cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mn5hn2s
title: Data from: Density-dependent changes in neophobia and stress-coping styles in the world’s oldest farmed fish

description: Farmed fish are typically reared at densities much higher than those
 observed in the wild, but to what extent crowding results in abnormal
 behaviours that can impact welfare and stress coping styles is subject to
 debate. Neophobia (i.e. fear of the ‘new’) is thought to be adaptive under
 natural conditions by limiting risks, but it is potentially maladapted in
 captivity, where there are no predators or novel foods. We reared juvenile
 Nile tilapia (Oreochromis niloticus) for six weeks at either high (50g/L)
 or low density (14g/L), assessed the extent of skin and eye darkening (two
 proxies of chronic stress), and exposed them to a novel object in an
 open-test arena, with and without cover, to assess the effects of density
 on neophobia and stress coping styles. Fish reared at high density were
 darker, more neophobic, less aggressive, less mobile and less likely to
 take risks than those reared at low density, and these effects were
 exacerbated when no cover was available. Thus, the reactive coping style
 shown by fish at high density was very different from the proactive coping
 style shown by fish at low density. Our findings provide novel insights
 into the plasticity of fish behaviour and the effects of aquaculture
 intensification on one of the world’s oldest farmed and most invasive
 fish, and highlight the importance of considering context. Crowding could
 have a positive effect on the welfare of tilapia by reducing aggressive
 behaviour, but it can also make fish chronically stressed and more
 fearful, which could make them less invasive.
description: Tilapia
 behaviourTilapia behaviour reared
 a low and high densityTilapia_Neophobia_data.xlsxTilapia_Body and skin darkeningSkin and body darkening of tilapia reared at low and high density
DOI: 10.5061/dryad.1jv55
title: Data from: Reconstructing the demographic history of orang-utans using approximate Bayesian computation

description: Investigating how different evolutionary forces have shaped patterns of
 DNA variation within and among species requires detailed knowledge of
 their demographic history. Orang-utans, whose distribution is currently
 restricted to the Southeast Asian islands of Borneo (Pongo pygmaeus) and
 Sumatra (Pongo abelii), have likely experienced a complex demographic
 history, influenced by recurrent changes in climate and sea levels,
 volcanic activities and anthropogenic pressures. Using the most extensive
 sample set of wild orang-utans to date, we employed an approximate
 Bayesian computation (ABC) approach to test the fit of 12 different
 demographic scenarios to the observed patterns of variation in autosomal,
 X-chromosomal, mitochondrial and Y-chromosomal markers. In the
 best-fitting model, Sumatran orang-utans exhibit a deep split of
 populations north and south of Lake Toba, probably caused by multiple
 eruptions of the Toba volcano. In addition, we found signals for a strong
 decline in all Sumatran populations ~24 ka, probably associated with
 hunting by human colonizers. In contrast, Bornean orang-utans experienced
 a severe bottleneck ~135 ka, followed by a population expansion and
 substructuring starting ~82 ka, which we link to an expansion from a
 glacial refugium. Therefore, we showed that orang-utans went through
 drastic changes in population size and connectedness, caused by the
 recurrent contraction and expansion of rainforest habitat during
 Pleistocene glaciations, and probably also by the impact of hunting by
 early humans. Our findings also emphasize the fact that important aspects
 of the evolutionary past of species with complex demographic histories
 might remain obscured when applying overly simplified models.
description: Sequence
 alignmentsFasta files containing
 alignments of all sequence loci.Sequence_alignments.zipMicrosatellite genotypesText files containing tab-delimited tables of microsatellite genotypes (one individual per row).Microsatellite_genotypes.zipSummary statistics for ABC analysisText files containing summary statistics used in the ABC analysis.ABC_summarystatistics.zipInput files for ABC analysisInput files used for ABC analysis with ABCtoolbox/fastsimcoal.ABC_inputfiles.zipScripts for ABC analysisCustom-made scripts used in the ABC analysis with ABCtoolbox/fastsimcoal.ABC_scripts.zip
DOI: 10.5061/dryad.6d87m
title: Data from: Recurrent myocardial infarction: mechanisms of free-floating adaptation and autonomic derangement in networked cardiac neural control

