cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397646
title: Data from: Photos provide information on age, but not kinship, of Andean bear

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Using photos of captive Andean bears of known age and pedigree, and photos of wild Andean bear cubs &lt;6 months old, we evaluated the degree to which visual information may be used to estimate bears’ ages and assess their kinship. We demonstrate that the ages of Andean bear cubs ≤6 months old may be estimated from their size relative to their mothers with an average error of &lt;0.01 ± 13.2 days (SD; n = 14), and that ages of adults ≥10 years old may be estimated from the proportion of their nose that is pink with an average error of &lt;0.01 ± 3.5 years (n = 41). We also show that similarity among the bears’ natural markings, as perceived by humans, is not associated with pedigree kinship among the bears (R2 &lt; 0.001, N = 1,043, p = 0.499). Thus, researchers may use photos of wild Andean bears to estimate the ages of young cubs and older adults, but not to infer their kinship. Given that camera trap photos are one of the most readily available sources of information on large cryptic mammals, we suggest that similar methods be tested for use in other poorly understood species.
DOI: 10.14288/1.0397647
title: Data from: Genetic signature of adaptive peak shift in threespine stickleback

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution as the same ancestor adapted to two lake types since the end of the ice age. A higher frequency of large effect genetic changes (quantitative trait loci) contributed to adaptive evolution in populations that adapted to lakes representing a more distant optimum than to lakes in which the optimum phenotype was nearer to the ancestral state. Our results also indicate that pleiotropy, not just optimum overshoot, contributes to this difference. These results suggest that a series of adaptive improvements to a new environment leaves a detectable mark in the genome of wild populations. Although not all assumptions of the theory are likely met in natural systems, the prediction may be robust enough to the complexities of natural environments to be useful when forecasting adaptive responses to large environmental changes.
DOI: 10.14288/1.0397648
title: Data from: No effect of environmental heterogeneity on the maintenance of genetic variation in wing shape in Drosophila melanogaster

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Theory suggests that heterogeneous environments should maintain more genetic variation within populations than homogeneous environments, yet experimental evidence for this effect in quantitative traits has been inconsistent. To examine the effect of heterogeneity on quantitative genetic variation, we maintained replicate populations of Drosophila melanogaster under treatments with constant temperatures, temporally variable temperature, or spatially variable temperature with either panmictic or limited migration. Despite observing differences in fitness and divergence in several wing traits between the environments, we did not find any differences in the additive genetic variance for any wing traits among any of the treatments. Although we found an effect of gene flow constraining adaptive divergence between cages in the limited migration treatment, it did not tend to increase within-population genetic variance relative to any of the other treatments. The lack of any clear and repeatable patterns of response to heterogeneous vs. homogeneous environments across several empirical studies suggests that a single general mechanism for the maintenance of standing genetic variation is unlikely; rather, the relative importance of putative mechanisms likely varies considerably from one trait and ecological context to another.
DOI: 10.14288/1.0397651
title: Data from: Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives.

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;• The development of modern crops typically involves both selection and hybridization, but to date most studies have focused on the former. In the present study we explore how both processes, and their interactions, have molded the genome of the cultivated sunflower, a globally important oilseed. • To identify genes targeted by selection during the domestication and improvement of sunflower, and to detect post-domestication hybridization with wild species, we analyzed transcriptome sequences of 80 genotypes, including wild, landrace, and modern lines of Helianthus annuus, as well as two cross-compatible wild relatives, H. argophyllus and H. petiolaris. • Outlier analyses identified 122 and 15 candidate genes associated with domestication and improvement, respectively. As in several previous studies, genes putatively involved in oil biosynthesis were the most extreme outliers. Additionally, several promising associations were observed with previously mapped QTLs, such as branching. Admixture analyses revealed that all of the modern cultivar genomes we examined contained one or more introgressions from wild populations, with every chromosome having evidence of introgression in at least one modern line. • Cumulatively, introgressions cover approximately 10% of the cultivated sunflower genome. Surprisingly, introgressions do not avoid candidate domestication genes likely because of the re-introduction of branching.
DOI: 10.14288/1.0397652
title: Data from: Rain, predators, and spider sociality: a manipulative experiment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Group-living organisms offer a unique perspective on how environmental gradients influence geographic distributions, as not only the properties of individuals, but also those of their groups interact with the environment to determine a species range. In turn, the ranges of group-living organisms should provide insights on the conditions that favor group versus solitary living. Here we show that rain intensity and predation by ants, factors postulated to exclude subsocial Anelosimus spiders from the lowland tropical rainforest, are greater in this habitat than at higher elevations. We further show that experimentally excluding these factors increases the survival of subsocial Anelosimus colonies when transplanted to the lowland rainforest, but not at their native higher elevation range. While providing a rare experimental test of the simultaneous importance of abiotic and biotic gradients on species range limits, these results provide direct evidence that adverse environmental factors may prevent solitary living and require group living in certain environments.
DOI: 10.14288/1.0397653
title: Data from: Integrating morphological characters, molecular markers, and distribution patterns to assess the identity of Blepharis species from Jordan

