cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j8058
title: Data from: Kind to kin: weak interference competition among white stork (Ciconia ciconia) broodmates

description: Altricial nestlings in structured families show a diverse array of
 behavioural mechanisms to compete for food, ranging from signalling
 scrambles to aggressive interference. Rates of filial infanticide are
 moderately high in white storks. It has been hypothesized that this
 unusual behaviour is an adaptive parental response to the absence of
 efficient mechanisms of brood reduction (aggression or direct physical
 interference) by nestlings. To test this latter assumption, we analyzed
 video recordings of 41 complete feeding episodes at 32 broods during the
 first half of the nestling period, when nestlings complete 90% of growth
 and chick mortality and size asymmetries are highest. Parents delivered
 food to all nestlings simultaneously by regurgitating on the nest floor.
 No direct (bill to bill) feeding was recorded. Senior nestlings were never
 observed to limit their junior nestlings from eating food, either by
 aggression or physical interference. Experimental feeding tests revealed
 that heavier nestlings handled prey items more efficiently and ate food at
 a higher speed. The high degree of tolerance shown by senior nestlings is
 unusual among birds with similar ecological and phylogenetic affinities,
 such as herons. Tolerance by seniors cannot be easily explained by absence
 of parental favouritism or proximate factors known to affect the
 occurrence of sibling aggression in other species (rate of food transfer,
 brood size, hatching asynchrony or length of nestling period).
description: White stork
 parent-offspring behavioural dataField data collected
 from video recordings at natural and experimental feeding events. The
 Excel file contains 5 sheets: variables for whole broods during natural
 feeding events (Brood data), variables for individual nestlings at natural
 feeding events (Nestling Behaviour), variables for individual nestlings at
 experimental feeding events including chick roles during tugs-of-war
 (1=winner) and assaults (1=actor) (Experimental feeding), occurrence of
 food disputes at broods (Food disputes) and chick mass and length of the
 largest food item at natural broods (Prey size)Dataset.xlsx
DOI: 10.5061/dryad.9ch60
title: Data from: Warming magnifies predation and reduces prey coexistence in a model litter arthropod system

description: Climate warming can destabilize interactions between competitors as
 smaller organisms gain advantages in warmer environments. Whether and how
 warming-induced effects on competitive interactions are modified by
 predation remains unknown. We hypothesized that predation will offset the
 competitive advantage of smaller prey species in warmer environments
 because of their greater vulnerability to predation. To test this, we
 assembled a litter arthropod community with two Collembola species
 (Folsomia candida and Proisotoma minuta) of different body sizes across a
 temperature gradient (three thermal environments) and in the presence and
 absence of predatory mites. Predatory mites reduced Collembola coexistence
 with increasing temperatures. Contradicting our hypothesis, the larger
 prey species always outperformed the smaller prey species in warmer
 environments with predators. Larger prey probably benefited as they
 expressed a greater trait (body length) plasticity to warming. Warming can
 thus magnify predation effects and reduce the probability of prey
 coexistence.
description: Thakur et al. - Prey and
 predator population dataThe data contains the
 population density of two prey species and the total population of
 predators in response to warming, predation and competition. Please check
 meta-data to get the abbreviation of codes.Thakuretal-RawData.xlsx
DOI: 10.5061/dryad.v2k50
title: Data from: Local plant adaptation across a subarctic elevational gradient

description: Predicting how plants will respond to global warming necessitates
 understanding of local plant adaptation to temperature. Temperature may
 exert selective effects on plants directly, and also indirectly through
 environmental factors that covary with temperature, notably soil
 properties. However, studies on the interactive effects of temperature and
 soil properties on plant adaptation are rare, and the role of abiotic
 versus biotic soil properties in plant adaptation to temperature remains
 untested. We performed two growth chamber experiments using soils and
 Bistorta vivipara bulbil ecotypes from a subarctic elevational gradient
 (temperature range: ±3°C) in northern Sweden to disentangle effects of
 local ecotype, temperature, and biotic and abiotic properties of soil
 origin on plant growth. We found partial evidence for local adaption to
 temperature. Although soil origin affected plant growth, we did not find
 support for local adaptation to either abiotic or biotic soil properties,
 and there were no interactive effects of soil origin with ecotype or
 temperature. Our results indicate that ecotypic variation can be an
 important driver of plant responses to the direct effects of increasing
 temperature, while responses to covariation in soil properties are of a
 phenotypic, rather than adaptive, nature.
description: Plant biomass and bulbil
 weight measurementsBistorta vivipara
 biomass data from Experiment 1 and Experiment 2. Dry weight of Bistorta
 vivipara bulbils collected from 450 m, 700 m, and 900 m elevation
 (Abisko).Data
 file.xlsx
DOI: 10.5061/dryad.2n97q
title: Data from: Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus) population in north-eastern Europe

