Find research datasets worth reusing

Data from: Seasonally varying contributions to urban CO2 in the Chicago, IL, USA region: insights from a high-resolution CO2 concentration and δ13C record

Understanding urban carbon cycling is essential given that cities sustain 54% of the global population and contribute 70% of anthropogenic CO2 emissions. When combined with CO2 concentration measurements ([CO2]), stable carbon isotope analyses (δ13C) can differentiate sources of CO2, including ecosystem respiration and combustion of fossil fuels, such as petroleum and natural gas. In this study, we used a wavelength scanned-cavity ringdown spectrometer to collect ~2x106 paired measurements for [CO2] and δ13C values in Evanston, IL for August 2011 through February 2012. Evanston is located immediately north of Chicago, IL, the third largest city in the United States. The measurements represent one of the longest records of urban [CO2] and δ13C values thus far reported. We also compiled local meteorological information, as well as complementary [CO2] and δ13C data for background sites in Park Falls, WI and Mauna Loa, HI. We use the dataset to examine how ecosystem processes, fossil fuel usage, wind speed, and wind direction control local atmospheric [CO2] and δ13C in a midcontinent urban setting on a seasonal to daily basis. On average, [CO2] and δ13C values in Evanston were 16–23 ppm higher and 0.97–1.13‰ lower than the background sites. While seasonal [CO2] and δ13C values generally followed broader northern hemisphere trends, the difference between Evanston and the background sites was larger in winter versus summer. Mixing calculations suggest that ecosystem respiration and petroleum combustion equally contributed CO2 in excess of background during the summer and that natural gas combustion contributed 80%–94% of the excess CO2 in winter. Wind speed and direction strongly influenced [CO2] and δ13C values on an hourly time scale. The highest [CO2] and lowest δ13C values occurred at wind speeds <3 m s−1 and when winds blew from the northwest, west, and south over densely populated neighborhoods.

opencc-zeroDec 2012View details →

Data from: Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome

The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints, but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the 'environmental relevance' of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.

opencc-zeroDec 2018View details →

Data from: The contribution of land tenure diversity to the spatial resilience of protected area networks

1. The relationship between diversity and resilience is relatively well-established for ecological systems, but remains much less explored for socioeconomic systems. Institutional diversity may have particular relevance for protected areas, whose managerial responses to environmental change depend on their legal basis, ability to make and enforce rules, and socio-political acceptance and endorsement. 2. Protected area expansion strategies are increasingly turning to private land conservation to increase the configuration and connectivity of national protected area networks. Yet we know little about the relative role of privately-owned protected areas in protecting threatened and poorly protected (under-represented) habitats, and in the overall connectivity of the national protected area network. 3. We present an empirical assessment of protected area tenure diversity across South Africa. 4. Privately-owned protected areas comprise 25.58% (2878422.26 ha) of the area of the total protected area estate. 5. Private nature reserves emerged as the dominant protected area type in under-represented and threatened habitats, protecting, on average, 32%, 38%, and 41%, respectively, of poorly protected, threatened and endangered vegetation classes. 6. Private nature reserves had the largest overall effect, compared to other protected area types, on connectivity within the national network. A spatially randomised comparison showed that privately-owned protected areas are over-dispersed and more strategically positioned to connect other types of protected areas than would be expected by chance from their extent and abundance. 7. Our results suggest that privately-owned protected areas enhance the resilience of the national protected area network, making it more extensive and better-connected, with greater levels of habitat redundancy. More generally, our analysis highlights the potentially valuable role of institutional diversity in building resilient habitat networks for biodiversity conservation.

opencc-zeroDec 2018View details →

Data from: Contribution of predation to the biological control of a key herbivorous pest in citrus agroecosystems

