http://hdl.handle.net/1903/16 2013-05-25T02:37:01Z 2013-05-25T02:37:01Z Heffer, Alison Pick, Leslie http://hdl.handle.net/1903/13359 2013-01-11T03:42:56Z 2011-03-01T00:00:00Z

Title: Rapid isolation of gene homologs across taxa: Efficient identification and isolation of gene orthologs from non-model organism genomes, a technical report Authors: Heffer, Alison; Pick, Leslie Abstract: Background: Tremendous progress has been made in the field of evo-devo through comparisons of related genes from diverse taxa. While the vast number of species in nature precludes a complete analysis of the molecular evolution of even one single gene family, this would not be necessary to understand fundamental mechanisms underlying gene evolution if experiments could be designed to systematically sample representative points along the path of established phylogenies to trace changes in regulatory and coding gene sequence. This isolation of homologous genes from phylogenetically diverse, representative species can be challenging, especially if the gene is under weak selective pressure and evolving rapidly. Results: Here we present an approach - Rapid Isolation of Gene Homologs across Taxa (RIGHT) - to efficiently isolate specific members of gene families. RIGHT is based upon modification and a combination of degenerate polymerase chain reaction (PCR) and gene-specific amplified fragment length polymorphism (AFLP). It allows targeted isolation of specific gene family members from any organism, only requiring genomic DNA. We describe this approach and how we used it to isolate members of several different gene families from diverse arthropods spanning millions of years of evolution. Conclusions: RIGHT facilitates systematic isolation of one gene from large gene families. It allows for efficient gene isolation without whole genome sequencing, RNA extraction, or culturing of non-model organisms. RIGHT will be a generally useful method for isolation of orthologs from both distant and closely related species, increasing sample size and facilitating the tracking of molecular evolution of gene families and regulatory networks across the tree of life.

2011-03-01T00:00:00Z Mooney, Kailen A Gruner, Daniel S Barber, Nicholas A Van Bael, Sunshine A Philpott, Stacy M Greenberg, Russ http://hdl.handle.net/1903/10059 2010-04-27T02:30:06Z 2010-04-01T00:00:00Z

Title: Interactions among predators and the cascading effects of vertebrate insectivores on arthropod communities and plants Authors: Mooney, Kailen A; Gruner, Daniel S; Barber, Nicholas A; Van Bael, Sunshine A; Philpott, Stacy M; Greenberg, Russ Abstract: Theory on trophic interactions predicts that predators increase plant biomass by feeding on herbivores, an indirect interaction called a trophic cascade. Theory also predicts that predators feeding on predators, or intraguild predation, will weaken trophic cascades. Although past syntheses have confirmed cascading effects of terrestrial arthropod predators, we lack a comprehensive analysis for vertebrate insectivores—which by virtue of their body size and feeding habits are often top predators in these systems—and of how intraguild predation mediates trophic cascade strength. We report here on a meta-analysis of 113 experiments documenting the effects of insectivorous birds, bats, or lizards on predaceous arthropods, herbivorous arthropods, and plants. Although vertebrate insectivores fed as intraguild predators, strongly reducing predaceous arthropods (38%), they nevertheless suppressed herbivores (39%), indirectly reduced plant damage (40%), and increased plant biomass (14%). Furthermore, effects of vertebrate insectivores on predatory and herbivorous arthropods were positively correlated. Effects were strongest on arthropods and plants in communities with abundant predaceous arthropods and strong intraguild predation, but weak in communities depauperate in arthropod predators and intraguild predation. The naturally occurring ratio of arthropod predators relative to herbivores varied tremendously among the studied communities, and the skew to predators increased with site primary productivity and in trees relative to shrubs. Although intraguild predation among arthropod predators has been shown to weaken herbivore suppression, we find this paradigm does not extend to vertebrate insectivores in these communities. Instead, vertebrate intraguild preda-tion is associated with strengthened trophic cascades, and insectivores function as dominant predators in terrestrial plant-arthropod communities.