description: Spatial genetics is a relatively new field in wildlife and conservation
 biology that is becoming an essential tool for unravelling the
 complexities of animal population processes, and for designing effective
 strategies for conservation and management. Conceptual and methodological
 developments in this field are therefore critical. Here we present two
 novel methodological approaches that further the analytical possibilities
 of STRUCTURE and DResD. Using these approaches we analyse structure and
 migrations in a grey wolf (Canis lupus) population in north-eastern
 Europe. We genotyped 16 microsatellite loci in 166 individuals sampled
 from the wolf population in Estonia and Latvia that has been under strong
 and continuous hunting pressure for decades. Our analysis demonstrated
 that this relatively small wolf population is represented by four genetic
 groups. We also used a novel methodological approach that uses linear
 interpolation to statistically test the spatial separation of genetic
 groups. The new method, which is capable of using program STRUCTURE
 output, can be applied widely in population genetics to reveal both core
 areas and areas of low significance for genetic groups. We also used a
 recently developed spatially explicit individual-based method DResD, and
 applied it for the first time to microsatellite data, revealing a
 migration corridor and barriers, and several contact zones.
description: Autosomal microsatellite
 data for Estonian-Latvian wolf populationThe data file includes
 16 microsatellite locus data for 166 wolves from Estonia and Latvia.
 Tissue samples were collected across the species range in Estonia and
 Latvia between 2004-2009.16_autosomal_microsat_loci_Estonian_Latvian_wolves.xlsx
DOI: 10.5061/dryad.c3b0260
title: Data from: Functional heterogeneity within the rodent lateral orbitofrontal cortex dissociates outcome devaluation and reversal learning deficits

description: The orbitofrontal cortex (OFC) is critical for updating reward-directed
 behaviours flexibly when outcomes are devalued or when task contingencies
 are reversed. Failure to update behaviour in outcome devaluation and
 reversal learning procedures are considered canonical deficits following
 OFC lesions in non-human primates and rodents. We examined the generality
 of these findings in rodents using lesions of the rodent lateral OFC (LO)
 in instrumental action-outcome and Pavlovian cue-outcome devaluation
 procedures. LO lesions disrupted outcome devaluation in Pavlovian but not
 instrumental procedures. Furthermore, although both anterior and posterior
 LO lesions disrupted Pavlovian outcome devaluation, only posterior LO
 lesions were found to disrupt reversal learning. Posterior but not
 anterior LO lesions were also found to disrupt the attribution of
 motivational value to Pavlovian cues in sign-tracking. These novel
 dissociable task- and subregion-specific effects suggest a way to
 reconcile contradictory findings between rodent and non-human primate OFC
 research.
description: PanayiKillcross2018_DatafilesData from all figures and analyses conducted in Panayi and Killcross (2018, eLife). See 'ReadMe' file for identification of each file. Data stored as .csv files.
DOI: 10.5061/dryad.t0554g0
title: Data from: Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota

description: Nutrient supply to ecosystems has major effects on ecological diversity,
 but it is unclear to what degree the shape of this relationship is general
 versus dependent on the specific environment or community. Although the
 diet composition in terms of the source or proportions of different
 nutrient types is known to affect gut microbiota composition, the
 relationship between the quantity of nutrients supplied and the abundance
 and diversity of the intestinal microbial community remains to be
 elucidated. Here we address this relationship using replicate populations
 of Drosophila melanogaster maintained over multiple generations on three
 diets differing in the concentration of yeast (the only source of most
 nutrients). While a 6.5-fold increase in yeast concentration led to a
 100-fold increase in the total abundance of gut microbes, it caused a
 major decrease in their alpha diversity (by 45-60 % depending on the
 diversity measure). This was accompanied by only minor shifts in the
 taxonomic affiliation of the most common operational taxonomic units
 (OTUs). Thus, nutrient concentration in host diet mediates a strong
 negative relationship between the nutrient abundance and microbial
 diversity in the Drosophila gut ecosystem.
description: Data File
 1The
 number of OTUs retained for the community analysis, with the numbers of
 reads attributed to them in each sample.Data File
 2Raw
 ct values from the qPCR used to quantify the abundance of
 microbiota
DOI: 10.5061/dryad.n914n
title: Data from: Population structure and seasonal migration of the spotted eagle ray, Aetobatus narinari

description: Few studies have reported on the fine-scale population genetics of batoid
 species in the Atlantic basin. Here, we investigate the genetic diversity
 and population structure of the spotted eagle ray, Aetobatus narinari,
 sampled in the northeastern and southwestern parts of the Gulf of Mexico
 and in the northwestern Caribbean Sea. Samples were collected from 286
 individuals sampled across 3 geographic localities. Estimates of
 divergence based on the mitochondrial cytochrome b gene and 10 nuclear
 microsatellite loci reveal weak but significant genetic structure among A.
 narinari populations in this region. Analysis of molecular variance
 estimates based on both marker types indicate significant differentiation
 between Florida and Mexico populations, while comparisons with Cuba
 suggest high levels of gene flow with rays from both Mexico and Florida.
 Conflicting results were found from the different marker types when sexes
 were analyzed separately underscoring the importance of applying multiple
 marker types when making inferences about population structure and
 sex-biased dispersal. Results from Bayesian clustering analyses suggest
 rays may be migrating south out of the Gulf of Mexico and into the
 northwestern Caribbean Sea. Given the impacts of fisheries on this
 species, coupled with the lack of population genetic data available, these
 findings offer valuable information to aid with conservation management
 strategies.
description: A. narinari unique
 haplotype sequencesMitochondrial DNA
 cytochrome b sequences containing 10 unique haplotypes from Aetobatus
 narinari collected in the Gulf of Mexico and northern Caribbean
 Sea.SERUNIQUEALIGN.fastaA. narinari microsatellite genotype dataNuclear genotype data from 10 microsatellite loci collected from A. narinari in the Gulf of Mexico and northern Carribean Sea.SER_msat_genotype_data.txt
DOI: 10.5061/dryad.c8mh3
title: Data from: Phylogeography of the snake pipefish, Entelurus aequoreus (Family: Syngnathidae) in the northeastern Atlantic Ocean

description: The snake pipefish, Entelurus aequoreus, is a widespread marine species
 occurring in pelagic and coastal environments in the northeastern Atlantic
 Ocean. Recently, the snake pipefish underwent a short-lived, yet
 substantial, increase in abundance and range expansion into arctic waters.
 However, little is known about the species’ population structure or if
 different ecotypes contributed to this outbreak. Specimens (n=178) were
 sampled from 25 locations from six regions spanning 1.9 million km2. A
 fragment of the mitochondrial cytochrome b gene and control region was
 used to assess population structure and genetic diversity. Both loci
 showed high haplotype diversity (Hd) and low nucleotide diversity (π) over
 all sampled locations. A genetic signature of population expansion was
 evident through mismatch distributions and tests for recent population
 expansion (Fu’s Fs, Tajima’s D, and R2). Effective population size
 analyses (Bayesian Skyline Plot) suggest an ancient expansion (50-100
 thousand years ago). However, we found neither significant population
 differentiation (AMOVA) among regions, nor evidence of genetically
 distinct ecotypes. This lack of structure is likely due to a pelagic life
 style, fast development and long distance dispersal aided by ocean
 currents. Our work highlights the need for further research to better
 understand the recent outbreak and how this species may respond to future
 environmental challenges.
description: Braga Goncalves et al.
 data for dryadEntelurus aequoreus
 specimens and voucher specimens used for DNA sequencing. Location,
 collection, habitat, collection date (m/d/yr), latitude, longitude,
 responsible persons for making collections (collected by), sex of
 individual (in most cases by visual inspection and not verified by gonad
 inspection), total length (TL) in mm, total wet weight (WT) in grams,
 reproductive status of males, notes, and gene bank assession #s for
 cytochrome b and control region sequences are listed for each individual.
 na = not applicable. ? = unknownBraga Goncalves et al data for
 dryad.csv
DOI: 10.5061/dryad.54sn3
title: Data from: Fuelwood sustainability revisited: integrating size structure and resprouting into a spatially realistic fuelshed model

