cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84v2f
title: Data from: Genetic sex assignment in wild populations using GBS data: a statistical threshold approach

description: Establishing the sex of individuals in wild systems can be challenging and
 often requires genetic testing. Genotyping-by-sequencing (GBS) and other
 reduced representation DNA sequencing (RRS) protocols (e.g., RADseq,
 ddRAD) have enabled the analysis of genetic data on an unprecedented
 scale. Here, we present a novel approach for the discovery and statistical
 validation of sex-specific loci in GBS datasets. We used GBS to genotype
 166 New Zealand fur seals (NZFS, Arctocephalus forsteri) of known sex. We
 retained monomorphic loci as potential sex-specific markers in the locus
 discovery phase. We then used (i) a sex-specific locus threshold (SSLT) to
 identify significantly male-specific loci within our dataset and (ii) a
 significant sex-assignment threshold (SSAT) to confidently assign sex in
 silico the presence or absence of significantly male-specific loci to
 individuals in our dataset treated as unknowns (98.9% accuracy for
 females; 95.8% for males, estimated via cross-validation). Furthermore, we
 assigned sex to 86 individuals of true unknown sex using our SSAT, and
 assessed the effect of SSLT adjustments on these assignments. From 90
 verified sex-specific loci, we developed a panel of three sex-specific PCR
 primers that we used to ascertain sex independently of our GBS data, which
 we show amplify reliably in at least three other pinniped species. Using
 monomorphic loci normally discarded from large SNP datasets is an
 effective way to identify robust sex-linked markers for non-model species.
 Our novel pipeline can be used to identify and statistically validate
 monomorphic and polymorphic sex-specific markers across a range of species
 and RRS datasets.
description: Sample IDs and Accession
 Numbers for each SRA BiosampleThis csv file includes
 each individual sample ID and its respective SRA biosample accession
 numberSample IDs and Accession
 Numbers.csvSex-Specific Locus
 ManagementThis zip file includes
 the commands to process data in Stacks, then isolate and visualise
 sex-specific loci. The files utilised by these commands are included in an
 "associated files" folder.Statistical Threshold
 ScriptsThis zip file includes
 the commands to determine the SSLT and SSAT for RRS data (to be run in R).
 The files we input into these commands are included in the
 "associated files" folder.Isolation and Alignment
 of Male-specific LociThis zip file includes
 the BLAST matches of our especially male-specific loci (individual
 frequency greater than or equal to 36 males). We ordered and tested primer
 pairs for the best 10 matches among these (NZFS loci
 1-10).
DOI: 10.5061/dryad.40r32
title: Data from: Population divergence in compensatory growth responses and their costs in sticklebacks

description: Compensatory growth (CG) may be an adaptive mechanism that helps to
 restore an organisms’ growth trajectory and adult size from deviations
 caused by early life resource limitation. Yet, few studies have
 investigated the genetic basis of CG potential and existence of
 genetically based population differentiation in CG potential. We studied
 population differentiation, genetic basis, and costs of CG potential in
 nine-spined sticklebacks (Pungitius pungitius) differing in their normal
 growth patterns. As selection favors large body size in pond and small
 body size in marine populations, we expected CG to occur in the pond but
 not in the marine population. By manipulating feeding conditions (viz.
 high, low and recovery feeding treatments), we found clear evidence for CG
 in the pond but not in the marine population, as well as evidence for
 catch-up growth (i.e., size compensation without growth acceleration) in
 both populations. In the marine population, overcompensation occurred
 individuals from the recovery treatment grew eventually larger than those
 from the high feeding treatment. In both populations, the recovery feeding
 treatment reduced maturation probability. The recovery feeding treatment
 also reduced survival probability in the marine but not in the pond
 population. Analysis of interpopulation hybrids further suggested that
 both genetic and maternal effects contributed to the population
 differences in CG. Hence, apart from demonstrating intrinsic costs for
 recovery growth, both genetic and maternal effects were identified to be
 important modulators of CG responses. The results provide an evidence for
 adaptive differentiation in recovery growth potential.
description: Primary data on growth,
 maturation and survivalThe data includes the
 cross-type, family and individual identifiers for all the 400 individual
 fish used in the experiment, as well as their size (standard length, in
 mm) at 15 different time points until day 510 after hatching when the
 experiments were terminated. Included is also information on day of
 maturation and survival. All the variables and their coding are described
 in second spread sheet of the file.AbGhani&Merila_2014_data.xlsx
DOI: 10.5061/dryad.1992
title: Data from: Heterozygosity-fitness correlations of conserved microsatellite markers in Kentish plovers Charadrius alexandrinus

