cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fh2hp7k4
title: Data from: Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses

description: Inbred mouse strains MRL and LG share the ability to fully heal ear hole
 punches with the full range of appropriate tissues without scarring. They
 also share a common ancestry, MRL being formed from a multi-strain cross
 with two final backcrosses to LG before being inbred by brother-sister
 mating. Many gene mapping studies for healing ability have been performed
 using these two strains, resulting in the location of about 20
 quantitative trait loci (QTLs). Here, we combine two of these crosses (N =
 638), MRL/lpr x C57BL/6NTac and LG/J x SM/J, in a single combined cross
 analysis to increase mapping power, decrease QTL support intervals,
 separate multiple QTLs, and establish allelic states at individual QTL.
 The combined cross analysis located 11 QTLs, 6 affecting only one cross (5
 LG x SM and 1 MRL x B6) and 5 affecting both crosses, approximately the
 number of common QTLs expected given strain SNP similarity. Amongst the 5
 QTLs mapped in both crosses, three had significantly different genetic
 effects, additive in one cross and over- or under-dominant in the other.
 It is possible that allelic states at these three loci are different in SM
 and B6 because they lead to differences in dominance interactions with the
 LG and MRL alleles. QTL support intervals are 40% smaller in the combined
 cross analysis than in either of the single crosses. Combined cross
 analysis was successful in enhancing the interpretation of earlier QTL
 results for these strains.
description: Genotype and Phenotype
 Data for Combined Cross Analysis of Wound HealingThis file includes
 animal IDs, demographic data, marker genotype data and both physical and
 recombination-based locations of markers for the LGxSM cross and for the
 MRLxB6 crossRaw
 Data.xlsx
DOI: 10.5061/dryad.db40p
title: Data from: Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus

description: The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species
 currently restricted to a single desert spring and a separate captive
 habitat in southwestern North America. Following establishment of the
 captive population from wild stock in 1976, the wild population has
 undergone natural population size fluctuations, intentional culling to
 purge genetic contamination from an invasive congener (Cyprinodon
 variegatus) and augmentation/replacement of wild fish from the captive
 stock. A severe population decline following the most recent introduction
 of captive fish prompted us to examine whether the captive and wild
 populations have differentiated during the short time they have been
 isolated from one another. If so, the development of divergent genetic
 and/or morphologic traits between populations could contribute to a
 diminished ability of fish from one location to thrive in the other.
 Examination of genomewide single nucleotide polymorphisms and morphologic
 variation revealed no evidence of residual C. variegatus characteristics
 in contemporary C. bovinus samples. However, significant genetic and
 morphologic differentiation was detected between the wild and captive
 populations, some of which might reflect local adaptation. Our results
 indicate that genetic and physical characteristics can diverge rapidly
 between isolated subdivisions of managed populations, potentially
 compromising the value of captive stock for future supplementation
 efforts. In the case of C. bovinus, our findings underscore the need to
 periodically inoculate the captive population with wild genetic material
 to help mitigate genetic, and potentially morphologic, divergence between
 them and also highlight the utility of parallel morphologic and genomic
 evaluation to inform conservation management planning.
description: GeneticsTwo GENEPOP files representing the filtered CB_GEN (1 990 SNPs) and CBV_GEN (3 313 SNPs) datasets. Sequential population factors for these files are: 1) DY, SNARRC and 2) DY, SNARRC, BL, respectively.MorphometricsTwo TPS files of raw Cartesian coordinates (CB_MORPH, CBV_MORPH), and the MORPHOJ project file used for morphometric analyses.
DOI: 10.5061/dryad.j2m3vm9
title: Data from: Response to joint selection on germination and flowering phenology depends on the direction of selection

