cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b563d
title: Data from: Temperature drives abundance fluctuations, but spatial dynamics is constrained by landscape configuration: implications for climate-driven range shift in a butterfly

description: 1. Prediction of species distributions in an altered climate requires
 knowledge on how global- and local-scale factors interact to limit their
 current distributions. Such knowledge can be gained through studies of
 spatial population dynamics at climatic range margins. 2. Here, using a
 butterfly (Pyrgus armoricanus) as model species, we first predicted based
 on species distribution modelling that its climatically suitable habitats
 currently extend north of its realized range. Projecting the model into
 scenarios of future climate, we showed that the distribution of
 climatically suitable habitats may shift northward by an additional 400 km
 in the future. 3. Second, we used a 13-year monitoring data set including
 the majority of all habitat patches at the species’ northern range margin
 to assess the synergetic impact of temperature fluctuations and spatial
 distribution of habitat, microclimatic conditions and habitat quality, on
 abundance and colonisation-extinction dynamics. 4. The fluctuation in
 abundance between years was almost entirely determined by the variation in
 temperature during the species’ larval development. In contrast,
 colonisation and extinction dynamics were better explained by patch area,
 between-patch connectivity, and host plant density. This suggests that the
 response of the species to future climate change may be limited by future
 land-use and how its host plants respond to climate change. It is thus
 probable that dispersal limitation will prevent P. armoricanus from
 reaching its potential future distribution. 5. We argue that models of
 range dynamics should consider the factors influencing metapopulation
 dynamics, especially at the range edges, and not only broad-scale climate.
 It includes factors acting at the scale of habitat patches such as habitat
 quality and microclimate, and landscape-scale factors such as the spatial
 configuration of potentially suitable patches. Knowledge of population
 dynamics under various environmental conditions, and the incorporation of
 realistic scenarios of future land-use, appear thus essential to provide
 predictions useful for actions mitigating the negative effects of climate
 change.
description: Monitoring
 dataPyrgus armoricanus
 abundance recorded in each site and each yearMonitoring_data.csvSite dataLocation and characteristics of each monitored siteSite_data.csv
DOI: 10.5061/dryad.k9f25
title: Data from: A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations

description: Genotypes are frequently used to assess alternative reproductive
 strategies such as extra-pair paternity and conspecific brood parasitism
 in wild populations. However, such analyses are vulnerable to genotyping
 error or molecular artefacts that can bias results. For example, when
 using multilocus microsatellite data, a mismatch at a single locus,
 suggesting the offspring was not directly related to its putative parents,
 can occur quite commonly even when the offspring is truly related. Some
 recent studies have advocated an ad-hoc rule that offspring must differ at
 more than one locus in order to conclude that they are not directly
 related. While this reduces the frequency with which true offspring are
 identified as not directly related young, it also introduces bias in the
 opposite direction, wherein not directly related young are categorized as
 true offspring. More importantly, it ignores the additional information on
 allele frequencies which would reduce overall bias. In this study, we
 present a novel technique for assessing extra-pair paternity and
 conspecific brood parasitism using a likelihood-based approach in a new
 version of program cervus. We test the suitability of the technique by
 applying it to a simulated data set and then present an example to
 demonstrate its influence on the estimation of alternative reproductive
 strategies.
description: R Code for Brood
 SimulationsThis file is the R code
 used to create the simulated data sets used in this
 manuscript.BroodSimulations.SupplementCode.txt
DOI: 10.5061/dryad.21gd2
title: Data from: Fitness consequences of boldness in juvenile and adult largemouth bass

description: To date, most studies investigating the relationship between personality
 traits and fitness have focused on a single measure of fitness (such as
 survival) at a specific life stage. However, many personality traits
 likely have multiple effects on fitness, potentially operating across
 different functional contexts and stages of development. Here, we address
 the fitness consequences of boldness, under seminatural conditions, across
 life stages and functional contexts in largemouth bass (Micropterus
 salmoides). Specifically, we report the effect of boldness on (1) juvenile
 survivorship in an outdoor pond containing natural prey and predators and
 (2) adult reproductive success in three outdoor ponds across three
 reproductive seasons (years). Juvenile survival was negatively affected by
 boldness, with bolder juveniles having a lower probability of survival
 than shyer juveniles. In contrast, bolder adult male bass had greater
 reproductive success than their shyer male counterparts. Female
 reproductive success was not affected by boldness. These findings
 demonstrate that boldness can affect fitness differently across life
 stages. Further, boldness was highly consistent across years and
 significantly heritable, which suggests that boldness has a genetic
 component. Thus, our results support theory suggesting that fitness
 trade-offs across life stages may contribute to the maintenance of
 personality variation within populations.
description: Data
DOI: 10.15468/dl.5admmr
title: Occurrence Download

description: A dataset containing 30996 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cottus perifretum"
 ]
}

