cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.td13jp3
title: Data from: Effect of canine oxytocin receptor gene polymorphism on the successful training of drug detection dogs

description: Drug detection dogs can be trained to locate various prohibited drugs with
 targeted odors, and they play an important role in interdiction of drug
 smuggling in human society. Recent studies provide the interesting
 hypothesis that the oxytocin system serves as a biological basis for
 co-evolution between dogs and humans. Here, we offer the new possibility
 that genetic variation of the canine oxytocin receptor (OXTR) gene may
 regulate the success of a dog’s training to become a drug detection dog. A
 total of 340 Labrador Retriever dogs that were trained to be drug
 detection dogs in Japan were analyzed. We genotyped an exonic SNP
 (rs8679682) in the OXTR gene and compared the training success rate of
 dogs with different genotypes. We also asked dog trainers in the training
 facility to evaluate subjective personality assessment scores for each
 dog, and examined how each dog’s training success was related to those
 scores. A significant effect of the OXTR genotype on the success of the
 dogs’ training was found, with a higher proportion of dogs carrying the C
 allele (T/C and C/C genotypes) being successful candidates than dogs
 carrying the T/T genotype. Dog personality scores of Training Focus
 (Factor 1) were positively correlated with an increased likelihood that a
 dog would successfully complete training. Although the molecular mechanism
 of the OXTR gene and its functional pathway related to dog behavior
 remains unknown, our findings suggest that canine OXTR gene variants may
 regulate individual differences between dogs in their responsiveness to
 training for drug detection.
description: dog phenotypes and
 genotypesThis file includes
 dog's ID, breed, sex, OXTR genotypes, and personality
 scores.data.xlsx
DOI: 10.5061/dryad.44kh3
title: Data from: Local genetic patchiness but no regional differences between Indo-West Pacific populations of the dogtooth tuna Gymnosarda unicolor

description: Physical barriers can have profound impacts on dispersal in marine
 species. Here, we investigate population structure and levels of
 relatedness among individuals of the coral reef associated fish, the
 dogtooth tuna Gymnosarda unicolor, collected from 15 sites across the
 Indo-West Pacific region. We screened 92 individuals for genetic variation
 at 13 nuclear microsatellite loci and the cytochrome oxidase subunit 1
 (CO1) mitochondrial DNA (mtDNA) gene. We detected no genetic
 differentiation between ocean basins or between sites within ocean basins,
 suggesting G. unicolor possesses a highly mobile larval or juvenile stage.
 In addition, the lack of deep evolutionary mtDNA divergences suggests gene
 flow was also not limited historically. However, comparisons of
 relatedness between pairs of individuals revealed that individuals
 collected from the same site were more related to each other, on average,
 than individuals collected from different sites. Such patterns are
 consistent with chaotic genetic patchiness, a possible consequence of high
 variance in reproductive success and patchy, local recruitment.
description: Microsatellite data -
 dogtoothExcel file containing
 microsatellite data. Missing data are coded with -9.mtDNA data
 fileThis is an is an
 ARLEQUIN input file containing mtDNA data for each
 populationmtDNA
 data.txt
DOI: 10.5061/dryad.12dp5
title: Data from: Vitamin D receptor gene expression and function in a South African population: ethnicity, vitamin D and FokI

