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Result data related to "Tröndle et al (2020) -- Trade-offs between geographic scale, cost, and infrastructure requirements for fully renewable electricity in Europe"
<p>The dataset contains aggregated result data of our study. See `README.md` for more information.</p> <p>If you use this data in an academic publication, please cite the following article:</p> <blockquote> <p>Tröndle, T., Lilliestam, J., Marelli, S., Pfenninger, S., 2020. Trade-offs between geographic scale, cost, and infrastructure requirements for fully renewable electricity in Europe. Joule.</p> </blockquote> <p>CHANGELOG:</p> <p>Version 1.2 (2020-09-28)</p> <p>* Add location name to scenario results.<br> * Add scenario results in CSV format, next to already existing NetCDF format.<br> * Remove capacity factors from scenario results.</p> <p>Version 1.1 (2020-07-17)</p> <p>* Remove macOS resource forks cluttering the zip file.</p> <p> </p>
The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover
<p>Zenodo deposit for Pozzi et al (2024) AJB</p> <p>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</p> <p><strong> _____________________________________________________________________________________________________________________________________</strong></p> <p><strong>The geographic scale of population level variation in growth and nodulation differs for two species of the prairie clover</strong></p> <p>Adrien C.M. Pozzi<sup>1,2</sup>, Ruth G. Shaw<sup>1</sup>, Georgiana May<sup>1,3</sup></p> <p><sup>1</sup> Department of Ecology, Evolution and Behavior, University of Minnesota Twin-Cities, St Paul, MN 55108. <sup>2</sup> Current affiliation: Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France. ORCID: 0000-0001-6765-4293. <sup>3</sup> Correspondence: Georgiana May (gmay@umn.edu)</p> <p><em><strong>Keywords:</strong></em></p> <p>conservation; <em>Dalea</em> spp.; habitat fragmentation; mutualism; nitrogen-fixing symbiosis; population level variation; native prairie legume; restoration; rhizobia</p> <p><em><strong>Description:</strong></em></p> <p>This Zenodo deposit is part of the MN LCCMR Healthy Prairies project granted to R. Shaw and G. May, UMN Twin-Cities. It contains the following files:</p> <p><span><span>·<span> </span></span></span>“Metadata & data” spreadsheet. <em>Contains metadata and data about the Twin Valley experiment (including the position of plants, an intermediary census, growth and nodulation traits for harvested plants, data on bacterial isolates from root nodules, and source modifiers for GenBank accessions OQ732394-OQ732572).</em></p> <p><span><span>·<span> </span></span></span>“Blast alignments output.txt” text file. <em>Contains ouput of Blastn alignements for the 16S rRNA genes of bacterial isolates against the rRNA_typestrains/16S_ribosomal_RNA 16S ribosomal RNA (Bacteria and Archaea type strains) database, to determine the genus as recommended by GenBank during sequence submission.</em></p> <p><span><span>·<span> </span></span></span>“General script.R”. <em>R script of the general statistical analyses produced for publication.</em></p> <p><span><span>·<span> </span></span></span>“General environment.RData”.<em> The companion RData (environment) of the above R script.</em></p> <p><span><span>·<span> </span></span></span>“Trait model script.R”. <em>R script of the plant trait models produced for publication</em></p> <p><span><span>·<span> </span></span></span>“Trait model environment.RData”. <em>The companion RData (environment) of the above R script.