cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/fokeug
title: Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

description: AbstractFew studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus spp.) and the factors that affect rates of protein evolution. We aligned 35 GB of transcriptome sequencing data and identified 433,257 polymorphic sites (SNPs) in a reference transcriptome comprising 16,312 genes. Using SNP markers, we identified strong population clustering largely corresponding to the three species analyzed here (Helianthus annuus, H. petiolaris, H. debilis), with one distinct early generation hybrid. Then, we calculated the proportions of adaptive substitution fixed by selection (alpha) and identified gene ontology categories with elevated values of alpha. The “response to biotic stimulus” category had the highest mean alpha across the three interspecific comparisons, implying that natural selection imposed by other organisms plays an important role in driving protein evolution in wild sunflowers. Finally, we examined the relationship between protein evolution (dN/dS ratio) and several genomic factors predicted to co-vary with protein evolution (gene expression level, divergence and specificity, genetic divergence [FST], and nucleotide diversity [pi]). We find that variation in rates of protein divergence was correlated with gene expression level and specificity, consistent with results from a broad range of taxa and timescales. This would in turn imply that these factors govern protein evolution both at a microevolutionary and macroevolutionary timescale. Our results contribute to a general understanding of the determinants of rates of protein evolution and the impact of selection on patterns of polymorphism and divergence.
DOI: 10.5683/sp2/fdhah7
title: Data from: The prevalence of MS in the United States: a population-based estimate using health claims data

description: AbstractObjective: To generate a national multiple sclerosis (MS) prevalence estimate for the United States by applying a validated algorithm to multiple administrative health claims (AHC) datasets. Methods: A validated algorithm was applied to private, military, and public AHC datasets to identify adult cases of MS between 2008 and 2010. In each dataset, we determined the 3-year cumulative prevalence overall and stratified by age, sex, and census region. We applied insurance-specific and stratum-specific estimates to the 2010 US Census data and pooled the findings to calculate the 2010 prevalence of MS in the United States cumulated over 3 years. We also estimated the 2010 prevalence cumulated over 10 years using 2 models and extrapolated our estimate to 2017. Results: The estimated 2010 prevalence of MS in the US adult population cumulated over 10 years was 309.2 per 100,000 (95% confidence interval [CI] 308.1–310.1), representing 727,344 cases. During the same time period, the MS prevalence was 450.1 per 100,000 (95% CI 448.1–451.6) for women and 159.7 (95% CI 158.7–160.6) for men (female:male ratio 2.8). The estimated 2010 prevalence of MS was highest in the 55- to 64-year age group. A US north-south decreasing prevalence gradient was identified. The estimated MS prevalence is also presented for 2017. Conclusion: The estimated US national MS prevalence for 2010 is the highest reported to date and provides evidence that the north-south gradient persists. Our rigorous algorithm-based approach to estimating prevalence is efficient and has the potential to be used for other chronic neurologic conditions.
DOI: 10.5683/sp2/qd1icg
title: Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.

description: AbstractRecent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of measurements that define corallite architecture, and could partition additive and non-additive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h² estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h² were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
DOI: 10.5683/sp2/cdizqq
title: Data from: The reciprocal relationship between competition and intraspecific trait variation

description: AbstractTrait differences among plants are expected to influence the outcome of competition; competition should be strongest between similar species (or individuals) under limiting similarity, and between dissimilar species within competitive hierarchies. These hypotheses are often used to infer competitive dynamics from trait patterns within communities. However, plant traits are frequently plastic in response to competition. This variation is poorly accounted for in trait-based studies of competition and community assembly. To explore the relationship between trait responses and competitive outcomes, we grew 15 species alone, in monoculture and in mixture. We measured traits relating to leaf and root tissue morphology as well as biomass allocation and related competition-induced changes in these traits to intra- and interspecific competition using multi-model inference. Additionally, we tested how traits from different competitive environments influenced potential community assembly inferences. The competitive environment had large effects on species’ traits, although many effects were species specific. Differences among species in how competition affected trait expression were linked to both intra- and interspecific competition, frequently affecting competitive hierarchies. Intraspecific competition was lower for species that limited competition-induced increases in root allocation and had less variability in this trait overall. Interspecific competition was lower for species with larger leaves and lower specific leaf area than their neighbours. Switching to more stress-tolerant strategies by increasing root diameter and leaf tissue density also reduced competition. However, dissimilarity in root tissue density also minimized competition, consistent with limiting similarity affecting competitive outcomes. Moreover, changes in these traits were linked to changes in functional diversity, suggesting that competition affects functional diversity by affecting trait expression. Synthesis. Both trait hierarchies and trait dissimilarity affect the outcome of competition by acting on different traits, although competition-induced changes in trait expression can alter competitive outcomes. Moreover, the magnitude of these trait changes suggests that the source environment where plant traits are collected can affect the inferences drawn from trait patterns within communities. Combined, our results suggest that considering the effect of competition on trait expression is critical to understanding the relationship between traits and community assembly.
DOI: 10.5683/sp2/kxz50p
title: Data from: The red queen coupled with directional selection favors the evolution of sex