description: Heterozygosity-fitness correlations (HFCs) are frequently used to examine
 the relationship between genetic diversity and fitness. Most studies have
 reported positive HFCs, although there is a strong bias towards
 investigating HFCs in genetically impoverished populations. We
 investigated HFCs in a large genetically diverse breeding population of
 Kentish plovers Charadrius alexandrinus in Southern Turkey. This small
 shorebird exhibits highly variable mating and care systems and it is
 becoming an ecological model species to understand breeding system
 evolution. Using eleven conserved and six anonymous microsatellite markers
 we tested whether and how heterozygosity was associated with chick
 survival, tarsus and body mass growth controlling for non-genetic effects
 (chick sex, hatching date, length of biparental care and site quality)
 that influence survival and growth. There was no genome-wide effect of
 heterozygosity on fitness and, we did not find any significant effects of
 heterozygosity on growth rates. However, two of the eleven conserved
 markers displayed an association with offspring survival: one marker
 showed a positive HFC whereas the other marker showed a negative HFC.
 Heterozygosity at three further conserved loci showed significant
 interaction with non-genetic variables. In contrast, heterozygosity based
 on anonymous microsatellite loci was not associated with fitness or
 growth. Markers that were correlated with chick survival were not more
 likely to be located in exons or introns than other markers that lacked
 this association.
description: HFC_KPHeterozygosity,
 survival, tarsus and mass growth of Kentish plover chicks hatched at
 Tuzla, Southern Turkey
DOI: 10.5061/dryad.bt5j6k4
title: Data from: Species-specific spatiotemporal patterns of leopard, lion and tiger attacks on humans

description: 1. Large carnivores of the genus Panthera can pose serious threats to
 public safety. Although the annual number of attacks on humans is rare
 compared to livestock depredation, such incidents undermine popular
 support for wildlife conservation and require immediate responses to
 protect human life. 2. We used a space-time scan method to perform a novel
 spatiotemporal analysis of 908 attacks on humans by lions, leopards and
 tigers to estimate the risks of further attacks in the same locales. 3. We
 found that a substantial proportion of attacks were clustered in time and
 space, but the dimension of these outbreaks varied between species. Lion
 outbreaks included more human fatalities, persisted for longer periods of
 time, and extended over larger areas than tiger or leopard outbreaks. 4.
 These techniques could be used by relevant agencies to warn local people
 of risks from further attacks within a certain time and distance following
 an initial incident by each species, as well as identify areas that
 require management interventions to address these threats.31-Oct-2018
description: Case file and coordinate
 data for big cat attack SatScan analysis (Packer et al)Attack data used for the
 SatScan analysis for each Panthera population. The first tab is the case
 file data with the first column: case number, second column: number of
 cases (attacks in this case), third column: Year/Month. The second tab is
 the coordinate data (Latitude/Longitude) for each
 attack.PackeretalDRYADdata.xlsx
DOI: 10.5061/dryad.b1366vs
title: Data from: Three-dimensional shape and velocity changes affect responses of a locust visual interneuron to approaching objects