description: Background and Aims. Flowering and germination time are components of
 phenology, a complex phenotype that incorporates a number of traits. In
 natural populations, selection is likely to occur on multiple components
 of phenology at once. However, we have little knowledge of how joint
 selection on several phenological traits influences evolutionary response.
 Methods. We conducted one generation of artificial selection for all
 combinations of early and late germination and flowering on replicated
 lines within two independent base populations in the herb Campanula
 americana. We then measured response to selection and realized
 heritability for each trait. Results. Response to selection and
 heritability were greater for flowering time than germination time,
 indicating greater evolutionary potential of this trait. Selection for
 earlier phenology, both flowering and germination, did not depend on the
 direction of selection on the other trait. Whereas response to selection
 to delay germination and flowering was greater when selection on the other
 trait was in the opposite direction (e.g. early germination, late
 flowering), indicating a negative genetic correlation between the traits.
 Conclusions. The extent to which correlations shaped response to selection
 depended on the direction of selection. Therefore the genetic correlation
 between timing of germination and flowering varies across the trait
 distributions. The negative correlation between germination and flowering
 time found when selecting for delayed phenology follows theoretical
 predictions of constraint for traits that jointly determine life history
 schedule. Whereas the lack of constraint found when selecting for an
 accelerated phenology suggests a reduction of the covariance due to strong
 selection favoring earlier flowering and a shorter life cycle. This
 genetic architecture, in turn, will facilitate further evolution of the
 early phenology often favored in warming climates.
description: Galloway et al Ecol Evol
 DataData for "Response
 to joint selection on germination and flowering phenology depends on the
 direction of selection". First sheet is data for Table 1/Figure 2.
 Remaining sheets contain data used to calculate heritability estimates.
 See comments on column headers for identification information if different
 from the text.
DOI: 10.5061/dryad.s4q6s
title: Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

description: The Convention on Biological Diversity (CBD) aims at the conservation of
 all three levels of biodiversity, i.e. ecosystems, species and genes.
 Genetic diversity represents evolutionary potential and is important for
 ecosystem functioning. Unfortunately, genetic diversity in natural
 populations is hardly considered in conservation strategies because it is
 difficult to measure and has been hypothesized to co-vary with species
 richness. This means that species richness is taken as a surrogate of
 genetic diversity in conservation planning, though their relationship has
 not been properly evaluated. We tested whether the genetic and species
 levels of biodiversity co-vary, using a large-scale and multi-species
 approach. We chose the high-mountain flora of the Alps and the Carpathians
 as study systems and demonstrate that species richness and genetic
 diversity are not correlated. Species richness thus cannot act as a
 surrogate for genetic diversity. Our results have important consequences
 for implementing the CBD when designing conservation strategies.
description: Data on species richness
 and genetic diversity in high-mountain vascular plants of the Alps and the
 Carpathians(i) Floristic data of
 vascular high-mountain plants from the Alps and the Carpathians, with
 occurrences of each species with a regular grid system (ii)
 Species-specific AFLP data (1/0 matrices) separately for samples from Alps
 and Carpathians, collected along the same grid system as the floristic
 dataTaberlet_etal_EcologyLetters2012.zip
DOI: 10.5061/dryad.nj3c0
title: Data from: Root biomass and exudates link plant diversity with soil bacterial and fungal biomass

description: Plant diversity has been shown to determine the composition and
 functioning of soil biota. Although root-derived organic inputs are
 discussed as the main drivers of soil communities, experimental evidence
 is scarce. While there is some evidence that higher root biomass at high
 plant diversity increases substrate availability for soil biota, several
 studies have speculated that the quantity and diversity of root inputs
 into the soil, i.e. though root exudates, drive plant diversity effects on
 soil biota. Here we used a microcosm experiment to study the role of plant
 species richness on the biomass of soil bacteria and fungi as well as
 fungal-to-bacterial ratio via root biomass and root exudates. Plant
 diversity significantly increased shoot biomass, root biomass, the amount
 of root exudates, bacterial biomass, and fungal biomass. Fungal biomass
 increased most with increasing plant diversity resulting in a significant
 shift in the fungal-to-bacterial biomass ratio at high plant diversity.
 Fungal biomass increased significantly with plant diversity-induced
 increases in root biomass and the amount of root exudates. These results
 suggest that plant diversity enhances soil microbial biomass, particularly
 soil fungi, by increasing root-derived organic inputs.
description: Eisenhauer et al 2017
 Sci Rep Data
DOI: 10.5061/dryad.8p0s7
title: Data from: Can latitudinal richness gradients be measured in the terrestrial fossil record?

