cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7mf14t0
title: Data from: Wild acorn woodpeckers recognize associations between individuals in other groups

description: According to the social intelligence hypothesis, understanding the
 cognitive demands of the social environment is key to understanding the
 evolution of intelligence. Many important socio-cognitive abilities,
 however, have primarily been studied in a narrow subset of the social
 environment—within-group social interactions—despite the fact that
 between-group social interactions often have a substantial effect on
 fitness. In particular, triadic awareness (knowledge about the
 relationships and associations between others) is critical for navigating
 many types of complex social interactions, yet no existing study has
 investigated whether wild animals can track associations between members
 of other social groups. We investigated inter-group triadic awareness in
 wild acorn woodpeckers (Melanerpes formicivorus), a socially complex
 group-living bird. We presented woodpeckers with socially incongruous
 playbacks that simulated two outsiders from different groups calling
 together, and socially congruous playbacks that simulated two outsiders
 from the same group calling together. Subjects responded more quickly to
 the incongruous playbacks, suggesting that they were aware that the
 callers belonged to two different groups. This study provides the first
 demonstration that animals can recognize associations between members of
 other groups under natural circumstances, and highlights the importance of
 considering how inter-group social selection pressures may influence the
 evolution of cognition.
description: Raw Data for Social
 Cognition PlaybackThis file contains the
 values of all response variables measured as part of a playback experiment
 to test whether acorn woodpeckers can recognize the associations between
 members of other social groups. The file also contains the identifying
 information for each subject and the specific stimuli to which she was
 exposed, the date and time of each playback trial, and a number of factors
 and covariates20180405_2016TriadicAwareness_Data_for_pub.csvDefinitions of all variables in raw data fileThis file contains the name and definition of each variable included in the raw data file20180310_2016TriadicAwareness_Metadata_for_pub.xlsxR code for data analysisThis file contains the R script used for all statistical analyses in this study, as well as the code used to create the figure in the paper20180614_2016TriadicAwareness_Rcode_for_pub.R
DOI: 10.5061/dryad.rr388
title: Data from: Metabolic traits of westslope cutthroat, introduced rainbow trout and their hybrids in an ecotonal hybrid zone along an elevation gradient

description: In the Upper Oldman River, Alberta, introduced non-native hatchery rainbow
 trout hybridize with native westslope cutthroat trout, resulting in a
 hybrid swarm. Rainbow trout dominate at low elevations (&lt;1250 m) in
 the river mainstem, cutthroat in high elevation tributaries (&gt;1400
 m), and hybrids are numerically dominant in the mid-elevation range. We
 hypothesized that metabolism of rainbow trout would exceed that of
 cutthroat trout, and that the elevation gradient in genetic makeup would
 be mirrored by a gradient in metabolic traits, with intermediate traits in
 the hybrid dominated ecotone. Metabolic traits were measured and regressed
 against the genetic makeup of individuals and elevation. Rainbow trout had
 higher oxygen consumption rates (OCR), higher white muscle lactate
 dehydrogenase (LDH) and citrate synthase (CS) activity, and higher plasma
 acetylcholinesterase (AchE) than cutthroat trout. Hybrids had intermediate
 OCR and AchE, but LDH activity as high as rainbow trout. While hybrid
 zones are usually modeled as a balance between cross species mating and
 selection against hybrids, ecotonal hybrid zones, where hybrids
 proliferate in intermediate habitats and have traits that appear well
 suited to ecotonal conditions, have been proposed for some plants and
 animals, and may have important implications for resource management and
 conservation.
description: Rasmussen et al data
 fileThe data set contains a
 number of measurements of metabolic traits measured on field caught fish
 (oxygen consumption rate, white muscle LDH and CS, and plasma
 acetylcholinesterase, together with the genotypes (pure rainbow trout,
 pure cutthroat trout or hybrid) body size data and the elevation of the
 site at which each was captured. These were the data used to generate the
 models presented in the paper.Rasmussen et al data
 file.xls
DOI: 10.5061/dryad.4p49n3mj
title: Data from: Evolutionary dynamics of separate and combined exposure of Pseudomonas fluorescens SBW25 to antibiotics and bacteriophage

