and camelids (2.0±0.1), likely representing “trophic omnivory”,
 wherein the condors consume plants (TP=1.0±0.1) and microbe-colonized
 carrion (2.3±0.1). Female condors exhibited a TP (2.8±0.2) lower than
 strict carnivory, suggesting that they consume more plant biomass in a
 carcass, while males (TP=3.1±0.3) are likely consuming more of the
 microbe-rich animal tissue. Our study highlights that carcasses represent
 a trophically heterogeneous resource, and that vertebrate scavengers can
 feed across trophic groups within the carcass, from autotrophs to
 secondary consumers, and from both the macro- and microbiome. Thus,
 integration of microbes in macroecological contexts can help to resolve
 trophic identity, and better characterize the importance of microbes in
 detritivorous and omnivorous species.
DOI: 10.15468/dl.p2vtw3
title: Occurrence Download

description: A dataset containing 396 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sinogentiana"
 ]
}

 The dataset includes 396 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002554-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xcfrq5
title: Occurrence Download

description: A dataset containing 2364 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((67.23176 22.92854,77.06707 5.88302,80.29428 7.40942,74.14721 25.8671,67.23176 22.92854))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Testudines"
 ]
}

 The dataset includes 2364 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002555-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4f4qrfj98
title: Cardinium localization during its parasitoid wasp host’s development provides insights into cytoplasmic incompatibility

description: Arthropods harbor heritable intracellular symbionts that may manipulate
 host reproduction to favor symbiont transmission. In cytoplasmic
 incompatibility (CI), the symbiont sabotages the reproduction of infected
 males such that high levels of offspring mortality result when they mate
 with uninfected females. In crosses with infected males and infected
 females, however, (the “rescue” cross), normal numbers of offspring are
 produced. A common CI-inducing symbiont, Cardinium hertigii, causes
 variable levels of CI mortality in the parasitoid wasp, Encarsia suzannae.
 Previous work correlated CI-induced mortality with male development time
 in this system, although the timing of Cardinium CI-induction and the
 relationship between development time and CI mortality was not well
 understood. Here, using a combination of crosses, manipulation of
 development time, and fluorescence microscopy, we identify the
 localization and the timing of the CI-induction step in the Cardinium-E.
 suzannae system. Antibiotic treatment of adult Cardinium-infected males
 did not reduce the mortality associated with the CI phenotype, suggesting
 that CI-alteration occurs prior to adulthood. Our results suggest that the
 alteration step occurs during the pupal period, and is limited by the
 duration of pupal development: 1) Encarsia produces most sperm prior to
 adulthood, 2), FISH localization of Cardinium in testes showed an
 association with sperm nuclei throughout spermatogenesis but not with
 mature sperm and 3) two methods of prolonging the pupal period (cool
 temperatures and the juvenile hormone analog methoprene) both caused
 greater CI mortality, suggesting the degree of alteration is limited by
 the duration of the pupal stage. Based on these results, we compare two
 models for potential mechanisms of Cardinium sperm modification in the
 context of what is known about analogous mechanisms of Wolbachia, a more
 extensively studied CI-inducing symbiont.
DOI: 10.5061/dryad.sj3tx9632
title: Collision between biological process and statistical analysis revealed by mean-centering

