cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.523t4
title: Data from: Long-term effect of yolk carotenoid levels on testis size in a precocial bird

description: Conditions experienced during prenatal development can have long-lasting
 organizational effects on offspring. Maternal carotenoids deposited in the
 eggs of birds and other oviparous species play an important role during
 fast embryonic growth and chick development through their antioxidant
 properties. However, the long-term consequences of variation in maternal
 carotenoid transfer for the offspring have seldom been considered. Since
 plasma carotenoid levels at adulthood are known to influence testis size
 and yolk carotenoid levels influence the ability to extract carotenoids
 later in life, we hypothesized that maternally transmitted carotenoids
 might influence gonad size at adulthood. Here, we showed that male
 Japanese quail (Coturnix japonica) originating from a carotenoid-enriched
 egg had smaller testes than control individuals at adulthood. This result
 shows that yolk carotenoids have long-term organizational effects. In
 addition, given that carotenoid intake at sexual maturity increases sperm
 quality and that a decreased testis size is associated with a lower sperm
 production, we propose that carotenoid exposure during embryo development
 might influence a trade-off between ejaculate size and sperm quality.
description: Data Biol.Lett_testes
 sizeData
DOI: 10.5061/dryad.1884
title: Data from: The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca)

description: Habitat fragmentation may disrupt original patterns of gene flow and lead
 to drift-induced differentiation among local population units. Top
 predators such as the jaguar may be particularly susceptible to this
 effect, given their low population densities, leading to small effective
 sizes in local fragments. On the other hand, the jaguar's high
 dispersal capabilities and relatively long generation time might
 counteract this process, slowing the effect of drift on local populations
 over the time frame of decades or centuries. In this study, we have
 addressed this issue by investigating the genetic structure of jaguars in
 a recently fragmented Atlantic Forest region, aiming to test whether loss
 of diversity and differentiation among local populations are detectable,
 and whether they can be attributed to the recent effect of drift. We used
 13 microsatellite loci to characterize the genetic diversity present in
 four remnant populations, and observed marked differentiation among them,
 with evidence of recent allelic loss in local areas. Although some migrant
 and admixed individuals were identified, our results indicate that recent
 large-scale habitat removal and fragmentation among these areas has been
 sufficiently strong to promote differentiation induced by drift and loss
 of alleles at each site. Low estimated effective sizes supported the
 inference that genetic drift could have caused this effect within a short
 time frame. These results indicate that jaguars' ability to
 effectively disperse across the human-dominated landscapes that separate
 the fragments is currently very limited, and that each fragment contains a
 small, isolated population that is already suffering from the effects of
 genetic drift.
description: Microsatellite data of
 the Atlantic Forest jaguar populationsMicrosatellite data of
 the four jaguar populations studied in Atlantic Forest.MicrosatelliteData.xls
DOI: 10.5061/dryad.pk7v8
title: Data from: Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift

description: Negative frequency dependent selection (NFDS) is supposed to be the main
 force controlling allele evolution at the gametophytic
 self-incompatibility locus (S-locus) in strictly outcrossing species.
 Genetic drift also influences S-allele evolution. In perennial sessile
 organisms, evolution of allelic frequencies over two generations is mainly
 shaped by individual fecundities and spatial processes. Using wild cherry
 populations between two successive generations, we tested whether
 S-alleles evolved following NFDS qualitative and quantitative predictions.
 We showed that allelic variation was negatively correlated with parental
 allelic frequency as expected under NFDS. However, NFDS predictions in
 finite population failed to predict more than half all S-allele
 quantitative evolution. We developed a spatially-explicit mating model
 which included the S-locus. We studied the effects of self-incompatibility
 and local drift within populations due to pollen dispersal in spatially
 distributed individuals, and variation in male fecundity on male mating
 success and allelic frequency evolution. Male mating success was
 negatively related to male allelic frequency as expected under NFDS.
 Spatial genetic structure combined with self-incompatibility resulted in
 higher effective pollen dispersal. Limited pollen dispersal in structured
 distributions of individuals and genotypes, non-random distribution of
 individuals and unequal pollen production significantly contributed to
 S-allele frequency evolution by creating local drift effects strong enough
 to counteract the NFDS effect on some alleles.
description: 2011 data Dryad Prunus
 S-allele Stoeckel et al.Observed
 Parents-offspring S-allele frequencies within populations of wild cherry
 trees
DOI: 10.5061/dryad.4nf75
title: Data from: Deer-mediated changes in environment compound the direct impacts of herbivory on understory plant communities