description: AbstractWhy sexual reproduction has evolved to be such a widespread mode of reproduction remains a major question in evolutionary biology. While previous studies have shown that increased sex and recombination can evolve in the presence of host-parasite interactions (the “Red Queen hypothesis” for sex), many of these studies have assumed that multiple loci mediate infection versus resistance. Data suggest, however, that a major locus is typically involved in antigen presentation and recognition. Here, we explore a model where only one locus mediates host-parasite interactions, but a second locus is subject to directional selection. Even though the effects of these genes on fitness are independent, we show that increased rates of sex and recombination are favored at a modifier gene that alters the rate of genetic mixing. This result occurs because of selective interference that occurs in finite populations (the “Hill-Robertson effect”), which also favors sex. These results suggest that the Red Queen hypothesis may help to explain the evolution of sex by contributing a form of persistent selection, which interferes with directional selection at other loci and thereby favors sex and recombination.
DOI: 10.5683/sp2/85tczj
title: Data from: The relationship between parasite fitness and host condition in an insect - virus system

description: AbstractResearch in host-parasite evolutionary ecology has demonstrated that environmental variation plays a large role in mediating the outcome of parasite infection. For example, crowding or low food availability can reduce host condition and make them more vulnerable to parasite infection. This observation that poor-condition hosts often suffer more from parasite infection compared to healthy hosts has led to the assumption that parasite productivity is higher in poor-condition hosts. However, the ubiquity of this negative relationship between host condition and parasite fitness is unknown. Moreover, examining the effect of environmental variation on parasite fitness has been largely overlooked in the host-parasite literature. Here we investigate the relationship between parasite fitness and host condition by using a laboratory experiment with the cabbage looper Trichoplusia ni and its viral pathogen, AcMNPV, and by surveying published host-parasite literature. Our experiments demonstrated that virus productivity was positively correlated with host food availability and the literature survey revealed both positive and negative relationships between host condition and parasite fitness. Together these data demonstrate that contrary to previous assumptions, parasite fitness can be positively or negatively correlated with host fitness. We discuss the significance of these findings for host-parasite population biology.
DOI: 10.5683/sp2/vsdxvk
title: Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

description: AbstractAlthough genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in ‘pair’ and ‘transect’ sampling strategies. We compared FST outlier and genetic–environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (FST or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and FST had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation and have important implications for the interpretation of genome scans based on landscape data.
DOI: 10.5683/sp2/tknvp2
title: Data from: The role of pleiotropy in the maintenance of sex in yeast

description: AbstractIn facultatively sexual species, lineages that reproduce asexually for a period of time can accumulate mutations that reduce their ability to undergo sexual reproduction when sex is favorable. We propagated Saccharomyces cerevisiae asexually for ~800 generations, after which we measured the change in sexual ﬁtness, measured as the proportion of asci observed in sporulation medium. The sporulation rate in cultures propagated asexually at small population size declined by 8%, on average, over this time period, indicating that the majority of mutations that affect sporulation rate are deleterious. Interestingly, the sporulation rate in cultures propagated asexually at large population size improved by 11%, on average, indicating that selection on asexual function effectively eliminated most of the mutations deleterious to sporulation ability. These results suggest that pleiotropy between mutations’ effects on asexual ﬁtness and sexual ﬁtness was predominantly positive, at least for the mutations accumulated in this experimental evolution study. A positive correlation between growth rate and sporulation rate among lines also pro- vided evidence for positive pleiotropy. These results demonstrate that, at least under certain circum- stances, selection acting on asexual ﬁtness can help to maintain sexual function.
DOI: 10.5683/sp2/ihbakz
title: Data from: The shortfall of sociality: group-living affects hunting performance of individual social spiders

