cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0nr72
title: Data from: Serum amyloid A protein concentration in blood is influenced by genetic differences in the cheetah (Acinonyx jubatus)

description: Systemic amyloid A (AA) amyloidosis is a major cause of morbidity and
 mortality among captive cheetahs. The self-aggregating AA protein
 responsible for this disease is a byproduct of serum amyloid A (SAA)
 protein degradation. Transcriptional induction of the SAA1 gene is
 dependent on both C/EBPβ and NF-κB cis-acting elements within the promoter
 region. In cheetahs, 2 alleles exist for a single guanine nucleotide
 deletion in the putative NF-κB binding site. In this study, a novel
 genotyping assay was developed to screen for the alleles. The results show
 that the SAA1A −97delG allele is associated with decreased SAA protein
 concentrations in the serum of captive cheetahs (n = 58), suggesting
 genetic differences at this locus may be affecting AA amyloidosis
 prevalence. However, there was no significant difference in the frequency
 of the SAA1A −97delG allele between individuals confirmed AA amyloidosis
 positive versus AA amyloidosis negative at the time of necropsy (n = 48).
 Thus, even though there is evidence that having more copies of the SAA1A
 −97delG allele results in a potentially protective decrease in serum
 concentrations of SAA protein in captive cheetahs, genotype is not
 associated with this disease within the North American population. These
 results suggest that other factors are playing a more significant role in
 the pathogenesis of AA amyloidosis among captive cheetahs.
description: SAA and Genotype
 DataThis excel file contains
 the genotypic data for the SAA1A SNP for cheetahs. Fixed factors and
 individual SAA concentrations are also provided.Franklin_JOH_DataFile.xlsxCaptive/Wild cheetah pedigree filePedigree file required for MENDEL software with full pedigree information available for captive/wild cheetahs measured in this study.Ped03.txt
DOI: 10.5061/dryad.68
title: Data from: Phylogeny of frogs of the Physalaemus pustulosus species group, with an examination of data incongruence

description: Characters derived from advertisement calls, morphology, allozymes, and
 the sequences of the small subunit of the mitochondrial ribosomal gene
 (12S) and the COI mitochondrial gene were used to estimate the phylogeny
 of frogs of the Physalaemus pustulosus group (Leptodactylidae). The
 combinability of these data partitions was assessed in several ways:
 measures of phylogenetic signal, character support for trees, congruence
 of tree topologies, compatibility of data partitions with suboptimal
 trees, and homogeneity of data partitions. Combined parsimony analysis of
 all data equally weighted yielded the same tree as the 12S partition
 analyzed under parsimony and maximum likelihood. The COI, allozyme, and
 morphology partitions were generally congruent and compatible with the
 tree derived from combined data. The call data were significantly
 different from all other partitions, whether considered in terms of tree
 topology alone, partition homogeneity, or compatibility of data with trees
 derived from other partitions. The lack of effect of the call data on the
 topology of the combined tree is probably due to the small number of call
 characters. The general incongruence of the call data with other data
 partitions is consistent with the idea that the advertisement calls of
 this group of frogs are under strong sexual selection.
description: Cannatella et al Data
 Matrixphysalaemus.nexus
DOI: 10.5061/dryad.f776h
title: Data from: Stocking activities for the Arctic charr in Lake Geneva: genetic effects in space and time