</em></p> <p><strong><em>Acknowledgments:</em></strong></p> <p>The authors thank members of the May Lab (Mai Beauclaire, Em Daily, Mara Demers, Kane Keller, Cedric Ndinga-Muniania, Liam Vertal, Monica Watson) for their help in field and lab work. We thank members of the Healthy Prairies project (Shelby Flint, Anna Peschel, Bill Peterson) who provided much of the infrastructure that made this project possible, as well as help in setting up field experiments. We also thank volunteer undergrads from University of Minnesota Morris (Amelia Nelson, Emily Job, Lily Fulton) for assistance in measuring harvested plants and counting nodules. Funding for this project was provided by the Minnesota Environment and Natural Resources Trust Fund as recommended by the Legislative-Citizen Commission on Minnesota Resources (LCCMR) Project 00086965, Healthy Prairies.</p> <p> </p>
Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence
<p>Aim: The need to forecast range shifts under future climate change has motivated an increasing interest in better understanding the role of biotic interactions in driving diversity patterns. The contribution of biotic interactions to shaping broad-scale species distributions is however, still debated, partly due to the difficulty of detecting their effects. We aim to test whether spatial exclusion between potentially competing species can be detected at the species range scale, and whether this pattern relates to fine-scale mechanisms of coexistence.</p> <p>Location: Western Palearctic</p> <p>Time period: Anthropocene</p> <p>Taxa: bats (Chiroptera)</p> <p>Methods: We develop and evaluate a measure of geographic avoidance that uses outputs of species distribution models to quantify geographic exclusion patterns expected if interspecific competition affects broad-scale distributions. We apply the measure to 10 Palearctic bat species belonging to four morphologically similar cryptic groups in which competition is likely to occur. We compare outputs to null models based on pairs of virtual species and to expectations based on ecological similarity and fine-scale coexistence mechanisms. We project changes in range suitability under climate change taking into account effects of geographic avoidance.</p> <p>Results: Values of geographic avoidance were above null expectations for two cryptic species pairs, suggesting that interspecific competition could have contributed to shaping their broad-scale distributions. These two pairs showed highest levels of ecological similarity and no trophic or habitat partitioning. Considering the role of competition modified predictions of future range suitability.</p> <p>Conclusions: Our results support the role of interspecific competition in limiting the geographic ranges of morphologically similar species in the absence of fine-scale mechanisms of coexistence. This study highlights the importance of incorporating biotic interactions into predictive models of range shifts under climate change, and the need for further integration of community ecology with species distribution models to understand the role of competition in ecology and biogeography.</p>
Figures 9–17 in Geographical distribution and phenotypic variation of Anovia punica Gordon (Coleoptera: Coccinellidae: Noviini), a predatory ladybeetle of fluted scales (Hemiptera: Coccoidea: Monophlebidae)
Figures 9–17. Male genitalia of Anovia punica. Peru: 9–11) San Martin State. Colombia: 12–14) San Andres Island. 15–17) Magdalena State. 9), 12), 15) Tegmen in ventral view. 10), 13), 16) Tegmen in lateral view. 11), 14), 17) Sipho.
Figures 1–8 in Geographical distribution and phenotypic variation of Anovia punica Gordon (Coleoptera: Coccinellidae: Noviini), a predatory ladybeetle of fluted scales (Hemiptera: Coccoidea: Monophlebidae)
Figures 1–8. Morphological variation of Anovia punica. Peru. 1–2) San Martín State. Colombia: 3) San Andres Island. 4) Magdalena State. 5) Valle del Cauca State. 6–7) Antioquia State. 8) Atlantico State.
Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
<p><strong>Aim</strong>: Patterns of evolutionary relatedness among co-occurring species are driven by scale-dependent contemporary and historical processes. Yet, we still lack a detailed understanding of how these drivers impact the phylogenetic structure of biological communities. Here, we focused on bats – one of the most speciose and vagile groups of mammals – and test the predictions of three general biogeographical hypotheses that are particularly relevant to understanding how paleoclimatic stability, local diversification rates, and geographical scales shaped their present-day phylogenetic community structure.</p> <p><strong>Location</strong>: Worldwide, across restrictive geographical extents: global, east-west hemispheres, biogeographical realms, tectonic plates, biomes, and ecoregions.</p> <p><strong>Time period</strong>: Last Glacial Maximum (~22,000 years ago) to the present.</p> <p><strong>Major taxa studied</strong>: Bats (Chiroptera)</p> <p><strong>Methods</strong>: We estimated bat phylogenetic community structure across restrictive geographical extents and modelled it as a function of paleoclimatic stability, and in situ net diversification rates.</p> <p><strong>Results</strong>: Limiting geographical extents from larger to smaller scales strongly changed the phylogenetic structure of bat communities. The magnitude of these effects is less noticeable in the western hemisphere, where frequent among-realm biota interchange could have been maintained through bats' adaptive traits. Highly phylogenetically related bat communities are generally more common in regions that changed less in climate since the last glacial maximum, supporting the expectation that stable climates allow for increased phylogenetic clustering. Finally, increased in situ net diversification rates are associated with greater phylogenetic clustering in bat communities.</p> <p><strong>Main conclusions</strong>: We show that the worldwide phylogenetic structure of bat assemblages varies as a function of geographical extents, dispersal barriers, paleoclimatic stability and in situ diversification. The integrative framework used in our study, which can be applied to other taxonomic groups, has proven useful to not only explain the evolutionary dynamics of community assembly but could also help tackle questions related to scale dependence in community ecology and biogeography.</p>
High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations
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Data from: Do biological control agents adapt to local pest genotypes? A multi-year test across geographic scales
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Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence
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Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
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Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales
<p>In parasites that strongly rely on a host for dispersal, geographic barriers that act on the host will simultaneously influence parasite distribution as well. If their association persists over macroevolutionary time it may result in congruent phylogenetic and phylogeographic patterns due to shared geographic histories. Here, we investigated the level of congruent evolutionary history at a regional and global scale in a highly specialised parasite taxon infecting hosts with limited dispersal abilities: the microsporidians <i>Dictyocoela</i> spp. and their amphipod hosts. <i>Dictyocoela</i> can be transmitted both vertically and horizontally and is the most common microsporidian genus occurring in amphipods in Eurasia. However, little is known about its distribution elsewhere. We started by conducting molecular screening to detect microsporidian parasites in endemic amphipod species in New Zealand; based on phylogenetic analyses, we identified nine species-level microsporidian taxa including six belonging to <i>Dictyocoela</i>. With a distance-based cophylogenetic analysis at the regional scale, we identified overall congruent phylogenies between <i>Paracalliope</i>, the most common New Zealand freshwater amphipod taxon, and their <i>Dictyocoela</i> parasites. Also, hosts and parasites showed similar phylogeographic patterns suggesting shared biogeographic histories. Similarly, at a global scale, phylogenies of amphipod hosts and their <i>Dictyocoela</i> parasites showed broadly congruent phylogenies. The observed patterns may have resulted from covicariance and/or codispersal, suggesting that the intimate association between amphipods and <i>Dictyocoela</i> may have persisted over macroevolutionary time. We highlight that shared biogeographic histories could play a role in the codiversification of hosts and parasites at a macroevolutionary scale.</p>
Dataset for "Study on Reference Frames and Geographic Scale"
<p>The analysis code was written in RStudio.</p> <p>The user data folder contains six .csv flies:</p> <ul> <li>Separate_pointing_errors.csv: participants' performance in the onsite pointing task</li> <li>Pre-Questionnaire.csv: participants' responses to the pre-questionnaire</li> <li>Post_Questionnaire.csv: participants' responses to the post-questionnaire</li> <li>Reference_frame_preference.csv: categorizing participants based on their reference frame proclivities</li> <li>LookingDirection_seperate.csv: participants' looking directions during maze learning</li> <li>Separate_time_data.csv: participants' time spent at each location in the virtual maze</li> </ul> <p> </p>