description: Animal ecologists often collect hierarchically-structured data and analyze
 these with linear mixed-effects models. Specific complications arise when
 the effect sizes of covariates vary on multiple levels (e.g., within vs
 among subjects). Mean-centering of covariates within subjects offers a
 useful approach in such situations, but is not without problems. A
 statistical model represents a hypothesis about the underlying biological
 process. Mean-centering within clusters assumes that the lower level
 responses (e.g. within subjects) depend on the deviation from the subject
 mean (relative) rather than on absolute values of the covariate. This may
 or may not be biologically realistic. We show that mismatch between the
 nature of the generating (i.e., biological) process and the form of the
 statistical analysis produce major conceptual and operational challenges
 for empiricists. We explored the consequences of mismatches by simulating
 data with three response-generating processes differing in the source of
 correlation between a covariate and the response. These data were then
 analyzed by three different analysis equations. We asked how robustly
 different analysis equations estimate key parameters of interest and under
 which circumstances biases arise.  Mismatches between generating
 and analytical equations created several intractable problems for
 estimating key parameters. The most widely misestimated parameter was the
 among-subject variance in response. We found that no single analysis
 equation was robust in estimating all parameters generated by all
 equations. Importantly, even when response-generating and analysis
 equations matched mathematically, bias in some parameters arose when
 sampling across the range of the covariate was limited. Our results have
 general implications for how we collect and analyze data. They also remind
 us more generally that conclusions from statistical analysis of data are
 conditional on a hypothesis, sometimes implicit, for the process(es) that
 generated the attributes we measure. We discuss strategies for real data
 analysis in face of uncertainty about the underlying biological process.
description: All data were generated through simulations, so included with
 this submission are a Read Me file containing general descriptions of data
 files, a code file that contains R code for the simulations and analysis
 data files (which will generate new datasets with the same parameters) and
 the analyzed results in the data files archived here. These data files
 form the basis for all results presented in the published paper. The code
 file (in R markdown) has more detailed descriptions of each file of
 analyzed results. 
description: All information should be contained in the Read Me file and the
 Markdown file posted here. Additional infomration is provided in
 the Supplementary Material for the publication.
DOI: 10.5061/dryad.sbcc2fr4g
title: Meta-analysis reveals materiomic relationships in major ampullate silk across the spider phylogeny

description: Spider Major Ampullate (MA) silk, with its combination of strength and
 extensibility, outperforms any synthetic equivalents. There is thus much
 interest in understanding its underlying materiome. While expression of
 the different silk proteins (spidroins) appears an integral component of
 silk performance, our understanding of the nature of the relationship
 between the spidroins, their constituent amino acids, and MA silk
 mechanics is ambiguous. To provide clarity on these relationships across
 spider species we performed a meta-analysis utilizing phylogenetic
 comparative methods. These showed that glycine and proline, both of which
 are indicators of differential spidroin expression, had effects on MA silk
 mechanics across the phylogeny. We also found serine to correlate with
 silk mechanics, probably via its presence within the carboxyl and amino
 terminal domains of the spidroins.  From our analyses we
 concluded that spidroin expression shifts across the phylogeny from
 predominantly MaSp1 in the MA silks of ancestral spiders to predominantly
 MaSp2 in the more derived spider’s silks. This trend was accompanied by an
 enhanced ultimate strain and decreased Young’s modulus in the silks. Our
 meta-analysis enabled us to decipher between real and apparent influences
 on MA silk properties, providing significant insights into spider silk and
 web co-evolution and enhancing our capacity to create spider silk-like
 materials.
description: Data was collecting using the PRISMA guidelines across Scopus and
 Web of science with the key (i) Spider silk, (ii) Amino acid, (iii)
 Protein, (iv) Composition, (v) Mechanical and (vi) Properties.
description: There are missing values in the data set. no=
 number of individuals
DOI: 10.5061/dryad.sn02v6x2d
title: Generating unbiased estimates of burrowing seabird populations

description: Maximising survey efficiency can help reduce the trade-off between
 spending limited conservation resources on identifying population changes
 and responding to those changes through management. Burrow-nesting
 seabirds are particularly challenging to survey because nests cannot be
 counted directly. We evaluated a stratified random survey design for
 generating unbiased population estimates simultaneously for four petrel
 species nesting on Macquarie Island, Australia, where the survey cue,
 burrow entrances, is similar for all species. We also compared the use of
 design-based and model-based analyses for minimising uncertainty in
 estimates. We recorded 2,845 Antarctic Prion burrows, 306 White-headed
 Petrel burrows and two Blue Petrel burrows while distance-sampling along
 154 km of transects. For Blue Petrels and Grey Petrels, we completed
 nocturnal searches along a further 71 km and searched 249 km of tracks
 during follow-up ground searches. We failed to generate unbiased
 population estimates for two rare and localised species, Blue and Grey
 Petrels, from our stratified random survey. Only for the most widespread
 and abundant species, Antarctic Prion, did the estimate have reasonable
 power to detect a rapid population change. Model-based analyses of the
 stratified random survey data did not improve upon traditional
 design-based analyses in terms of uncertainty in population estimates, but
 they did provide useful spatial representation of current populations.
 Models that used the targeted survey data did not reflect current
 population sizes and distributions of the two rare and localised species.
 We found that when species ecologies, distributions and abundances vary, a
 multi-method approach to surveys is needed. Species with low abundance
 that occur patchily across large islands are likely to be best estimated
 using targeted surveys, whereas widespread and abundant species can be
 accurately and precisely estimated from randomised surveys using
 informative model-based analyses.
description: Data are supplied as an .RData file with an .Rmd file that will
 run analyses in RStudio.
DOI: 10.5061/dryad.2ngf1vhkw
title: Data from: 346 target gene sequences from Vitaceae for Hyb-Seq