 The dataset includes 30996 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001403-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.27832
title: Data from: Individual variation in the oxidative costs of personality traits

description: 1.‘Personality traits’ are behavioural differences between individuals
 that are stable within individuals. Different combinations of personality
 traits can correlate with fitness variation but the mechanisms remain
 unclear. There is the suggestion that personality reflects variation in
 physiology. For example, ‘fast’ (bold, active, fast exploring) individuals
 are predicted to maintain a higher metabolic rate than ‘slow’ animals. A
 raised metabolic rate can result in a proliferation of reactive oxygen
 species (ROS) which, if unchecked, cause oxidative stress. Thus, the
 ‘extended pace of life theory’ predicts that ‘fast’ individuals will pay
 higher oxidative costs than ‘slow’ ones. Alternatively, stress hormones,
 which are often relatively high in ‘slow’ individuals, can also cause
 proliferation of ROS and subsequent oxidative damage. Here, we assessed
 co-variation between personality and oxidative profile in wild blue tits.
 2.The personality traits neophobia (latency to approach food near novel
 objects), activity level in a novel environment and exploratory tendency
 (controlling for differences in activity) assayed in captivity were
 repeatable within individuals but were uncorrelated with each other.
 Reactive oxygen metabolites (ROMs an index of pro-oxidant status) and OXY
 (antioxidant capacity) were also uncorrelated with each other and did not
 vary with age or sex. Blood sampling birds within three minutes of capture
 from their familiar cage versus after 15 minutes of exposure to a
 standardised stressor did not affect ROMs or OXY. 3.Wintering blue tits
 that were both highly neophobic and exploratory had low OXY defences and
 individuals that showed low neophobia and low exploration had high OXY
 defences. Variation in ROMs was not explained by any personality trait.
 High exploratory tendency also correlated with a reduction in body
 condition in captivity, but body condition did not predict ROMs or OXY.
 Activity level in the exploration trial did not vary with oxidative
 profile or change in body condition. 4.Personality types differed in
 antioxidant defences, and it was the combination of an individual's
 personality traits that proved important. ROS production and antioxidant
 defences will vary due to many processes e.g. resource allocation, not
 just metabolic rate and stress responsiveness. Consequently, the costs of
 personality traits and thus the predictions regarding fitness are complex.
 This article is protected by copyright. All rights reserved.
description: Arnold et al summary of
 dataSummary of main data
 used
DOI: 10.5061/dryad.64m4n
title: Data from: Population genetics of overwintering monarch butterflies, Danaus plexippus (Linnaeus), from central Mexico inferred from mitochondrial DNA and microsatellite markers

description: Population genetic variation and demographic history in Danaus plexippus
 (L.), from Mexico were assessed based on analyses of mitochondrial
 cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp)
 gene segments and seven microsatellite loci. The sample of 133 individuals
 included both migratory monarchs, mainly from four overwintering sites
 within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico
 (states of Michoacán and México), and a nonmigratory population from
 Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were
 relatively low, averaging 0.466 and 0.00073, respectively, for COI, and
 0.629 and 0.00245 for COII. Analysis of molecular variance (AMOVA) of the
 COI data set, which included additional GenBank sequences from a
 nonmigratory Costa Rican population, showed significant population
 structure between Mexican migratory monarchs and nonmigratory monarchs
 from both Mexico and Costa Rica, suggesting limited gene flow between the
 two behaviorally distinct groups. Interestingly, while the COI haplotype
 frequencies of the nonmigratory populations differed from the migratory,
 they were similar to each other, despite the great physical distance
 between them. Microsatellite analyses, however, suggested a lack of
 structure between the two groups, possibly owing to the number of
 significant deviations from Hardy Weinberg equilibrium resulting from
 heterzoygote deficiencies found for most of the loci. Estimates of
 demographic history of the combined migratory MBBR monarch population,
 based on the mismatch distribution and Bayesian skyline analyses of the
 concatenated COI and COII data set (n = 89) suggested a population
 expansion dating to the late Pleistocene (~35,000 to 40,000 years before
 present) followed by a stable effective female population size (Nef) of
 about six million over the last 10,000 years.
description: Monarch butterfly
 microsatellitesMicrosatellite genotypes
 of Danaus plexxipus from MexicoData
 Availability.txt
DOI: 10.15468/dl.p4vvkc
title: Occurrence Download

description: A dataset containing 7423 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Homalodisca vitripennis"
 ]
}

