17 Works

Data from: Fast and cost-effective genetic mapping in apple using next-generation sequencing

Kyle M. Gardner, Thomas F. Cooke, Patrick J. Brown, Scott Cann, Fabrizio Costa, Carlos D. Bustamante, Riccardo Velasco, Michela Troggio, Sean Myles, P. Brown & C. Bustamante
Next-generation DNA sequencing (NGS) produces vast amounts of DNA sequence data, but it is not specifically designed to generate data suitable for genetic mapping. Recently developed DNA library preparation methods for NGS have helped solve this problem, however, by combining the use of reduced representation libraries with DNA sample barcoding to generate genome-wide genotype data from a common set of genetic markers across a large number of samples. Here we use such a method, called...

Data from: Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

Daniel J. Hasselman, Emily E. Argo, Meghan C. McBride, Paul Bentzen, Thomas F. Schultz, Anna A. Perez-Umphrey & Eric P. Palkovacs
Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry has received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites we examined hybridization between...

Data from: Grazing damage and encrustation by an invasive bryozoan reduce the ability of kelps to withstand breakage by waves

Kira A. Krumhansl, J. Michael Lee & Robert E. Scheibling
Increased breakage of macroalgal fronds during large wave events can significantly reduce canopy cover and biomass. We examined the effects of encrustation by the invasive bryozoan Membranipora membranacea and damage by the snail Lacuna vincta on the ability of kelp blades (Saccharina longicruris, Laminaria digitata, and Laminaria complanata) to withstand wave forces. Using standard materials testing procedures, we documented significant reductions in the maximum stress before breakage, toughness, and extensibility of blade material following bryozoan...

Data from: Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Dylan J. Fraser, Paul V. Debes, Louis Bernatchez & Jeffrey A. Hutchings
Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population...

Data from: Detrital subsidy from subtidal kelp beds is altered by the invasive green alga Codium fragile ssp. fragile

Kira A. Krumhansl, Robert E. Scheibling, KA Krumhansl & RE Scheibling
Invasive species have the potential to alter the dynamics of detrital subsidy from high to low productivity areas through changes in quantity and nutritional quality of detrital material. We examined the effect of the invasive alga Codium fragile ssp. fragile on the nature of detrital export from subtidal algal beds off Nova Scotia, Canada, by comparing changes in mass, nutritional quality (%C, %N, C/N ratio), concentration of dimethylsulfoniopropionate (DMSP, a secondary metabolite that deters grazers),...

Data from: Emergent global patterns of ecosystem structure and function from a mechanistic General Ecosystem Model

Michael Brian James Harfoot, Tim Newbold, Derek P. Tittensor, Stephen Emmott, Jon Hutton, Vassily Lyutsarev, Matthew J. Smith, Jorn P. W. Scharlemann & Drew W. Purves
Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global, and...

Data from: Bayesian long branch attraction bias and corrections

Edward Susko
Previous work on the star-tree paradox has shown that Bayesian methods suffer from a long branch attraction bias. That work is extended to settings involving more taxa and partially resolved trees. The long branch attraction bias is confirmed to arise more broadly and an additional source of bias is found. A by-product of the analysis is methods that correct for biases toward particular topologies. The corrections can be easily calculated using existing Bayesian software. Posterior...

Data from: Detrital production in Nova Scotian kelp beds: patterns and processes

K. A. Krumhansl, R. E. Scheibling, KA Krumhansl & RE Scheibling
Connectivity via the transport of detrital material from areas of high to low productivity may be an important determinant of secondary productivity and biodiversity in receiving communities. On the Atlantic coast of Nova Scotia, detritus exported from subtidal kelp beds contributes to food webs in communities inhabiting deeper waters offshore. To estimate the amount of energy available via this pathway, we measured rates of detrital production via erosion of kelp blades in kelp beds at...

Data from: Genetic divergence and signatures of natural selection in marginal populations of a keystone, long-lived conifer, eastern white pine (Pinus strobus) from northern Ontario

Vikram E. Chhatre & Om P. Rajora
Marginal populations are expected to provide the frontiers for adaptation, evolution and range shifts of plant species under the anticipated climate change conditions. Marginal populations are predicted to show genetic divergence from central populations due to their isolation, and divergent natural selection and genetic drift operating therein. Marginal populations are also expected to have lower genetic diversity and effective population size (Ne) and higher genetic differentiation than central populations. We tested these hypotheses using eastern...