description: Adaptive collision avoidance behaviours require accurate detection of
 complex spatiotemporal properties of an object approaching in an
 animal's natural, 3-dimensional environment. Within the locust, the
 lobula giant movement detector (LGMD) and its postsynaptic partner, the
 descending contralateral movement detector (DCMD) respond robustly to
 images that emulate an approaching 2-dimensional object and exhibit firing
 rate modulation correlated with changes in object trajectory. It is not
 known how this pathway responds to visual expansion of a 3-dimensional
 object or an approaching object that changes velocity, both of which
 representing natural stimuli. We compared DCMD responses to images that
 emulate the approach of a sphere with those elicited by a 2-dimensional
 disc. A sphere evoked later peak firing and deceased sensitivity to the
 ratio of the half size of the object to the approach velocity, resulting
 in an increased threshold subtense angle required to generate peak firing.
 We also presented locusts with a sphere that decreased or increased
 velocity against either a white or flow field background. A velocity
 decrease resulted in transition-associated peak firing followed by a
 firing rate increase that resembled the response to a constant, slower
 velocity. A velocity increase resulted in an earlier increase in the
 firing rate that was more pronounced with an earlier transition. For the
 flow field contrast used here, we observed no effect of background motion
 on responses to approaches along constant or changing velocities. These
 results further demonstrate that this pathway can provide motor circuits
 for behaviour with salient information about complex stimulus dynamics.
description: Stott et al Python
 codePython code to calculate
 stimulus parameters of a disc and sphere based on experimenter input to
 GUI.Stott et al Matlab
 codeMatlab code to
 autodetect DCMD firing parameters
DOI: 10.5061/dryad.d3b3t
title: Data from: Simulated moult reduces flight performance but overlap with breeding does not affect breeding success in a long-distance migrant

description: 1. Long-distance migrants are time-constrained as they need to incorporate
 many annual cycle stages within a year. Migratory passerines moult in the
 short interval between breeding and migration. To widen this interval,
 moult may start while still breeding, but this results in flying with
 moulting wings when food provisioning. 2. We experimentally simulated wing
 gaps in breeding male pied flycatchers by plucking 2 primary feathers from
 both wings. We quantified the nest visitations of both parents, proportion
 of high-quality food brought to the nestlings and adults and nestlings
 condition. Differences in oxidative damage caused by a possible reduction
 in flight efficiency were measured in amounts of ROMs and OXY in the
 blood. We also measured how flight performance was affected with
 recordings of the male`s escape flight using high-speed cameras. Finally,
 we collected data on adult survival, clutch size and laying date in the
 following year. 3. “Plucked” males travelled a 5% shorter distance per
 wingbeat, showing that our treatment reduced flight performance. In line
 with this, “plucked” males visited their nests less often. Females of
 “plucked” males, however, visited the nest more often than controls, and
 fully compensated their partner’s reduced visitation rate. As a result,
 there were no differences between treatments in food quality brought to
 the nest, adult or chick mass or number of successfully fledged chicks.
 Males did not differ in their oxidative damage or local survival to the
 following year. In contrast, females paired with plucked males tended to
 return less often to breed in the next year in comparison to controls, but
 this difference was not significant. For the birds that did return there
 were no effects on breeding. 5. Our results reveal that wing gaps in male
 pied flycatchers reduce their flight performance, but when it occurs
 during breeding they prioritise their future reproduction by reducing
 parental care. As a result, there is no apparent detriment to their
 condition during breeding. Because non-moulting females are able to
 compensate their partner’s reduced care, there is also no immediate costs
 to the offspring, but females may pay the cost suffering from a reduced
 survival.
description: Field and flight
 performance dataExcel tables containing:
 a) Field and oxidative stress data, b) Flight performance data, c) A brief
 explanation about each column.Tomotani_etal_Data.xlsx
DOI: 10.5061/dryad.2c506
title: Data from: Determinants of flammability in savanna grass species

