13 Works

Data from: A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R. Botigue, Robyn S. Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T. Kim, James Leebens-Mack, Ilia J. Leitch, Olivier Maurin, Doug Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker & Norman Wickett
Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used...

Data from: Flower preferences and pollen transport networks for cavity nesting solitary bees: implications for the design of agri-environment schemes

Catherine E.A. Gresty, Elizabeth Clare, Dion S. Devey, Robyn S. Cowan, Laszlo Csiba, Panagiota Malakasi, Owen T. Lewis, Katherine J. Willis & Catherine E. A. Gresty
Floral foraging resources are valuable for pollinator conservation on farmland, and their provision is encouraged by agri-environment schemes in many countries. Across Europe, wildflower seed mixtures are widely sown on farmland to encourage pollinators, but the extent to which key pollinator groups such as solitary bees exploit and benefit from these resources is unclear. We used high-throughput sequencing of 164 pollen samples extracted from the brood cells of 6 common cavity nesting solitary bee species...

Data from: Environment and host as large-scale controls of ectomycorrhizal fungi

Sietse Van Der Linde, Laura M. Suz, C. David L. Orme, Filipa Cox, Henning Andreae, Endla Asi, Bonnie Atkinson, Sue Benham, Christopher Carroll, Nathalie Cools, Bruno De Vos, Hans-Peter Dietrich, Johannes Eichhorn, Joachim Germann, Tine Grebenc, Hyun S. Gweon, Karin Hansen, Frank Jacob, Ferdinand Kristöfel, Pawel Lech, Miklos Manninger, Jan Martin, Henning Meesenburg, Päivi Merilä, Manuel Nicolas … & Martin I. Bidartondo
Explaining the large-scale diversity of soil organisms that drive biogeochemical processes—and their responses to environmental change—is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is—to our knowledge—unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds...

Data from: The search for loci under selection: trends, biases and progress

Collin W. Ahrens, Paul D. Rymer, Adam Stow, Jason Bragg, Shannon Dillon, Kate D. L. Umbers & Rachael Y. Dudaniec
Detecting genetic variants under selection using FST outlier analysis (OA) and environmental association analyses (EAA) are popular approaches that provide insight into the genetic basis of local adaptation. Despite the frequent use of OA and EAA approaches and their increasing attractiveness for detecting signatures of selection, their application to field-based empirical data have not been synthesized. Here, we review 66 empirical studies that use Single Nucleotide Polymorphisms (SNPs) in OA and EAA. We report trends...

Data from: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

Gerardo A. Salazar, Joao A.N. Batista, Lidia I. Cabrera, Cassio Van Den Berg, W. Mark Whitten, Eric C. Smidt, Cristiano R. Buzatto, Rodrigo B. Singer, Gunter Gerlach, Rolando Jimenez-Machorro, Jose A. Radins, Irma S. Insaurralde, Leonardo R.S. Guimaraes, Fabio De Barros, Francisco Tobar, Jose L. Linares, Ernesto Mujica, Robert L. Dressler, Mario A. Blanco, Eric Hagsater & Mark W. Chase
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the...

Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction

James S. Borrell, Nian Wang, Richard A. Nichols & Richard J. A. Buggs
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys....

Data from: C4 anatomy can evolve via a single developmental change

Marjorie R. Lundgren, Luke T. Dunning, Jill K. Olofsson, Jose J. Moreno Villena, Jacques W. Bouvier, Tammy L. Sage, Roxana Khosravesh, Stefanie Sultmanis, Matt Stata, Brad S. Ripley, Maria S. Vorontsova, Guillaume Besnard, Claire Adams, Nicholas Cuff, Anthony Mapaura, Matheus E. Bianconi, Christine M. Long, Pascal-Antoine Christin, Colin P. Osborne, Roxana Khoshravesh & Jose J. Moreno-Villena
C4 photosynthesis boosts productivity in warm environments. Paradoxically, this complex physiological process evolved independently in numerous plant lineages, despite requiring specialized leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besides those needed for C4 functionality. Here, we quantify the anatomical changes accompanying the transition between non-C4 and C4 phenotypes by sampling widely across the continuum of leaf anatomical traits in the grass Alloteropsis semialata....