description: Studying the deep-time origins of macroecological phenomena can help us to
 understand their long-term drivers. Given the considerable spatiotemporal
 bias of the terrestrial fossil record, it behooves us to understand how
 much biological information is lost. The aim of this study is to establish
 whether latitudinal diversity gradients are detectable in a biased
 terrestrial fossil record. I develop a simulated fossilization approach,
 weighting the probability of terrestrial mammal species appearing in the
 fossil record based on body size and geographic-range size; larger species
 with larger range sizes are more likely to enter the fossil record. I
 create simulated fossil localities from the modern North American mammal
 record. I vary the percentage of species successfully fossilized and
 estimate the magnitude of the latitudinal diversity gradient (slope of the
 richness gradient and degree of species turnover). I find that estimates
 of the latitudinal diversity gradient are sensitive to the loss of species
 with small body size and geographic-range sizes. In some cases, simulated
 fossil-record bias completely obliterates evidence of declining richness
 with latitude, a phenomenon that is not ameliorated by the application of
 nonparametric richness estimation. However, if the rate of preservation is
 medium (50% of species) to high (75% of species), the magnitude of the
 latitudinal diversity gradient can be reliably estimated. Similarly,
 changes in the diversity gradient estimates are largely explained by
 differences in the diversity–climate relationship among iterations,
 suggesting that these relationships may be measurable in the fossil
 record.
description: Appendix A R markdown
 January 2017R code and associated
 descriptions for simulated fossilization.Appendix I R markdown January
 2017.pdfAppendix B Body Size
 ProbabilitiesProbabilities of
 appearance in a simulated fossil record based on body size
 categories.Appendix
 2.xlsx
DOI: 10.5061/dryad.34h7v
title: Data from: Specialization of a polyphenism switch gene following serial duplications in Pristionchus nematodes

description: Polyphenism is an extreme manifestation of developmental plasticity,
 requiring distinct developmental programs and the addition of a switch
 mechanism. Because the genetic basis of polyphenism switches has only
 begun to be understood, how their mechanisms arise is unclear. In the
 nematode Pristionchus pacificus, which has a mouthpart polyphenism
 specialized for alternative diets, a gene (eud-1) executing the
 polyphenism switch was recently identified as the product of
 lineage-specific duplications. Here, we infer the role of gene
 duplications in producing a switch gene. Using reverse genetics and
 population genetic analyses, we examine evidence for competing scenarios
 of degeneration and complementation, neutral evolution, and functional
 specialization. Of the daughter genes, eud-1 alone has assumed switch-like
 regulation of the mouth polyphenism. Measurements of life-history traits
 in single, double, and triple sulfatase mutants did not, given a benign
 environment, identify alternative or complementary roles for eud-1
 paralogs. Although possible roles are still unknown, selection analyses of
 the sister species and 104 natural isolates of P. pacificus detected
 purifying selection on the genes, suggesting their functionality by their
 fixation and evolutionary maintenance. Our approach shows the tractability
 of reverse genetics in a nontraditional model system to study evolution by
 gene duplication.
description: Sulfatase_mutant_sequencesSequence data for three CRISPR/Cas9 generated mutants: 1) sul-2.2.1(iub1); eud-1(iub14) 2) sul-2.2.1(iub2); eud-1(california/wild-type) 3) sul-2.1(iub3). Please note: The experimental data reported in Figures 3 and 4 of the associated publication (Ragsdale and Ivers. 2016. Evolution. doi:10.1111/evo.13011) are available at http://dx.doi.org/10.5061/dryad.dh38s
DOI: 10.5061/dryad.br86d
title: Data from: Random versus game trail-based camera trap placement strategy for monitoring terrestrial mammal communities

