cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2386p
title: Data from: Troubleshooting the potential pitfalls of cross-fostering

description: 1. Cross-fostering is the transfer of offspring between their natal
 environment and a new social environment. This method allows researchers
 to disentangle the genetic and interacting environmental effects that
 influence phenotypes, and is popular in both wild and laboratory studies.
 Here, we discuss three factors that might bias cross-fostering and
 influence ecological and evolutionary conclusions if not accommodated. 2.
 First, cross-fostering tends to be spatially and temporally non-random
 because heterogeneous breeding conditions can result in clustered breeding
 attempts. Second, cross-fostering will often change the brood composition
 because the exchanged broods are unlikely to be precisely matched in age,
 size, and composition. Third, some methods can introduce bias by using a
 systematically structured subset of the population, leading to a
 systematically structured data-set. 3. We use a 12-year case study of wild
 house sparrows (Passer domesticus) to demonstrate how to identify these
 biases with statistical modelling and how to adjust the cross-fostering
 protocol according to the identified biases. 4. In our dataset,
 cross-fostered nestlings were more likely to survive than
 non-cross-fostered nestlings, but post-fledging and overall survival were
 not affected. Survival differed between cross-fostering treatments,
 partially due to temporally non-random breeding conditions and non-random
 offspring selection, demonstrating two of the three forms of bias in data
 from a wild population. 5. In all cases, we suggest using statistical
 models to examine whether cross-fostering opportunities and offspring
 fitness are affected by non-random breeding, changes to the brood
 composition, and biased methodology. We provide guidelines for optimising
 a cross-fostering design and reducing inherent bias.
description: Models 1,3,4, paired
 analysis, supplement models, figures - nestling survival and
 recruitmentNestling survival and
 recruitment in relation to morphometrics and demographic data. Data to
 produce models 1,3,4, and the paired analysis in the main text, models in
 the supplementary information, and figures in the main text and
 supplementary information. For a description of the column names, advice
 on using the data, and units, see the README file.models134pairedandsupplement.txtexplanation-of-columns-20150210.txtModel 2 - recruitmentNestling recruitment in relation to morphometrics and demographic data. Slightly more individuals in this file than the data set for models 1,2,3 etc because the condition of knowing mass on day 2 is relaxed. Data to produce model 2 in the main text. For a description of the column names, advice on using the data, and units, see the second half of the README file.model2.txtexplanation-of-columns-20150210.txt
DOI: 10.5061/dryad.n94sg
title: Data from: Molecular evidence for hybridization in Colias (Lepidoptera: Pieridae): are Colias hybrids really hybrids?

description: Gene flow and hybridization among species dramatically affect our
 understanding of the species as a biological unit, species relationships,
 and species adaptations. In North American Colias eurytheme and Colias
 eriphyle, there has been historical debate over the extent of
 hybridization occurring and the identity of phenotypically intermediate
 individuals as genetic hybrids. This study assesses the population
 structure of these two species to measure the extent of hybridization and
 the genetic identity of phenotypic intermediates as hybrids. Amplified
 fragment length polymorphism (AFLP) marker analysis was performed on 378
 specimens collected from northern California and Nevada. Population
 structure was inferred using a Bayesian/Markov chain Monte Carlo method,
 which probabilistically assigns individuals to genetic clusters. Three
 genetic clusters provided the best fit for the data. C. eurytheme
 individuals were primarily assigned to two closely related clusters, and
 C. eriphyle individuals were mostly assigned to a third, more distantly
 related cluster. There appeared to be significant hybridization between
 the two species. Individuals of intermediate phenotype (putative hybrids)
 were found to be genetically indistinguishable from C. eriphyle,
 indicating that previous work based on the assumption that these
 intermediate forms are hybrids may warrant reconsideration.
description: DWYER_AFLP_Data_for_DryadThis file contains AFLP presence/absence data for the individual insects included in this study. Each individual has a unique identification number and is designated to a number between 1 and 11 according to phenotypic species identification and collection region. Details are included in the key/legend contained within the Excel file.
DOI: 10.5061/dryad.596k1
title: Data from: The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler

description: Translocations are an increasingly common tool in conservation. The
 maintenance of genetic diversity through translocation is critical for
 both the short and long term persistence of populations and species.
 However, the relative spatio-temporal impacts of translocations on neutral
 and functional genetic diversity and how this affects genetic structure
 among the conserved populations overall has received little investigation.
 We compared the impact of translocating different numbers of founders on
 both microsatellite and major histocompatibility complex (MHC) class I
 diversity over a 23-year period in the Seychelles warbler (Acrocephalus
 sechellensis). We found low and stable microsatellite and MHC diversity in
 the source population and evidence for only a limited loss of either type
 of diversity in the four new populations. However, we found evidence of
 significant, but low to moderate, genetic differentiation between
 populations with those populations established with fewer founders
 clustered separately. Stochastic genetic capture (as opposed to subsequent
 drift) was the main determinant of translocated population diversity.
 Further, a strong correlation between microsatellite and MHC
 differentiation suggested that neutral processes outweighed selection in
 shaping MHC diversity in the new populations. These data provide important
 insights into how to optimise the use of translocation as a conservation
 tool.
description: Wright et
 al_DRYADdata_110314An excel file containing
 two sheets. One sheet of microsatellite genotypes and one sheet of major
 histocompatibility (MHC) genotypes of Seychelles warblers, along with a
 unique individual identifier, the island and year of
 sampling.
DOI: 10.5061/dryad.8j0kf
title: Data from: Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer

description: Elucidation of tumour suppression mechanisms is a major challenge in
 cancer biology. Therefore, Peto's paradox, or low cancer incidence in
 large animals, has attracted focus. According to the gene-abundance
 hypothesis, which considers the increase/decrease in cancer-related genes
 with body size, researchers evaluated the associations between gene
 abundance and body size. However, previous studies only focused on a few
 specific gene functions and have ignored the alternative hypothesis
 (metabolic rate hypothesis): in this hypothesis, the cellular metabolic
 rate and subsequent oxidative stress decreases with increasing body size.
 In this study, we have elected to explore the gene-abundance hypothesis
 taking into account the metabolic rate hypothesis. Thus, we
 comprehensively investigated the correlation between the number of genes
 in various functional categories and body size while at the same time
 correcting for the mass-specific metabolic rate (Bc). A number of gene
 functions that correlated with body size were initially identified, but
 they were found to be artefactual due to the decrease in Bc with
 increasing body size. By contrast, immune system-related genes were found
 to increase with increasing body size when the correlation included this
 correction for Bc. These findings support the gene-abundance hypothesis
 and emphasize the importance of also taking into account the metabolic
 rate when evaluating gene abundance–body size relationships. This finding
 may be useful for understanding cancer evolution and tumour suppression
 mechanisms as well as for determining cancer-related genes and functions.
description: supplementary_material_KTMISSN
DOI: 10.5061/dryad.8311n
title: Data from: Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

description: The crop seed is a complex organ that may be composed of the diploid
 embryo, the triploid endosperm and the diploid maternal tissues. According
 to the genetic features of seed characters, two genetic models for mapping
 quantitative trait loci (QTLs) of crop seed traits are proposed, with
 inclusion of maternal effects, embryo or endosperm effects of QTL,
 environmental effects and QTL-by-environment (QE) interactions. The
 mapping population can be generated either from double back-cross of
 immortalized F2 (IF2) to the two parents, from random-cross of IF2 or from
 selfing of IF2 population. Candidate marker intervals potentially
 harboring QTLs are first selected through one-dimensional scanning across
 the whole genome. The selected candidate marker intervals are then
 included in the model as cofactors to control background genetic effects
 on the putative QTL(s). Finally, a QTL full model is constructed and model
 selection is conducted to eliminate false positive QTLs. The genetic main
 effects of QTLs, QE interaction effects and the corresponding P-values are
 computed by Markov chain Monte Carlo algorithm for Gaussian mixed linear
 model via Gibbs sampling. Monte Carlo simulations were performed to
 investigate the reliability and efficiency of the proposed method. The
 simulation results showed that the proposed method had higher power to
 accurately detect simulated QTLs and properly estimated effect of these
 QTLs. To demonstrate the usefulness, the proposed method was used to
 identify the QTLs underlying fiber percentage in an upland cotton IF2
 population. A computer software, QTLNetwork-Seed, was developed for QTL
 analysis of seed traits.
description: A software for mapping
 QTL of seed traitsThis software was
 developed by Qi, Tiang and Xu, Haiming, which could be used to mapping QTL
 of seed traits for several designs including biparental backcross design,
 IF2 designe, random mating or selfing of IF2. The mixed linear model based
 composite interval mapping is used in mapping QTL. The software can
 simultaneously analyze the QTL maternal effects and embryo or endosperm
 effects, as well as their interaction effects with
 environmentsQTLNetwork-Seed.rar
DOI: 10.5061/dryad.d1h318n
title: Data from: Host cues mediate growth and establishment of oak mistletoe (Phoradendron leucarpum, Viscaceae), an aerial parasitic plant.