description: Much concern has been expressed about the sustainability of fuelwood
 harvesting in Africa. Most models predict that demand will outstrip supply
 within a few decades, resulting in severe deforestation. However, despite
 substantial impacts of harvesting on woody vegetation structure, the
 ‘fuelwood crisis’ predicted since the 1970s has not materialized. We
 propose that this is at least partially because regeneration through
 coppicing has been poorly accounted for in most models. We developed a
 local fuelwood model that is demographically and spatially explicit, and
 that incorporates coppice dynamics. The model simulates the dynamics of
 multiple stem size classes (seedling, sapling, pole and adult), the
 harvesting decisions of villagers based on fuelwood availability and
 village demand across the landscape. Importantly, we specify
 size-dependent coppice production of cut stems, and the probability of
 progression of coppice shoots into larger size classes, after accounting
 for self-thinning of shoots. In general, our model projections for a rural
 South African savanna system suggest that current levels of harvesting
 (barring changes in human population size) are relatively sustainable.
 Declines in total woody biomass were predicted to be modest (˜20%), and
 the loss of intact stems of sapling size was predicted to be more than
 offset by increases in coppiced stems. Synthesis and applications. The
 results from our local fuelwood model clearly demonstrate that the impact
 of deforestation and wood removal on tree populations and wood resources
 is strongly influenced by the resprouting ability of trees. This
 highlights the importance of considering coppice dynamics when assessing
 the sustainability of wood harvesting. Our model is not system specific,
 and can be transferred to other systems, with the relevant parameters and
 geographic information system layers specified. Because of the
 transferability of this model, it can help address key international
 concerns about deforestation and sustainable fuelwood management.
description: Matlab code and data
 files for executing fuelwood harvesting modelZipped file containing
 main Matlab script, two user-contributed functions, and three text raster
 files containing input data for running the model.Twine_Holdo_Fuelshed_Model.zip
DOI: 10.15468/dl.hkaf9c
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gonatus antarcticus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 115 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001141-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.03g17
title: Data from: The effect of population bottlenecks on mutation rate evolution in asexual populations

description: In the absence of recombination, a mutator allele can spread through a
 population by hitchhiking with beneficial mutations that appear in its
 genetic background. Theoretical studies over the past decade have shown
 that the survival and fixation probability of beneficial mutations can be
 severely reduced by population size bottlenecks. Here, we use
 computational modelling and evolution experiments with the yeast S.
 cerevisiae to examine whether population bottlenecks can affect mutator
 dynamics in adapting asexual populations. In simulation, we show that
 population bottlenecks can inhibit mutator hitchhiking with beneficial
 mutations and are most effective at lower beneficial mutation supply
 rates. We then subjected experimental populations of yeast propagated at
 the same effective population size to three different bottleneck regimes
 and observed that the speed of mutator hitchhiking was significantly
 slower at smaller bottlenecks, consistent with our theoretical
 expectations. Our results, thus, suggest that bottlenecks can be an
 important factor in mutation rate evolution and can in certain
 circumstances act to stabilize or, at least, delay the progressive
 elevation of mutation rates in asexual populations. Additionally, our
 findings provide the first experimental support for the theoretically
 postulated effect of population bottlenecks on beneficial mutations and
 demonstrate the usefulness of studying mutator frequency dynamics for
 understanding the underlying dynamics of fitness-affecting mutations.
description: simulator_v1_5Wright-Fisher implementing population simulation (in python)simExample parameter fileExperimental ResultsMutator frequencies in experimental yeast populations
DOI: 10.5061/dryad.2k527b8
title: Data from: Cardiac plasticity influences aerobic performance and thermal tolerance in a tropical, freshwater fish at elevated temperatures