description: 1. Tropical grasses fuel the majority of fires on Earth. In fire-prone
 landscapes, enhanced flammability may be adaptive for grasses via the
 maintenance of an open canopy and an increase in spatiotemporal
 opportunities for recruitment and regeneration. In addition, by burning
 intensely but briefly, high flammability may protect resprouting buds from
 lethal temperatures. Despite these potential benefits of high flammability
 to fire-prone grasses, variation in flammability among grass species, and
 how trait differences underpin this variation, remains unknown. 2. By
 burning leaves and plant parts, we experimentally determined how five
 plant traits (biomass quantity, biomass density, biomass moisture content,
 leaf surface-area-to-volume ratio and leaf effective heat of combustion)
 combined to determine the three components of flammability (ignitability,
 sustainability and combustibility) at the leaf and plant scales in 25
 grass species of fire-prone South African grasslands at a time of peak
 fire occurrence. The influence of evolutionary history on flammability was
 assessed based on a phylogeny built here for the study species. 3. Grass
 species differed significantly in all components of flammability.
 Accounting for evolutionary history helped to explain patterns in
 leaf-scale combustibility and sustainability. The five measured plant
 traits predicted components of flammability, particularly leaf
 ignitability and plant combustibility in which 70% and 58% of variation,
 respectively, could be explained by a combination of the traits. Total
 above-ground biomass was a key driver of combustibility and sustainability
 with high biomass species burning more intensely and for longer, and
 producing the highest predicted fire spread rates. Moisture content was
 the main influence on ignitability, where species with higher moisture
 contents took longer to ignite and once alight burnt at a slower rate.
 Biomass density, leaf surface-area-to-volume ratio and leaf effective heat
 of combustion were weaker predictors of flammability components. 4.
 Synthesis. We demonstrate that grass flammability is predicted from easily
 measurable plant functional traits and is influenced by evolutionary
 history with some components showing phylogenetic signal. Grasses are not
 homogenous fuels to fire. Rather, species differ in functional traits that
 in turn demonstrably influence flammability. This diversity is consistent
 with the idea that flammability may be an adaptive trait for grasses of
 fire-prone ecosystems.
description: Plant trait
 dataIndividual-level data of
 measured plant traitsClump-scale flammability
 traitsIndividual-level data
 for clump-scale flammability traitsPhylogenyPhylogeny of the 25 Poaceae species. The time scale is arbitrary.smallphylogenyLeaf-scale flammability traitsIndividual-level data of leaf-scale flammmability traits
DOI: 10.5061/dryad.6g53s
title: Data from: Quantifying relative fish abundance with eDNA: a promising tool for fisheries management

description: Assessment and monitoring of exploited fish populations are challenged by
 costs, logistics and negative impacts on target populations. These factors
 therefore limit large-scale effective management strategies. Evidence is
 growing that the quantity of eDNA may be related not only to species
 presence/absence, but also to species abundance. In this study, the
 concentrations of environmental DNA (eDNA) from a highly prized sport fish
 species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in
 water samples from 12 natural lakes and compared to abundance and biomass
 data obtained from standardized gillnet catches as performed routinely for
 fisheries management purposes. To reduce environmental variability among
 lakes, all lakes were sampled in spring, between ice melt and water
 stratification. The eDNA concentration did not vary significantly with
 water temperature, dissolved oxygen, pH and turbidity, but was
 significantly positively correlated with relative fish abundance estimated
 as catch per unit effort (CPUE), whereas the relationship with biomass per
 unit effort (BPUE) was less pronounced. The value of eDNA to inform about
 local aquatic species distribution was further supported by the similarity
 between the spatial heterogeneity of eDNA distribution and spatial
 variation in CPUE measured by the gillnet method. Synthesis and
 applications. Large-scale empirical evidence of the relationship between
 the eDNA concentration and species abundance allows for the assessment of
 the potential to integrate eDNA within fisheries management plans. As
 such, the eDNA quantitative method represents a promising population
 abundance assessment tool that could significantly reduce the costs
 associated with sampling and increase the power of detection, the spatial
 coverage and the frequency of sampling, without any negative impacts on
 fish populations.
description: eDNA DATA_ALR et al.
 JAppEcol2015The environmental DNA
 (eDNA) concentration (pg/L) of each sample is provided, including
 replicate measurements. For each site, the latitude, longitude and site
 depth (m) are also provided.DATA_ALR et al.
 JAppEcol2015.xls
DOI: 10.5061/dryad.ck5p92b
title: Data from: Peripherally injected ghrelin and leptin reduce food hoarding and mass gain in the coal tit (Periparus ater)