description: 1. In forests of eastern North America, white-tailed deer (Odocoileus
 virginianus) can directly affect, via herbivory, the presence, abundance,
 and reproductive success of many plant species. In addition, deer
 indirectly influence understory communities by altering environmental
 conditions. 2. To examine how deer indirectly influence understory plants
 via environmental modification, we sampled vegetation and environmental
 variables in- and outside deer exclosures (10-20 years old) located in
 temperate forests in northern Wisconsin and the Upper Peninsula of
 Michigan, USA. We assessed how excluding deer affected understory
 community composition and structure, the soil and light environment, and
 relationships between direct and indirect effects using non-metric
 multidimensional scaling (NMDS), mixed linear models and non-parametric
 multiplicative regression (NPMR). 3. Excluding deer altered sapling
 communities and several aspects of the understory environment. Excluding
 deer from plots with lower overstory basal area increased sapling
 abundance, decreasing the amount of light available to groundlayer plants.
 Exclusion also reduced soil compaction and the thickness of the soil E
 horizon. 4. The composition of understory communities and the frequencies
 of various species and groups covaried in apparent response to the
 environmental factors affected by exclusion. In several common species and
 groups, E horizon thickness, compaction, openness, and/or total (sapling
 and overstory) basal area were significant predictors of plant frequency.
 5. Complementary analyses revealed that deer exclusion also altered the
 frequency distributions of several species and groups across environmental
 space. Synthesis: Deer alter many facets of the understory environment,
 such as light availability, soil compaction and depth of the soil E
 horizon, which, in turn, appear to mediate variation in plant communities.
 Those environmental modifications likely compound direct impacts of
 herbivory as drivers of understory community change, having important
 implications for forest composition. Thus, we suggest a reexamination of
 the common assumption that understory community shifts stem primarily from
 tissue removal.
description: Vegetation and
 environmental data from deer exclosures in the Upper
 MidwestVegetation data include
 sapling basal area and proportion of quadrats where each species was found
 (&gt; 5% abundance) as well as several species groups that were developed
 by adding together all relevant species frequencies. Environmental data
 include soil physical and chemical properties, coarse woody debris, canopy
 conditions and earthworm invasion levels.Sabo_etal_JoE_2017_data.csv
DOI: 10.5061/dryad.70m1r
title: Data from: Growing up with feces: benefits of allo-coprophagy in families of the European earwig

description: An important issue in the evolution of group living is the risk of
 pathogen and predator exposure entailed by the inherent accumulation of
 feces within a nesting site. While many group living species limit this
 risk by cleaning the nest, others do not, raising questions about the
 benefits of maintaining feces in the nest and their importance in social
 evolution. Here, we investigated whether one of these benefits could be
 mediated by coprophagy in families of the European earwig, Forficula
 auricularia. In this insect species, mothers and mobile juveniles (nymphs)
 line their nests with feces and consume them. In a first experiment, we
 tested whether access to feces produced by either nymphs or mothers
 affects nymph survival in both presence and absence of food. The results
 showed that access to sibling feces, but not mother feces, enhanced
 offspring survival under food deprivation. Such an effect did not occur
 when regular food was available. We then conducted a food-choice
 experiment to reveal whether nymphs prefer food to feces, and if they
 discriminate between feces from their mother, unrelated adult females,
 unrelated nymphs, or their siblings. We found that offspring generally
 preferred regular food to feces, but nevertheless always consumed some
 feces. By contrast, nymphs showed no preference between related sibling or
 mother feces and did not discriminate between feces from related and
 unrelated individuals. Overall, our results suggest that the benefits of
 coprophagy could favor the maintenance of feces within the nest and
 promote the evolution of social life.
description: DRYAD_survival_dataThis is the data file associated with the survival experiment. Please check the second sheet in the file for further details regarding the individual columns.DRYAD_food_choiceThis data file contains our data regarding the food choice experiment. Please consult the second sheet within the file for further explanations regarding the individual columns.
DOI: 10.15468/dl.njbk3q
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acrothamnus maccraei",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 169 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001178-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3562g
title: Data from: Higher-order interactions capture unexplained complexity in diverse communities