Biological control has traditionally simplified the view of trophic relationships between herbivorous pests and their natural enemies in agriculture. The success or failure of this pest management strategy is still mainly attributed to the ability of a few key natural enemies to suppress the pest density. For example, successful regulation of the California red scale (Aonidiella aurantii) a key citrus pest, is generally credited to specific parasitoids of the Aphytis genus. Currently, research is revealing how herbivore regulation in agroecosystems can be alternatively achieved with a greater number of trophic associations within the system. The goals of the present study were: i) to unravel species‐specific trophic links between A. aurantii, and its natural enemies in citrus agroecosystems, and ii) to assess their contribution to control of A. aurantii. Predation and parasitism of this herbivorous pest were assessed through exclusion experiments. Species‐specific trophic links between this herbivorous pest and its natural enemies were studied using gut‐content analysis of field collected predators employing prey specific DNA molecular markers. Relative predation rates of the species involved in A. aurantii regulation were estimated. Predation was found to be the main biotic component of A. aurantii mortality, causing reductions of more than 75% in recently settled cohorts. Aonidiella aurantii DNA was detected in the digestive system of 11 species of predators. Generalist and stenophagous predators, mainly associated with other citrus pests such as aphids, proved to be the most important biological control agents of this pest. Complex trophic relationships, such as apparent competition between two key citrus pests, were revealed. The present study highlights the role of predation as biotic mortality factor of key pests in perennial agroecosystems; wherein, it is a rich complex of indigenous or naturalized generalist predators that are primarily responsible for this mortality. The results herein presented may therefore offer another perspective on the biological control of one of the key worldwide citrus pests; at least in those regions where specific parasitoids are not able to successfully regulate the scale populations.

opencc-zeroDec 2015View details →

Data from: New insights into the history of domesticated and wild apricots and its contribution to Plum pox virus resistance

Studying domesticated species and their wild relatives allows understanding of the mechanisms of population divergence and adaptation, and identifying valuable genetic resources. Apricot is an important fruit in the Northern hemisphere, where it is threatened by the Plum pox virus (PPV), causing the sharka disease. The histories of apricot domestication and of its resistance to sharka are however still poorly understood. We used 18 microsatellite markers to genotype a collection of 230 wild trees from Central Asia and 142 cultivated apricots as representatives of the worldwide cultivated apricot germplasm; we also performed experimental PPV inoculation tests. The genetic markers revealed highest levels of diversity in Central Asian and Chinese wild and cultivated apricots, confirming an origin in this region. In cultivated apricots, Chinese accessions were differentiated from more Western accessions, while cultivated apricots were differentiated from wild apricots. An approximate Bayesian approach indicated that apricots likely underwent two independent domestication events, with bottlenecks, from the same wild population. Central Asian native apricots exhibited genetic subdivision and high frequency of resistance to sharka. Altogether, our results contribute to the understanding of the domestication history of cultivated apricot and point to valuable genetic diversity in the extant genetic resources of wild apricots.

opencc-zeroNov 2019View details →

Natural variation in the contribution of microbial density to inducible immune dynamics

Immune responses evolve to balance the benefits of microbial killing against the costs of autoimmunity and energetic resource use. Models that explore the evolution of optimal immune responses generally include a term for constitutive immunity, or the level of immunological investment prior to microbial exposure, and for inducible immunity, or investment in immune function after microbial challenge. However, studies rarely consider the functional form of inducible immune responses with respect to microbial density, despite the theoretical dependence of immune system evolution on microbe- versus immune-mediated damage to the host. In this study, we analyze antimicrobial peptide (AMP) gene expression from seven wild-caught flour beetle populations (Tribolium spp.) during acute infection with the virulent bacteria Bacillus thuringiensis (Bt) and Photorhabdus luminescens (P.lum) to demonstrate that inducible immune responses mediated by the humoral IMD pathway exhibit natural variation in both microbe density-dependent and independent temporal dynamics. Beetle populations that exhibited greater AMP expression sensitivity to Bt density were also more likely to die from infection, while populations that exhibited higher microbe density-independent AMP expression were more likely to survive P. luminescens infection. Reduction in pathway signaling efficiency through RNAi-mediated knockdown of the imd gene reduced the magnitude of both microbe-independent and dependent responses and reduced host resistance to Bt growth, but had no net effect on host survival. This study provides a framework for understanding natural variation in the flexibility of investment in inducible immune responses and should inform theory on the contribution of non-equilibrium host-microbe dynamics to immune system evolution.

Data from: Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage

Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages.

opencc-zeroDec 2012View details →

Data from: Host resistance, population structure and the long-term persistence of bubonic plague: contributions of a modelling approach in the Malagasy focus

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.