2010-04-01T00:00:00Z Hillebrand, Helmut Borer, Elizabeth Bracken, Matthew Cardinale, Brad Cebrian, Just Cleland, Elsa Elser, James Gruner, Daniel Harpole, Stanley Ngai, Jackie Sandin, Stuart Seabloom, Eric Shurin, Jonathan Smith, Jennifer Smith, Melinda http://hdl.handle.net/1903/9414 2009-07-22T02:30:19Z 2009-01-01T00:00:00Z

Title: Herbivore metabolism and stoichiometry each constrain herbivory at different organizational scales across ecosystems Authors: Hillebrand, Helmut; Borer, Elizabeth; Bracken, Matthew; Cardinale, Brad; Cebrian, Just; Cleland, Elsa; Elser, James; Gruner, Daniel; Harpole, Stanley; Ngai, Jackie; Sandin, Stuart; Seabloom, Eric; Shurin, Jonathan; Smith, Jennifer; Smith, Melinda Abstract: Plant-herbivore interactions mediate the trophic structure of ecosystems. We use a comprehensive data set extracted from the literature to test the relative explanatory power of two contrasting bodies of ecological theory, the metabolic theory of ecology (MTE) and ecological stoichiometry (ES), for per-capita and population-level rates of herbivory across ecosystems. We found that ambient temperature and herbivore body size (MTE) as well as stoichiometric mismatch (ES) both constrained herbivory, but at different scales of biological organization. Herbivore body size, which varied over 11 orders of magnitude, was the primary factor explaining variation in per-capita rates of herbivory. Stoichiometric mismatch explained more variation in population-level herbivory rates and also in per-capita rates when we examined data from within functionally similar trophic groups (e.g. zooplankton). Thus, predictions from metabolic and stoichiometric theories offer complementary explanations for patterns of herbivory that operate at different scales of biological organization.

2009-01-01T00:00:00Z Gruner, Daniel Kolekar, Arunima McLaughlin, John Strong, Donald http://hdl.handle.net/1903/9413 2009-07-22T02:30:16Z 2009-01-01T00:00:00Z

Title: Host resistance reverses the outcome of competition between microparasites Authors: Gruner, Daniel; Kolekar, Arunima; McLaughlin, John; Strong, Donald Abstract: Predators and parasites can control the abundance or biomass of herbivores with indirect effects on producer communities and ecosystems, but the interplay of multiple natural enemies may yield unexpected dynamics. We experimentally examined interactions between two microparasites (entomopathogenic nematodes) isolated from sandy grassland soils of coastal California: Heterorhabditis marelatus (Heterorhabditidae) and Steinernema feltiae (Steinernematidae). Heterorhabditis marelatus drives trophic cascades by attacking root- and stem-boring ghost moth caterpillars (Hepialus californicus, Hepialidae), thereby indirectly protecting bush lupine shrubs (Lupinus arboreus, Fabaceae). Extensive field surveys demonstrated sympatric overlap in microhabitat use under lupine canopies and similar mean prevalence of the two nematode species. Using a response-surface design in the laboratory, we varied relative and absolute microparasite densities to test for competitive outcomes within an evolutionary naı¨ve host, larvae of the greater wax moth Galleria mellonella (Pyralidae), and within the native host Hepialus californicus. Independent of conspecific or interspecific density, S. feltiae dominated as expected over H. marelatus within the naı¨ve Galleria, but S. feltiae infected hosts at low frequency and showed lower reproductive fitness than H. marelatus within native Hepialus hosts. Contrary to studies that demonstrate the pairwise dominance of steinernematid over heterorhabditid species in laboratory hosts, host resistance to S. feltiae may provide a mechanism for coexistence of multiple microparasite species. We hypothesize that the ubiquitous field prevalence and rapid life history of S. feltiae imply its use of widespread, abundant but small-bodied hosts and indicate the lack of direct competition with H. marelatus in the Hepialus–Lupinus trophic cascade.

2009-01-01T00:00:00Z