cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2631p
title: Data from: Space use by 4 strains of laying hens to perch, wing flap, dust bathe, stand and lie down

description: The laying hen industry is implementing aviary systems intended to improve
 welfare by providing hens with more space and resources to perform
 species-specific behaviors. To date, limited research has examined spatial
 requirements of various strains of laying hens for performing key
 behaviors and none has been conducted within an alternative housing
 system. This study investigated the amount of space used by 4 strains of
 laying hens (Hy-Line Brown [HB], Bovans Brown [BB], DeKalb White [DW], and
 Hy-Line W36) to perform 5 different behaviors in the litter area of a
 commercial-style aviary. Hens were recorded standing [S], lying [L],
 perching [P], wing flapping [WF], and dust bathing [DB] on an open-litter
 area with an outer perch between 12:00 and 15:00 at peak lay (28wk). Still
 images of each behavior were analyzed using ImageJ software for 16 hens
 per strain, and maximum hen length and width were used to calculate total
 area occupied per hen for each behavior. Brown hens required, on average,
 89.6cm2 more space for S (P≤0.021) and 81.5cm2 more space for L (P≤0.013)
 than white hens. White hens used, on average, 572cm2 more space to perform
 WF than brown hens (P≤0.024) while brown hens used 170.3cm2 more space for
 DB than white hens (P≤0.022). On average, hens of all strains were wider
 while perching than the 15cm commonly recommended per hen (e.g., DW:
 18.03; HB: 21.89cm), and brown hens required, on average, 3.38cm more
 space while perching than white hens (P≤0.01). Brown and white hens occupy
 different amounts of space when performing key behaviors. These
 differences, along with factors such as behavioral synchrony, clustering,
 and preferred inter-bird distances associated with these behaviors, should
 be considered when creating industry guidelines, crafting legislation and
 designing and stocking laying hen facilities to ensure hens can fulfill
 their behavioral needs.
description: Raw Data: Space use by 4
 strains laying hensSpreadsheet containing
 information on length, width and area occupied by 4 genetic strains of
 laying hens performing the behaviors of lying, standing, perching, wing
 flapping and dust bathing.Raw Data Space use 4 strains
 laying hens.xlsx
DOI: 10.5061/dryad.2qp80
title: Data from: A unified model explains commonness and rarity on coral reefs

description: Abundance patterns in ecological communities have important implications
 for biodiversity maintenance and ecosystem functioning. However,
 ecological theory has been largely unsuccessful at capturing multiple
 macroecological abundance patterns simultaneously. Here, we propose a
 parsimonious model that unifies widespread ecological relationships
 involving local aggregation, species-abundance distributions, and species
 associations, and we test this model against the metacommunity structure
 of reef-building corals and coral reef fishes across the western and
 central Pacific. For both corals and fishes, the unified model
 simultaneously captures extremely well local species-abundance
 distributions, interspecific variation in the strength of spatial
 aggregation, patterns of community similarity, species accumulation, and
 regional species richness, performing far better than alternative models
 also examined here and in previous work on coral reefs. Our approach
 contributes to the development of synthetic theory for large-scale
 patterns of community structure in nature, and to addressing ongoing
 challenges in biodiversity conservation at macroecological scales.
description: Species-by-sites
 abundance matricesThis zip file contains
 the coral and fish species-by-sites matrices of counts analyzed in the
 linked publication in Ecology Letters. Please see the Data_Readme.txt for
 details.Abunds.zipR code to fit the unified modelThis ZIP file contains 5 files needed to fit the unified model to the data in the CSV files (or similar data, formatted in the same way), to conduct parametric bootstrap goodness-of-fit testing, and to generate out-of-sample predictions of unshared species.Code.zip
DOI: 10.5061/dryad.3d271
title: Data from: Assembly patterns of mixed-species avian flocks in the Andes