description: Natural communities are well known to be maintained by many complex
 processes. Despite this, the practical aspects of studying them often
 require some simplification, such as the widespread assumption that
 direct, additive competition captures the important details about how
 interactions between species impact community diversity. On the other
 hand, more complex non-additive ‘higher-order’ interactions, are assumed
 to be negligible or absent. Notably, these assumptions are poorly
 supported and have major consequences for the accuracy with which patterns
 of natural diversity are modelled and explained. We present a
 mathematically simple framework for incorporating biologically meaningful
 complexity into models of diversity by including non-additive higher-order
 interactions. We further provide empirical evidence that such higher-order
 interactions strongly influence species’ performance in natural plant
 communities, with variation in seed production (as a proxy for per capita
 fitness) explained dramatically better when at least some higher-order
 interactions are considered. Our study lays the groundwork for a
 long-overdue shift in how species interactions are used to study the
 diversity of natural communities.
description: York Gum woodland focal
 plant fecundity and neighbourhood dataThis file contains
 estimated seed set (fecundity) data on 773 individuals of six focal annual
 plant species common to the York Gum woodlands in SW Western Australia.
 Seed set per focal plant was estimated for each plant by counting up the
 total number of flowers (or inflorescences) on each plant and multiplying
 that number by the average number of seeds produced per flower(infor.)
 using 1-3 flowers(inflor.) per plant. In addition to seed production
 values, this dataset also includes the identity and abundance of all
 plants within a 7.5 cm radius around each focal plant. More details are
 available in the readme file and in the methods of the paper associated
 with this dataset.complete.Rdata
DOI: 10.5061/dryad.7b92c
title: Data from: Dominant and subordinate outside options alter help and eviction in a pay-to-stay negotiation model

description: In several cooperatively breeding species, subordinates that do not help
 sufficiently are punished or evicted from the group by dominant
 individuals. The credibility of dominant eviction threats may vary with
 the social context beyond the group level: when subordinates can easily
 breed in a neighboring territory, dominant may be less able to demand help
 from subordinates. Further, dominant ability to enforce subordinate
 cooperation may be reduced when it is difficult to replace evicted
 subordinates or in small groups where each subordinate makes a large
 contribution to group productivity. Here, we develop a two-player game
 theoretic model to examine how the social context influences subordinate
 help and the threshold of help at which dominants evict subordinates. In
 contract to predictions, we found that dominants demand more help when
 dominants are less able to replace evicted subordinates, suggesting that
 dominants punish a dereliction of helping behavior more strongly when they
 are unable to compensate for the loss of an evicted subordinate. In single
 sealed-bid games, subordinates help less than the fitness costs they
 impose on dominants and help does not vary with subordinate breeding
 opportunities outside the group. However, when subordinates can
 plastically increase help in response to demanding dominants (akin to
 pay-to-stay dynamics), subordinates provide more help overall, but
 decrease their help as breeding opportunities outside of the group
 increase. Our results demonstrate the importance of incorporating
 negotiation into theoretical models of helping strategies and demonstrate
 that plasticity is a key mechanism underlying pay-to-stay mechanisms of
 cooperation.
description: SimulationsSimulation files examining ESS and CSSModelsolveplasticevolsim.mModel_solve_final_DryadParameter filefitevictplasticitycompEquationsModel outputModel results- final Dryad.txt
DOI: 10.5061/dryad.r02h8
title: Data from: Biogeography predicts macro-evolutionary patterning of gestural display complexity in a passerine family

description: Gestural displays are incorporated into the signaling repertoire of
 numerous animal species. These displays range from complex signals that
 involve impressive and challenging maneuvers, to simpler displays or no
 gesture at all. The factors that drive this evolution remain largely
 unclear, and we therefore investigate this issue in New World blackbirds
 by testing how factors related to a species’ geographical distribution and
 social mating system predict macro-evolutionary patterns of display
 elaboration. We report that species inhabiting temperate regions produce
 more complex displays than species living in tropical regions, and we
 attribute this to i) ecological factors that increase the competitiveness
 of the social environment in temperate regions, and ii) different
 evolutionary and geological contexts under which species in temperate and
 tropical regions evolved. Meanwhile, we find no evidence that social
 mating system predicts species differences in display complexity, which is
 consistent with the idea that gestural displays evolve independently of
 social mating system. Together, these results offer some of the first
 insight into the role played by geographic factors and evolutionary
 context in the evolution of the remarkable physical displays of birds and
 other vertebrates.
description: Miles et al (2017)
 Evoltuion_Display Complexity DataDisplay complexity
 scores
DOI: 10.5061/dryad.s9m4qt0
title: Data from: The insensitive dormouse: reproduction skipping is not caused by chronic stress in Glis glis