description: Polymorphisms of the vitamin D receptor gene (VDR) have been associated
 inconsistently with various diseases, across populations of diverse
 origin. The T(f) allele of the functional SNP FokI, in exon 2 of VDR,
 results in a longer vitamin D receptor protein (VDR) isoform, proposed to
 be less active. Genetic association of VDR with disease is likely
 confounded by ethnicity and environmental factors such as plasma 25(OH)D3
 status. We hypothesized that VDR expression, VDR level and transactivation
 of target genes, CAMP and CYP24A1, depend on vitamin D, ethnicity and FokI
 genotype. Healthy volunteers participated in the study (African, n = 40
 and White, n = 20). Plasma 25(OH)D3 levels were quantified by LC-MS and
 monocytes cultured, with or without 1,25(OH)2D3. Gene expression and
 protein level was quantified using qRT-PCR and flow cytometry,
 respectively. Mean plasma 25(OH)D3 status was normal and not significantly
 different between ethnicities. Neither 25(OH)D3 status nor 1,25(OH)2D3
 supplementation significantly influenced expression or level of VDR.
 Africans had significantly higher mean VDR protein levels
 (P&lt;0.050), nonetheless transactivated less CAMP expression than
 Whites. Genotyping the FokI polymorphism by pyrosequencing together with
 HapMap data, showed a significantly higher (P&lt;0.050) frequency of
 the CC genotype in Africans than in Whites. FokI genotype, however, did
 not influence VDR expression or VDR level, but influenced overall
 transactivation of CAMP and 1,25(OH)2D3-elicited CYP24A1 induction; the
 latter, interacting with ethnicity. In conclusion, differential VDR
 expression relates to ethnicity, rather than 25(OH)D3 status and FokI
 genotype. Instead, VDR transactivation of CAMP is influenced by FokI
 genotype and, together with ethnicity, influence 1,25(OH)2D3-elicited
 CYP24A1 expression. Thus, the expression and role of VDR to transactivate
 target genes is determined not only by genetics, but also by ethnicity and
 environment involving complex interactions which may confound disease
 association.
description: Data for Vitamin D
 receptor gene expression and function in a South African
 populationThe raw data presented
 is in excel format with sheet one containing the data of the larger study
 comprising 60 South African individuals, while sheet two contains data for
 a smaller study in which the effect of increased vitamin D on VDR function
 was assessed (n = 8).DATA for open
 access.xlsx
DOI: 10.5061/dryad.m15k5
title: Data from: Seasonality maintains alternative life history phenotypes

description: Many organisms express discrete alternative phenotypes (polyphenisms) in
 relation to predictable environmental variation. However, the evolution of
 alternative life history phenotypes remains poorly understood. Here, we
 analyze the evolution of alternative life histories in seasonal
 environments by using temperate insects as a model system. Temperate
 insects express alternative developmental pathways of diapause and direct
 development, the induction of a certain pathway affecting fitness through
 its life history correlates. We develop a methodologically novel and
 holistic simulation model and optimize development time, growth rate, body
 size, reproductive effort and adult lifespan simultaneously in both
 developmental pathways. The model predicts that direct development should
 be associated with shorter development time (duration of growth) and adult
 life span, higher growth rate and reproductive effort, smaller body size
 as well as lower fecundity compared to the diapause pathway, because the
 two generations divide the available time unequally. These predictions are
 consistent with many empirical data. Our analysis shows that seasonality
 alone can explain the evolution of alternative life histories.
description: Kivelä et al.
 2013_EVOLUTION_R-codeKivelä et al.
 2013_EVOLUTION_R-code.R
DOI: 10.5061/dryad.gj5b7
title: Data from: In search of genetic constraints limiting the evolution of egg size: Direct and correlated responses to artificial selection on a prenatal maternal effector

description: Maternal effects are an important force in nature, but the evolutionary
 dynamics of the traits that cause them are not well understood. Egg size
 is known to be a key mediator of prenatal maternal effects with an
 established genetic basis. Contrary to theoretical expectations for
 fitness-related traits, there is a large amount of additive genetic
 variation in egg size observed in natural populations. One possible
 mechanism for the maintenance of this variation is through genetic
 constraints caused by a shared genetic basis among traits. Here we created
 replicated, divergent selection lines for maternal egg investment in
 Japanese quail (Coturnix japonica) to quantify the role of genetic
 constraints in the evolution of egg size. We found that egg size responds
 rapidly to selection, accompanied by a strong response in all egg
 components. Initially, we observed a correlated response in body size, but
 this response declined over time, showing that egg size and body size can
 evolve independently. Furthermore, no correlated response in fecundity
 (i.e. the number of eggs laid over a 10 day period) was observed. However,
 the response to selection was asymmetrical, with egg size plateauing after
 one generation of selection in the high but not the low investment lines.
 We attribute this pattern to the presence of genetic asymmetries, caused
 by directional dominance or unequal allele frequencies. Such asymmetries
 may contribute to the evolutionary stasis in egg size observed in natural
 populations, despite a positive association between egg size and fitness.
description: Measurements of Japanese
 quail (Coturnix japonica) from an artificial selection experiment for
 relative egg sizeExcel file with 4
 sheets, containing data collected from replicated divergent artificial
 selection lines for relative egg size, created in a captive population of
 Japanese quail (Coturnix japonica) at the University of Zurich. The first
 sheet contains information about subsequent sheets. The second sheet
 contains data mean values for each generation, repeat and line
 combinations for all traits used in analysis. The third sheet contains
 data of dried egg components from the fourth generation of the selection
 lines. The fourth sheet contains data of laying intervals from the fourth
 generation of the selection lines.all_dryad.xlsx
DOI: 10.5061/dryad.jg57k
title: Data from: Kinship and association in a highly social apex predator population, killer whales at Marion Island