description: The cardiac nervous system continuously controls cardiac function whether
 or not pathology is present. While myocardial infarction typically has a
 major and catastrophic impact, population studies have shown that
 longer-term risk for recurrent myocardial infarction and the related
 potential for sudden cardiac death depends mainly upon standard
 atherosclerotic variables and autonomic nervous system maladaptations.
 Investigative neurocardiology has demonstrated that autonomic control of
 cardiac function includes local circuit neurons for networked control
 within the peripheral nervous system. The structural and adaptive
 characteristics of such networked interactions define the dynamics and a
 new normal for cardiac control that results in the aftermath of recurrent
 myocardial infarction and/or unstable angina that may or may not
 precipitate autonomic derangement. These features are explored here via a
 mathematical model of cardiac regulation. A main observation is that the
 control environment during pathology is an extrapolation to a setting
 outside prior experience. Although global bounds guarantee stability, the
 resulting closed-loop dynamics exhibited while the network adapts during
 pathology are aptly described as ‘free-floating’ in order to emphasize
 their dependence upon details of the network structure. The totality of
 the results provide a mechanistic reasoning that validates the clinical
 practice of reducing sympathetic efferent neuronal tone while aggressively
 targeting autonomic derangement in the treatment of ischemic heart
 disease.
description: Networked Mathematical
 ModelThe mathematical model
 is stored in a zip file. The model is written in JAVA. There is a readme
 file that explains how to compile and run the file. If there are any
 questions please contact the first author and full assistance will be
 supplied.DryadRepository.zip
DOI: 10.5061/dryad.fn02v
title: Data from: Arboreality increases reptile community resistance to disturbance from livestock grazing

description: Domestic livestock grazing directly alters ground-level habitat but its
 effects on arboreal habitat are poorly known. Similarly, the response to
 grazing of ground-dwelling fauna has been examined, but there are few
 studies of arboreal fauna. Globally, grazing has been implicated in the
 decline of vertebrate fauna species, but some species appear resistant to
 the effects of grazing, either benefiting from the structural changes at
 ground level or avoiding them, as may be the case with arboreal species.
 Here we examine arboreal and terrestrial habitat responses and reptile
 community responses to grazing, to determine whether arboreal reptile
 species are more resistant than terrestrial reptile species. We conducted
 arboreal and terrestrial reptile surveys on four different grazing
 treatments, at a 19-year experimental grazing trial in northern Australia.
 To compare the grazing response of arboreal and terrestrial reptile
 assemblages, we used community, functional group and individual
 species-level analyses. Species responses were modelled in relation to
 landscape-scale and microhabitat variables. Arboreal reptile species were
 resistant to the impact of grazing, whereas terrestrial reptiles were
 negatively affected by heavy grazing. Terrestrial reptiles were positively
 associated with complex ground structures, which were greatly reduced in
 heavily grazed areas. Arboreal lizards responded positively to
 microhabitat features such as tree hollows. Synthesis and applications.
 Arboreal and terrestrial reptiles have different responses to the impact
 of livestock grazing. This has implications for rangeland management,
 particularly if management objectives include goals relating to conserving
 certain species or functional groups. Arboreal reptiles showed resistance
 in a landscape that is grazed, but where trees have not been cleared. We
 highlight the importance of retaining trees in rangelands for both
 terrestrial and arboreal microhabitats.
description: Wambiana Reptile
 CommunityThe abundance of reptile
 species and micro-habitat measures at the Wambiana Grazing Trial. Data
 comes from biodiversity surveys conducted in April 2014, October 2014,
 April 2015 and October 2015.Dryad_JApEc_ReptilePaperData.xlsx
DOI: 10.5061/dryad.792r3k1
title: Data from: The significance of prey avoidance behaviour for the maintenance of a predator colour polymorphism