description: Artificial stocking practices are widely used by resource managers
 worldwide, in order to sustain fish populations exploited by both
 recreational and commercial activities, but their benefits are
 controversial. Former practices involved exotic strains, although current
 programs rather consider artificial breeding of local fishes (supportive
 breeding). Understanding the complex genetic effects of these management
 strategies is an important challenge with economic and conservation
 implications, especially in the context of population declines. In the
 present study, we focus on the declining Arctic charr (Salvelinus alpinus)
 population from Lake Geneva (Switzerland and France), which has initially
 been restocked with allochtonous fishes in the early eighties, followed by
 supportive breeding. In this context, we conducted a genetic survey to
 document the evolution of the genetic diversity and structure throughout
 the last 50 years, before and after the initiation of hatchery
 supplementation, using contemporary and historical samples. We show that
 the introduction of exotic fishes was associated with a genetic bottleneck
 in the 1980-1990s, a break of Hardy-Weinberg Equilibrium (HWE), a
 reduction of genetic diversity, an increase of genetic structure among
 spawning sites, and a change in their genetic composition. Together with
 better environmental conditions, three decades of subsequent supportive
 breeding using local fishes allowed to re-establish HWE and the initial
 levels of genetic variation. However, current spawning sites have not
 fully recovered their original genetic composition and were extensively
 homogenized across the lake. Our study demonstrates the drastic genetic
 consequences of different restocking tactics in a comprehensive
 spatio-temporal framework, and suggests that genetic alteration by
 non-local stocking may be partly reversible through supportive breeding.
 We recommend that conservation-based programs consider local diversity and
 implement adequate protocols to limit the genetic homogenization of this
 Arctic charr population.
description: Salvelinus_GenotypesGenotypes (N=378) of Salvelinus alpinus for 8 microsatellite loci
DOI: 10.5061/dryad.1ct56
title: Data from: Genetic components to caste allocation in a multiple-queen ant species

description: Reproductive division of labor and the coexistence of distinct castes are
 hallmarks of insect societies. In social insect species with multiple
 queens per colony, the fitness of nestmate queens directly depends on the
 process of caste allocation (i.e., the relative investment in queen,
 sterile worker and male production). The aim of this study is to
 investigate the genetic components to the process of caste allocation in a
 multiple-queen ant species. We conducted controlled crosses in the
 Argentine ant Linepithema humile and established single-queen colonies to
 identify maternal and paternal family effects on the relative production
 of new queens, workers and males. There were significant effects of
 parental genetic backgrounds on various aspects of caste allocation: the
 paternal lineage affected the proportion of queens and workers produced
 while the proportions of queens and males, and females and males were
 influenced by the interaction between parental lineages. In addition to
 revealing non-additive genetic effects on female caste determination in a
 multiple-queen ant species, this study reveals strong genetic
 compatibility effects between parental genomes on caste allocation
 components.
description: DATA_Libbrecht_et_al_2011_EVOLUTIONNumber of individuals produced for each caste, associated with both parental lineages.
DOI: 10.5061/dryad.73pv8
title: Data from: Morphological variation in different populations of Aceria anthocoptes (Acari: Eriophyoidea) associated with the Canada thistle, Cirsium arvense, in Serbia

description: The russet mite, Aceria anthocoptes (Nal.), is the only eriophyid that has
 been recorded on Canada thistle, Cirsium arvense (L.) Scop. It has been
 noted in several European countries and recently in the USA. With its
 apparent host specificity and because of the damage it causes to its host
 plant, A. anthocoptes is being studied as a potential candidate for
 classical biological control. The aim of the present study was to examine
 quantitative morphological traits in four populations of A. anthocoptes
 living on two infraspecific host plant taxa (C. arvense var. arvense and
 C. arvense var. vestitum) in two geographically separate areas of Serbia
 in order to test the hypothesis of absence of the possible host plant
 impact on mite morphology. MANOVA analysis revealed significant
 differences between populations from different localities in Serbia.
 Populations of A. anthocoptes inhabiting two thistle varieties in the
 vicinity of Belgrade differed significantly from mites inhabiting the same
 two host varieties in the vicinity of the town of Ivanjica. Canonical
 discriminant analysis showed that the trait which best discriminates the
 populations of A. anthocoptes is the number of dorsal annuli. It was not
 possible to ascribe morphological differences to the impact of the host
 plant.
description: Morphological
 measurements of Aceria anthocoptesMorphological
 measurements of Aceria anthocoptes, original data. Abbreviations for
 column headings: please see in the publication.2007_EAA_Magud_et_al_data.xls
DOI: 10.5061/dryad.1529d
title: Data from: Genetic structure and expansion of golden jackals (Canis aureus) in the north-western distribution range (Croatia and eastern Italian Alps)

