cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g29pr
title: Data from: Quantification and comparison of anti-fibrotic therapies by polarized SRM and SHG-based morphometry in rat UUO model

description: Renal interstitial fibrosis (IF) is an important pathologic manifestation
 of disease progression in a variety of chronic kidney diseases (CKD).
 However, the quantitative and reproducible analysis of IF remains a
 challenge, especially in experimental animal models of progressive IF. In
 this study, we compare traditional polarized Sirius Red morphometry (SRM)
 to novel Second Harmonic Generation (SHG)-based morphometry of unstained
 tissues for quantitative analysis of IF in the rat 5 day unilateral
 ureteral obstruction (UUO) model. To validate the specificity of SHG for
 detecting fibrillar collagen components in IF, co-localization studies for
 collagens type I, III, and IV were performed using IHC. In addition, we
 examined the correlation, dynamic range, sensitivity, and ability of
 polarized SRM and SHG-based morphometry to detect an anti-fibrotic effect
 of three different treatment regimens. Comparisons were made across three
 separate studies in which animals were treated with three mechanistically
 distinct pharmacologic agents: enalapril (ENA, 15, 30, 60 mg/kg),
 mycophenolate mofetil (MMF, 2, 20 mg/kg) or the connective tissue growth
 factor (CTGF) neutralizing antibody, EX75606 (1, 3, 10 mg/kg). Our results
 demonstrate a strong co-localization of the SHG signal with fibrillar
 collagens I and III but not non-fibrillar collagen IV. Quantitative IF,
 calculated as percent cortical area of fibrosis, demonstrated similar
 response profile for both polarized SRM and SHG-based morphometry. The two
 methodologies exhibited a strong correlation across all three pharmacology
 studies (r2 = 0.89–0.96). However, compared with polarized SRM, SHG-based
 morphometry delivered a greater dynamic range and absolute magnitude of
 reduction of IF after treatment. In summary, we demonstrate that SHG-based
 morphometry in unstained kidney tissues is comparable to polarized SRM for
 quantitation of fibrillar collagens, but with an enhanced sensitivity to
 detect treatment-induced reductions in IF. Thus, performing SHG-based
 morphometry on unstained kidney tissue is a reliable alternative to
 traditional polarized SRM for quantitative analysis of IF.
description: Summary of SHG and SRM
 dataRaw data of quantitative
 imaging analysis of SRM and SHGCorrelation between SRM
 and SHG for three UUO studies (2-10-16)Correlation between SRM
 and SHG analysis
DOI: 10.5061/dryad.sr4rm
title: Data from: Genetic variation in adaptive traits and seed transfer zones for Pseudoroegneria spicata (bluebunch wheatgrass) in the northwestern United States

description: A genecological approach was used to explore genetic variation in adaptive
 traits in Pseudoroegneria spicata, a key restoration grass, in the
 intermountain western United States. Common garden experiments were
 established at three contrasting sites with seedlings from two maternal
 parents from each of 114 populations along with five commercial releases
 commonly used in restoration. Traits associated with size, flowering
 phenology and leaf width varied considerably among populations and were
 moderately correlated to the climates of the seed sources. P. spicata
 populations from warm, arid source environments were smaller with earlier
 phenology and had relatively narrow leaves than those from mild climates
 with cool summers, warm winters, low seasonal temperature differentials,
 high precipitation, and low aridity. Later phenology was generally
 associated with populations from colder climates. Releases were larger and
 more fecund than most of the native ecotypes, but were similar to native
 populations near their source of origin. Differences among native
 populations associated with source climates that are logical for survival,
 growth and reproduction indicate that genetic variation across the
 landscape is adaptive and should be considered during restoration. Results
 were used to delineate seed transfer zones and population movement
 guidelines to ensure adapted plant materials for restoration activities.
description: Raw Trait
 ValuesRaw trait data for a
 bluebunch wheatgrass genecology study conducted in 2007-2008. SITE =
 garden site: CF = Central Ferry, WA; LP = Lucky Peak Nursery, ID; PU =
 Pullman, WA. YEAR = year of data collection. BLOCK = block within site.
 POP = population ID. FAM = maternal family within population. UID = unique
 ID for each individual. Description of trait values can be found in the
 associated paper.bluebunch1.csvGermination DataPer run germination data for a bluebunch wheatgrass genecology study conducted in 2007-2008. UID = for each germination run. SITE = garden site: CF = Central Ferry, WA; LP = Lucky Peak Nursery, ID; PU = Pullman, WA. POP = population ID. FAM = maternal family within population. Description of trait values can be found in the associated paper.bluebunch2.csvPopulation location and climate dataPopulation location and associated climate data for a bluebunch wheatgrass genecology study conducted in 2007-2008. POP = population ID. Description of climate variables can be found on the climateWNA website: http://www.genetics.forestry.ubc.ca/cfcg/ClimateWNA/ClimateWNA.htmlbluebunch3.csv
DOI: 10.5061/dryad.tn4r0
title: Data from: Insect temperature-body size trends common to laboratory, latitudinal and seasonal gradients are not found across altitudes