description: The existence of conspicuous colour polymorphisms in animals provides an
 ideal opportunity to examine the mechanisms which determine genetic and
 phenotypic variation in populations. It is well known that directional and
 negative frequency-dependent selection by predators can influence the
 persistence of colour polymorphisms in their prey, but much less attention
 has been paid to the idea that prey behaviour could generate selection on
 predator colour morphs. In this study, we examine the role that avoidance
 behaviour by honeybees might play in selection on a colour-polymorphic
 sit-and-wait predator, the crab spider Synema globosum. In two field
 experiments, we offered flowers harbouring spiders of different colour
 morphs to foraging honeybees. In the first, we tested for a pre-existing
 propensity in honeybees to avoid one spider morph over another, and
 whether this behaviour is influenced by the flower species on which
 spiders hunt. In the second, we tested the ability of bees to learn to
 avoid spider morphs associated with a previous simulated attack. Our
 results suggest that honeybees do not impose strong directional selection
 on spider morphs in our study population, and that avoidance behaviour is
 not influenced by flower species. However, we find evidence that honeybees
 learn to avoid spiders of a colour morph that has previously been
 associated with a simulated attack. These findings are the first empirical
 evidence for a mechanism by which prey behaviour might generate negative
 frequency-dependent selection on predator colour morphs, and hence
 potentially influence the long-term persistence of genetic and phenotypic
 diversity in predator populations.
description: Data from prey avoidance
 and predator colour polymorphismData from two
 experiments designed to test the impact of predator colour polymorphism on
 prey behaviour.
DOI: 10.5061/dryad.627
title: Data from: The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda)

description: The importance of fossils to phylogenetic reconstruction is well
 established. However, analyses of fossil data sets are confounded by
 problems related to the less complete nature of the specimens. Taxa that
 are incompletely known are problematic because of the uncertainty of their
 placement within a tree, leading to a proliferation of most parsimonious
 solutions and wild card behavior. Problematic taxa are commonly deleted
 based on a priori criteria of completeness. Paradoxically, a taxon's
 problematic behavior is tree dependent, and levels of completeness are not
 directly associated with problematic behavior. Exclusion of taxa based on
 completeness eliminates real character conflict and, by not allowing
 incomplete taxa to determine tree topology, the phylogenetic hypothesis is
 diminished. The phylogenetic trunk approach is proposed to allow
 optimization of taxonomic inclusion and tree stability. This method is
 used in an analysis of the Paleozoic Lepospondyli. A single most
 parsimonious tree, or trunk, is found after removal of one taxon
 identified as being problematic. The 38 trees found one additional step
 from this primary trunk are reduced to two by removal of one additional
 taxon. These trunks are compared to the trees found by excluding taxa with
 various degrees of completeness. Effects of incomplete taxa are explored
 in light of the trunk. Correlated characters associated with limblessness
 are discussed regarding the assumption of character independence, but
 inclusion of intermediate taxa is found to be the single best method for
 breaking down long branches.
description: Anderson Data
 SetAnderson.txt
DOI: 10.5061/dryad.hb15m
title: Data from: Contrasting effects of specialist and generalist herbivores on resistance evolution in invasive plants

description: Invasive alien plants are likely to be released from specialist herbivores
 and at the same time encounter biotic resistance from resident generalist
 herbivores in their new ranges. The Shifting Defense Hypothesis predicts
 that this will result in evolution of decreased defense against specialist
 herbivores and increased defense against generalist herbivores. To test
 this, we performed a comprehensive meta-analysis of 61 common garden
 studies that provide data on resistance and/or tolerance for both
 introduced and native populations of 32 invasive plant species. We
 demonstrate that introduced populations, relative to native populations,
 decreased their resistance against specialists, and increased their
 resistance against generalists. These differences were significant when
 resistance was measured in terms of damage caused by the herbivore, but
 not in terms of performance of the herbivore. Furthermore, we found the
 first evidence that the magnitude of resistance differences between
 introduced and native populations depended significantly on herbivore
 origin (i.e. whether the test herbivore was collected from the native or
 non-native range of the invasive plant). Finally, tolerance to generalists
 was found to be higher in introduced populations, while neither tolerance
 to specialists nor that to simulated herbivory differed between introduced
 and native plant populations. We conclude that enemy release from
 specialist herbivores and biotic resistance from generalist herbivores
 have contrasting effects on resistance evolution in invasive plants. Our
 results thus provide strong support for the Shifting Defense Hypothesis.
description: data
DOI: 10.5061/dryad.34dr2
title: Data from: Finding the gap: A brightness-based strategy for guidance in cluttered environments