description: Entire populations of edible dormice (Glis glis) can skip reproduction in
 years without mast seeding of deciduous trees (particularly beech or oak
 seed), because juveniles require high caloric seeds for growth and
 fattening prior to hibernation. We hypothesized that, in mast failure
 years, female dormice may be forced to spend larger amounts of time
 foraging for low-quality food, which should increase their exposure to
 predators, mainly owls. This may lead to chronic stress, i.e., long-term
 increased secretion of Glucocorticoids (GC), which can have inhibitory
 effects on reproductive function in both female and male mammals. We
 monitored reproduction in free-living female dormice over three years with
 varying levels of food availability, and performed a supplemental feeding
 experiment. To measure stress hormone levels, we determined fecal GC
 metabolite (GCM) concentrations collected during the day, which reflect
 hormone secretion rates in the previous nocturnal activity phase. We found
 that year-to-year differences in beech mast significantly affected fecal
 GCM levels and reproduction. However, contrary to our hypothesis, GCM
 levels were lowest in a non-mast year without reproduction, and
 significantly elevated in full-mast and intermediate years, as well as
 under supplemental feeding. Variation in owl density in our study area had
 no influence on GCM levels. Consequently, we conclude that down-regulation
 of gonads and reproduction skipping in mast-failure years in this species
 is not caused by chronic stress. Thus, in edible dormice, delayed
 reproduction apparently is profitable in response to the absence of
 energy-rich food in non-mast years, but not in response to chronic stress.
description: Validation experiment
 femalesValidation experiment
 females, biological validationanimals_ACTH_females_jeb.xlsxGlucocorticoid data field Glis glis femalesfield data, Glis glis females, glucocorticoids, animal parameters and environmental factorshormon_analysis_females_jeb.csv
DOI: 10.5061/dryad.2k16k4b
title: Data from: Nitrate or ammonium: influences of nitrogen source on the physiology of a green alga

description: In freshwaters, algal species are exposed to different inorganic nitrogen
 (Ni) sources whose incorporation varies in biochemical energy demand. We
 hypothesized that due to the lesser energy requirement of ammonium
 (NH4+)-use, in contrast to nitrate (NO3-)-use, more energy remains for
 other metabolic processes, especially under CO2- and phosphorus (Pi)
 limiting conditions. Therefore, we tested differences in cell
 characteristics of the green alga Chlamydomonas acidophila grown on NH4+
 or NO3- under covariation of CO2 and Pi-supply in order to determine
 limitations, in a full-factorial design. As expected, results revealed
 higher carbon fixation rates for NH4+-grown cells compared to growth with
 NO3- under low CO2 conditions. NO3--grown cells accumulated more of the
 nine analysed amino acids, especially under Pi-limited conditions,
 compared to cells provided with NH4+. This is probably due to a slower
 protein synthesis in cells provided with NO3-. In contrast to our
 expectations, compared to NH4+-grown cells NO3--grown cells had higher
 photosynthetic efficiency under Pi-limitation. In conclusion, growth on
 the Ni-source NH4+ did not result in a clearly enhanced Ci-assimilation,
 as it was highly dependent on Pi and CO2 conditions (replete or limited).
 Results are potentially connected to the fact that C. acidophila is able
 to use only CO2 as its inorganic carbon (Ci) source.
description: data_nitrate_ammonium
DOI: 10.5061/dryad.648jt
title: Data from: Threshold effect of habitat loss on bat richness in cerrado-forest landscapes

description: Understanding how animal groups respond to contemporary habitat loss and
 fragmentation is essential for development of strategies for species
 conservation. Until now, there has been no consensus about how landscape
 degradation affects the diversity and distribution of Neotropical bats.
 Some studies demonstrate population declines and species loss in impacted
 areas, although the magnitude and generality of these effects on bat
 community structure are unclear. Empirical fragmentation thresholds
 predict an accentuated drop in biodiversity, and species richness in
 particular, when less than 30% of the original amount of habitat in the
 landscape remains. In this study, we tested whether bat species richness
 demonstrates this threshold response, based on 48 sites distributed across
 12 landscapes with 9 to 88% remaining forest in Brazilian cerrado-forest
 formations. We also examined the degree to which abundance was similarly
 affected within four different feeding guilds. The threshold value for
 richness, below which bat diversity declines precipitously, was estimated
 at 47% of remaining forest. To verify if the response of bat abundance to
 habitat loss differed among feeding guilds, we used a model selection
 approach based on Akaike's information criterion. Models accounted
 for the amount of riparian forest, semideciduous forest, cerrado, tree
 plantations, secondary forest, and the total amount of forest in the
 landscape. We demonstrate a nonlinear effect of the contribution of tree
 plantations to frugivores, and a positive linear effect of the amount of
 cerrado to nectarivores and animalivores, the groups that responded most
 to decreases in amount of forest. We suggest that bat assemblages in
 interior Atlantic Forest and cerrado regions of southeastern Brazil are
 impoverished, since we found lower richness and abundance of different
 groups in landscapes with lower amounts of forest. The relatively higher
 threshold value of 47% suggests that bat communities have a relatively
 lower resistance to habitat degradation than other animal groups.
 Accordingly, conservation and restoration strategies should focus on
 increasing the amount of native vegetation of landscapes so as to enhance
 species richness of bats.
description: Bat community data for
 15 landscapes in southeastern BrazilAll information on bats
 was collected in the field by Renata Muylaert. Metadata is described on
 file.Muylaert et al 2016
 Dryad.xlsx