cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hv4db
title: Data from: Short-term disturbance by a commercial two-dimensional seismic survey does not lead to long-term displacement of harbour porpoises

description: Assessments of the impact of offshore energy developments are constrained
 because it is not known whether fine-scale behavioral responses to noise
 lead to broader-scale displacement of protected small cetaceans. We used
 passive acoustic monitoring and digital aerial surveys to study changes in
 the occurrence of harbour porpoises across a 2000 km2 study area during a
 commercial 2-D seismic survey in the North Sea. Acoustic and visual data
 provided evidence of group responses to air-gun noise from the 470 cu inch
 array over ranges of 5-10 km, at received peak-to-peak sound pressure
 levels of 165-172 dB re 1 µPa and sound exposure levels of 145-151 dB re.
 1µPa2 s. However, animals were typically detected again at affected sites
 within a few hours, and the level of response declined through the 10 day
 survey. Overall, acoustic detections decreased significantly during the
 survey period in the impact area compared to a control area, but this
 effect was small in relation to natural variation. These results
 demonstrate that prolonged seismic survey noise did not lead to
 broader-scale displacement into sub-optimal or higher-risk habitats, and
 suggest that impact assessments should focus on sub-lethal effects
 resulting from changes in foraging performance of animals within affected
 sites.
description: responses to seismic
 surveysZIP file containing 10
 .txt data files as described in readme.txt
DOI: 10.5061/dryad.74tr3
title: Data from: The effect of historical legacy on adaptation: do closely related species respond to the environment in the same way?

description: The many documented examples of parallel and convergent evolution in
 similar environments are strong evidence for the role of natural selection
 in the evolution of trait variation. However, species may respond to
 selection in different ways; idiosyncrasies of their evolutionary history
 may affect how different species respond to the same selective pressure.
 To determine whether evolutionary history affects trait-environment
 associations in a recently diverged lineage, we investigated
 within-species trait-environment associations in the white proteas, a
 closely related monophyletic group. We first used MANOVAs to determine the
 relative importance of shared response to selection, evolutionary history,
 and unique responses to selection on trait variation. We found that on
 average, similar associations to the environment across species explained
 trait variation, but that the species had different mean trait values. We
 also detected species-specific associations of traits to the environmental
 gradients. To identify the traits associated uniquely to the environment
 we used a structural equation model. Our analysis showed that the species
 differed in how their traits were associated with each of the
 environmental variables. Further, in the cases of two root traits (root
 mass and root length:mass ratio), two species differed in the direction of
 their associations (e.g. populations in one species had heavier roots in
 warmer areas, and populations in the other species had lighter roots in
 warmer areas). Our study shows that even in a closely related group of
 species, evolutionary history may have an effect on both the size and
 direction of adaptations to the environment.
description: Roots
 DataRaw data from plants
 grown in the greenhouse.roots_data.csvEnvironmental dataData for collection locales. Soil data were collected, environmental variables were extracted from the South African Atlas of Argohydrology.soil_env.csvEnvironmental PCAs for all white protea locationsPCA values drawn from South African of Agrohydrology for all known locations of the white proteas.all-points-PCA.csv
DOI: 10.15468/dl.tvayzc
title: Occurrence Download

description: A dataset containing 7440 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is Specimen",
 "TaxonKey is one of (Hymenophyllum capillare, Hymenophyllum hirsutum, Hymenophyllum kuhnii, Crepidomanes africanum, Didymoglossum ballardianum, Didymoglossum chamaedrys, Crepidomanes chevalieri, Crepidomanes clarenceanum, Trichomanes crispiforme, Polyphlebium diaphanum, Abrodictyum dregei, Didymoglossum erosum, Crepidomanes fallax, Vandenboschia gigantea, Abrodictyum guineense, Didymoglossum liberiense, Crepidomanes parvulum, Crepidomanes melanotrichum, Crepidomanes mettenii)"
 ]
}

 The dataset includes 7440 records from 219 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000529-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6tv82c4
title: Data from: Metapopulation dynamics of Roseate Terns: sources, sinks and implications for conservation management decisions