description: The relative contribution of deterministic and stochastic processes in the
 assembly of biotic communities is a central issue of controversy in
 community ecology. However, several studies have shown patterns of species
 segregation that are consistent with the hypothesis that deterministic
 factors such as competition and niche-partitioning structure species
 assemblages in animal communities. Community assembly provides a
 theoretical framework for understanding these processes, but it has been
 seldom applied to social aggregations within communities. In this research
 we assessed patterns of non-randomness in Andean mixed-species flocks
 using three assembly models: (a) co-occurrence patterns (b) guild
 proportionality; and (c) constant body-size ratios using data from 221
 species of resident and Neotropical migrant birds participating in 311
 mixed-species flocks at 13 regions distributed in Venezuela, Colombia,
 Ecuador, and Peru. Significant assembly patterns for mixed-species flocks
 based on co-occurrence models and guild proportionality models suggest
 that competitive interactions play an important role in structuring this
 social system in the Andes. Distribution of species among foraging guilds
 (i.e. insectivore, frugivore, omnivore, nectivore) was generally similar
 among flocks, though with some regional variation. In contrast, we found
 little evidence that structuring of mixed-species flocks in the Andes was
 mediated by body size. Rather, we found greater than expected variance of
 body-size ratios within flocks, indicating that birds did not segregate
 morphologically. Overall, our findings suggest that deterministic factors
 associated to competitive interactions are important contributors to
 mixed-species flock assemblages across the Andes.
description: datafiles_Colorado_&_Rodewald_2014Presence-absence matrix for mixed-species bird flocks from 13 regions in Colombia, Venezuela, Ecuador and Peru. Data is presented with scientific names of birds.
DOI: 10.5061/dryad.tq43g
title: Data from: Fluorescent sperm in a transparent worm: validation of a GFP marker to study sexual selection

description: Background: Sexual selection has initially been thought to occur
 exclusively at the precopulatory stage in terms of contests among males
 and female mate choice, but research over the last four decades revealed
 that it often continues after copulation through sperm competition and
 cryptic female choice. However, studying these postcopulatory processes
 remains challenging because they occur internally and therefore are often
 difficult to observe. In the transparent free-living flatworm Macrostomum
 lignano, a recently established transgenic line that expresses green
 fluorescent protein (GFP) in all cell types, including sperm, offers a
 unique opportunity to non-invasively visualise and quantify the sperm of a
 GFP-expressing donor inside the reproductive tract of wild-type recipients
 in vivo. We here test several aspects of the reproductive performance of
 the transgenic individuals and the accuracy of the techniques involved in
 assessing the GFP-expressing worms and their sperm. We then show the
 usefulness of these methods in a study on sperm displacement. Results:
 GFP-expressing worms do not differ from wild-type worms in terms of
 morphology, mating rate and reproductive success. In addition, we show
 that the GFP signal is reliably and unequivocally expressed by all
 GFP-expressing individuals observed under epifluorescence illumination.
 However, the intensity of the GFP signal emitted by sperm of GFP
 expressing donors can vary (which we show to be at least in part due to
 sperm ageing) and the GFP marker is inherited according to Mendel’s laws
 in most, but not all, of the individuals. Nevertheless, we argue these two
 issues can be addressed with an appropriate experimental design. Finally,
 we demonstrate the value of the GFP-techniques by comparing the number of
 GFP-expressing sperm in a wild-type recipient before and after mating with
 a competing sperm donor, providing clear experimental evidence for sperm
 displacement in M. lignano. This result suggests that sperm donors can
 displace previously stored sperm and replace it with their own.
 Conclusion: The availability of the GFP-techniques in a transparent
 organism provide unique opportunities to visualise and quantify internal
 processes in the female reproductive tract after mating, which opens new
 avenues in the study of sexual selection.
description: Datasets,
 Marie-Orleach.et.al., BMC.Evol.BiolDatasetsMarie-Orleach.et.al_BMC.Evol.Biol_datasets.xlsx
DOI: 10.5061/dryad.7h5q8
title: Data from: Social costs enforce honesty of a dynamic signal of motivation