description: The ability to move safely between obstacles is critical for animals that
 fly rapidly through cluttered environments but surprisingly little is
 known about how they achieve this. Do they reactively avoid obstacles or
 do they instead fly towards the gaps between them? If they aim towards
 gaps, what information do they use to detect and fly through them? Here,
 we aim to answer these questions by presenting orchid bees with different
 apertures. When negotiating gaps, orchid bees locate and fly close to the
 point that gives them greatest clearance from the edges. The cue that they
 use to pinpoint this spot is the brightness gradient formed across the
 aperture. Furthermore, we find that orchid bees also rely on brightness
 cues to locate gaps that are sufficiently large to safely negotiate. The
 advantage of using brightness for locating and negotiating gaps in a
 cluttered environment is that it provides information about the safest
 path through obstacles, at least in a forest environment. This
 brightness-based guidance strategy for gap detection and negotiation
 represents a fast, computationally simple and efficient mechanism to
 identify the clearest path through a forest and is therefore likely to
 represent a more general mechanism used by other animals.
description: Data for manuscript
 RSPB-2015-2988.R1This file contains all
 of the raw data presented in the manuscript 'Finding the Gap: A
 brightness-based strategy for guidance in cluttered
 environments'.RSPB
 data.xlsx
DOI: 10.5061/dryad.1kv63
title: Data from: Loss of reproductive output caused by an invasive species

description: We investigated whether Neogobius melanostomus, an invader of biodiversity
 ‘hot-spots’ in the Laurentian Great Lakes region, facilitates or inhibits
 unionid mussel recruitment by serving as a host or sink for their
 parasitic larvae (glochidia). Infestation and metamorphosis rates of four
 mussel species with at-risk (conservation) status (Epioblasma torulosa
 rangiana, Epioblasma triquetra, Lampsilis fasciola and Villosa iris) and
 one common species (Actinonaias ligamentina) on N. melanostomus were
 compared with rates on known primary and marginal hosts in the laboratory.
 All species successfully infested N. melanostomus, but only E. triquetra,
 V. iris and A. ligamentina successfully metamorphosed into juveniles,
 albeit at very low rates well below those seen on even the marginal hosts.
 Neogobius melanostomus collected from areas of unionid occurrence in the
 Grand and Sydenham rivers (Ontario, Canada) exhibited glochidial infection
 rates of 39.4% and 5.1%, respectively, with up to 30 glochidia
 representing as many as six unionid species per fish. A mathematical model
 suggests that N. melanostomus serve more as a sink for glochidia than as a
 host for unionids, thereby limiting recruitment success. This represents a
 novel method by which an invasive species affects a native species.
description: Tremblay-et-al-ESMDimensions of female unionids used for infestation experiments, and the viability of their glochidia Unionid mussel and fish pairings, and total lengths of experimental fish
DOI: 10.5061/dryad.8c4196f
title: Data from: Reproductive success of a keystone herbivore is more variable and responsive to climate in habitats with lower resource diversity