 The dataset includes 7423 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001400-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k95p5
title: Data from: A positive genetic correlation between hypoxia tolerance and heat tolerance supports a controversial theory of heat stress

description: We used quantitative genetics to test a controversial theory of heat
 stress, in which animals overheat when the demand for oxygen exceeds the
 supply. This theory, referred to as oxygen- and capacity-limited thermal
 tolerance, predicts a positive genetic correlation between hypoxia
 tolerance and heat tolerance. We demonstrate the first genetic correlation
 of this kind in a model organism, Drosophila melanogaster. Genotypes more
 likely to fly under hypoxic stress (12% O2) were also more likely to fly
 under heat stress (39°C). This finding prompts new questions about
 mechanisms and limits of adaptation to heat stress.
description: Excel sheet with flight
 probabilities for isofemale lines under three treatmentsline = ID for DPRG line;
 hypoxia25C = % flight at 25C and hypoxia; normoxia39C = % flight at 39C
 and normoxia; normoxia25C = % flight at 25C and
 normoxiadata for
 Dryad.xlsx
DOI: 10.5061/dryad.k2r40
title: Data from: Unifying concepts of biological function from molecules to ecosystems

description: The concept of function arises at all levels of biological study and is
 often loosely and variously defined, especially within ecology. This has
 led to ambiguity, obscuring the common structure that unites levels of
 biological organisation, from mol- ecules to ecosystems. Here we build on
 already successful ideas from molecular biology and complexity theory to
 create a precise definition of biological function which spans levels of
 biological organisation and can be quantified in the unifying currency of
 biomass, enabling comparisons of functional effectiveness (irrespective of
 the specific function) across the field of ecology. We give precise
 definitions of ecological and ecosystem function that bring clarity and
 precision to studies of biodiversity-ecosystem function relationships and
 questions of ecological redundancy. To illustrate the new concepts and
 their unifying power, we construct a simple community-level model with
 nutrient cycling and animal-plant mutualism, emphasising the importance of
 its network structure in determining overall functioning. This type of
 network structure is that of an autocatalytic set of functional
 relationships, which also appears at biochemical, cellular and organism
 levels of organisation, creating a nested hierarchy. This enables a common
 and unifying concept of function to apply from molecular interaction
 networks up to the global ecosystem.
description: Mathematica script for
 community dynamics modelThis script runs in
 Mathematica by Wolfram. It is used to implement the model community
 described in the Appendix as an illustration of an autocatalytic
 ecological system.Community_Dynamics_Model
DOI: 10.5061/dryad.n4g95
title: Data from: Diversity of MHC DQB and DRB genes in the endangered Australian sea lion (Neophoca cinerea)

description: Major histocompatibility complex (MHC) class II molecules have an
 important role in vertebrate adaptive immunity, being responsible for
 recognizing, binding, and presenting specific antigenic peptides to T
 lymphocytes. Here, we study the MHC class II DQB and DRB exon 2 genes of
 the Australian sea lion (Neophoca cinerea), an endangered pinniped species
 that experiences high pup mortality. Following characterization of N.
 cinerea DQB and DRB by molecular cloning, and evaluation of diversity in
 pups across 2 colonies using variant screening (n = 47), 3 DQB alleles and
 10 DRB variants (including 1 pseudogene allele) were identified. The
 higher diversity at DRB relative to DQB is consistent with other studies
 in marine mammals. Despite overall lower MHC class II allelic diversity
 relative to some other pinniped species, we observed similar levels of
 nucleotide diversity and selection in N. cinerea. In addition, we provide
 support for recent divergence of MHC class II alleles. The
 characterization of MHC class II diversity in the Australian sea lion
 establishes a baseline for further investigation of associations with
 disease, including endemic hookworm infection, and contributes to the
 conservation management of this species.
description: Australian sea lion MHC
 DQB and DRB genotypesInformation includes
 list of all individual pups that were genotyped, sample location (Seal Bay
 or Dangerous Reef), and DQB and DRB alleles identified in each
 individual.
DOI: 10.5061/dryad.71n0h48
title: Data from: Electrically induced verbal perseveration: a striatal deafferentation model

description: Objective: The present study aimed to elucidate the neural correlates of
 the deafferentation cognitive model of verbal perseveration (VP) by
 analyzing the connectomics of the sites where electrical stimulation
 elicited VP during awake left glioma surgery. Methods: We retrospectively
 reviewed the anatomical sites that generated VP when electrically
 stimulated, in a series of 21 patients operated on while awake for a left
 glioma. Each stimulation point was manually located on the postoperative
 MRI and then registered to the Montreal Neurological Institute template.
 Connectomics of these sites were further analyzed using Tractotron and
 disconnectome maps. Results: VP stimulation sites were located within the
 white matter surrounding the postero-superior head of the caudate nucleus,
 as well as within the white matter of the external capsule and the
 supero-lateral wall of the temporal horn of the ventricle. Furthermore,
 tractotron and disconnectome maps revealed the connectome of these
 stimulation sites: the inferior fronto-occipital fasciculus,
 fronto-striatal tract, and anterior thalamic radiations. Conclusion: Based
 on these results and other data, we propose the following anatomical
 implementation of the deafferentation cognitive model: the lexico-semantic
 system – comprising different areas linked together through direct
 cortico-cortical connections – sends information to the striatum; the
 striato-thalamic system acts as a tunable filter of this lexico-semantic
 input; and the thalamus projects back to the lexico-semantic system,
 amplifying the targeted response and inhibiting its competitors.
description: Table2MNI coordinates of white
 matter functional sites other than verbal perseveration
 sites.
DOI: 10.5281/zenodo.17978755
title: SHM_415393_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic boat axe collected from Broby in Skåne, currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=690