description: 1. Habitat management to restore or create breeding sites may allow
 metapopulations to increase in size and reduce the risk of demographic
 stochasticity or disasters causing metapopulation extinction. However, if
 newly restored or created sites are of low quality, they may act as sinks
 that draw individuals away from better quality sites to the detriment of
 metapopulation size. 2. Following intensive conservation effort, the
 metapopulation of roseate tern (Sterna dougallii) in NW Europe is
 recovering from a large crash in numbers, but most former colonies remain
 unoccupied and hence are potential targets for restoration. To inform
 conservation efforts, we studied the dynamics of this metapopulation with
 a multistate integrated population model to assess each of the three main
 colonies for important demographic contributors to population growth rate,
 source/sink status and possible density dependence. 3. All three study
 colonies are managed for roseate terns (and other tern species) in similar
 ways but the demographic processes vary considerably between colonies. The
 largest colony is a source involved in almost all dispersal, and its
 growth is determined by survival rates and productivity. 4. Productivity
 and juvenile apparent survival at the largest colony appear to be density
 dependent. Although the mechanisms are unclear, this may provide an
 increasing impetus for emigration of recruits to other colonies in the
 future. 5. The smallest of the three colonies is a sink, relying on
 immigration for its growth. Simulation models suggest the metapopulation
 would be ~10 % larger in the absence of dispersal to the sink colony. 6.
 This work indicates that, due to variable site quality, aims to enhance
 both distribution and size of metapopulations may be mutually exclusive.
 In this case, before future attempts to encourage recolonisation of former
 sites, assessments of site suitability should be undertaken, focusing on
 food availability and isolation from predators to maximise the likelihood
 of attaining levels of productivity and survival that avoid creation of a
 sink population to the detriment of the overall metapopulation size.
description: Capture-mark-resighting
 history of roseate terns ringed as fledglingsCapture-mark-resighting
 history of individual roseate terns ringed as fledglings in the colonies
 Rockabill (R), Lady's Island Lake (L) and Coquet Island (C) from 1992
 to 2016. A '0' denotes that the individual was not observed that
 year.CH_RLC_Ringed_as_J.txtPopulation count and productivity data for roseate terns in NW EuropeThe data file includes data on breeding pairs and number of fledglings of roseate terns on Rockabill, Lady's Island Lake and Coquet Island, in NW Europe.popcounts.txt
DOI: 10.5061/dryad.t9n0r
title: Data from: Persistence, impacts and environmental drivers of covert infections in invertebrate hosts

description: Background: Persistent covert infections of the myxozoan, Tetracapsuloides
 bryosalmonae, in primary invertebrate hosts (the freshwater bryozoan,
 Fredericella sultana) have been proposed to represent a reservoir for
 proliferative kidney disease in secondary fish hosts. However, we have
 limited understanding of how covert infections persist and vary in
 bryozoan populations over time and space and how they may impact these
 populations. In addition, previous studies have likely underestimated
 covert infection prevalence. To improve our understanding of the dynamics,
 impacts and implications of covert infections we employed a highly
 sensitive polymerase chain reaction (PCR) assay and undertook the first
 investigation of covert infections in the field over an annual period by
 sampling bryozoans every 45 days from three populations within each of
 three rivers. Results: Covert infections persisted throughout the year and
 prevalence varied within and between rivers, but were often &gt; 50%.
 Variation in temperature and water chemistry were linked with changes in
 prevalence in a manner consistent with the maintenance of covert
 infections during periods of low productivity and thus poor growth
 conditions for both bryozoans and T. bryosalmonae. The presence and
 increased severity of covert infections reduced host growth but only when
 bryozoans were also investing in the production of overwintering
 propagules (statoblasts). However, because statoblast production is
 transitory, this effect is unlikely to greatly impact the capacity of
 bryozoan populations to act as persistent sources of infections and hence
 potential disease outbreaks in farmed and wild fish populations.
 Conclusions: We demonstrate that covert infections are widespread and
 persist over space and time in bryozoan populations. To our knowledge,
 this is the first long-term study of covert infections in a field setting.
 Review of the results of this and previous studies enables us to identify
 key questions related to the ecology and evolution of covert infection
 strategies and associated host-parasite interactions.
description: Colony sampling
 dataThis file contains the
 results for each bryozoan colony collected (1 colony = 1 row) during this
 study. Various infection and environmental parameters are presented for
 each colony collected in each river, tree and trip. The first tab contains
 the data and the second tab contains the legend of the first
 tab.Colony_sampling_data.xlsxEnvironmental parameters dataThis file contains the results from the water chemistry analyses for each trip in each river along with water flow measurements taken on-site. The first two tabs contain the data (for water chemistry and flow, respectively) and the third tab contains the legend for the data tabs.Environmental_parameters_data.xlsx
DOI: 10.5061/dryad.j075c
title: Data from: Brain size in birds is related to traffic accidents