description: Understanding the processes that promote signal reliability may provide
 important insights into the evolution of diverse signaling strategies
 among species. The signals that animals use to communicate must comprise
 mechanisms that prohibit or punish dishonesty, and social costs of
 dishonesty have been demonstrated for several fixed morphological signals
 (e.g. color badges of birds and wasps). The costs maintaining the honesty
 of dynamic signals, which are more flexible and potentially cheatable, are
 unknown. Using an experimental manipulation of the dynamic visual signals
 used by male veiled chameleons (Chamaeleo calyptratus) during aggressive
 interactions, we tested the idea that the honesty of rapid color change
 signals is maintained by social costs. Our results reveal that social
 costs are an important mechanism maintaining the honesty of these dynamic
 color signals − 'dishonest' chameleons whose experimentally
 manipulated coloration was incongruent with their contest behavior
 received more physical aggression than 'honest' individuals.
 This is the first demonstration that the honesty of a dynamic signal of
 motivation − physiological color change − can be maintained by the social
 costliness of dishonesty. Behavioral responses of signal receivers,
 irrespective of any specific detection mechanisms, therefore prevent
 chameleon cheaters from prospering.
description: Trial data +
 metadataThis excel file has two
 tabs. First, a tab with a key for all column headings in the second tab.
 Second, a table of data for the individuals, behaviors, and experimental
 treatments for the trials analyzed in this manuscript.
DOI: 10.15468/dl.eu574r
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Cordia myxa"
 ]
}

 The dataset includes 171 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001133-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.63n3f
title: Data from: Individual variation in parental workload and breeding productivity in female European starlings: is the effort worth it?

description: We analyzed individual variation in work load (nest visit rate) during
 chick-rearing, and the consequences of this variation in terms of breeding
 productivity, in a highly synchronous breeder, the European starling
 (Sturnus vulgaris) focusing on female birds. There was marked (10- to
 16-fold) variation in total, female and male nest visit rates, among
 individuals, but individual variation in female nest visit rate was
 independent of environment (rainfall, temperature) and metrics of
 individual quality (laying date, clutch size, amount of male provisioning
 help), and was only weakly associated with chick demand (i.e., day 6 brood
 size). Female nest visit rate was independent of date and experimentally
 delayed birds provisioned at the same rate as peak-nesting birds;
 supporting a lack of effect of date per se. Brood size at fledging was
 positively but weakly related to total nest visit rate (male + female),
 with &gt;fivefold variation in nest visit rate for any given brood
 size, and in females brood size at fledging and chick mass at fledging
 were independent of female nest visit rate, that is, individual variation
 in workload was not associated with higher productivity. Nevertheless,
 nest visit rate in females was repeatable among consecutive days (6–8
 posthatching), and between peak (first) and second broods, but not among
 years. Our data suggest that individual females behave as if committed to
 a certain level of parental care at the outset of their annual breeding
 attempt, but this varies among years, that is, behavior is not fixed
 throughout an individual's life but represents an annually variable
 decision. We suggest females are making predictable decisions about their
 workload during provisioning that maximizes their overall fitness based on
 an integration of information on their current environment (although these
 cues currently remain unidentified).
description: European Starling
 Provisioning DataNest visit rates,
 individual identifying bands,environmental data and reproductive success
 in European starlings. See ReadMe file for further
 description.Fowler_Williams_EUST
 data.csv
DOI: 10.5061/dryad.t1b051ph
title: Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