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/8EA4688A-BF71-461E-97C5-AB31659B993B
DOI: 10.5281/zenodo.17978756
title: SHM_415393_HST_3D

description: Photogrammetric 3D model of a Middle Neolithic boat axe collected from Broby in Skåne, currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=690

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/8EA4688A-BF71-461E-97C5-AB31659B993B
DOI: 10.5061/dryad.36vq2
title: Data from: Reconciling timber extraction with biodiversity conservation in tropical forests using reduced-impact logging

description: 1. Over 20% of the world's tropical forests have been selectively
 logged, and large expanses are allocated for future timber extraction.
 Reduced-impact logging (RIL) is being promoted as best practice forestry
 that increases sustainability and lowers CO2 emissions from logging, by
 reducing collateral damage associated with timber extraction. RIL is also
 expected to minimize the impacts of selective logging on biodiversity,
 although this is yet to be thoroughly tested. 2. We undertake the most
 comprehensive study to date to investigate the biodiversity impacts of RIL
 across multiple taxonomic groups. We quantified birds, bats and large
 mammal assemblage structures, using a before-after control-impact (BACI)
 design across 20 sample sites over a 5-year period. Faunal surveys
 utilized point counts, mist nets and line transects and yielded
 &gt;250 species. We examined assemblage responses to logging, as well
 as partitions of feeding guild and strata (understorey vs. canopy), and
 then tested for relationships with logging intensity to assess the primary
 determinants of community composition. 3. Community analysis revealed
 little effect of RIL on overall assemblages, as structure and composition
 were similar before and after logging, and between logging and control
 sites. Variation in bird assemblages was explained by natural rates of
 change over time, and not logging intensity. However, when partitioned by
 feeding guild and strata, the frugivorous and canopy bird ensembles
 changed as a result of RIL, although the latter was also associated with
 change over time. Bats exhibited variable changes post-logging that were
 not related to logging, whereas large mammals showed no change at all. 4.
 Indicator species analysis and correlations with logging intensities
 revealed that some species exhibited idiosyncratic responses to RIL,
 whilst abundance change of most others was associated with time. 5.
 Synthesis and applications. Our study demonstrates the relatively benign
 effect of reduced-impact logging (RIL) on birds, bats and large mammals in
 a neotropical forest context, and therefore, we propose that forest
 managers should improve timber extraction techniques more widely. If RIL
 is extensively adopted, forestry concessions could represent sizeable and
 important additions to the global conservation estate – over 4 million
 km2.
description: Bicknell et al.
 dataDetection rates of
 birds, bats, and large mammals at each site before and after logging, as
 well as site details and metrics. Each table includes a description to
 interpret the data.
DOI: 10.5061/dryad.143sp
title: Data from: Interactive effects of predation risk and conspecific density on the nutrient stoichiometry of prey

description: The mere presence of predators (i.e., predation risk) can alter consumer
 physiology by restricting food intake and inducing stress, which can
 ultimately affect prey-mediated ecosystem processes such as nutrient
 cycling. However, many environmental factors, including conspecific
 density, can mediate the perception of risk by prey. Prey conspecific
 density has been defined as a fundamental feature that modulates perceived
 risk. In this study, we tested the effects of predation risk on prey
 nutrient stoichiometry (body and excretion). Using a constant predation
 risk, we also tested the effects of varying conspecific densities on prey
 responses to predation risk. To answer these questions, we conducted a
 mesocosm experiment using caged predators (Belostoma sp.), and small
 bullfrog tadpoles (Lithobates catesbeianus) as prey. We found that L.
 catesbeianus tadpoles adjust their body nutrient stoichiometry in response
 to predation risk, which is affected by conspecific density. We also found
 that the prey exhibited strong morphological responses to predation risk
 (i.e., an increase in tail muscle mass), which were positively correlated
 to body nitrogen content. Thus, we pose the notion that in risky
 situations, adaptive phenotypic responses rather than behavioral ones
 might partially explain why prey might have a higher nitrogen content
 under predation risk. In addition, the interactive roles of conspecific
 density and predation risk, which might result in reduced perceived risk
 and physiological restrictions in prey, also affected how prey
 stoichiometry responded to the fear of predation.
description: DataData used for analysis
 and graphs