description: The golden jackal, widely distributed in Europe, Asia and Africa, is one
 of the less studied carnivores in the world and the genetic structure of
 the European populations is unknown. In the last century jackals strongly
 declined mainly due to human persecution, but recently they expanded again
 in eastern Europe. With the aim to determine the genetic structure and the
 origin of expanding jackals, we analyzed population samples obtained from
 Bulgaria, Serbia, Croatia (Dalmatia and Slavonia) and individuals sampled
 in north-eastern Italy. Samples were typed at the hypervariable part of
 the mitochondrial DNA control-region (mtDNA CR1) and at 15 canine
 autosomal microsatellite loci (STR), and analyzed using multivariate,
 Bayesian and landscape genetic methods. The mtDNA CR1 was monomorphic,
 showing a single haplotype shared among all the populations. The STR loci
 were variable, with 2–14 alleles and intermediate values of heterozygosity
 (Ho = 0.47; He = 0.51). Genetic diversity was significantly partitioned
 (θST = 0.07; P &lt; 0.001) and the populations were partially
 distinct, perhaps in consequence of recent fragmentations. Jackals from
 Dalmatia were the most genetically differentiated. Assignment testing and
 gene flow analyses suggested that jackals colonizing Italy have admixed
 origins from Dalmatian and Slavonian populations. They are not first
 generation migrants, suggesting that dispersal towards north-eastern Italy
 is a stepping-stone process. Golden jackal and wolf colonization patterns
 might be different, with prevalent short-distance dispersal in jackals
 versus prevalent long distance dispersal in wolves. The admixed origin of
 jackals in the Alps ensures abundant genetic variability, which may
 enhance adaptive fitness and expectancy of population growth. The
 intersections between Dinaric–Balkan and Eastern Alps are areas of
 population expansion and admixture, highlighting their conservation,
 ecological and evolutionary values.
description: Golden_Jackal_GenotypesGenotypes table at 15 canine microsatellites. The first column includes the sample identifiers, the second column the country of origin of samples.Table_Jackal_Genotypes.xls
DOI: 10.5061/dryad.rb75g
title: Data from: Hybridization promotes color polymorphism in the aposematic harlequin poison frog, Oophaga histrionica

description: Whether hybridization can be a mechanism that drives phenotypic diversity
 is a widely debated topic in evolutionary biology. In poison frogs
 (Dendrobatidae), assortative mating has been invoked to explain how new
 color morphs persist despite the expected homogenizing effects of natural
 selection. Here, we tested the complementary hypothesis that new morphs
 arise through hybridization between different color morphs. Specifically,
 we (1) reconstructed the phylogenetic relationships among the studied
 populations of a dart-poison frog to provide an evolutionary framework,
 (2) tested whether microsatellite allele frequencies of one putative
 hybrid population of the polymorphic frog O. histrionica are intermediate
 between O. histrionica and O. lehmanni, and (3) conducted mate-choice
 experiments to test whether putatively intermediate females prefer
 homotypic males over males from the other two populations. Our findings
 are compatible with a hybrid origin for the new morph and emphasize the
 possibility of hybridization as a mechanism generating variation in
 polymorphic species. Moreover, because coloration in poison frogs is
 aposematic and should be heavily constrained, our findings suggest that
 hybridization can produce phenotypic novelty even in systems where
 phenotypes are subject to strong stabilizing selection.
description: Microsatellite
 DatasetMicrosatellite
 information for three different populations, O. histrionica, pHYB
 (putative hybrid) and O. lehmanni. Data for seven microsatellite markers,
 two columns per locus, one column per allele. Column names are locus
 markers as named by the authors of the primers. References are listed at
 the bottom of the list. Missing values= 0.Dryad_EcoandEvo.xls
DOI: 10.5061/dryad.ft12r
title: Data from: Maternal investment increases with altitude in a frog on the Tibetan plateau