description: The cheetah (Acinonyx jubatus) has been described as a species with low
 levels of genetic variation. This has been suggested to be the consequence
 of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to
 the assumption that only small genetic differences exist between the
 described subspecies. However, analysing mitochondrial DNA and
 microsatellites in cheetah samples from most of the historic range of the
 species we found relatively deep phylogeographic breaks between some of
 the investigated populations, and most of the methods assessed divergence
 time estimates predating the postulated bottleneck. Mitochondrial DNA
 monophyly and overall levels of genetic differentiation support the
 distinctiveness of Northern-East African cheetahs (Acinonyx jubatus
 soemmeringii). Moreover, combining archaeozoological and contemporary
 samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are
 unambiguously separated from African subspecies. Divergence time estimates
 from mitochondrial and nuclear data place the split between Asiatic and
 Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya
 using an average mammalian microsatellite mutation rate and at 4700–44 000
 ya employing human microsatellite mutation rates. Cheetahs are vulnerable
 to extinction globally and critically endangered in their Asiatic range,
 where the last 70–110 individuals survive only in Iran. We demonstrate
 that these extant Iranian cheetahs are an autochthonous monophyletic
 population and the last representatives of the Asiatic subspecies A. j.
 venaticus. We advocate that conservation strategies should consider the
 uncovered independent evolutionary histories of Asiatic and African
 cheetahs, as well as among some African subspecies. This would facilitate
 the dual conservation priorities of maintaining locally adapted ecotypes
 and genetic diversity.
description: Microsatellite_scores-67cheetahsScores of 67 cheetahs screened at 18 microsatellite lociDryad-67cheetahs.xls
DOI: 10.5061/dryad.pt886
title: Data from: Sperm competitive ability evolves in response to experimental alteration of operational sex ratio

description: In naturally polygamous organisms such as Drosophila, sperm competitive
 ability is one of the most important components of male fitness and is
 expected to evolve in response to varying degrees of male–male
 competition. Several studies have documented the existence of ample
 genetic variation in sperm competitive ability of males. However, many
 experimental evolution studies have found sperm competitive ability to be
 unresponsive to selection. Even direct selection for increased sperm
 competitive ability has failed to yield any measurable changes. Here we
 report the evolution of sperm competitive ability (sperm defense-P1,
 offense-P2) in a set of replicate populations of Drosophila melanogaster
 subjected to altered levels of male–male competition (generated by varying
 the operational sex ratio) for 55–60 generations. Males from populations
 with female-biased operational sex ratio evolved reduced P1 and P2,
 without any measurable change in the male reproductive behavior. Males in
 the male-biased regime evolved increased P1, but there was no significant
 change in P2. Increase in P1 was associated with an increase in copulation
 duration, possibly indicating greater ejaculate investment by these males.
 This study is one of the few to provide empirical evidence for the
 evolution of sperm competitive ability of males under different levels of
 male–male competition.
description: Nandy et al. Sperm
 competitive ability and associated dataNandy et al.
 data.xlsx
DOI: 10.5061/dryad.3324n
title: Data from: Free-ranging dogs show age related plasticity in their ability to follow human pointing

description: Differences in pet dogs’ and captive wolves’ ability to follow human
 communicative intents have led to the proposition of several hypotheses
 regarding the possession and development of social cognitive skills in
 dogs. It is possible that the social cognitive abilities of pet dogs are
 induced by indirect conditioning through living with humans, and studying
 free-ranging dogs can provide deeper insights into differentiating between
 innate abilities and conditioning in dogs. Free-ranging dogs are mostly
 scavengers, indirectly depending on humans for their sustenance. Humans
 can act both as food providers and as threats to these dogs, and thus
 understanding human gestures can be a survival need for the free-ranging
 dogs. We tested the responsiveness of such dogs in urban areas toward
 simple human pointing cues using dynamic proximal points. Our experiment
 showed that pups readily follow proximal pointing and exhibit weaker
 avoidance to humans, but stop doing so at the later stages of development.
 While juveniles showed frequent and prolonged gaze alternations, only
 adults adjusted their behaviour based on the reliability of the human
 experimenter after being rewarded. Thus free-ranging dogs show a tendency
 to respond to human pointing gestures, with a certain level of behavioural
 plasticity that allows learning from ontogenic experience.
description: RAW DATA_Pointing
 Gesture Experiment-Free-ranging dogsAll data decoded from
 the videos used for the pointing gesture experiment.
DOI: 10.5061/dryad.85g00
title: Data from: Nest inheritance is the missing source of direct fitness in a primitively eusocial insect