description: The oak mistletoe (Phoradendron leucarpum, Viscaceae) is well-documented
 to exhibit preference for a few potential host species in a given
 locality, even when many potential host species are present. In trying to
 explain this distribution, we examined the mechanisms by which mistletoe
 seedlings recognize potentially suitable hosts in the Piney Woods
 ecoregion of east Texas. An initial survey of patterns of infection on the
 campus of Sam Houston State University revealed that water oak (Quercus
 nigra) was host to nearly half of the mistletoes observed, despite
 comprising less than 15% of trees surveyed. Field experiments demonstrated
 that light, host physiochemistry, and volatiles released from potential
 host trees serve as cues affecting the viability and establishment of
 mistletoe seedlings. These results provoked further study in controlled
 laboratory settings, in which it was demonstrated that chemical compounds
 in the bark of local host trees (compared to trees that serve as hosts
 elsewhere, but not in our survey) induce significantly although slightly
 greater seedling viability. Establishment of haustoria depended only on
 the presence of these chemicals, regardless of host species. Importantly,
 we demonstrated that three common monoterpenes, limonene, β-myrcene, and
 β-phellandrene induce a positive growth response of mistletoe radicles.
 These results taken together suggest a model to explain local host
 preference in P. leucarpum, in which covariation between mistletoe fruit
 maturity and monoterpene production by hosts determines the distribution
 of successful haustorial establishment.
description: Phoradendron_data_analaysisFiles contain raw data and analysis output
DOI: 10.5061/dryad.4464n
title: Data from: Smaller beaks for colder winters: Thermoregulation drives beak size evolution in Australasian songbirds

description: Birds’ beaks play a key role in foraging, and most research on their size
 and shape has focused on this function. Recent findings suggest that beaks
 may also be important for thermoregulation, and this may drive
 morphological evolution as predicted by Allen's rule. However, the
 role of thermoregulation in the evolution of beak size across species
 remains largely unexplored. In particular, it remains unclear whether the
 need for retaining heat in the winter or dissipating heat in the summer
 plays the greater role in selection for beak size. Comparative studies are
 needed to evaluate the relative importance of these functions in beak size
 evolution. We addressed this question in a clade of birds exhibiting wide
 variation in their climatic niche: the Australasian honeyeaters and allies
 (Meliphagoidea). Across 158 species, we compared species’ climatic
 conditions extracted from their ranges to beak size measurements in a
 combined spatial-phylogenetic framework. We found that winter minimum
 temperature was positively correlated with beak size, while summer maximum
 temperature was not. This suggests that while diet and foraging behavior
 may drive evolutionary changes in beak shape, changes in beak size can
 also be explained by the beak's role in thermoregulation, and winter
 heat retention in particular.
description: CharactersCharacter matrix of morphological traits and climate values averaged to species level.ChoroplethShape files of spatial grid with beak size values attached as attributes of each grid cell. Used to produce choropleth in QGIS.TreesPhylogenetic trees used in this study, stored in Newick format.
DOI: 10.5061/dryad.6nk15
title: Data from: Female Soay sheep do not adjust their maternal care behaviour to the quality of their home range

description: Resource availability, through its impact on the costs and benefits of
 parental care, is expected to influence parental care behaviour. There
 has, to our knowledge, been no attempt to understand how variation in the
 resource use of wild individuals influences individual parental care
 behaviour. To understand how natural resource variability affects maternal
 care in female St. Kilda Soay sheep, we selected 69 females whose home
 ranges varied in quality (measured as the mean percentage cover of Holcus
 lanatus), and recorded the behaviour of each individual and her lamb over
 the period of maternal care. Home range quality did not influence suckling
 or non-suckling behaviours of the female or her lamb, suggesting that
 maternal care did not vary with a female’s access to resources. Growth
 rate analyses confirmed the behavioural results, with no association
 between home range quality and the weight gain of lambs between birth and
 weaning. This work suggests that female Soay sheep faced with poorer
 resources do not favour their own future success over that of their lamb,
 and thereby do not exhibit a conservative reproductive strategy. This may
 be because when resource levels are high during the summer, females are
 able to offset the costs of lactation by consuming additional resources,
 regardless of the location of their home range. Our results suggest that
 more studies characterizing the environment experienced by individual
 animals will be necessary to fully understand how individuals alter their
 behaviour in response to temporal and spatial variation in the
 environment.
description: Lamb behavioural
 dataThis file contains all
 the data necessary to replicated all the lamb behavioural
 analyses.Lamb
 data.csvEwe
 dataThis file contains all
 the data necessary to replicate the analyses of female behavioural
 dataGrowth
 dataThis file contains all
 the data necessary to replicate the analyses of early lamb
 growthCondition
 dataThis file contains all
 the data necessary to repeat the analyses of female body
 condition
DOI: 10.5061/dryad.fc109
title: Data from: Disruptive camouflage impairs object recognition