description: Camera trap surveys exclusively targeting features of the landscape that
 increase the probability of photographing one or several focal species are
 commonly used to draw inferences on the richness, composition and
 structure of entire mammal communities. However, these studies ignore
 expected biases in species detection arising from sampling only a limited
 set of potential habitat features. In this study, we test the influence of
 camera trap placement strategy on community-level inferences by carrying
 out two spatially and temporally concurrent surveys of medium to large
 terrestrial mammal species within Tanzania’s Ruaha National Park,
 employing either strictly game trail-based or strictly random camera
 placements. We compared the richness, composition and structure of the two
 observed communities, and evaluated what makes a species significantly
 more likely to be caught at trail placements. Observed communities
 differed marginally in their richness and composition, although
 differences were more noticeable during the wet season and for low levels
 of sampling effort. Lognormal models provided the best fit to rank
 abundance distributions describing the structure of all observed
 communities, regardless of survey type or season. Despite this, carnivore
 species were more likely to be detected at trail placements relative to
 random ones during the dry season, as were larger bodied species during
 the wet season. Our findings suggest that, given adequate sampling effort
 (&gt; 1400 camera trap nights), placement strategy is unlikely to
 affect inferences made at the community level. However, surveys should
 consider more carefully their choice of placement strategy when targeting
 specific taxonomic or trophic groups.
description: Cusack_et_al_random_versus_trail_camera_trap_dataCamera trap data on medium to large terrestrial mammals ("Species") collected at 54 camera stations ("Station") in Ruaha National Park, southern Tanzania. Sampling was carried out for two months during the dry season of 2013 (D under "Season") and two months during the wet season of 2014 (W under "Season"). Each camera station is associated with a randomly placed camera (Random under "Placement") and a trail-based camera (Trail under "Placement"), with the aim of comparing communities resulting from the two camera trap placement strategies. The date and time of each photographic event is also given ("DateTime").
DOI: 10.5061/dryad.1qh3k
title: Data from: Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.)

description: Most eukaryotes reproduce sexually and a wealth of different sex
 determination mechanisms have evolved in this lineage. Dioecy or separate
 sexes are rare among flowering plants but have repeatedly evolved from
 hermaphroditic ancestors possibly involving male or female sterility
 mutations. Willows (Salix spp.) and poplars (Populus spp.) are
 predominantly dioecious and are members of the Salicaceae family. All
 studied poplars have sex determination loci on chromosome XIX, however,
 the position differs among species and both male and female heterogametic
 system exists. In contrast to the situation in poplars, knowledge of sex
 determination mechanisms in willows is sparse. In the present study, we
 have for the first time positioned the sex determination locus on
 chromosome XV in S. viminalis using quantitative trait locus mapping. All
 female offspring carried a maternally inherited haplotype, suggesting a
 system of female heterogamety or ZW. We used a comparative mapping
 approach and compared the positions of the markers between the S.
 viminalis linkage map and the physical maps of S. purpurea, S. suchowensis
 and P. trichocarpa. As we found no evidence for chromosomal rearrangements
 between chromosome XV and XIX between S. viminalis and P. trichocarpa, it
 shows that the sex determination loci in the willow and the poplar most
 likely do not share a common origin and has thus evolved separately. This
 demonstrates that sex determination mechanisms in the Salicaceae family
 have a high turnover rate and as such it is excellent for studies of
 evolutionary processes involved in sex chromosome turnover.
description: popIIImap141023Genetic map of Salix viminalis population S3Genotypes+sex_141013Genotypes of S3 mapping population in Joinmap infile format. Sex as morphological marker is included in this file too.mapqtl-sex_141023Phenotypic data on the sex of the individuals in the mapping population S3. Male = 1, Female = 2
DOI: 10.5061/dryad.0mg7h
title: Data from: Within-population polymorphism of sex-determination systems in the common frog (Rana temporaria)