description: Social structure is a core element of population biology, influenced by
 intrinsic and environmental factors. Intra-taxon comparisons of social
 organization are useful in elucidating the role of such ecological
 determinants of sociality. Killer whales Orcinus orca are widely
 distributed, social delphinids with diverse morphology, diet, behaviour,
 and genetics, but few studies have quantitatively examined social
 structure in this species. We used 7 years of individual identification
 data on killer whales at Marion Island, Southern Ocean, to calculate the
 half-weight association index among 39 individuals, creating a weighted
 association network. There were long-term associations between
 individuals, though associations were dynamic over time. We defined 8
 social modules using a community detection algorithm and these typically
 contained 3 individuals of various ages and sexes. Pairwise genetic
 relatedness among 20 individuals was not significantly correlated with
 association index. Individuals were on average more related within than
 between social modules, but social modules contained related as well as
 unrelated individuals. Likely parent pairs of 6 individuals indicated
 mating between social modules.
description: Individual photographic
 identification data of killer whales at Marion IslandThe file contains
 individual photographic identification data for killer whales observed at
 Marion Island, 2006-2013. Each row in the file represents a sighting of a
 group of killer whales. "Date" is the date and time (UTC +03:00)
 of the sighting, "Site" is a code representing the locality of
 the sighting and "IDs" contains the alphanumeric individual IDs
 of all animals in the group (IDs are separated by spaces). For further
 methodological details see Reisinger et al. (2011)
 http://dx.doi.org/10.3354/ab00340.Reisinger et al - Data - Photo
 ID.csvGenotype data of killer
 whales sampled at Marion IslandThis file contains
 genotype data for 20 killer whales biopsy sampled at Marion Island,
 2011-2013. Individuals were genotyped at 12 microsatellite loci.
 Individuals, identified by the column "Individual ID", are
 represented in rows, with loci represented in the columns 4-27. The sex
 (column "Sex") and age class (column "Class") of each
 individual is given as male ("M"), female ("F") or
 unknown ("U") and adult ("A") or juvenile
 ("J"), respectively.Reisinger et al - Data -
 Genotype.csv
DOI: 10.5061/dryad.rd47d
title: Data from: Territorial males can sire more offspring in nests with smaller doors in the cichlid Lamprologus lemairii

description: To examine how territorial males counter reproductive parasites, we
 examined the paternity of broods guarded by territorial males using 5
 microsatellite loci and factors that determine siring success in a wild
 population of the Lake Tanganyika cichlid Lamprologus lemairii. Females
 enter rock holes (nests) and spawn inside, and territorial males release
 milt over the nest openings. Sneakers attempt to dart into the nests, but
 territorial males often interrupt the attempt. The body size of
 territorial males (territorial defense ability) and the size of nest
 opening (the ability to prevent sneakers from nest intrusions) are
 predicted to be factors that affect paternity at the premating stage,
 whereas milt quality traits are factors that affect paternity at the
 postmating stage. Parentage analyses of 477 offspring revealed that most
 clutches have few or no cuckolders, and territorial males sired
 &gt;80% of eggs in 7 of the 10 analyzed clutches. Larger territorial
 males that spawned in nests with narrower openings had greater siring
 success. In contrast, none of the milt traits affected the siring success.
 These suggest that territorial male L. lemairii adopt premating strategies
 whereby they effectively prevent reproductive parasitism.
description: AlleleSizeLamprologuslemairiigenotype data underlying the paternity analysis in Lamprologus lemairii
DOI: 10.5061/dryad.rm317
title: Data from: Desynchronizations in bee-plant interactions cause severe fitness losses in solitary bees