description: 1. Body size affects rates of most biological and ecological processes,
 from individual performance to ecosystem function, and is fundamentally
 linked to organism fitness. Within species, size at maturity can vary
 systematically with environmental temperature in the laboratory and across
 seasons, as well as over latitudinal gradients. Recent meta-analyses have
 revealed a close match in the magnitude and direction of these size
 gradients in various arthropod orders, suggesting that these size
 responses share common drivers. 2. As with increasing latitude,
 temperature also decreases with increasing altitude. Although the general
 direction of body size clines along altitudinal gradients has been
 examined previously, to our knowledge altitude-body size (A-S) clines have
 never been synthesised quantitatively, nor compared with temperature-size
 (T-S) responses measured under controlled laboratory conditions. 3. Here
 we quantitatively examine variation in intraspecific A-S clines among 121
 insect species from 50 different global locations, representing 12
 taxonomic orders. While some taxa were better represented in the
 literature than others, our analysis reveals extensive variation in the
 magnitude and direction of A-S clines. Following the assumption that
 temperature on average declines by 1°C per 150m increase in altitude,
 order-specific A-S clines in the field appear to deviate from laboratory
 T-S responses. Specifically, the magnitude of A-S clines and T-S responses
 are more closely matched in some taxonomic orders (e.g. Diptera) than
 others (e.g. Orthoptera). These findings contrast with the strong
 co-variation observed between latitude-size clines and T-S responses, and
 between laboratory and seasonal T-S responses. 4. The lack of clear size
 relationships with elevation, and hence temperature, is likely due to the
 counteracting effects of other major drivers with altitude, including
 season length and oxygen partial pressure. Switches in voltinism within
 species across altitude, and the dispersal of individuals across different
 elevations, may also obscure trends.
description: Horne et al. Data
 SetRaw data used to
 calculate altitude-size clines.
DOI: 10.5061/dryad.6t7t6
title: Data from: Revisiting Darwin’s naturalization conundrum: explaining invasion success of non-native trees and shrubs in southern Africa

description: 1. Invasive species are detrimental ecologically and economically. Their
 negative impacts in Africa are extensive and call for a renewed commitment
 to better understand the correlates of invasion success. 2. Here, we
 explored several putative drivers of species invasion among woody
 non-native trees and shrubs in southern Africa, a region of high floristic
 diversity. We tested for differences in functional traits between plant
 categories using a combination of phylogenetic independent contrasts and a
 simulation-based phylogenetic anova. 3. We found that non-native species
 generally have longer flowering duration compared with native species and
 are generally hermaphroditic, and their dispersal is mostly abiotically
 mediated. We also revealed that non-native trees and shrubs that have
 become invasive are less closely related to native trees and shrubs than
 their non-invasive non-native counterparts. Non-natives that are more
 closely related to the native species pool may be more likely to possess
 traits suited to the new environment in which they find themselves and
 thus have greater chance of establishment. However, successful invaders
 are less closely related to the native pool, indicating evidence for
 competitive release or support for the vacant niche theory. 4. Synthesis.
 Non-native trees and shrubs in southern Africa are characterized by a
 suite of traits, including long flowering times, a hermaphroditic sexual
 system and abiotic dispersal, which may represent important adaptations
 promoting establishment. We suggest that differences in the evolutionary
 distances separating the native species pool from invasive and
 non-invasive species might help resolve Darwin's naturalization
 conundrum.
description: Table
 S2Trait database used in
 this analysisPhylogenetic
 treePhylogeny of southern
 African trees and shrubs speciesPhD_final_final.treTable S1
DOI: 10.5061/dryad.8tb7r
title: Data from: Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway

description: Background and Aims - Investigating species distributions across
 geographic barriers is a commonly utilized method in biogeography to help
 understand the functional traits that allow plants to disperse
 successfully. Here the biogeographic pattern analysis approach is extended
 by using chloroplast DNA whole-genome ‘mining’ to examine the functional
 traits that have impacted the dispersal of widespread temperate forest
 species across an intermittent seaway, the 200 km wide Bass Strait of
 south-eastern Australia. Methods - Multiple, co-distributed species of
 both dry and wet forests were sampled from five regions on either side of
 the Strait to obtain insights into past dispersal of these biomes via
 seed. Using a next-generation sequencing-based pool-seq method, the
 sharing of single nucleotide polymorphisms (SNPs) was estimated between
 all five regions in the chloroplast genome. Key Results - A total of 3335
 SNPs were detected in 20 species. SNP sharing patterns between regions
 provided evidence for significant seed-mediated gene flow across the study
 area, including across Bass Strait. A higher proportion of shared SNPs in
 dry forest species, especially those dispersed by birds, compared with wet
 forest species suggests that dry forest species have undergone greater
 seed-mediated gene flow across the study region during past climatic
 oscillations and sea level changes associated with the
 interglacial/glacial cycles. Conclusions - This finding is consistent with
 a greater propensity for long-distance dispersal for species of open
 habitats and proxy evidence that expansive areas of dry vegetation
 occurred during times of exposure of Bass Strait during glacials. Overall,
 this study provides novel genetic evidence that habitat type and its
 interaction with dispersal traits are major influences on dispersal of
 plants.
description: Worth et al. 22 species
 chloroplast DNA reference genomesThis zip file contains
 the chloroplast DNA reference genomes assembled for the 22 species
 investigated in this study. These genomes were used as references to map
 reads for SNP discovery. For details on how the reference genomes were
 assembled please refer to the paper 'Habitat type and dispersal mode
 underlie the capacity for plant migration across an intermittent
 seaway' in Annals of Botany.
DOI: 10.5061/dryad.3df12
title: Data from: Palaeo-precipitation is a major determinant of palm species richness patterns across Madagascar: a tropical biodiversity hotspot

description: The distribution of rainforest in many regions across the Earth was
 strongly affected by Pleistocene ice ages. However, the extent to which
 these dynamics are still important for modern-day biodiversity patterns
 within tropical biodiversity hotspots has not been assessed. We employ a
 comprehensive dataset of Madagascan palms (Arecaceae) and climate
 reconstructions from the last glacial maximum (LGM; 21 000 years ago) to
 assess the relative role of modern environment and LGM climate in
 explaining geographical species richness patterns in this major tropical
 biodiversity hotspot. We found that palaeoclimate exerted a strong
 influence on palm species richness patterns, with richness peaking in
 areas with higher LGM precipitation relative to present-day even after
 controlling for modern environment, in particular in northeastern
 Madagascar, consistent with the persistence of tropical rainforest during
 the LGM primarily in this region. Our results provide evidence that
 diversity patterns in the World's most biodiverse regions may be
 shaped by long-term climate history as well as contemporary environment.
description: Richness_analyses_02_all_cells_5records_nodataRichness_analyses_02_all_cells_10records_nodataRichness_analyses_05_all_cells_5records_nodataRichness_analyses_05_all_cells_10records_nodata
DOI: 10.5061/dryad.8bq71011
title: Data from: Quantitative genetics of female mate preferences in an ancestral and a novel environment