description: In sharp contrast with birds and mammals, the sex chromosomes of
 ectothermic vertebrates are often undifferentiated, for reasons that
 remain debated. A linkage map was recently published for Rana temporaria
 (Linnaeus, 1758) from Fennoscandia (Eastern European lineage), with a
 proposed sex-determining role for linkage group 2 (LG2). We analysed
 linkage patterns in lowland and highland populations from Switzerland
 (Western European lineage), with special focus on LG2. Sibship analyses
 showed large differences from the Fennoscandian map in terms of
 recombination rates and loci order, pointing to large-scale inversions or
 translocations. All linkage groups displayed extreme heterochiasmy (total
 map length was 12.2 cM in males, versus 869.8 cM in females). Sex
 determination was polymorphic within populations: a majority of families
 (with equal sex ratios) showed a strong correlation between offspring
 phenotypic sex and LG2 paternal haplotypes, whereas other families (some
 of which with female-biased sex ratios) did not show any correlation. The
 factors determining sex in the latter could not be identified. This
 coexistence of several sex-determination systems should induce frequent
 recombination of X and Y haplotypes, even in the absence of male
 recombination. Accordingly, we found no sex differences in allelic
 frequencies on LG2 markers among wild-caught male and female adults,
 except in one high-altitude population, where nonrecombinant Y haplotypes
 suggest sex to be entirely determined by LG2. Multifactorial sex
 determination certainly contributes to the lack of sex-chromosome
 differentiation in amphibians.
description: Table genotypes aLG
 pj2011 dryadTable of the genotypes
 from 10 pedigrees, including parents and juveniles with known phenotypic
 sex. Genotypes include 47 polymorphic microsatellite markers. Genotyping
 was conducted with an ABI3000 Prism sequencer.Table Genotypes LG2
 familles11 dryadTable of genotypes from
 10 full pedigrees, including parents, sexed juveniles, and tadpoles.
 Genotypes include 10 polymorphic microsatellite markers. Genotypes were
 obtained with an ABI3000 Prism sequencer.Table Genotypes LG2
 adultes11 dryadTable of genotypes from
 adults from five different populations. Genotypes include 11 polymorphic
 microsatellite markers.
DOI: 10.5061/dryad.f542t16
title: Data from: Grazing and resource availability control soil nematode body size and abundance-mass relationship in semi-arid grassland

description: 1. Body size is a central functional trait in ecological communities.
 Despite recognition of the importance of above-belowground interactions,
 effects of aboveground herbivores on size and abundance-size relationships
 in soil fauna are almost uncharted. Depending on climate and soil
 properties, herbivores may increase basal resources of soil food webs, or
 reduce pore space, mechanisms expected to have contrasting effects on soil
 animal body size. 2. We investigated how body size and shape of soil
 nematodes responded to mammalian grazers in three semi-arid grassland
 sites, along a gradient of soil texture and organic matter (OM) in a
 long-term herbivore removal study. We analysed nematode mass, length,
 diameter, body size distribution, and biomass distribution. We formulated
 two mechanistic hypotheses to assess whether resource availability or pore
 space was the dominant abiotic control and modulated the effects of
 grazing. 3. In ungrazed soils, average and maximum nematode size, as well
 as abundance and biomass of large nematodes, were greater in the high-OM
 than in the low-OM soil, and intermediate in the medium-OM soil. Grazing
 promoted larger sizes in the low-OM soil, where it had been shown to
 increase organic matter and microbial biomass, and led to more homogeneous
 average size and body size distribution across sites. The results support
 the hypothesis that nematode size was controlled by basal resource
 availability rather than by pore space. However, body shape might have
 been constrained by small pores in the fine-texture, high-OM soil, where
 nematodes were more elongated. 4. Grazing may facilitate larger sizes in
 soil nematode communities by boosting basal resources where these are
 limiting, with important implications for estimations of nematode biomass
 and contribution to carbon and nutrient cycling. These findings contribute
 to the insofar-limited mechanistic understanding of how herbivores can
 shape functional traits of soil fauna, and demonstrate that animals at one
 trophic level may control patterns in body size and abundance-size
 relationships in other trophic levels without a direct predator-prey or
 competitive linkage between them.
description: Data_Andriuzzi_Wall_J_Animal_EcolNematode body size and abundance data for article "Grazing and resource availability control soil nematode body size and abundance-mass relationship in semi-arid grassland"Andriuzzi & Wall JAE data.xlsx