description: 1. Global warming can disrupt mutualistic interactions between solitary
 bees and plants when increasing temperature differentially changes the
 timing of interacting partners. One possible scenario is for insect
 phenology to advance more rapidly than plant phenology. 2. However,
 empirical evidence for fitness consequences due to temporal mismatches is
 lacking for pollinators and it remains unknown if bees have developed
 strategies to mitigate fitness losses following temporal mismatches. 3. We
 tested the effect of temporal mismatches on the fitness of three
 spring-emerging solitary bee species, including one pollen specialist.
 Using flight cages, we simulated (i) a perfect synchronization (from a bee
 perspective): bees and flowers occur simultaneously, (ii) a mismatch of
 three days and (iii) a mismatch of six days, with bees occurring earlier
 than flowers in the latter two cases. 4. A mismatch of six days caused
 severe fitness losses in all three bee species, as few bees survived
 without flowers. Females showed strongly reduced activity and reproductive
 output compared to synchronized bees. Fitness consequences of a three day
 mismatch were species-specific. Both the early-spring species Osmia
 cornuta and the mid-spring species Osmia bicornis produced the same number
 of brood cells after a mismatch of three days as under perfect
 synchronization. However, O. cornuta decreased the number of female
 offspring, whereas O. bicornis spread the brood cells over fewer nests,
 which may increase offspring mortality e.g. due to parasitoids. The
 late-spring specialist Osmia brevicornis produced fewer brood cells even
 after a mismatch of three days. Additionally, our results suggest that
 fitness losses after temporal mismatches are higher during warm than cold
 springs, as the naturally occurring temperature variability revealed that
 warm temperatures during starvation decreased the survival rate of O.
 bicornis. 5. We conclude that short temporal mismatches can cause clear
 fitness losses in solitary bees. Although our results suggest that bees
 have evolved species-specific strategies to mitigate fitness losses after
 temporal mismatches, the bees were not able to completely compensate for
 impacts on their fitness after temporal mismatches with their food
 resources.
description: Survival rate, Activity
 Index, brood cells, nests, female offspring, TempSurvival rate, Activity
 Index, Temp. until day 6 and no. of brood cells, nests and female
 offspring of three different spring-emerging bee species (O. cornuta, O.
 bicornis, O. brevicornis) after perfect synchronization and
 desynchronization with their host plants.Activity Index (early
 vs. late activity)Activity Index (divided
 into early and late activity) of three different spring-emerging bee
 species (O. cornuta, O. bicornis, O. brevicornis) after perfect
 synchronization and desynchronization with their host
 plants.
DOI: 10.5061/dryad.td30f
title: Data from: How do seasonality, substrate, and management history influence macrofungal fruiting assemblages in a central Amazonian Forest?

description: Worldwide, fungal richness peaks in tropical forest biomes where they are
 the primary drivers of decomposition. Understanding how environmental and
 anthropogenic factors influence tropical macrofungal fruiting patterns
 should provide insight as to how, for example, climate change and
 deforestation may impact their long-term demographic stability and
 evolutionary potential. However, in Amazonia no studies have yet to
 disentangle the effects of substrate, seasonality and forest history on
 phenology. Here, we quantitate spatial and temporal variation in community
 structure of fruiting macrofungi in relation to these factors at a
 long-term forest management research site in central Amazonia: the Biomass
 and Nutrients of Tropical Rain Forest (BIONTE's). Basidiome surveys
 of four substrate classes (leaves, soil, branches and trunks) were
 conducted along 250 m2 transects in primary and secondary (managed)
 forests, between 2012–13. From the 669 basidiomes collected, 290 taxa were
 identified of which 44 percent were restricted to primary and 36 percent
 to secondary forests. Although species-accumulation curves did not
 asymptote, rarefaction analyses and Fisher's alpha indicate
 contrasting differences in richness among forests in relation to substrate
 type. For example, leaf litter basidiome richness was higher in secondary
 forests, whereas the contrary was observed for soil communities,
 suggesting that variation in fruiting patterns in relation to disturbance
 is substrate-dependent possibly due to differences in necromass quality
 and/or understory micro-climates. Furthermore, secondary forests harbored
 significantly lower basidiome richness and abundance in dry months,
 suggesting synergistic impacts of seasonality and management history on
 fruiting regimes.
description: Agaricales mushroom at
 BIONTE area from Central AmazoniaAgaricales mushroom
 separated by species and/ or morphotype and its respective collection
 number, according to substrate type (trunk, branches, leaf and soil),
 season (dry or rainy), month, year (2012 and 2013), forest stage
 (secondary= transects S1, S2, S3 and S4) and primary = transects P1, P2,
 P3 and P4DIRCE_dados_atualizados.csv
DOI: 10.5061/dryad.11cj1
title: Data from: Susceptibility of amphibians to chytridiomycosis is associated with MHC class II conformation