description: Estimates suggest that perhaps a quarter of a billion birds are killed by
 traffic annually across the world. This is surprising because birds have
 been shown to learn speed limits. Birds have also been shown to adapt to
 the direction of traffic and lane use, and this apparently results in
 reduced risks of fatal traffic accidents. Such behavioural differences
 suggest that individual birds that are not killed in traffic should have
 larger brains for their body size. We analysed the link between being
 killed by traffic and relative brain mass in 3521 birds belonging to 251
 species brought to a taxidermist. Birds that were killed in traffic indeed
 had relatively smaller brains, while there was no similar difference for
 liver mass, heart mass or lung mass. These findings suggest that birds
 learn the behaviour of car drivers, and that they use their brains to
 adjust behaviour in an attempt to avoid mortality caused by rapidly and
 predictably moving objects.
description: Data for
 paperxls
DOI: 10.5061/dryad.6b678210
title: Data from: The effect of cost surface parameterization on landscape resistance estimates

description: A cost or resistance surface is a representation of a landscape’s
 permeability to animal movement or gene flow and is a tool for measuring
 functional connectivity in landscape ecology and genetics studies.
 Parameterizing cost surfaces by assigning weights to different landscape
 elements has been challenging however, because true costs are rarely
 known; thus, expert opinion is often used to derive relative weights.
 Assigning weights would be made easier if the sensitivity of different
 landscape resistance estimates to relative costs was known. We carried out
 a sensitivity analysis of three methods to parameterize a cost surface and
 two models of landscape permeability: least cost path and effective
 resistance. We found two qualitatively different responses to varying cost
 weights: linear and asymptotic changes. The most sensitive models (i.e.
 those leading to linear change) were accumulated least cost and effective
 resistance estimates on a surface coded as resistance (i.e. where
 high-quality elements were held constant at a low-value, and low-quality
 elements were varied at higher values). All other cost surface scenarios
 led to asymptotic change. Developing a cost surface that produces a linear
 response of landscape resistance estimates to cost weight variation will
 improve the accuracy of functional connectivity estimates, especially when
 cost weights are selected through statistical model fitting procedures. On
 the other hand, for studies where cost weights are unknown and model
 selection is not being used, methods where resistance estimates vary
 asymptotically with cost weights may be more appropriate, because of their
 relative insensitivity to parameterization.
description: Forested landscape -
 conductance gridAscii file representing
 costs to movement for the forested landscape. Values are conductances,
 where high values represent low cost (high conductance). In Canada Lambert
 Conformal Conic projection.Settled landscape -
 conductance gridAscii file representing
 costs to movement for the settled landscape. Values are conductances,
 where high values represent low cost (high conductance). In Canada Lambert
 Conformal Conic projection.forested_landscape_30ptscoordinates of the 30 random points for the forested landscape, in North America Lambert Conformal Conic projectionsettled_landscape_30ptscoordinates of the 30 points for the settled landscape, in North America Lambert Conformal Conic projection
DOI: 10.15468/dl.bu8s3d
title: Occurrence Download

description: A dataset containing 49228 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-143.09 59.19,-95.32 59.19,-95.32 71.49,-143.09 71.49,-143.09 59.19))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi"
 ]
}

 The dataset includes 49228 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000530-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n0k69
title: Data from: Zeno’s paradox in decision making

description: Classical probability theory has been influential in modeling decision
 processes, despite empirical findings that have been persistently
 paradoxical from classical perspectives. For such findings, some
 researchers have been successfully pursuing decision models based on
 quantum theory. One unique feature of quantum theory is the collapse
 postulate, which entails that measurements (or in decision making,
 judgments) reset the state to be consistent with the measured outcome. If
 there is quantum structure in cognition, then there has to be evidence for
 the collapse postulate. A striking, a priori prediction, is that opinion
 change will be slowed down (under idealized conditions frozen) by
 continuous judgments. In physics, this is the quantum Zeno effect. We
 demonstrate a quantum Zeno effect in decision making in humans and so
 provide evidence that advocates the use of quantum principles in decision
 theory, at least in some cases.
description: Experiment 1 Data
 SetData for the first
 experimentExperiment 2 Data
 SetData for the second
 experimentRead
 MeDescription of the
 variables reported in the data sets
DOI: 10.5061/dryad.b0p66dn
title: Data from: Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