description: A female’s mate preference is a potentially complex function relating
 variation in multiple male phenotypes with her probability of accepting
 individual males as a mate. Estimating the quantitative genetic basis of
 preference functions within a population is empirically challenging yet
 key to understanding preference evolution. We employed a recently
 described approach that uses random-coefficient mixed models in the
 analysis of function-valued traits. Using a half-sibling breeding design
 in a laboratory-adapted Drosophila serrata population, we estimated the
 genetic (co)variance function of female preference for male sexual
 displays composed of nine contact pheromones. The breeding design was
 performed across two environments: the food to which the population was
 well adapted and a novel food that reduced average female productivity by
 35%. Significant genetic variance in female preference was detected and
 the majority (64.2%) was attributable to a single genetic dimension
 (eigenfunction), suggesting that preferences for different pheromones are
 not genetically independent. The second eigenfunction, accounting for 24%
 of the total genetic variance, approached significance in a conservative
 test, suggesting the existence of a second, independent genetic dimension.
 There was no evidence that the genetic basis of female preference differed
 between the two environments, suggesting the absence of
 genotype-by-environment interactions and hence a lack of
 condition-dependent preference expression.
description: Rundle_Mate_preference_dataSee associated ReadMe text file.
DOI: 10.5061/dryad.d6620
title: Data from: A gene with major phenotypic effects as a target for selection versus homogenizing gene flow

description: Genes with major phenotypic effects facilitate quantifying the
 contribution of genetic vs. plastic effects to adaptive divergence. A
 classical example is Ectodysplasin (Eda), the major gene controlling
 lateral plate phenotype in three-spined stickleback. Completely plated
 marine stickleback populations evolved repeatedly towards low-plated
 freshwater populations, representing a prime example of parallel evolution
 by natural selection. However, many populations remain polymorphic for
 lateral plate number. Possible explanations for this polymorphism include
 relaxation of selection, disruptive selection, or a balance between
 divergent selection and gene flow. We investigated 15 polymorphic
 stickleback populations from brackish and freshwater habitats in coastal
 North-western Europe. At each site, we tracked changes in allele frequency
 at the Eda gene between subadults in fall, adults in spring, and juveniles
 in summer. Eda genotypes were also compared for body size and reproductive
 investment. We observed a fitness advantage for the Eda allele for
 low-platedness in freshwater, and for the allele for completely-platedness
 in brackish water. Despite these results, the differentiation at the Eda
 gene was poorly correlated with habitat characteristics. Neutral
 population structure was the best predictor of spatial variation in
 lateral plate number, suggestive of a substantial effect of gene flow. A
 meta-analysis revealed that the signature of selection at Eda was weak
 compared to similar studies in stickleback. We conclude that a balance
 between divergent selection and gene flow can maintain stickleback
 populations polymorphic for lateral plate number, and that ecologically
 relevant genes may not always contribute much to local adaptation, even
 when targeted by selection.
description: Raeymaekers et
 al-MolEcol-2014 EdaSee first
 sheet
DOI: 10.5061/dryad.qv275
title: Data from: Laboratory maintenance does not alter ecological and physiological patterns among species: a Drosophila case study