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Background: Blepharis constitutes an important vegetative part of the Jordanian arid and semi-arid regions, yet whether one or more species occurs in this area is debatable. We addressed this question by assessing morphological characters and employing Inter-Simple Sequence Repeat (ISSR) markers on three populations of Blepharis: two Northern (lower slopes of Kufranjah valley and the Dead Sea region) and one Southern (Wadi al Yutm). Results: Shoots from 19 randomly chosen Blepharis plants per population were harvested for morphological and molecular analyses. Spikes were lax and bract width was considerably shorter than length of the longest lateral spine in the Northern populations compared to the Southern population (P &lt; 0.001). A multivariate linear discriminant analysis (LDA) distinguished the Northern populations from the Southern one largely by internode length, bract width, longest lateral spine length, and bract width to spine length ratio (P &lt; 0.001). The ISSR analysis revealed that 44 markers across eight primers were polymorphic with major allele frequency of 83.6% and an average of 5.5 polymorphic markers per primer. The genetic resemblance among individuals ranged from 0.27 to 0.96. The three Blepharis populations were accordingly clustered into two distinct groups, similar to the analysis of morphological differences. Conclusions: Our results strongly indicate the occurrence of two discrete Blepharis species in Jordan and the hypothesis that the genus is represented by only one species is not supported. The species in Jordan are B. attenutata Napper (represented by the Northern populations) and B. ciliaris [L.] B. L. Burtt (represented by the Southern population). These findings are important for informing floristic work within the region and an updated key has been included in our findings.
DOI: 10.14288/1.0397654
title: Data from: A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
DOI: 10.14288/1.0397655
title: Data from: Herbivory enhances the resistance of mangrove forest to cordgrass invasion

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The biotic resistance hypothesis proposes that biotic interactions, such as competition and herbivory, resist the establishment and spread of non-native species. The relative and interactive role of competition and herbivory in resisting plant invasions, however, remains poorly understood. We investigated the interactive role of competition and herbivory (by the native rodent Rattus losea) in resisting Spartina alterniflora (cordgrass) invasions into mangrove forests. In southern China, although exotic cordgrass numerically dominates intertidal mudflats and open gaps in mangrove forests, intact forests appear to be highly resistant to cordgrass invasion. A field transplant and rodent exclusion experiment showed that while the impact of rodent grazing on cordgrass was weak on mangrove forest edges and open mudflats, rodent grazing strongly suppressed cordgrass in mangrove understory habitats. A greenhouse experiment confirmed a synergistic interaction between grazing and light availability (a proxy for mangrove shading/competition) in suppressing cordgrass establishment, with the strongest impacts of grazing in low light conditions that likely weakened cordgrass to survive and resprout. When both were present, as in mangrove understory habitats, grazing and low light acted in concert to eliminate cordgrass establishment, resulting in resistance of mangrove forests to cordgrass invasion. Our results reveal that grazing by native herbivores can enhance the resistance of mangrove forests to cordgrass invasion in southern China, and suggest that investigating multifactor interactions may be critical to understanding community resistance to exotic invasions.
DOI: 10.14288/1.0397656
title: Data from: Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [ 1, 2 ]. Many traits previously considered “animal specific” were subsequently found in other holozoans [ 3, 4 ], showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [ 2, 5 ]. Here we report the morphology and transcriptome sequencing from three novel unicellular holozoans: Pigoraptor vietnamica and Pigoraptor chileana, which are related to filastereans, and Syssomonas multiformis, which forms a new lineage with Corallochytrium in phylogenomic analyses. All three species are predatory flagellates that feed on large eukaryotic prey, and all three also appear to exhibit complex life histories with several distinct stages, including multicellular clusters. Examination of genes associated with multicellularity in animals showed that the new filastereans contain a cell-adhesion gene repertoire similar to those of other species in this group. Syssomonas multiformis possessed a smaller complement overall but does encode genes absent from the earlier-branching ichthyosporeans. Analysis of the T-box transcription factor domain showed expansion of T-box transcription factors based on combination with a non-T-box domain (a receiver domain), which has not been described outside of vertebrates. This domain and other domains we identified in all unicellular holozoans are part of the two-component signaling system that has been lost in animals, suggesting the continued use of this system in the closest relatives of animals and emphasizing the importance of studying loss of function as well as gain in major evolutionary transitions.
DOI: 10.14288/1.0397659
title: Data from: Origins of food crops connect countries worldwide