Data from: Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France

Species distribution models (SDM) have often been used to predict the potential ranges of introduced species and prioritize management strategies. However, this approach assumes equilibrium between occurrences and environmental gradients, an assumption which is violated during the invasion process, where many suitable sites are empty because the species has not yet reached them. Here we considered the invasive ladybird Harmonia axyridis as a case study to show the benefits of using a dynamic colonization–extinction model that does not assume equilibrium. We used a multi-year occupancy model incorporating environmental, anthropogenic and neighborhood effects, to identify factors that explained spreading variation of this species in France from 2004, when only a few occupied sites were detected, to 2011. We found that anthropogenic factors (urbanization, agriculture, vineyards, and presence/absence of highways) explained more variation in the diffusion process than environmental factors (winter and summer temperatures, wind-speed, and rainfall). The surface of urbanization was the major anthropogenic factor increasing the probability of colonization. The average summer temperature was the main environmental factor affecting colonization, with a negative effect when high or low. The neighborhood effect revealed that colonization was mostly influenced by contributions coming from a radius of 24 km around the focal cell. The contribution of neighborhood decreases over time, suggesting that H. axyridis is reaching its equilibrium in France. This is confirmed by the small discrepancy observed between the performance of our approach and a SDM approach when predicting a single year occupancy pattern at the end of the study period. Our approach has the advantage of explicitly modelling the state of the biological system during the spatial expansion and identifying colonization constraints. This allows managers to explore the effect of different actions on the system at key moments of the invasion process, hence providing a powerful approach to prioritize management strategies.

Data from: When does intraspecific trait variation contribute to functional beta-diversity?

1. Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional-trait composition of communities (functional β-diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales. 2. We examined how ITV contributes to functional β-diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across scales, we compared patterns of functional β-diversity across soil-resource and topographic gradients at three spatial grains and three spatial extents. To quantify the contribution of ITV to functional β-diversity, we compared patterns that included ITV in five traits (leaf area, specific leaf area, leaf water content, leaf toughness, and chlorophyll content) to patterns based on species-mean trait values. 3. Functional β-diversity that included ITV increased with spatial extent and decreased with spatial grain, suggesting stronger environmental filtering within spatially extensive landscapes that contain populations locally adapted to different habitats. In contrast, functional β-diversity based on species-mean trait values increased with spatial extent but did not change with spatial grain, suggesting weaker environmental filtering among larger communities which each contain a variety of habitats and locally adapted populations. 4. Synthesis. Although studies typically infer community assembly mechanisms from species-mean trait values, our study suggests that mean trait values may mask the strength of assembly mechanisms such as environmental filtering, especially in landscape-scale studies that encompass strong environmental gradients and locally adapted populations. Our study highlights the utility of integrating ITV into studies of functional β-diversity to better understand the ecological conditions under which trait variation within and among species contributes most strongly to patterns of biodiversity across spatial scales.

opencc-zeroDec 2017View details →

Data from: Towards smarter harvesting from natural palm populations by sparing the individuals that contribute most to population growth or productivity

1. Natural populations deliver a wide range of products that provide income for millions of people and need to be exploited sustainably. Large heterogeneity in individual performance within these exploited populations has the potential to improve population recovery after exploitation and thus help sustaining yields over time. 2. We explored the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity and population growth, using the understorey palm Chamaedorea elegans as a model system. Leaves of this palm are an important non-timber forest product and long-term inter-individual growth variability can be evaluated from internode lengths. 3. We studied a population of 830 individuals, half of which was subjected to a 67 % defoliation treatment for three years. We measured effects of defoliation on vital rates and leaf size – a trait that determines marketability. We constructed integral projection models in which vital rates depended on stem length, past growth rate, and defoliation, and evaluated transient population dynamics to quantify population development and leaf yield. We then simulated scenarios in which we spared individuals that were either most important for population growth or had leaves smaller than marketable size. 4. Individuals varying in size or past growth rate responded similarly to leaf harvesting in terms of growth and reproduction. By contrast, defoliation-induced reduction in survival chance was smaller in large individuals than in small ones. Simulations showed that harvest-induced population decline was much reduced when individuals from size and past growth classes that contributed most to population growth were spared. Under this scenario cumulative leaf harvest over 20 years was somewhat reduced, but long-term leaf production was sustained. A three-fold increase in leaf yield was generated when individuals with small leaves are spared. 5. Synthesis and applications This study demonstrates the potential to create smarter systems of palm leaf harvest by accounting for individual heterogeneity within exploited populations. Sparing individuals that contribute most to population growth ensured sustained leaf production over time. The concepts and methods presented here are generally applicable to exploited plant and animal species which exhibit considerable individual heterogeneity.