description: AbstractIneffective hunters in cooperative foraging groups may be shielded from natural selection by their more effective group mates, whereas those living solitarily would starve and thus be removed from the population. The problem may be exacerbated in large groups where it may be easier for individuals to withhold participation. Group foragers may thus be ineffective individual hunters or exhibit greater inter-individual variation in hunting abilities, in particular when living in large groups. We test these hypotheses in spider species of the genus Anelosimus that differ in their level of sociality and, among social species, in colonies of different sizes. We found that individuals from the more social species, and those from larger groups, reacted more slowly to prey than those from solitary species or small groups. Individuals from these categories also had greater inter-individual variation in reaction times. Individuals from large social groups also had lower prey capture success than those from small ones. These differences may have been driven by the size of the group from which the social individuals were taken, as those from small colonies behaved similarly to individuals of the two less social species. This finding suggests that hunting ability may develop as a phenotypically plastic trait.
DOI: 10.5683/sp2/7ng4in
title: Data from: Theory, practice, and conservation in the age of genomics: the Galápagos giant tortoise as a case study

description: AbstractHgh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in non-model organisms. Using &gt;20,000 genome-wide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
DOI: 10.5683/sp2/rkkazq
title: Data from: Thermal tolerances and species interactions determine the elevational distributions of insects

description: AbstractAim: While physiological limits to thermal extremes are often thought to determine the abundance and geographic distribution of species, more recent evidence suggests that species interactions may be equally important. Moreover, the relative importance of these constraints may shift with changing abiotic conditions, such as climate change. Here, we explore the relative importance of physiological tolerances to heat and species interactions in determining the distribution of insects along two elevational gradients. The gradients contrast in precipitation but not temperature, allowing us to separate these two climatic factors. Location: Montane rainforest in Costa Rica. Time period: 2015-2016. Major taxa studied: Bromeliad-dwelling aquatic insect larvae. Methods: We estimated the elevation preferences of five insect taxa by surveying 170 bromeliads along the moist Atlantic and the dry Pacific slopes of Monteverde, and experimentally determined their critical thermal maxima (CTmax). We determined if species-specific heat tolerances predict their elevation preferences, using Deming regressions, and tested if potential predators mediated elevation effects on species distributions, using structural equation models. Results: On the moist Atlantic slope, heat tolerances of insects explained their elevational distributions: taxa with high heat tolerances preferred low elevations where conditions are warmest, while taxa with low heat tolerances preferred high elevations where it is coldest. By contrast, on the drier Pacific slope, the elevational abundance pattern of many insects reflected negative interactions from cranefly larvae. These larvae are known to become predatory under drought conditions and were disproportionally abundant at low elevations on the Pacific slope. Main conclusions: We show that under drought, indirect effects mediated by species interactions can override any direct physiological effects of environmental conditions on insect distributions. The relative importance of limits to physiological tolerance and species interactions thus depends on environmental context, an important insight given that environmental conditions are expected to shift with climate change.
DOI: 10.5683/sp2/ymexcm
title: Data from: They are likely to be there: using a family-centered index-testing approach to identify HIV-positive children in Kenya

description: AbstractIn Kenya, only half of children with an HIV-positive parent have been tested for HIV. The effectiveness of a family-centred index-testing approach to identify children (0-14 years) living with HIV was examined. A retrospective clinical record review was conducted among adult index patients newly enrolled in HIV care between May–July 2015 and family outcomes were followed through May 2016 at 60 high-volume clinics in western Kenya. HIV testing uptake and results, health facility level, enrollment into care and antiretroviral therapy (ART) initiation were abstracted. Chi-square test compared yield (percentage of HIV tests positive) among children tested through family-centred index testing to outpatient and inpatient testing approaches for the same age category, health facilities and time period. Review of 1,937 index client charts led to the identification of 3,005 eligible children for testing. Of 2,848 (94.8%) children tested through family-centred index testing, 127 (4.5%) were HIV-positive, 100 (78.7%) were linked to care, and 85 of those eligible (91.4%) had initiated ART by May 2016. Family testing resulted in higher yield as compared with inpatient 1.8% (p&lt;0.001) or outpatient testing 1.6% (p&lt;0.001). The absolute number of HIV positive children identified, however, was highest with outpatient testing (338 HIV positive children identified out of 27,402 tested). The family testing approach resulted in a high HIV identification yield for children and demonstrated promise in achieving the first two 90’s of the 90-90-90 targets for children, with additional effort required to improve linkage from testing to treatment.
DOI: 10.5683/sp2/hhhb1s
title: Data from: Three keys to the radiation of angiosperms into freezing environments

description: AbstractEarly flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species’ traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits5 and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile6, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.