Data from: Multiple independent origins of intermediate species between Sorbus aucuparia and S. hybrida (Rosaceae) in the Baltic region

Joel Levin, Michael F. Fay, Jaume Pellicer & Mikael Hedrén
Populations intermediate between the diploid and sexual Sorbus aucuparia and the tetraploid and facultative apomictic Sorbus hybrida are scattered in coastal regions of southern Scandinavia. Our aims were to investigate whether these populations were of local and independent origins, whether they were morphologically and molecularly distinct from each other and whether they could give rise to constant offspring by apomixis. Six intermediate populations from the Baltic Sea basin were studied for variation at nuclear and...

Data from: Development of 15 nuclear EST microsatellite markers for the palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae)

James R. P. Worth, James R. Marthick, Maurizio Rossetto, Joel Cohen, Greg Bourke & Gregory J. Jordan
Premise of the study: Nuclear microsatellite markers were developed for population genetic analysis of the threatened palaeoendemic conifer Pherosphaera hookeriana W. Archer (Podocarpaceae). Methods and Results: Fifteen variable loci were identified showing 1 to 13 alleles per population with seven loci displaying over four alleles in all populations and the average number of alleles per locus ranging from 4.8 to 5.93 per population. The observed heterozygosity per locus varied from 0.00 to 0.91 and overall...

Data from: PROTAX-fungi: a web-based tool for probabilistic taxonomic placement of fungal ITS sequences

Kessy Abarenkov, Panu Somervuo, R. Henrik Nilsson, Paul M. Kirk, Tea Huotari, Nerea Abrego & Otso Ovaskainen
• Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed PROTAX-fungi, a general tool for taxonomic placement of fungal ITS sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. • PROTAX-fungi outperformed the SINTAX and RDB classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence...

Data from: Plant controls on Late Quaternary whole ecosystem structure and function

Elizabeth S. Jeffers, Nicki J. Whitehouse, Adrian Lister, Gill Plunkett, Phil Barratt, Emma Smyth, Philip Lamb, Michael W. Dee, Stephen J. Brooks, Katherine J. Willis, Cynthia A. Froyd, Jenny E. Watson & Michael B. Bonsall
Plants and animals influence biomass production and nutrient cycling in terrestrial ecosystems; however their relative importance remains unclear. We assessed the extent to which mega-herbivore species controlled plant community composition and nutrient cycling, relative to other factors during and after the Late Quaternary extinction event in Britain and Ireland, when two-thirds of the region’s mega-herbivore species went extinct. Warmer temperatures, plant-soil and plant-plant interactions, and reduced burning contributed to the expansion of woody plants and...

Data from: Disease where you dine: plant species and floral traits associated with pathogen transmission in bumble bees

Lynn S. Adler, Kristen M. Michaud, Stephen P. Ellner, Scott H. McArt, Phillip C. Stevenson, Rebecca E. Irwin & Philip C. Stevenson
Hotspots of disease transmission can strongly influence pathogen spread. Bee pathogens may be transmitted via shared floral use, but the role of plant species and floral trait variation in shaping transmission dynamics is almost entirely unexplored. Given the importance of pathogens for the decline of several bee species, understanding whether and how plant species and floral traits affect transmission could give us important tools for predicting which plant species may be hotspots for disease spread....

Data from: Matching symbiotic associations of an endangered orchid to habitat to improve conservation outcomes

Noushka Reiter, Ann C. Lawrie & Celeste C. Linde
Background and Aims: An understanding of mycorrhizal variation, orchid seed germination temperature and the effect of co-occurring plant species could be critical for optimising conservation translocation of endangered plants with specialised mycorrhizal associations. Methods: Focussing on the orchid Thelymitra epipactoides we isolated mycorrhizal fungi from ten plants within each of three sites; Shallow Sands Woodland (SSW), Damp Heathland (DH) and Coastal Heathland Scrub (CHS). Twenty-seven fungal isolates were tested for symbiotic germination under three temperature...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Royal Botanic Gardens
  • University of Western Australia
  • University of Massachusetts Amherst
  • University of Greenwich
  • Queen's University Belfast
  • Research Institute for Nature and Forest
  • Northwestern University
  • University of Georgia
  • Lund University
  • University of Alberta