description: Animals that co-operate with non-relatives represent a challenge to
 inclusive fitness theory, unless co-operative behavior is shown to provide
 direct fitness benefits. Inheritance of breeding resources could provide
 such benefits, but this route to co-operation has been little investigated
 in the social insects. We show that nest inheritance can explain the
 presence of unrelated helpers in a classic social insect model, the
 primitively eusocial wasp Polistes dominulus. We found that subordinate
 helpers produced more direct offspring than lone breeders, some while
 still subordinate but most after inheriting the dominant position. Thus,
 while indirect fitness obtained through helping relatives has been the
 dominant paradigm for understanding eusociality in insects, direct fitness
 is vital to explain co-operation in P. dominulus.
description: Subordinate co-foundress
 productivitySUMMARY.txt
DOI: 10.5061/dryad.r2cc3
title: Data from: Song rate as a signal of male aggressiveness during territorial contests in the wood warbler

description: Aggressive signaling is an important component in animal communication, as
 it provides an efficient mechanism for settling conflicts over resources
 between competitors. In songbirds, a number of singing behaviors have been
 proposed to be aggressive signals used in territory defense, including
 song rate. Although aggressive signaling in songbirds has received
 considerable research attention, adequate evidence for most putative
 aggressive signals is not available. In this study, we experimentally
 investigated whether the song rate of male wood warblers (Phylloscopus
 sibilatrix) is a signal of their aggressive intent in male-male
 interactions. We found that males responded differentially to simulated
 territorial intrusions depending on the song rate of an intruder.
 Moreover, males that continued to sing during territorial contests
 increased their song rates, and this behavior predicted the strength of
 aggressive escalation by the signaler. These results suggest that song
 rate is an aggressive signal during male-male interactions in the wood
 warbler. We also found high intra-individual repeatability in the strength
 of aggressive response to simulated intrusions, likely reflecting
 differences in personality (aggressiveness) or quality of male wood
 warblers. We conclude that changes in singing rate may be an efficient
 mechanism of signaling immediate shifts in motivation of signalers during
 territorial contests, especially in species that lack large repertoires or
 have simple songs.
description: Szymkowiak and Kuczyński
 - dataIncludes data worksheet
 that detail: (1) behavioral responses of wood warblers to experimental
 treatment; (2) changes in male song rate, average song duration, number of
 syllables per song, and maximum song frequency between experimental
 stages.Szymkowiak and Kuczyński
 dataset.xlsx
DOI: 10.5061/dryad.17371h3
title: Data from: Pathogen shifts in a honey bee predator following arrival of the Varroa mite

description: Emerging infectious diseases (EIDs) are a global threat to honey bees, and
 spillover from managed bees threaten wider insect populations. Deformed
 wing virus (DWV), a widespread virus that has become emergent in
 conjunction with the spread of the mite Varroa destructor, is thought to
 be partly responsible for global colony losses. The arrival of Varroa in
 honey bee populations causes a dramatic loss of viral genotypic diversity,
 favoring a few virulent strains. Here, we investigate DWV spillover in an
 invasive Hawaiian population of the wasp, Vespula pensylvanica, a honey
 bee predator and honey-raider. We show that Vespula underwent a parallel
 loss in DWV variant diversity upon the arrival of Varroa, despite the mite
 being a honey bee specialist. The observed shift in Vespula DWV, and the
 variant-sharing between Vespula and Apis, suggest that these wasps can
 acquire DWV directly or indirectly from honey bees. Apis prey items
 collected from Vespula foragers were positive for DWV, indicating
 predation is a possible route of transmission. We also sought cascading
 effects of DWV shifts in a broader Vespula pathogen community. We
 identified concurrent changes in a suite of additional pathogens, as well
 as shifts in the associations between these pathogens in Vespula and in
 Apis. These findings reveal how hidden effects of the Varroa mite can, via
 spillover, transform the composition of pathogens in interacting species,
 with potential knock-on effects for entire pathogen communities.
description: Pathogen
 dataThis file contains the
 DWV variant sequences and data, as well as the broad pathogen screen data
 for Vespula pensylvanica and Apis mellifera from Hawaii Volcanoes National
 Park.Loope_et_al_pathogen_data.xlsx