description: The use of bacteriophages against pathogenic bacteria in health care and
 in the food industry is now being advocated as an alternative to the use
 of antibiotics. But what is the evolutionary response for a bacterial
 population if both antibiotics and phages are used in combination? We
 employ an experimental evolution approach to address these questions and
 exposed Pseudomonas fluorescens SBW25 and a related hypermutator strain
 (mutS-) to the action of the antibiotic rifampicin and the lytic
 bacteriophage SBW25φ2. We then compared the densities, growth rates, and
 the mutations at the rpoB locus leading to rifampicin resistance of the
 evolved bacterial populations. We observed that the evolutionary response
 of populations under different treatments varied depending on the order in
 which the antimicrobials were added and whether the bacterium was a
 hypermutator. We found that wild type rifampicin-resistant populations
 involved in biofilm formation often reverted to rifampicin sensitivity
 when stresses were added sequentially. In contrast, when the mortality
 agents were added simultaneously, phage populations frequently went
 extinct and the bacteria evolved antibiotic resistance. Finally,
 populations of the hypermutator mutS- converged to a single genotype at
 the rpoB locus. Future investigation on other bacteria and using different
 antibiotics and bacteriophage are needed to evaluate the generality of our
 findings.
description: Data for
 Datadryad
DOI: 10.15468/dl.yptee9
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nothocestrum latifolium",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 30 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000964-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2m6t6
title: Data from: Functionally relevant responses to human facial expressions of emotion in the domestic horse (Equus caballus)

description: Whether non-human animals can recognize human signals, including emotions,
 has both scientific and applied importance, and is particularly relevant
 for domesticated species. This study presents the first evidence of
 horses' abilities to spontaneously discriminate between positive
 (happy) and negative (angry) human facial expressions in photographs. Our
 results showed that the angry faces induced responses indicative of a
 functional understanding of the stimuli: horses displayed a left-gaze bias
 (a lateralization generally associated with stimuli perceived as negative)
 and a quicker increase in heart rate (HR) towards these photographs. Such
 lateralized responses towards human emotion have previously only been
 documented in dogs, and effects of facial expressions on HR have not been
 shown in any heterospecific studies. Alongside the insights that these
 findings provide into interspecific communication, they raise interesting
 questions about the generality and adaptiveness of emotional expression
 and perception across species.
description: Smith et al. Raw
 Data
DOI: 10.5061/dryad.br360
title: Data from: Are Brazil nut populations threatened by fruit harvest?

description: Harvest of Brazil nuts from the large, iconic tree Bertholletia excelsa
 generates substantial income for smallholders, providing a strong
 incentive to conserve the mature forests where it grows. Although much
 previous work has focused on the impact of nut harvest on new seedling
 recruits into B. excelsa populations, the connection between harvest rates
 and long-term population stability is still unclear. Moreover, there is
 additional uncertainty for Brazil nut management in terms of population
 response to climate change and other anthropogenic influences. We drew on
 14 years of research in two sites in Acre, Brazil with different B.
 excelsa nut harvest intensities (39% and 81%), to produce stochastic and
 deterministic matrix population models which incorporated parameter
 uncertainty in vital rates. Adult abundance was projected to remain close
 to the current observed abundance or higher through the next 50 years.
 Elasticity analyses revealed that the asymptotic population growth rate
 (λ) was most sensitive to stasis vital rates in sapling, juvenile, and
 adult stages. Deterministic transition matrices calculated using diameter
 growth rates dependent on rainfall yielded average λ values around 1.0
 under extreme high, extreme low, and average annual rainfall. While
 sustained high rates of Brazil nut harvest and climate change could
 potentially negatively impact B. excelsa populations, changes in human use
 of the forested landscape are more immediate concern. To reduce the risk
 of population decline, smallholders and managers of B. excelsa rich
 forests should focus on conservation of pre-mature and mature individuals.
description: Cachoeira growth and
 fruit productionDBH growth and fruit
 production data for trees in the Cachoeira study site from 2008 to
 2015.Cachoeira regeneration
 Oliveira 2011Filipinas regeneration
 Oliveira 2011Cachoeira
 survivalFilipinas
 survival
DOI: 10.5061/dryad.5dd67
title: Data from: Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species

description: Host–parasite interactions are ubiquitous in nature. However, how parasite
 population genetic structure is shaped by the interaction between host and
 parasite life history remains understudied. Studies comparing multiple
 parasites infecting a single host can be used to investigate how different
 parasite life history traits interplay with host behaviour and life
 history. In this study, we used 10 newly developed microsatellite loci to
 investigate the genetic structure of a parasitic bat fly (Basilia nana).
 Its host, the Bechstein's bat (Myotis bechsteinii), has a social
 system and roosting behaviour that restrict opportunities for parasite
 transmission. We compared fly genetic structure to that of the host and
 another parasite, the wing-mite, Spinturnix bechsteini. We found little
 spatial or temporal genetic structure in B. nana, suggesting a large,
 stable population with frequent genetic exchange between fly populations
 from different bat colonies. This contrasts sharply with the genetic
 structure of the wing-mite, which is highly substructured between the same
 bat colonies as well as temporally unstable. Our results suggest that
 although host and parasite life history interact to yield similar
 transmission patterns in both parasite species, the level of gene flow and
 eventual spatiotemporal genetic stability is differentially affected. This
 can be explained by the differences in generation time and winter survival
 between the flies and wing-mites. Our study thus exemplifies that the
 population genetic structure of parasites on a single host can vary
 strongly as a result of how their individual life history characteristics
 interact with host behaviour and life history traits.
description: BasiliaNanaMicrosatelliteDataThis file contains the microsatellite data for Basilia nana analyzed in the paper: van Schaik J, Dekeukeleire D, Kerth G (2015) Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species. Molecular Ecology.
DOI: 10.5061/dryad.82hs7
title: Data from: When east meets west: population structure of a high- latitude resident species, the boreal chickadee (Poecile hudsonicus)