description: Understanding the spatial scale of local adaptation and the factors
 associated with adaptive diversity are important objectives for ecology
 and evolutionary biology, and have significant implications for effective
 conservation and management of wild populations and natural resources. In
 this study, we used an environmental association analysis (EAA) to
 identify important bioclimatic variables correlated with putatively
 adaptive genetic variation in a benthic marine invertebrate – the giant
 California sea cucumber (Parastichopus californicus) – spanning coastal
 British Columbia and southeastern Alaska. We used a redundancy analysis
 (RDA) with 3,699 SNPs obtained using RAD sequencing to detect candidate
 markers associated with 11 bioclimatic variables, including sea bottom and
 surface conditions, across two spatial scales (entire study area and
 within sub-regions). At the broadest scale, RDA revealed 59 candidate
 SNPs, 86% of which were associated with mean bottom temperature. Similar
 patterns were identified when population structure was accounted for.
 Additive polygenic scores, which provide a measure of the cumulative
 signal across all candidate SNPs, were strongly correlated with mean
 bottom temperature, consistent with spatially varying selection across a
 thermal gradient. At a finer scale, 23 candidate SNPs were detected,
 primarily associated with surface salinity (26%) and bottom current
 velocity (17%). Our findings suggest that environmental variables may play
 a role as drivers of spatially varying selection for P. californicus.
 These results provide context for future studies to evaluate the genetic
 basis of local adaptation in P. californicus and help inform the relevant
 scales and environmental variables for in situ field studies of putative
 adaptive variation in marine invertebrates.
description: 01-RDA_candidate_snpsscript to perform RDA for detecting candidate SNPs02-compute_polygenic_scoresscript to compute polygenic scores across candidate SNPs3699snps_freqsallele frequencies for RDAcandidates.frqcandidate frequencies for polygenic scoresmeanbottomtemp_atsitesbottom temperature at sites for polygenic scores
DOI: 10.5061/dryad.856rc00
title: Data from: Acoustic adaptation to city noise through vocal learning by a songbird

description: Anthropogenic noise imposes novel selection pressures, especially on
 species that communicate acoustically. Many animals – including insects,
 frogs, whales, and birds – produce sounds at higher frequencies in areas
 with low-frequency noise pollution. Although there is support for animals
 changing their vocalizations in real time in response to noise (i.e.,
 immediate flexibility), other evolutionary mechanisms for animals that
 learn their vocalizations remain largely unexplored. We hypothesize that
 cultural selection for signal structures less masked by noise is a
 mechanism of acoustic adaptation to anthropogenic noise. We test this
 hypothesis by presenting nestling white-crowned sparrows (Zonotrichia
 leucophyrs) less-masked (higher frequency) and more masked (lower
 frequency) tutor songs either during playback of anthropogenic noise
 (noise-tutored treatment) or at a different time from noise playback
 (control treatment). As predicted, we find that noise-tutored males learn
 less-masked songs significantly more often, whereas control males show no
 copying preference, providing strong experimental support for cultural
 selection in response to anthropogenic noise. Further, noise-tutored males
 reproduce songs at higher frequencies than their tutor, indicating a
 distinct mechanism to increase signal transmission in a noisy environment.
 Notably, noise-tutored males achieve lower performance songs than their
 tutors, suggesting potential costs in a sexual selection framework.
description: Background noise L90
 valuesCity-like noise L90
 values used for estimating masking of tutor songsESM_2_RSPB-2018-1356.csvPeak frequency SNRs for tutor songsThe signal-to-noise ratio (SNR) of the peak frequency for each 5ms of sound in each tutor song and which of these time periods the SNR was above the critical ratio in noise.ESM_3_RSPB-2018-1356.csvSong data analyzedSPCC, trill frequency and vocal performance dataESM4_RSPB-2018-1356.xlsx
DOI: 10.5061/dryad.cv507
title: Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

description: How do mutation and gene flow influence population persistence, niche
 expansion, and local adaptation in spatially heterogeneous environments?
 In this article, we analyse a demographic and evolutionary model of
 adaptation to an environment containing two habitats in equal frequencies,
 and we bridge the gap between different theoretical frameworks.
 Qualitatively, our model yields four qualitative types of outcomes: (i)
 global extinction of the population (ii) adaptation to one habitat only,
 but also adaptation to both habitats with (iii) specialized phenotypes, or
 (iv) with generalized phenotypes; and we determine the conditions under
 which each equilibrium is reached. We derive new analytical approximations
 for the local densities and the distributions of traits in each habitat
 under a migration--selection--mutation balance, compute the equilibrium
 values of the means, variances and asymmetries of the local distributions
 of phenotypes, and contrast the effects of migration and mutation on the
 evolutionary outcome. We then check our analytical results by solving our
 model numerically, and also assess their robustness in the presence of
 demographic stochasticity. While increased migration results in a decrease
 in local adaptation, mutation in our model does not influence the values
 of the local mean traits. Yet, both migration and mutation can have
 dramatic effects on population size and even lead to metapopulation
 extinction when selection is strong. Niche expansion, the ability for the
 population to adapt to both habitats, can also be prevented by small
 migration rates and a reduced evolutionary potential characterised by rare
 mutation events of small effects; but niche expansion is otherwise the
 most likely outcome. Although our results are derived under the assumption
 of clonal reproduction, we finally show and discuss the links between our
 model and previous quantitative genetics models.
description: Debarre-etal_2013_JEB_CodesZipped folder containing R and Mathematica codes.