description: The Vitaceae (the grape family) consists of 16 genera and ca. 950 species.
 It is best known for the economically important fruit crop -- the grape
 Vitis vinifera. The deep phylogenetic relationships and character
 evolution of the grape family have attracted the attention of researchers
 in recent years. We herein reconstruct the phylogenomic relationships
 within Vitaceae using nuclear and plastid genes based on the Hyb-Seq
 approach and test the newly proposed classification system of the family.
 The five tribes of the grape family, including Ampelopsideae, Cayratieae,
 Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both
 nuclear and chloroplast genomic data. The cupular floral disc (raised
 above and free from ovary at the upper part) is an ancestral state of
 Vitaceae, with the inconspicuous floral disc as derived in the tribe
 Parthenocisseae, and the state of adnate to the ovary as derived in the
 tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral
 in Vitaceae, with the 4-merous flowers evolved at least two times in the
 family. The compound dichasial cyme (cymose with two secondary axes) is
 ancestral in Vitaceae and the thyrse inflorescence (a combination of
 racemose and cymose branching) in tribe Viteae is derived. The ribbon-like
 trichome only evolved once in Vitaceae, as a synapomorphy for the tribe
 Viteae.
DOI: 10.5061/dryad.tx95x69w2
title: Raw data from: Consumer-resource interactions along urbanization gradients drive natural selection

description: Urbanization is an important component of global change. Urbanization
 affects species interactions, but the evolutionary implications are rarely
 studied. We investigate the evolutionary consequences of a common pattern:
 the loss of high trophic-level species in urban areas. Using a
 gall-forming fly, Eurosta solidaginis, and its natural enemies that select
 for opposite gall sizes, we test for patterns of enemy loss, selection,
 and local adaptation along five urbanization gradients. Eurosta declined
 in urban areas, as did predation by birds, which preferentially consume
 gallmakers that induce large galls. These declines were linked to changes
 in habitat availability, namely reduced forest cover in urban areas.
 Conversely, a parasitoid which attacks gallmakers that induce small galls
 was unaffected by urbanization. Changes in patterns of attack by birds and
 parasitoids resulted in stronger directional selection, but loss of
 stabilizing selection in urban areas, a pattern which we suggest may be
 general. Despite divergent selective regimes, gall size did not very
 systematically with urbanization, suggesting but not conclusively
 demonstrating that environmental differences, gene flow, or drift, may
 have prevented the adaptive divergence of phenotypes. We argue that the
 evolutionary effects of urbanization will have predictable consequences
 for patterns of species interactions and natural selection.
description: Data were collected by both Denon Start and I, as well as a
 number of undergraduate volunteers and researchers.
description: This is the raw data I pulled from the working dropbox folder for
 this project. Some errors are present in the GPS coordinates in the
 "Coordinates for Waypoints..." excel files, which were corrected
 manually by Denon Start by merging accidental duplicate waypoints and
 moving inaccurate ones on Google Earth. The waypoints & polygons
 on the "Gall Places.kmz" file are accurate to my understanding.
 The "urban_gall_data.xlsx" file contains the gall dissection
 & diameter data.
DOI: 10.5061/dryad.f1vhhmgv2
title: Maternal and paternal age effects on male antler flies: a field experiment