description: Large comparative studies in animal ecology, physiology, and evolution
 often use animals reared in the laboratory for many generations; however,
 the relevance of these studies hinges on the assumption that laboratory
 populations are still representative for their wild living conspecifics.
 In the present study, we investigate if laboratory-maintained and
 freshly-collected animal populations are fundamentally different and if
 data from laboratory-maintained animals are valid to use in large
 comparative investigations of ecological and physiological patterns. Here,
 we obtained nine species of Drosophila with paired populations of
 laboratory-maintained and freshly-collected flies. These species,
 representing a range of ecotypes, were then assayed for four stress
 tolerance traits, two body size traits, and six life history traits. For
 all of these traits, we observed small differences in species-specific
 comparisons between field and laboratory populations; however, these
 differences were unsystematic and laboratory maintenance did not eclipse
 fundamental species characteristics. To investigate if laboratory
 maintenance influence the general patterns in comparative studies, we
 correlated stress tolerance and life history traits with environmental
 traits for the laboratory-maintained and freshly-collected populations.
 Based on this analysis we found that the comparative physiological and
 ecological trait correlations are largely similar irrespective of
 provenience. This finding is important for comparative biology in general
 because it validates comparative meta-analyses based on
 laboratory-maintained populations.
description: Cor.Mat.2LabAdapt.3.11.16Raw data for all 12 traits in field/lab comparison
DOI: 10.5061/dryad.6ss84
title: Data from: The good, the bad, and the ugly: the influence of skull reconstructions and intraspecific variability in studies of cranial morphometrics in theropods and basal saurischians

description: Several studies investigating macroevolutionary skull shape variation in
 fossil reptiles were published recently, often using skull reconstructions
 taken from the scientific literature. However, this approach could be
 potentially problematic, because skull reconstructions might differ
 notably due to incompleteness and/or deformation of the material.
 Furthermore, the influence of intraspecific variation has usually not been
 explored in these studies. Both points could influence the results of
 morphometric analyses by affecting the relative position of species to
 each other within the morphospace. The aim of the current study is to
 investigate the variation in morphometric data between skull
 reconstructions based on the same specimen, and to compare the results to
 shape variation occurring in skull reconstructions based on different
 specimens of the same species (intraspecific variation) and skulls of
 closely related species (intraspecific variation). Based on the current
 results, shape variation of different skull reconstructions based on the
 same specimen seems to have generally little influence on the results of a
 geometric morphometric analysis, although it cannot be excluded that some
 erroneous reconstructions of poorly preserved specimens might cause
 problems occasionally. In contrast, for different specimens of the same
 species the variation is generally higher than between different
 reconstructions based on the same specimen. For closely related species,
 at least with similar ecological preferences in respect to the dietary
 spectrum, the degree of interspecific variation can overlap with that of
 intraspecific variation, most probably due to similar biomechanical
 constraints.
description: ERROR_test_22LMMorphoJ file
DOI: 10.5061/dryad.5d19r
title: Data from: A morphometric analysis of vegetation patterns in dryland ecosystems

description: Vegetation in dryland ecosystems often forms remarkable spatial patterns.
 These range from regular bands of vegetation alternating with bare ground,
 to vegetated spots and labyrinths, to regular gaps of bare ground within
 an otherwise continuous expanse of vegetation. It has been suggested that
 spotted vegetation patterns could indicate that collapse into a bare
 ground state is imminent, and the morphology of spatial vegetation
 patterns, therefore, represents a potentially valuable source of
 information on the proximity of regime shifts in dryland ecosystems. In
 this paper, we have developed quantitative methods to characterize the
 morphology of spatial patterns in dryland vegetation. Our approach is
 based on algorithmic techniques that have been used to classify pollen
 grains on the basis of textural patterning, and involves constructing
 feature vectors to quantify the shapes formed by vegetation patterns. We
 have analysed images of patterned vegetation produced by a computational
 model and a small set of satellite images from South Kordofan (South
 Sudan), which illustrates that our methods are applicable to both
 simulated and real-world data. Our approach provides a means of
 quantifying patterns that are frequently described using qualitative
 terminology, and could be used to classify vegetation patterns in
 large-scale satellite surveys of dryland ecosystems.
description: Model images of
 patterned vegetationThis zip file contains a
 dataset of images of patterned vegetation produced by a computational
 model. These images are: (1) raw model output images, (2) images that have
 been cropped to 50x50 pixels, and (3) binary images derived from these
 cropped images. These images are all in .tif format. The images show
 patterns produced at 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3 and
 1.4 mm per day.