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.
DOI: 10.14288/1.0397663
title: Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.
DOI: 10.14288/1.0397665
title: Data from: Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;We developed a new modeling framework to assess how the local abundance of one species influences the local abundance of a potential competitor while explicitly accounting for differential responses to environmental conditions. Our models also incorporate imperfect detection as well as abundance estimation error for both species. As a case study, we applied the model to four pairs of mammal species in Borneo, surveyed by extensive and spatially widespread camera trapping. We detected different responses to elevation gradients within civet, macaque, and muntjac deer species pairs. Muntjac and porcupine species varied in their response to terrain ruggedness, and the two muntjac responded different to river proximity. Bornean endemic species of civet and muntjac were more sensitive than their widespread counterparts to habitat disturbance (selective logging). Local abundance within several species pairs was positively correlated, but this is likely due to the species having similar responses to (unmodeled) environmental conditions or resources rather than representing facilitation. After accounting for environment and correcting for false absences in detection, negative correlations in local abundance appear rare in tropical mammals. Direct competition may be weak in these species, possibly because the ‘ghost of competition past’ or habitat filtering have already driven separation of the species in niche space. The analytical framework presented here could increase basic understanding of how ecological interactions shape patterns of abundance across the landscape for a range of taxa, and also provide a powerful tool for forecasting the impacts of global change..
DOI: 10.14288/1.0397667
title: Data from: Development of an ultra-dense genetic map of the sunflower genome

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.
DOI: 10.14288/1.0397669
title: Data from: Ecological mechanisms and phylogeny shape invertebrate stoichiometry: a test using detritus-based communities across Central and South America

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Stoichiometric differences among organisms can affect trophic interactions and rates of nutrient cycling within ecosystems. However, we still know little about either the underlying causes of these stoichiometric differences, or the consistency of these differences across large geographic extents. 2. Here we analyze elemental (carbon, nitrogen, phosphorus) composition of 872 aquatic macroinvertebrates (71 species) inhabiting tank bromeliads (n = 140) from five distantly located sites across Central and South America to (1) test phylogenetic, trophic and body size scaling explanations for why organisms differ in elemental composition, and (2) determine if patterns in elemental composition are universal or context-dependent. 3. Taxonomy explained most variance in elemental composition, even though phylogenetic signals were weak and limited to regional spatial extents and to the family level. The highest elemental contents and lowest carbon:nutrient ratios were found in organisms at high trophic levels and with smaller body size, regardless of geographic location. 4. Carnivores may have higher nutrient content and lower carbon:nutrient ratios than their prey, as organisms optimize growth by choosing the most nutrient-rich resources to consume and then preferentially retain nutrients over carbon in their bodies. Smaller organisms grow proportionally faster than large organisms, and so are predicted to have higher nutrient requirements to fuel RNA and protein synthesis. Geography influenced the magnitude, more than the direction, of the ecological and/or phylogenetic effects on elemental composition. 5. Overall, our results show that both ecological (i.e., trophic group) and evolutionary drivers explain among-taxa variation in the elemental content of invertebrates, whereas intraspecific variation is mainly a function of body size. Our findings also demonstrate that restricting analyses of macroinvertebrate stoichiometry solely to either the local scale or species level affects inferences of the patterns in invertebrate elemental content, and their underlying mechanisms.
DOI: 10.15468/dl.qmqskc
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((88 31,103 31,103 38,88 38,88 31))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Canis lupus Linnaeus, 1758"
 ]
}

 The dataset includes 57 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004329-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.