description: In birds little is known about the hormonal signals that communicate
 nutritional state to the brain and regulate appetitive behaviours. In
 mammals, the peptide hormones ghrelin and leptin elevate and inhibit
 consumption and food hoarding, respectively. In birds, administration of
 both ghrelin and leptin inhibit food consumption. The role of these
 hormones in the regulation of food hoarding in avian species has not been
 examined. To investigate this, we injected wild caught coal tits
 (Periparus ater) with leptin, high-dose ghrelin, low-dose ghrelin and a
 saline control in the laboratory. We then measured food hoarding and mass
 gain, as a proxy of food consumption, every 20 mins for two hours
 post-injection. Both high-dose ghrelin and leptin injections significantly
 reduced hoarding and mass gain compared with controls. Our results provide
 the first evidence that hoarding behaviour can be reduced by both leptin
 and ghrelin in a wild bird. These findings add to evidence that the
 hormonal control of food consumption and hoarding in avian species differs
 from that in mammals. Food hoarding and consumptive behaviours
 consistently show the same response to peripheral signals of nutritional
 state, suggesting that the hormonal regulation of food hoarding has
 evolved from the consumption regulatory system.
description: DataBehavioural response to
 leptin and ghrelin treatment in coal tits.
DOI: 10.5061/dryad.8fg6664
title: Data from: Eggshell spotting pattern is related to hatching asynchrony, hematocrit value and growth of nestling great tits (Parus major)

description: Eggshell pigmentation may signal the quality of the egg, that of the
 female and the environment, and thus nestling development may be related
 to this egg trait. However, so far, few studies have investigated the
 relationship between eggshell pigmentation and nestling development. Our
 aim was to study in a partial cross-fostering experiment whether the
 protoporphyrin-based eggshell pigmentation (spot intensity and spot
 distribution) showed any significant associations with several traits
 related to the development of nestling great tits (Parus major). We found
 that nestlings from clutches with darker spotted eggshells hatched more
 synchronously, had higher hematocrit value and shorter wings. Females
 under adverse environmental circumstances were previously shown to lay
 darker-spotted eggs, and these females probably delayed the start of
 incubation due to energetic constraints, resulting in a more synchronous
 hatching. The shorter wings of fledglings originating from clutches with
 darker-spotted eggs may be caused by the lower general quality of their
 mothers, mediated through either genetic factors or early maternal
 effects. Darker spotted eggs may contain different levels of some
 biomolecules than paler spotted eggs, which could have an effect on
 nestling metabolism and activity, resulting in an elevated hematocrit
 value. More aggregated eggshell spotting was related to faster bone growth
 and slightly longer fledging tarsus length. Eggs with aggregated spotting
 may have thinner eggshells that could lead to hatchlings with smaller
 bones due to the lower availability of calcium during development.
 Neslings may increase bone growth rate to compensate for their smaller
 initial size. Overall, our results indirectly suggest lower fitness for
 nestlings hatched from darker spotted eggs and for nestlings hatched from
 eggs with more aggregated spotting distribution due to the possible
 long-term costs of synchronous hatching, shorter wings, and accelerated
 tarsus growth rate.
description: Hargitai-2018JAV-Eggshell-spotting-pattern-DataDetailed information is in the xls file in the ReadMe worksheet.