description: 1. The effects of climate on wild populations are often channeled through
 species interactions. Population responses to climate variation can
 therefore differ across habitats, owing to variation in the biotic
 community. Theory predicts that consumer demography should be less
 variable and less responsive to climate in habitats with greater resource
 diversity. 2. We tested these predictions using a long-term study of
 breeding lesser snow geese along the western coast of Hudson Bay,
 Manitoba, Canada. Reproductive success was measured in 22 years from 114
 locations, in either coastal or inland habitat types. We used Bayesian
 analysis to estimate the response of reproductive success to climate in
 each habitat type, along with residual variation not explained by climate.
 We then quantified gosling diet composition in each habitat type to test
 the prediction that reproductive success would be less variable and more
 responsive to climate in habitats with lower resource diversity. 3.
 Reproductive success responded positively to seasonal warmness, but this
 response was much stronger in inland habitats than in coastal habitats.
 Site- and year-level random effects were also three to five times more
 variable in inland habitats. Simultaneously, land cover diversity and
 gosling diet diversity were lower in inland habitats. 4. Our study
 illustrates that spatial variation in resource diversity (and thus,
 species interactions) can have important effects on consumer responses to
 climate. In this system, climate change is expected to disproportionately
 increase the reproductive success of snow geese in vast inland habitats,
 potentially counteracting management efforts to reduce the abundance of
 this keystone herbivore.
description: Counts of gosling and
 adult lesser snow geese from banding drivesCounts of goslings and
 adults at banding drives along the west coast of Hudson Bay. Data
 collected in the field as part of a long-term banding effort. Please
 contact David Iles (david.thomas.iles@gmail.com) or Robert Rockwell
 (rfrockwell@gmail.com) with questions about data collection procedures,
 sources of error, and proper use.juv_ad_for_archive.csvLesser snow gosling diet contents collected in western Hudson BayProventriculus contents from lesser snow goslings collected in representative coastal and inland habitat areas.gosling_diet_data_for_archive.csv
DOI: 10.5061/dryad.s1502
title: Data from: Contact networks structured by sex underpin sex-specific epidemiology of infection

description: Contact networks are fundamental to the transmission of infection and host
 sex often affects the acquisition and progression of infection. However,
 the epidemiological impacts of sex-related variation in animal contact
 networks have rarely been investigated. We test the hypothesis that
 sex-biases in infection are related to variation in multilayer contact
 networks structured by sex in a population of European badgers Meles meles
 naturally infected with Mycobacterium bovis. Our key results are that
 male-male and between-sex networks are structured at broader spatial
 scales than female-female networks and that in male-male and between-sex
 contact networks, but not female-female networks, there is a significant
 relationship between infection and contacts with individuals in other
 groups. These sex differences in social behaviour may underpin male-biased
 acquisition of infection and may result in males being responsible for
 more between-group transmission. This highlights the importance of
 sex-related variation in host behaviour when managing animal diseases.
description: Contact_networks_structured_by_sex_underpin_sex_specific_epidemiology_of_infection_Data+RcodeZip folder containing all necessary data and code to replicate the analysis in Contact networks structured by sex underpin sex-specific epidemiology of infection published in Ecology Letters
DOI: 10.5061/dryad.3d727
title: Data from: From the field to the lab: best practices for field preservation of bat specimens for molecular analyses

description: Studies in molecular ecology depend on field-collected samples for genetic
 information, and the tissue sampled and preservation conditions strongly
 affect the quality of the DNA obtained. DNA yields from different tissue
 types have seldom been compared, and the relative performance of storage
 media has never been directly tested, even though these media may
 influence DNA degradation under field conditions. We analyzed DNA yield
 from buccal swabs and wing punches harvested from live bats using nucleic
 acid quantification as well as quantitative PCR for a single-copy nuclear
 locus. We also compared DNA yields from wing tissue preserved in three
 media: ethanol, NaCl-saturated dimethyl sulfoxide (DMSO), and silica
 desiccant. Wing punches yielded more total DNA than did buccal swabs, and
 wing tissues preserved in silica beads yielded significantly more total
 and nuclear DNA than those preserved in DMSO or ethanol. These results
 show that tissue type and preservation media strongly influence the
 quantity of DNA obtained from non-lethal genetic samples, and based on
 these effects we provide recommendations for field collection of tissues
 for genetic analyses.
description: DNA quantification by
 Nanodrop SpectrophotometerAnalysis data of DNA
 yield from buccal swabs and wing punches harvested from live bats using
 nucleic acid quantification as well as DNA yields from wing tissue
 preserved in three media: ethanol, NaCl-saturated dimethyl sulfoxide
 (DMSO), and silica desiccant.corthals_etal_DNAquant_dryad.xlsxDNA quantification qPCRAnalysis data of DNA yield from buccal swabs and wing punches harvested from live bats using quantitative PCR for a single-copy nuclear locus.corthals_etal_qPCR_dryad.xlsx