11 Works

Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)

Hanna Larsson, Emanuele De Paoli, Michele Morgante, Martin Lascoux & Niclas Gyllenstrand
To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the repetitive fraction of the genome, which is commonly hypermethylated. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison a standard shotgun library was constructed and samples of the respective libraries were obtained...

Data from: The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Dimitrios Floudas, Manfred Binder, Robert Riley, Kerrie Barry, Robert A. Blanchette, Bernard Henrissat, Angel T. Martínez, Robert Ortillar, Joseph W. Spatafora, Jagjit S. Yadav, Andrea Aerts, Isabelle Benoit, Alex Boyd, Alexis Carlson, Alex Copeland, Pedro M. Coutinho, Ronald P. De Vries, Patricia Ferreira, Keisha Findley, Brian Foster, Jill Gaskell, Dylan Glotzer, Paweł Górecki, Joseph Heitman, Cedar Hesse … & David S. Hibbett
Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non–lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as...

Data from: Selection on variance-controlling genes – adaptability or stability

Mats Emanuel Pettersson, Ronald Michael Nelson & Örjan Carlborg
Simulations on a model system where a variance-controlling master locus scales the effects of a set of effector loci show that selection affects the variance-controlling locus more strongly than the effector loci, and that the direction of selection is dependent on the frequency of environmental changes.

Data from: Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies)

Jun Chen, Thomas Källman, Xiaofei Ma, Niclas Gyllenstrand, Giusi Zaina, Michele Morgante, Jean Bousquet, Andrew Eckert, Jill Wegrzyn, David B. Neale, Ulf Lagercrantz, Martin Lascoux & David Neale
Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties are clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We...

Data from: Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.)

Dan W. Bean, Peter Dalin & Tom L. Dudley
In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on post release evolution of beneficial life history traits. In this study we measure evolution of...

Data from: Fine-grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of non-random gene flow in restricting effective migration among wetlands

Alex Richter-Boix, María Quintela, Marcin Kierczak, Marc Franch & Anssi Laurila
Adaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High gene flow, on the other hand, is expected to homogenize genetic variation among populations and therefore prevent local adaptation. Understanding how local adaptation can persist at the spatial scale at which gene flow occurs has remained an elusive goal, especially for wild vertebrate populations. Here, we explore the roles of natural selection and nonrandom gene flow...

Data from: Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms

Jun Chen, Severin Uebbing, Niclas Gyllenstrand, Ulf Lagercrantz, Martin Lascoux & Thomas Källman
BACKGROUND: A detailed knowledge about spatial and temporal gene expression is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now simultaneously identify the transcribed part of a species genome and estimate...

Data from: Browsed twig environmental DNA: diagnostic PCR to identify ungulate species

Ruth V. Nichols, Helena Königsson, Kjell Danell & Göran Spong
Ungulate browsing can have a strong effect on ecological processes by affecting plant community structure and composition, with cascading effects on nutrient cycling and animal communities. However, in the absence of direct observations of foraging, species-specific foraging behaviors are difficult to quantify. We therefore know relatively little about foraging competition and species specific browsing patterns in systems with several browsers. However, during browsing, a small amount of saliva containing buccal cells is deposited at the...

Data from: Strong divergence in trait means but not in plasticity across hatchery and wild populations of sea-run brown trout Salmo trutta

Björn Rogell, Johan Dannewitz, Stefan Palm, Erik Petersson, Jonas Dahl, Tore Prestegaard, Torbjörn Järvi & Anssi Laurila
There is ample evidence that organisms adapt to their native environment when gene flow is restricted. However, evolution of plastic responses across discrete environments is less well examined. We studied divergence in means and plasticity across wild and hatchery populations of sea-run brown trout (Salmo trutta) in a common garden experiment with two rearing environments (hatchery and a nearly natural experimental stream). Since natural and hatchery environments differ, this arrangement provides an experiment in contemporary...

Data from: Retracing the routes of introduction of invasive species: the case of the Sirex noctilio woodwasp.

Emilie Boissin, Brett Hurley, Michael J. Wingfield, Rimvydas Vasaitis, Jan Stenlid, Chuck Davis, Peter De Groot, Rodrigo Ahumeda, Angus Carnegie, Arturo Goldarazena, Paula Klasmer, Beat Wermelinger & Bernard Slippers
Understanding the evolutionary histories of invasive species is critical to adopt appropriate management strategies, but this process can be exceedingly complex to unravel. As illustrated in this study of the worldwide invasion of the woodwasp Sirex noctilio, population genetic analyses using coalescent-based scenario testing together with Bayesian clustering and historical records provide opportunities to address this problem. The pest spread from its native Eurasian range to the Southern Hemisphere in the 1900’s and recently to...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Registration Year

  • 2012
    11

Resource Types

  • Dataset
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Affiliations

  • Swedish University of Agricultural Sciences
    11
  • Uppsala University
    4
  • University of California, Santa Barbara
    2
  • Swiss Institute of Bioinformatics
    1
  • University of Pretoria
    1
  • Department of Plant Biology
    1
  • Oregon State University
    1
  • Lund University
    1
  • University of Zaragoza
    1
  • University of California, San Diego
    1