description: Reproducing females can allocate energy between the production of eggs or
 offspring of different size or number, both of which can strongly
 influence fitness. The physical capacity to store developing offspring
 imposes constraints on maximum clutch volume, but individual females and
 populations can trade off whether more or fewer eggs or offspring are
 produced, and their relative sizes. Harsh environments are likely to
 select for larger egg or offspring size, and many vertebrate populations
 compensate for this reproductive investment through an increase in female
 body size. We report a different trade-off in a frog endemic to the
 Tibetan Plateau, Rana kukunoris. Females living at higher altitudes (n =
 11 populations, 2000–3500 m) produce larger eggs, but without a
 concomitant increase in female body size or clutch size. The reduced diel
 and seasonal activity at high altitudes may impose constraints on the
 maximum body size of adult frogs, by limiting the opportunity for energy
 accumulation. Simultaneously, producing larger eggs likely helps to
 increase the rate of embryonic development, causing tadpoles to hatch
 earlier. The gelatinous matrix surrounding eggs, more of which is produced
 by large females, may help buffer developing embryos from temperature
 fluctuations or offer protection from ultraviolet radiation. High-altitude
 frogs on the Tibetan Plateau employ a reproductive strategy that favours
 large egg size independent of body size, which is unusual in amphibians.
 The harsh and unpredictable environmental conditions at high altitudes can
 thus impose strong and opposing selection pressures on adult and embryonic
 life stages, both of which can simultaneously influence fitness.
description: data-JEB
DOI: 10.34740/kaggle/dsv/14637753
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.gg526
title: Data from: Quantifying the effect of gape and morphology on bite force: biomechanical modeling and in vivo measurements in bats

description: Maximum bite force is an important metric of feeding performance that
 defines the dietary ecology of many vertebrates. In mammals, theoretical
 analyses and empirical studies suggest a trade-off between maximum bite
 force and gape at behavioural and evolutionary scales; in vivo bite force
 is expected to decrease at wide gapes, and cranial morphologies that
 enable high mechanical advantage are thought to have a lower ability to
 generate high bite forces at wide gapes, and vice versa. However, very few
 studies have confirmed these relationships in free-ranging mammals. This
 study uses an ecologically diverse sample of bats to document the
 variation in bite force with respect to gape angle, and applies
 three-dimensional models of the feeding apparatus to identify the major
 morphological and biomechanical predictors of the gape-bite force
 relationship. In vivo and model data corroborated that bite force
 decreases significantly at wide gapes across species, but there is
 substantial intraspecific variation in the data obtained from live bats.
 Results from biomechanical models, analysed within a phylogenetic
 framework, revealed that species with larger temporalis muscles, higher
 temporalis stretch factors and high mechanical advantages experience a
 steeper reduction in bite force with increasing gape. These trends are
 illustrated by short-faced durophagous frugivores. The results from this
 study suggest that gape-mediated changes in bite force can be explained
 both by behavioural effects and cranial morphology, and that these links
 are relevant for functional analyses of mammal dietary ecology.
description: Model and in vivo bite
 force dataField measurements of
 bite forces at low and wide gapes for bats, and input and output data of
 3D bite force models of bat skulls at low and wide
 gapes.Santana_Gape_FE_Field &
 Model data for Dryad.xls
DOI: 10.5061/dryad.d2g8v
title: Data from: Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

description: Species that have been translocated and otherwise manipulated by humans
 may show patterns of population structure that reflect those interactions.
 At the same time, natural processes shape populations, including
 behavioural characteristics like dispersal potential and breeding system.
 In Europe, a key factor is the geography and history of climate change
 through the Pleistocene. During glacial maxima throughout that period,
 species in Europe with temperate distributions were forced south, becoming
 distributed among the isolated peninsulas represented by Anatolia, Italy
 and Iberia. Understanding modern patterns of diversity depends on
 understanding these historical population dynamics. Traditionally,
 European fallow deer (Dama dama dama) are thought to have been restricted
 to refugia in Anatolia and possibly Sicily and the Balkans. However, the
 distribution of this species was also greatly influenced by human-mediated
 translocations. We focus on fallow deer to better understand the relative
 influence of these natural and anthropogenic processes. We compared modern
 fallow deer putative populations across a broad geographic range using
 microsatellite and mitochondrial DNA loci. The results revealed highly
 insular populations, depauperate of genetic variation and significantly
 differentiated from each other. This is consistent with the expectations
 of drift acting on populations founded by small numbers of individuals,
 and reflects known founder populations in the north. However, there was
 also evidence for differentiation among (but not within) physically
 isolated regions in the south, including Iberia. In those regions we find
 evidence for a stronger influence from natural processes than may be
 expected for a species with such strong, known anthropogenic influence.
description: Dama dama dama Dryad
 submissionEuropean fallow deer
 (Dama dama dama) microsatellite data genotyped across 10
 loci
DOI: 10.5061/dryad.0mr42
title: Data from: Environmental stress linked to consumption of maternally derived carotenoids in brown trout embryos (Salmo trutta)