description: Whether hiding from predators, or avoiding battlefield casualties,
 camouflage is widely employed to prevent detection. Disruptive coloration
 is a seemingly well-known camouflage mechanism proposed to function by
 breaking up an object’s salient features (such as their characteristic
 outline), rendering objects more difficult to recognise. However, while a
 wide range of animals are thought to evade detection using disruptive
 patterns, there is no direct experimental evidence that disruptive
 coloration impairs recognition. Using humans searching for
 computer-generated moth targets, we demonstrate that the number of
 edge-intersecting patches on a target reduces the likelihood of it being
 detected, even at the expense of reduced background matching. Crucially,
 eye-tracking data show that targets with more edge-intersecting patches
 were looked at for longer periods prior to attack, and passed-over more
 frequently during search tasks. We therefore show directly that edge
 patches enhance survivorship by impairing recognition, confirming that
 disruptive coloration is a distinct camouflage strategy, not simply an
 artefact of background matching.
description: fullData_DryadSee attached file for information about variables.
DOI: 10.5061/dryad.37rt1
title: Data from: Transition from conventional to light-emitting diode street lighting changes activity of urban bats

description: Light pollution is rapidly increasing and can have deleterious effects on
 biodiversity, yet light types differ in their effect on wildlife. Among
 the light types used for street lamps, light-emitting diodes (LEDs) are
 expected to become globally predominant within the next few years. In a
 large-scale field experiment, we recorded bat activity at 46 street lights
 for 12 nights each and investigated how the widespread replacement of
 conventional illuminants by LEDs affects urban bats: we compared bat
 activity at municipal mercury vapour (MV) street lamps that were replaced
 by LEDs with control sites that were not changed. Pipistrellus
 pipistrellus was the most frequently recorded species; it was 45% less
 active at LEDs than at MV street lamps, but the activity did not depend on
 illuminance level. Light type did not affect the activity of Pipistrellus
 nathusii, Pipistrellus pygmaeus or bats in the
 Nyctalus/Eptesicus/Vespertilio (NEV) group, yet the activity of P.
 nathusii increased with illuminance level. Bats of the genus Myotis
 increased activity 4·5-fold at LEDs compared with MV lights, but
 illuminance level had no effect. Decreased activity of P. pipistrellus,
 which are considered light tolerant, probably paralleled insect densities
 around lights. Further, our results suggest that LEDs may be less
 repelling for light-averse Myotis spp. than MV lights. Accordingly, the
 transition from conventional lighting techniques to LEDs may greatly alter
 the anthropogenic impact of artificial light on urban bats and might
 eventually affect the resilience of urban bat populations. Synthesis and
 applications. At light-emitting diodes (LEDs), the competitive advantage –
 the exclusive ability to forage on insect aggregations at lights – is
 reduced for light-tolerant bats. Thus, the global spread of LED street
 lamps might lead to a more natural level of competition between
 light-tolerant and light-averse bats. This effect could be reinforced if
 the potential advantages of LEDs over conventional illuminants are applied
 in practice: choice of spectra with relatively little energy in the short
 wavelength range; reduced spillover by precisely directing light; dimming
 during low human activity times; and control by motion sensors. Yet, the
 potential benefits of LEDs could be negated if low costs foster an overall
 increase in artificial lighting.
description: Lewanzik_Voigt_2016_data
DOI: 10.5061/dryad.91qd114b
title: Data from: Genetic structure and differentiation of the Italian Catria horse

description: Catria is one of the 22 native Italian horse breeds that now survive from
 a larger number. 30 individuals, representative of the Catria horse, were
 analyzed for 11 microsatellites and compared to data of 10 breeds reared
 in Italy. Three different approaches, genetic distances, correspondence
 analysis and clustering methods, were considered to study genetic
 relationships among Catria and the other horse populations. Genetic
 differentiation among breeds was highly significant (P &lt; 0.01) for
 all loci. Average FST values indicate that around 10% of the total genetic
 variation was explained by the between-breed differences and the three
 approaches utilized gave similar results. Italian native breeds are
 clearly separated from the other examined breeds. However, by the
 correspondence analysis, the Catria appears closer to Maremmano and
 Murgese. The results of Bayesian approaches give further information
 showing for Catria a common origin with Maremmano and Italian Heavy
 Draught. Genetic relationships among Catria and the other breeds are
 consistent with the breed’s documented history. The data and information
 found here can be utilized in the organization of conservation programmes
 planned to reduce inbreeding and to minimize loss of genetic variability.
description: Bigi - Catria 2011r2 -
 Supplementary Table 1Supplementary Table 1:
 Genetic distances among 11 horse populations; the Reynolds’s distance (Dr)
 is given above the diagonal, below the Nei’s distance
 (Ds).Bigi - Catria 2011r2 -
 Supplementary Table 2Supplementary Table 2:
 Pairwise comparisons of 11 horse populations using FST estimates. All
 pairwise FST differences were significantly larger than 0
 (p&lt;0.001).Bigi - Catria 2011r2 -
 Supplementary Figure 1Supplementary Figure 1:
 Correspondence analysis of allele frequencies for the 11 populations
 studied. The projection is shown on the first two axes.