description: The population genetic structure of northern boreal species has been
 strongly influenced both by the Quaternary glaciations and the presence of
 contemporary barriers, such as mountain ranges and rivers. We used a
 combination of mitochondrial DNA (mtDNA), nuclear microsatellites and
 spatial distribution modelling to study the population genetic structure
 of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to
 investigate whether historical or contemporary barriers have influenced
 this northern species. MtDNA data showed evidence of eastern and western
 groups, with secondary admixture occurring in central Canada. This
 suggests that the boreal chickadee probably persisted in multiple glacial
 refugia, one in Beringia and at least one in the east. Palaeo-distribution
 modelling identified suitable habitat in Beringia (Alaska), Atlantic
 Canada and the southern United States, and correspond to divergence dates
 of 60–96 kya. Pairwise FST values for both mtDNA and microsatellites were
 significant for all comparisons involving Newfoundland, though mtDNA data
 suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear
 data support population connectivity among the continental populations,
 possibly due to male-biased dispersal. Although both are significant, the
 isolation-by-distance signal is much stronger for mtDNA (r2=0.51) than for
 microsatellites (r2=0.05), supporting the hypothesis of male-biased
 dispersal. The population structure of the boreal chickadee was influenced
 by isolation in multiple refugia and contemporary barriers. In addition to
 geographical distance, physical barriers such as the Strait of Belle Isle
 and northern mountains in Alaska are restricting gene flow, whereas the
 Rocky Mountains in the west are a porous barrier.
description: Microsatellite raw data
 of 6 loci for boreal chickadees across North AmericaThe file contains the
 raw sizes for six microsatellite loci. Regions were isolated using
 M13-labelled target-site specific primers and run on a 6% gel using a
 LI-COR 4300 DNA Analyzer. Sizes were scored by hand relative to 4
 standards and a mystery plate. Samples were either collected in the field
 or were provided by museums (see SI).HDY-12-OR0281-microsatellite
 raw data.xlsx
DOI: 10.5061/dryad.6hb7j
title: Data from: Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

description: Knowledge of phylogenetic relationships among species is fundamental to
 understanding basic patterns in evolution and underpins nearly all
 research programs in biology and paleontology. However, most methods of
 phylogenetic inference typically used by paleontologists do not
 accommodate the idiosyncrasies of fossil data and therefore do not take
 full advantage of the information provided by the fossil record. The
 advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is
 especially promising for paleosystematists because time-stamped
 comparative data can be combined with probabilistic models tailored to
 accommodate the study of fossil taxa. Under a Bayesian framework, the
 recently developed fossilized birth–death (FBD) process provides a more
 realistic tree prior model for paleontological data that accounts for
 macroevolutionary dynamics, preservation, and sampling when inferring
 phylogenetic trees containing fossils. In addition, the FBD tree prior
 allows for the possibility of sampling ancestral morphotaxa. Although
 paleontologists are increasingly embracing probabilistic phylogenetic
 methods, these recent developments have not previously been applied to the
 deep-time invertebrate fossil record. Here, I examine phylogenetic
 relationships among Ordovician through Devonian crinoids using a Bayesian
 tip-dating approach. Results support several clades recognized in previous
 analyses sampling only Ordovician taxa, but also reveal instances where
 phylogenetic affinities are more complex and extensive revisions are
 necessary, particularly among the Cladida. The name Porocrinoidea is
 proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids
 and hybocrinids. The Eucladida is proposed as a clade name for the sister
 group of the Flexibilia herein comprised of cladids variously considered
 ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.
description: Supplementary Data
 1Characters used in
 phylogenetic analysis.Supplementary Data
 2Nexus file containing
 the character matrix and age range calibrations.Supplementary Data
 3Comparison of marginal
 log-likelihood scores and Bayes Factors for phylogenetic model
 selection.Supplementary Data
 4Tree
 file containing the maximum clade credibility tree from the best fit
 model.
DOI: 10.5061/dryad.m23c6
title: Data from: The role of host phenology in determining the incidence of an insect sexually transmitted infection

