Insects
A. Scaptomyza flava
Life-cycle of Scaptomyza flava on Arabidopsis thaliana. From upper left, clockwise: A pair mating on a leaf, a female creating a feeding puncture with her dentate ovipositor, eggs laid within feeding punctures on the underside of a leaf, serpentine mine of a first instar larva in a leaf, a blotch mine of a second or third instar larva, a puparium under the epidermis of a leaf. Egg to adult development time is 21 days at 22°C. The fly is holarctic and feeds on many plants in the order Brassicales, and reportedly on a few plants in other families. The fly is a pest of mustards in New Zealand where it was introduced recently. Herbivory has evolved several times in the family Drosophilidae and feeding on leaves a few times. We study the interaction between S. flava and A. thaliana, which has the benefit of the tremendous genetic resources available for the host plant, as well the advantages of newly sequenced transcriptome, capturing over half of the 'gene space' of and the availability of genetic tools in the closely related Drosophila melanogaster, which allows us to express S. flava transgenes in the D. melanogaster background. We also study many other species in the lineage Scaptomyza, which exhibit tremendous variation in feeding ecology. The fly lines used for these studies were found in Massachusetts by Noah. We are currently inbreeding lines of flies for genomic analyses and we are happy to share these lines with interested researchers.
B. Scaptomyza nigrita
We study a fly called Scaptomyza nigrita very similar in phenotype to S. flava, and the two are close relatives. This fly occurs throughout the inter-mountain western U.S. and is a specialist on a single lineage of plant, a mustard Cardamine cordifolia. The fly completes one or two generations/year on this plant, and the two live above 6,000 feet in the Rockies, Cascades and Sierra Nevadas. This is the system that Svata Louda and colleagues studied in detail at RMBL. We have found 100+ year old herbarium specimens of C. cordifolia with S. nigrita mines from across the range of the host plant suggesting that there is opportunity for co-evolutionary interactions between these species. Because each species is closely related to species with genomic resources, our goal is identify host plant resistance genes as well as insects detoxification genes and other loci involved in host specificity and to study their evolutionary histories across North America. We are developing genomics tools for this species and we keep a laboratory colony of these flies.
Plants
A. Arabidopsis thaliana
Thale cress, or Arabidopsis thaliana was the first plant species to have its genome sequenced, and is the main model for plant molecular biology, and increasingly is being used a model for ecology and evolutionary biology. More generally, the order Brassicales is now a model plant order, with many species being sequenced. Plant defense pathways common to all plants were first discovered in this species, there are many genetic resources available, transgenesis is easily conducted, and the genomes of thousands of wild accessions are currently being sequenced. We primarily use mutant phenotypes that are deficient in defense pathways or reporter lines that yield information on how host plants and natural enemies interact. We maintain lines of S. flava on this plant.
B. Cardamine cordifolia
A close relative of Arabidopsis thaliana, the mustard Cardamine cordifolia is a member of Lineage I of the Brassicaceae (in the water-loving lineage; www.amjbot.org/cgi/reprint/95/10/1307.pdf) and has a haploid chromosome number of 12. This species occurs from New Mexico to British Columbia, mostly above 6,000 feet in elevation. Svata Louda and colleauges showed that this plant is distributed primarily in the shade of trees throughout its distribution, in large part because herbivores are less abundant in the shade. Her and colleagues' elegant experiments showed that natural enemies, including the fly S. nigrita were primarily responsible for the shade-skewed distribution of the plant. Plants in the sun are heavily attacked by herbivores. We are using this system as a model co-evolutionary interaction system. It is highly compelling ecologically and the evolutionary proximity to A. thaliana renders it appealing from a comparative genomics perspective. We are developing genomics resources for this species and maintain rootstock of this plant that we've collected from throughout the range in the U.S. (Washington, Oregon, Idaho, California, Nevada, Utah, Arizona and New Mexico) and from sun and shade sites at our main field sites near Gothic, Colorado.
C. Phoradendron californicum and its host plants in the Fabaceae family.
Phoradendron species are in the family Viscaceae and are hemi-parasitic on trees and shrubs. They obtain water and minerals from hosts. In the Sonoran desert, we study the desert mistletoe, P. californicum, which lives in leguminous trees including Palo Verde species, mesquites, acacias and ironwood. Leaves are scale-like and plants are dioecious, females produce beautiful golden/pink fruits in the winter. We're interested in understanding the population genetic structure and phylogeographic history of mistletoe and factors shaping local adaptation to different host plants in sympatry. We are studying the population structure and phylogeographic history of the Phainopepla (Phainopepla nitens), the main disperser of the desert mistletoe's fruits. Comparing population genetic structures and phylogeographic histories of these interacting species will give us important insight into the evolution and ecology of a keystone species interaction in the Sonoran Desert.
Bacteria
We mainly study Pseudomonas bacteria in the phyllosphere (leaves) of C. cordifolia (photo to the left of endophytic bacteria from a single leaf growing on King's B media) as well as lab model strains in A. thaliana. In addition, we study the microbes associated with the guts of Scaptomyza flies, including Wolbachia and free-living species. We are recovering lineages new to science and attempting to understand their ecological interactions and evolutionary histories, particularly with respect to mediating plant-insect interactions directly and indirectly. A field study in Colorado aims to study ecology and evolution of Pseudomonas spp. isolates that naturally infect C. cordifolia and how these bacteria interact directly and indirectly with S. nigrita flies. For example, we study how previous infection with a Pseudomonas strain influences whether a plant is resistant or susceptible to herbivory by S. nigrita and vice versa. Conveniently, many Pseudomonas strains are easily manipulated genetically; knockouts and transgenic lines are easily created.
Birds
The lab continues to work on interactions between the Galapagos hawk (Buteo galapagoensis) but our involvement this wonderful project is nearly complete. We haven't quite given up on birds yet though, and are studying population genetics and phylogeography of the Phainopepla (Phainopepla nitens) which is the main dispersal agent for the desert mistletoe Phoradendron californicum. These birds are in the silky flycatcher family (Ptilogonatidate) and, interestingly, nest in the lowland desert in the winter and nest in the higher elevation oak scrub in the late spring and summer. They are year-round residents in the desert around Tucson. Processing over 1000 fruits a day is correlated with a specially adapted crop that allows efficient removal of mistletoe exocarps. Seeds are deposited on host plant branches after passing through the bird's digestive tract. Mistletoes are aggregated in their distribution, as are most macroparasites, most hosts have no or a few mistletoes and a few hosts have a lot of mistletoes. This is due in large part to bird behavior and a positive feedback loop of feeding on mistletoes and passing fruits on productive trees. Whether mistletoes on the same host tree individual are also close relatives though, is unknown and something we are testing.