Data from: Genetic connectivity among swarming sites in the wide ranging and recently declining little brown bat (Myotis lucifugus)

Lynne E. Burns, Timothy R. Frasier & Hugh G. Broders
Characterizing movement dynamics and spatial aspects of gene flow within a species permits inference on population structuring. As patterns of structuring are products of historical and current demographics and gene flow, assessment of structure through time can yield an understanding of evolutionary dynamics acting on populations that are necessary to inform management. Recent dramatic population declines in hibernating bats in eastern North America from white-nose syndrome have prompted the need for information on movement dynamics...

Data from: Food-limited mothers favor offspring quality over offspring number: a principal components approach

Zachary R. Stahlschmidt & Shelley A. Adamo
Mothers are expected to balance the tradeoff between the number and quality of offspring, and many theoretical studies describe how the maternal environment might influence the evolution of the number-quality tradeoff. However, few empirical studies attempt to test these theories (and their assumptions) by measuring the fitness consequences of variation in investment per offspring. Part of the problem is that measuring offspring fitness is difficult, which frequently leads experimenters to measure several proxies of offspring...

Data from: Bay-scale patterns in the distribution, aggregation and spatial variability of larvae of benthic invertebrates

Remi M. Daigle, Anna Metaxas, Brad DeYoung & RM Daigle
This study aimed to investigate mechanisms of pattern formation in the larval distributions of benthic invertebrates by relating the spatial and temporal variability in the larval distributions to that in physical and biological variables, such as temperature, salinity, fluorescence and current velocity. Larvae were sampled at 11 sites on 7-8, and 11-12 Aug 2008 and at 16 sites on Aug 2-4, 2009, with a 200-μm plankton ring net (0.75-m diameter) towed for 5 min at...

Data from: Effects of domestication on parr maturity, growth, and vulnerability to predation in Atlantic salmon

Paul V. Debes & Jeffrey A. Hutchings
Domestication can change fitness-related traits. We investigated domestication-induced changes in fitness-related traits in Atlantic salmon (Salmo salar) under naturally enriched laboratory conditions with and without threat of predation. Selection in two strains for rapid growth for 3 and 5 generations resulted in 2 and 3 times larger sizes of under-yearling parr relative to their wild ancestor. An initially larger size and ability to outgrow prey size more rapidly resulted in lower size-selective predation mortality for...

Data from: Modeling effects of climate change and phase shifts on detrital production of a kelp bed

Kira A. Krumhansl, Jean-Sébastien Lauzon-Guay & Robert E. Scheibling
The exchange of energy and nutrients between ecosystems (i.e., resource subsidies) plays a central role in ecological dynamics over a range of spatial and temporal scales. Little attention has been paid to the role of anthropogenic impacts on natural systems in altering the magnitude, timing, and quality of resource subsidies. Kelp ecosystems are highly productive on a local scale and export over 80% of kelp primary production as detritus, subsidizing consumers across broad spatial scales....

Data from: Spatial and temporal variation in grazing damage by the gastropod Lacuna vincta in Nova Scotian kelp beds

Kira A. Krumhansl, Robert E. Scheibling, KA Krumhansl & RE Scheibling
Population increases of the gastropod Lacuna vincta have been associated with significant damage to kelp blades and decreases in kelp biomass in subtidal kelp beds off Nova Scotia, Canada. We measured the total level and along-blade distribution of grazing damage by Lacuna vincta on the dominant kelp species at 5 sites in Nova Scotia, Canada, over a 15 mo period. Grazing was typically low or absent in the basal regions of blades, consistent with seasonal...

Data from: A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success

G. Christopher Cutler, Cynthia D. Scott-Dupree, Maryam Sultan, Andrew D. McFarlane & Larry Brewer
In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of...

Data from: Supertrees based on the subtree prune-and-regraft distance

Chris Whidden, Norbert Zeh, Robert G. Beiko & Christopher Whidden
Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Although they often work well in practice, existing supertree approaches use optimality criteria that do not reflect underlying processes, have known biases and may be unduly influenced by LGT....

Registration Year

  • 2014

Resource Types

  • Dataset


  • Dalhousie University
  • University of Sussex
  • Stanford University
  • Duke University
  • Saint Mary's University
  • United Nations Environment Programme
  • University of Guelph
  • University of Oslo
  • Fisheries and Oceans Canada
  • Fondazione Edmund Mach