description: The yellow, orange, or red colors of salmonid eggs are due to maternally
 derived carotenoids whose functions are not sufficiently understood yet.
 Here, we studied the significance of naturally acquired carotenoids as
 maternal environmental effects during embryo development in brown trout
 (Salmo trutta). We collected eggs from wild females, quantified their egg
 carotenoid content, fertilized them in vitro in full-factorial breeding
 blocks to separate maternal from paternal effects, and raised 3,278
 embryos singly at various stress conditions until hatching. We found
 significant sire effects that revealed additive genetic variance for
 embryo survival and hatching time. Dam effects were 5.4 times larger than
 these sire effects, indicating that maternal environmental effects play an
 important role in determining embryo stress tolerance. Of the eight
 pigment molecules that we targeted, only astaxanthin, zeaxanthin (that
 both affected egg redness), and lutein were detected above our confidence
 thresholds. No strong link could be observed between carotenoid content in
 unfertilized eggs and embryo mortality or hatching timing. However, the
 consumption of carotenoids during our stress treatment was negatively
 correlated to embryo survival among sib groups and explained about 14% of
 the maternal environmental variance. We conclude that maternally derived
 carotenoids play a role in the ability of embryos to cope with
 environmental stress, but that the initial susceptibility to the organic
 pollution was mainly determined by other factors.
description: dryad_LGEW_EE17This file contains the R-script we used to analyze our data for this manuscript (details of the analysis are given in the manuscript). It also contains two different input files for R. 'parental_characteristics.txt' is a text file with all the measurements we took for the brown trout parents and 'embryo_stats.txt' are all the traits of the embryos.
DOI: 10.5061/dryad.d03nf
title: Data from: Phylogenetic patterns of skeletal morphometrics and pelvic traits in relation to locomotor mode in frogs

description: Frogs are one of the most speciose groups of vertebrate tetrapods
 (&gt; 6200sp) with a diverse array of locomotor behaviours. Despite
 the impressive diversity in frog locomotor behaviours, there remains a
 paucity of information on the relationship between skeletal variation and
 locomotor mode in frogs and the evolutionary patterns in which these
 relationships are framed across the frog phylogeny. Our current
 understanding of the evolution of frog locomotion shows that hopping
 transitioned into jumping within the Neobatrachia where a variety of
 pelvic/hindlimb length patterns and locomotor niches have appeared, but
 this has yet to be studied over a broad taxonomic sample of frogs.
 Although limb length remains as the primary predictor of leaping
 performance, pelvic and sacral morphometrics have not been quantified in
 relation to limb proportions, body size and locomotor mode and previous
 studies have not sampled more than 24 families. We present a large-scale
 phylogenetic comparison of skeletal morphometrics in relation to locomotor
 mode in 188 genera from 37 families. Osteological variation in limb/pelvic
 girdle morphometrics and pelvic traits that are posited to be associated
 with locomotor mode were analysed to identify which aspects of the frog
 skeleton are the best descriptors of locomotor mode. Our results, contrary
 to previous work, reveal that the greatest axis of variation in frogs is
 represented by the shape of the sacrum with two pelvic morphologies
 evident in qualitative and quantitative ancestral trait reconstructions.
 Limb morphology was not significantly different across most locomotor
 modes, but we identified several outliers in hindlimb phylomorphospace.
 Patterns of sacral evolution together with hindlimb length outliers reveal
 how the general bauplan of this successful group of vertebrate tetrapods
 is constrained, has radiated and has converged on certain phenotypes to
 fill an array of locomotor modes.
description: Jorgensen and Reilly
 datasetGenus averages of
 morphological traits, size-removed residuals, and phylogenetic
 PCA.