opencc-by-nc-4.0Jun 2016View details →

Microphone Perceptual Attribute Elicitation & Contribution Dataset

Data generated as part of research to determine the perceptual attributes in terms of which recordings made with alternative microphones differ, and the degree to which each of these attributes contributes to perceived inter-microphone differences. Data comprise audio files, listening test instructions and MaxMSP interfaces , MATLAB code and listening test results. References A.Pearce. T.Brookes, M.Dewhirst, R.Mason, "Eliciting the most prominent perceived differences between microphones", J. Acoust. Soc. Am. 139 (5), May 2016, pp.2970-2981

opennotspecifiedNov 2002View details →

FIGURES 34 in Contribution to the knowledge of Parantiteuchus (Heteroptera, Pentatomidae, Discocephalinae): description of the male of P. hemitholus Ruckes, 1962

FIGURES 34, male genitalia. Pygophore: dorsal and ventral view respectively. (dr dorsal rim; lpdr lateral process of dorsal rim; paparamere; plap posterolateral angle process; pr proctiger; vrlp ventral rim lateral process).

FIGURES 60–66 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 60–66. Details of Macrolycus flabellatus (Motschulsky). 60 — metendosternite; 61 — metacoxa, internally; 62 — male ultimate tergites; 63 — male ultimate sternite; 64 — female ultimate sternite; 65 — aedeagus, laterally; 66 — same, ventrally.

FIGURES 55–59 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 55–59. Details of Macrolycus flabellatus (Motschulsky). 55 — head, ventrally; 56 — head, dorsally; 57 — head, laterally; 58 — thorax, ventrally; 59 — mesepimeron and mesepisternum, internally. CS — coronal suture; PM — prementum; SaS — subantennal suture; TN — trochantin.

FIGURES 32–39 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 32–39. Aedeagi of Mesolycus. 32 — M. obscurus (Pic), dorsally; 33 — same, laterally; 34 — same, ventrally; 35 — same, apically; 36 — M. discoidalis (Pic), laterally; 37 — same, apically; 38 — M. vitalisi Pic, laterally; 39 — same, inner sac structures, apically.

FIGURES 25–31 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 25–31. Details of Mesolycus shelfordi (Bourgeois). 25 — metathoracic wing; 26 — metendosternite; 27 — metacoxa, internally; 28 — female ultimate sternite; 29 — female genitalia; 30 — aedeagus, ventrally; 31 — same, laterally. MR — meron; TN — trochantin.

FIGURES 12–17 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 12–17. Aedeagi of Dilophotes species. 12 — D. basalis Pic, dorsally; 13 — D. pubescens Pic, ventrally; 14 — same, laterally; 15 — D. sexualis (Pic), dorsally; 16 — D. corporaali Pic, ventrally; 17 — D. luteus Bic, laterally.

FIGURES 18–24 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 18–24. Details of Mesolycus shelfordi (Bourgeois). 18 — head, ventrally; 19 — labium; 20 — head, dorsally; 21 — head, laterally; 22 — thorax, ventrally; 23 — mesoscutum, internally; 24 — mesepimeron and mesepisternum, internally. CS — coronal suture; MR — meron; PM — prementum; SaS — subantennal suture; TN — trochantin.

FIGURES 40–47 in Contribution to the knowledge of Macrolycini with description of Calcaeron, new genus (Coleoptera, Lycidae)

FIGURES 40–47. Aedeagi of Mesolycus. 40 — M. mediozonatus Nakane, ventrally; 41 — same, laterally; 42 — M. hubeicus sp. nov., laterally; 43 — same, inner sac structures, apically; 44 — M. nanensis sp. nov., laterally; 45 — same, inner sac structures, apically; 46 — M. murzini sp. nov., laterally; 47 — same, inner sac structures, apically. UP — upper plate.