A large-scale assessment of ant diversity across the Brazilian Amazon Basin: integrating geographic, ecological, and morphological drivers of sampling bias
<p>Tropical ecosystems are often biodiversity hotspots, and invertebrates represent the main underrepresented component of diversity in large-scale analyses. This problem is partly related to the scarcity of data widely available to conduct these studies and the lack of systematic organization of knowledge about invertebrates' distributions in biodiversity hotspots. Here, we introduce and analyze a comprehensive data compilation of Amazonian ant diversity. Using records from 1817 to 2020 from both published and unpublished sources, we describe the diversity and distribution of ant species in the Brazilian Amazon Basin. Further, using high-definition images and data from taxonomic publications, we build a comprehensive database of morphological traits for the ant species that occur in the region. In total, we recorded 1,067 nominal species in the Brazilian Amazon Basin, with sampling locations strongly biased by access routes, urban centers, research institutions, and major infrastructure projects. Large areas where ant sampling is non-existent represent about 52% of the basin and are concentrated mainly in the North, Southeastern, and Western Brazilian Amazon. We found that distance to roads is the main driver of ant sampling in the Amazon. Contrary to our expectations, morphological traits had lower predictive power in predicting sample bias than purely geographic variables. However, when geographic predictors were controlled, habitat stratum and traits contribute to explain the remaining variance. More species were recorded in better-sampled areas, but species richness estimation models suggest that areas in South Amazonian edge forests are associated with especially high species richness. Our results represent the first trait-based, large-scale study for insects in Amazonian forests and a starting point for macroecological studies focusing on insect diversity in the Amazon Basin.</p>
Data for: (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions
<p><span>Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (<em>Ciona intestinalis</em>) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of </span><span>divergent selection</span><span>. </span><span>In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, gene ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.</span></p>
Data for "Testing for variation in photoperiodic plasticity in a butterfly: inconsistent effects of circadian genes between geographic scales" (Ecology and Evolution, accepted manuscript)
<p>Raw data and analysis scripts belonging to <em>Testing for variation in photoperiodic plasticity in a butterfly: inconsistent effects of circadian genes between geographic scales</em> (Ecology and Evolution, accepted manuscript).</p> <p>Includes data from a photoperiodic assay with larvae of the speckled wood butterfly, <em>Pararge aegeria</em>, as well as a small bioinformatic analysis of SNP variation in two circadian candidate genes.</p> <p>List of files:</p> <table> <tbody> <tr> <td>statistics_and_figures.R</td> <td>Statistical analysis of phenotyping experiment; drawing figures</td> </tr> <tr> <td>variant_calling.sh</td> <td>Shell script for mapping sequencing reads; calling and tabulating SNPs</td> </tr> <tr> <td>experiment_diapause.txt</td> <td>Data from phenotyping experiment, for analysis of diapause induction</td> </tr> <tr> <td>experiment_larval</td> <td>Data from phenotyping experiment, for analysis of larval development</td> </tr> <tr> <td>snptable_timeless</td> <td>Tabulated allele frequencies for exonic SNPs in timeless</td> </tr> <tr> <td>snptable_period</td> <td>Tabulated allele frequencies for exonic SNPs in period</td> </tr> </tbody> </table>
Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 in Digenetic Trematodes From Marine Fishes Off The Coast Of Kuwait, Arabian Gulf: Fellodistomidae And Some Smaller Families, New Host And Geographic Records
Fig. 4. Transversotrema licinum MANTER, 1970 from Diplodus noct. Ventral view. Scale 1.00 mm
Fig. 5. Treptodemus latus MANTER, 1961 from Hemiramphus marginatus. Ventral view. Scale 1.00 in Digenetic Trematodes From Marine Fishes Off The Coast Of Kuwait, Arabian Gulf: Fellodistomidae And Some Smaller Families, New Host And Geographic Records
Fig. 5. Treptodemus latus MANTER, 1961 from Hemiramphus marginatus. Ventral view. Scale 1.00 mm
Dataset 2 for Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly
<p>Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographical areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here we consider these issues in the Sooty Copper butterfly (<i>Lycaena tityrus</i>) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the West may result from (1) admixture of different western refuges, (2) more recent demographic changes, or (3) introgression of lowland <i>L. tityrus</i> populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine <i>L. tityrus </i>should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow and selection in a region that is expected to be particularly vulnerable to climate change.</p>
Dataset 1 for Large- and small-scale geographic structures affect genetic patterns across populations of an Alpine butterfly
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Evolutionary trajectories of multiple defense traits across phylogenetic and geographic scales in Vitis
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