description: Fishes faced with novel thermal conditions often modify physiological
 functioning to compensate for elevated temperatures. This physiological
 plasticity (thermal acclimation) has been shown to improve metabolic
 performance and extend thermal limits in many species. Adjustments in
 cardiorespiratory function are often invoked as mechanisms underlying
 thermal plasticity because limitations in oxygen supply have been
 predicted to define thermal optima in fishes, however few studies have
 explicitly linked cardiorespiratory plasticity to metabolic compensation.
 Here we quantify thermal acclimation capacity in the commercially
 harvested Nile perch (Lates niloticus) of East Africa, and investigate
 mechanisms underlying observed changes. We reared juvenile Nile perch for
 3 months under two temperature regimes, and then measured a series of
 metabolic traits (e.g., aerobic scope, AS) and critical thermal maximum
 (CTmax) upon acute exposure to a range of experimental temperatures. We
 also measured morphological traits of heart ventricles, gills, and brains
 to identify potential mechanisms for compensation. We found that long-term
 (3-months) exposure to elevated temperature induced compensation in upper
 thermal tolerance (CTmax) and metabolic performance (SMR, MMR and AS), and
 induced cardiac remodeling in Nile perch. Furthermore, variation in heart
 morphology influenced variations in metabolic function and thermal
 tolerance. These results indicate that plastic changes enacted over longer
 exposures lead to differences in metabolic flexibility when acutely
 exposed to temperature variation. Furthermore, we established functional
 links between cardiac plasticity, metabolic performance, and thermal
 tolerance, providing evidence that plasticity in cardiac capacity may be
 one mechanism for coping with climate change.
description: Metabolic rate and organ
 measurements of Nile perch reared under different
 temperaturesMetabolic rate (SMR,
 MMR, AS), critical thermal maximum (CTmax), and organ (liver, heart, gill,
 brain) measurements of Nile perch (Lates niloticus) reared under two
 temperature regimes (average and warm) and then acutely exposed to a range
 of temperatures in the laboratory.Nyboer&Chapman-JEB2018-CardiacPlasticity-MetabolicPerformance.xlsx
DOI: 10.5061/dryad.1n1kc
title: Data from: Curvilinear telomere length dynamics in a squamate reptile

description: The lack of consensus concerning the impact of telomere length (TL)
 dynamics on survival emphasizes the need for additional studies to
 evaluate the effect of TL on key life-history processes. Using both
 cross-sectional and longitudinal data, we therefore explored age-specific
 TL dynamics in a squamate reptile: the frillneck lizard (Chlamydosaurus
 kingii). Our cross-sectional analyses revealed that young lizards had
 short TL, TL increased in medium-aged lizards, but TL decreased in older
 age cohorts, revealing a curvilinear relationship between TL and frillneck
 lizard age. Neither our cross-sectional nor our longitudinal analyses
 revealed any association between TL dynamics and lizard survival. We
 observed a significant positive relationship between TL and telomerase
 expression (TE), suggesting that TE is a significant determinant of
 frillneck lizard TL dynamics. Importantly, our longitudinal analyses
 revealed a positive relationship between initial TL and telomere attrition
 rate within individual lizards, that is lizards with short initial
 telomeres were subjected to reduced telomere attrition rates compared to
 lizards with long initial TL. Our results strongly suggest that TL and TE
 dynamics in frillneck lizards is not associated with lizard survival but
 rather reflect an adaptation to maintain TL above a critical minimum
 length in order to sustain cellular homeostasis.
description: Telomere and telomere
 expression data used in the manuscript(1) Cross sectional and
 (2) longitudinal data on frillneck lizards telomere length in relation to
 sex, age, survival and temporal change in telomere length. (3) Telomere
 length (TL) in relation to telomerase expression (TE).DRYAD
 data.xls