description: The pathogenic chytrid fungus Batrachochytrium dendrobatidis (Bd) can
 cause precipitous population declines in its amphibian hosts. Responses of
 individuals to infection vary greatly with the capacity of their immune
 system to respond to the pathogen. We used a combination of comparative
 and experimental approaches to identify major histocompatibility complex
 class II (MHC-II) alleles encoding molecules that foster the survival of
 Bd-infected amphibians. We found that Bd-resistant amphibians across four
 continents share common amino acids in three binding pockets of the MHC-II
 antigen-binding groove. Moreover, strong signals of selection acting on
 these specific sites were evident among all species co-existing with the
 pathogen. In the laboratory, we experimentally inoculated Australian tree
 frogs with Bd to test how each binding pocket conformation influences
 disease resistance. Only the conformation of MHC-II pocket 9 of surviving
 subjects matched those of Bd-resistant species. This MHC-II conformation
 thus may determine amphibian resistance to Bd, although other MHC-II
 binding pockets also may contribute to resistance. Rescuing amphibian
 biodiversity will depend on our understanding of amphibian immune defence
 mechanisms against Bd. The identification of adaptive genetic markers for
 Bd resistance represents an important step forward towards that goal.
description: DataS1-AAAlignment of the β1 domain of the MHC class II in worldwide amphibiansdataset2-lvaGenotyping results for 9 microsatellite markers and the exon2 of one MHC class II locus for Litoria verreauxii alpina wild populationsdataset3-NAGenotyping results for 9 microsatellite markers and the exon2 of one MHC class II locus for Litoria verreauxii alpina wild populations-corrected for null alleles using the so-called INA method described in Chapuis and Estoup (2007), GENEPOP format
DOI: 10.5061/dryad.f4245
title: Data from: Spatial correlations between browsing on balsam fir by white-tailed deer and the nutritional value of neighboring winter forage

description: Associational effects, that is, the influence of neighboring plants on
 herbivory suffered by a plant, are an outcome of forage selection.
 Although forage selection is a hierarchical process, few studies have
 investigated associational effects at multiple spatial scales. Because the
 nutritional quality of plants can be spatially structured, it might
 differently influence associational effects across multiple scales. Our
 objective was to determine the radius of influence of neighbor density and
 nutritional quality on balsam fir (Abies balsamea) herbivory by
 white-tailed deer (Odocoileus virginianus) in winter. We quantified
 browsing rates on fir and the density and quality of neighboring trees in
 a series of 10-year-old cutovers on Anticosti Island (Canada). We used
 cross-correlations to investigate relationships between browsing rates and
 the density and nutritional quality of neighboring trees at distances up
 to 1,000 m. Balsam fir and white spruce (Picea glauca) fiber content and
 dry matter in vitro true digestibility were correlated with fir browsing
 rate at the finest extra-patch scale (across distance of up to 50 m) and
 between cutover areas (300–400 m). These correlations suggest
 associational effects, that is, low nutritional quality of neighbors
 reduces the likelihood of fir herbivory (associational defense). Our
 results may indicate associational effects mediated by intraspecific
 variation in plant quality and suggest that these effects could occur at
 scales from tens to hundreds of meters. Understanding associational
 effects could inform strategies for restoration or conservation; for
 example, planting of fir among existing natural regeneration could be
 concentrated in areas of low nutritional quality.
description: crosscorr_browsingData used in cross-correlation to test the impact of the abundance and nutritional quality of neighbours on balsam fir browsing in Champagne, Moore, Côté and Tremblay. Spatial correlations between browsing on balsam fir by white-tailed deer and the nutritional value of neighbouring winter foragelandscape_configData used to investigate the effect of landscape configuration on balsam fir browsing by deer in Champagne, Moore, Côté and Tremblay. Spatial correlations between browsing on balsam fir by white-tailed deer and the nutritional value of neighbouring winter forage