description: In many species, parental age at reproduction can influence offspring
 performance and lifespan, but the direction of these effects and the
 traits affected vary among studies. Data on parental age effects are still
 scarce in non-captive populations, especially insects, despite species
 such as fruit flies being models in laboratory-based aging research. We
 performed a biologically relevant experimental manipulation of maternal
 and paternal age at reproduction of antler flies (Protopiophila litigata)
 in the laboratory and tracked the adult lifespan and reproductive success
 of their male offspring released in the wild. Increased paternal, but not
 maternal, age somewhat increased sons’ adult lifespan, while parental ages
 did not influence sons’ mating rate or reproductive senescence. Our
 results indicate that while parental age effects do exist in an insect in
 the field, they may be beneficial in such a short-lived animal, in
 contrast to results from most wild vertebrates and laboratory
 invertebrates.
DOI: 10.5061/dryad.mkkwh70xd
title: Correlation of giant earthquakes with the lunar phase in seven Indo-Pacific subduction zones and around Mongolia

description: Lunar phases of earthquakes worldwide with MW ≥ 8 between 1900 and
 November 15, 2016, were calculated. The null hypothesis that the
 occurrences of the giant earthquakes are random was assumed and tested for
 some subduction zones and around Mongolia. The null hypothesis was
 statistically rejected for Southern Chile, Alaska, Peru, the Japan Trench,
 the Kuril Islands, and Around Mongolia. The rejection of the random null
 hypothesis means that the occurrences of the giant earthquakes are not
 random. However, there are statistically significant specific lunar phase
 ranges (dangerous lunar phase, DLP) in which the giant earthquakes
 concentrate for each subduction zone and around Mongolia. DLPs for
 Southern Chile, Alaska, and Peru are almost around the spring tides.
 However, DLPs of the Japan Trench, the Kuril Islands, and around Mongolia
 are rather around the neap tides. A method to evaluate the DLP for the
 next giant earthquake with a significance level of 0.01 and 0.05 was
 proposed. The lower limit of MW for the analysis was investigated for
 Peruvian earthquakes, and MW = 7.5 was considered the best. The DLP was
 calculated for the giant earthquakes in the Japan Trench before Tohoku
 2011. It was found that the foreshocks of Tohoku 2011 and the mainshock
 occurred in the DLP. Heightened attention during the DLP in each seismic
 zone, primarily when seismicity occurs, should reduce the damage from
 giant earthquakes.
DOI: 10.5061/dryad.1ns1rn8rv
title: The last moves: the effect of hunting and culling on the risk of disease spread from a population of reindeer

description: 1. Hunting and culling are frequently used to combat infectious wildlife
 diseases. The aim is to markedly lower population density in order to
 limit disease transmission or to eradicate the host. Massive host culling
 can yield a trade-off when combating wildlife disease; it follows that
 intrusive actions may have unintended behavioural side-effects, leading to
 the geographic spread of disease. The manner in which such excessive
 hunting and culling of hosts can affect the movement and dispersion of
 cervids has not been studied. 2. In this study, we quantified the
 behaviour (daily movements and habitat use) and dispersion of GPS-marked
 reindeer (n = 24) before and during the eradication of an entire
 population (&gt;2000 reindeer) infected with chronic wasting disease
 (CWD) in Norway. We compared behaviour and dispersion during 10 ordinary
 hunting seasons (2007-16), an extended hunt in 2017 and marksmen culling
 (2017/18). 3. Seasonality had a major impact on movements. Reindeer
 movements during the early hunting season (20 August–20 September) did not
 increase the overall movements compared to that in the pre-hunt season (20
 July–19 August), while extended hunting into October (as in 2017) and
 marksmen culling from November to February markedly increased daytime
 movements relative to that normally observed in this time of the year.
 Towards the end of the eradication, the remaining reindeer sought refuge
 at restricted high-elevation areas with limited forage production.
 Reindeer used novel areas towards the perimeter of the range, but active
 herding during culling stopped one herd from leaving the CWD zone. 4.
 Synthesis and applications: With emerging wildlife diseases, host culling
 is becoming a more frequently used tool for managers in Europe. Our study
 highlights the potential trade-off between combating disease transmission
 within a population and the risk of geographic spread. Such insight is
 important to design mitigation measures, such as perimeter fencing or
 herding, to avoid the risk of the geographic spread of disease in cases of
 severe and economically important wildlife diseases.
description: GPS-data used to
 calculate step length, elevation and home range size.
description: cfr. Readme file