description: Changes in the timing of life history events within the year alter the
 degree to which the activity patterns of different species coincide,
 making the dynamics of interspecific interactions sensitive to the
 phenology of the interacting parties. For parasites, the availability of
 suitable hosts to infect represents a crucial determinant of dynamics, and
 changes in the host (and parasite) phenology may thus alter disease
 epidemiology and the conditions for disease maintenance. We tested the
 hypothesis that the incidence of a sexually transmitted mite infection,
 Coccipolipus hippodamiae, in Adalia bipunctata ladybird beetles in Sweden
 was determined by host phenology, namely presence/absence of sexual
 contact between cohorts of the host. We observed that the pattern of mite
 presence/absence across Swedish A. bipunctata populations was highly
 reproducible between years, implying a persistent biological/ecological
 basis underlying the incidence. Further, ladybirds from populations where
 the mite was absent were able to acquire mites during copulation, develop
 a mite infection, and transmit infection onward, indicating an ecological
 (rather than biological) driver of mite incidence. Observations of
 ladybird phenology in natural populations provided evidence of sexual
 contact between overwintered and new cohort adults in populations where
 the mite was present. In contrast, new cohort ladybirds in the two
 northern Swedish populations where the mite was not present had not had
 sexual contact with the overwintered generation, creating a ‘hard stop’ to
 mite transmission. We conclude that variation in host phenology may be an
 important driver of the incidence of sexually transmitted infections
 (STIs) by determining the presence/absence of sexual contact between
 generations. More generally, we hypothesize that sensitivity to variation
 in host phenology will be highest for parasites like STIs that infect one
 host species, one host life stage and are directly transmitted on contact
 between host individuals.
description: Pastok et al Stockholm
 phenologyData supporting Figure 2
 and Figure 3.
DOI: 10.5061/dryad.26s85
title: Data from: Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

description: The extent of genetic diversity loss and former connectivity between
 fragmented populations are often unknown factors when studying endangered
 species. While genetic techniques are commonly applied in extant
 populations to assess temporal and spatial demographic changes, it is no
 substitute for directly measuring past diversity using ancient DNA (aDNA).
 We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci
 from 64 historical fossil and skin samples of the critically endangered
 Western Australian woylie (Bettongia penicillata ogilbyi), and compared
 them with 231 (n=152 for mtDNA) modern samples. In modern woylie
 populations 15 mitochondrial control region (CR) haplotypes were
 identified. Interestingly, mtDNA CR data from only 29 historical samples
 demonstrated 15 previously unknown haplotypes and detected an extinct
 divergent clade. Through modelling, we estimated the loss of CR mtDNA
 diversity to be between 46% and 91% and estimated this to have occurred in
 the past 2000-4000 years in association with a dramatic population
 decline. Additionally, we obtained near-complete 11-loci microsatellite
 profiles from 21 historical samples. In agreement with the mtDNA data, a
 number of ‘new’ microsatellite alleles was only detected in the historical
 populations despite extensive modern sampling, indicating a nuclear
 genetic diversity loss greater than 20%. Calculations of genetic diversity
 (heterozygosity and allelic rarefaction) showed that these were
 significantly higher in the past and that there was a high degree of gene
 flow across the woylie's historical range. These findings have an
 immediate impact on how the extant populations are managed and we
 recommend the implementation of an assisted migration program to prevent
 further loss of genetic diversity. Our study demonstrates the value of
 integrating aDNA data into current-day conservation strategies.
description: Pacioni_etal_dataData associated with Pacioni, C., Hunt, H., Allentoft, M.E., Vaughan, T.G., Wayne, A.F., Baynes, A., Haouchar, D., Dortch, J., Bunce, M., in press. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Molecular Ecology. Please refer to ReadMe.txt (within the zipped folder) for additional information.
DOI: 10.5061/dryad.g44g3
title: Data from: The narrow gap between norms and cooperative behaviour in a reindeer herding community

description: Cooperation evolves on social networks and is shaped, in part, by norms:
 beliefs and expectations about the behaviour of others or of oneself.
 Networks of cooperative social partners and associated norms are vital for
 pastoralists, such as Saami reindeer herders in northern Norway. However,
 little is known quantitatively about how norms structure
 pastoralists' social networks or shape cooperation. Saami herders
 reported their social networks and participated in field experiments,
 allowing us to gauge the overlap between reported and emergent
 cooperation. We show that individuals' perceptions of reciprocal
 cooperation within their social networks exceeded actual reciprocity,
 although both occurred frequently and were concentrated within herding
 groups. Herders with more extensive cooperation networks received more
 rewards in an economic game. Although herders overestimated reciprocal
 helping, cooperation in this community was still extensive, suggesting
 that perceived norms potentially allow network structures promoting
 cooperation to emerge and be maintained.
description: Cleaned, processed
 data.zip file contains: (1)
 data about herders; (2) gift giving edgelist; (3) social network edgelist;
 (4) dyadic data.saami norms paper
 data.zip