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faculty research

Ecology and Evolution

Faculty research interests in the area of ecology and evolution include conservation and evolutionary genetics (Aguilar Lab), plant evolutionary biology (Barrett Lab), theoretical population biology (Desharnais Lab), bryophyte ecology and evolution (Fisher Lab), evolutionary ecology of marine invertebrates (Krug Lab), conservation biology and ecology of tree squirrels (Muchlinski Lab), benthic marine ecology (Robles Lab), and evolutionary history of marine organisms (Torres Lab). An asterisk following a name in a publication citation indicates a student coauthor.

Conservation and Evolutionary Genetics

Prickly sculpin     Contact:  Andres Aguilar, Ph.D.
Office:  ASCL 215, ext: 3-2078
Laboratory:  ASCB 346
E-mail:  aaguil67@calstatela.edu
Prickly sculpin (Cottus asper) are a native freshwater fish species in California. Genetic evidence suggests isolation of coastal and inland forms may represent the early stages of speciation.

Research Summary
Our current work studies evolutionary, ecological and conservation based questions. We employ a variety of molecular genetic, genomic, computational and field approaches. Major areas of study include the evolution and conservation of California's native freshwater ichthyofauna and evolutionary genomic studies of diverse group of marine fishes (rockfish). We also work on endangered vernal pool crustaceans, amphibians, and sea birds.

Representative Publications
Baumsteiger, J.D., Kinziger, A.P., and Aguilar, A. 2012. Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach. Molecular Phylogenetics and Evolution, in press.
Heras, J., Koop, B., and Aguilar, A. 2011. A transcriptomic scan for positively selected genes in two closely related marine fishes: Sebastes caurinus and S. rastrelliger. Marine Genomics 4: 93-98.
Aguilar, A. 2011. Weak phylogeographic structure in the endemic western North American fairy shrimp Branchinecta lynchi (Eng, Belk and Erickson 1990). Aquatic Sciences 73: 15-20.
Aguilar, A., and Jones, W.J. 2009. Nuclear and mitochondrial diversification in two native California minnows: insights into taxonomic identity and regional phylogeography. Molecular Phylogenetics and Evolution 51: 373-381.
Aguilar, A., Roemer, G., Debenham, S., Binns, M., Garcelon, D., and Wayne, R.K. 2004. High MHC diversity maintained in an otherwise genetically monomorphic mammal. Proceedings of the National Academy of Sciences USA 101: 3490-3494.

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Plant Evolutionary Biology

Parasitic orchid     Contact:  Craig Barrett, Ph.D.
Office:  ASCL 214, ext: 3-2049
Laboratory:  ASCB 345
E-mail:  cbarret5@calstatela.edu
Web:  http://cbshotgun99.wix.com/barrett
Corallorhiza striata variety vreelandii, an obligate fungus-eating, parasitic orchid.

Research Summary
Our research is in plant systematics and evolution, ranging from higher-level phylogenetic questions to those at the population level. We further have interests in molecular and genome evolution, population/conservation genetics, phylogeography, and symbiosis/coevolution. We study a diversity of plant groups, including legumes and their mutualistic nitrogen-fixing bacteria, fungus-eating (mycoheterotrophic) orchids, and monocots as a whole. Our current focus is on the phylogenomics of monocot order Arecales (the palms), order Zingiberales (bananas, gingers, and relatives), family Orchidaceae (orchids, particularly the leafless fungus-eating members), and the branching order at the base of the commelinid monocots.

Representative Publications
Taylor, D.L., Barrett, C.F., Beatty, G., Hopkins, S.E., Kennedy, A.H., and Klooster, M.F. 2012. Progress and prospects for the ecological genetics of mycoheterotrophs. In Biology of Mycoheterotrophic Flowering Plants. V.F. Merckx (ed), Springer (in press).
Barrett, C.F., Davis, J.I., Leebens-Mack, J., Stevenson, D.W., and Conran, J.G. 2012. Plastid genomes and deep relationships among the commelinid monocot angiosperms. Cladistics (in press).
Barrett, C.F., and Davis, J.I. 2012. The plastid genome of the fully mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. American Journal of Botany 99: 1513-1523.
Barrett, C.F., and Freudenstein, J.V. 2011. An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Molecular Ecology 20: 2771-2786.
Barrett, C.F., Freudenstein, J.V., Taylor, D.L., and Kõljalg, U. 2010. Rangewide analysis of fungal associations in the fully mycoheterotrophic Corallorhiza striata complex (Orchidaceae) reveals extreme specificity on ectomycorrhizal Tomentella (Thelephoraceae) across North America. American Journal of Botany 97: 628-643.

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Theoretical Population Biology

Adult flour beetle     Contact:  Robert A. Desharnais, Ph.D.
Office:  ASCB 323D, ext: 3-2056
Laboratory:  ASCB 342, ext: 3-2033
E-mail:  rdeshar@calstatela.edu
Web:  http://caldera.calstatela.edu/rdeshar
Ventral view of an adult flour beetle, Tribolium castaneum. Populations of these insects are used as a laboratory model for testing ecological theory.

Research Summary
Our research interests are in the area of theoretical and experimental population biology. We use of insect populations to test predictions of nonlinear population models, including phenomena such as chaos, the effects of stochasticity, and metapopulation synchrony. We are also working with the Robles laboratory on models of the dynamics of marine mussel beds. Our methods involve mathematical models, computer simulations, and laboratory population experiments with flour beetles.

Representative Publications
Donahue, M.J., Desharnais, R.A., Robles, C.D., Arriola, P.* 2011. Mussel bed boundaries as dynamic equilibria: thresholds, phase shifts, and alternative states. The American Naturalist 178: 612-625.
Robles, C.D., Desharnais, R.A., Garza, C., Donahue, M.J., and Martinez, C.A.* 2009. Complex equilibria in the maintenance of boundaries: experiments with mussel beds. Ecology 90: 985-995.
Desharnais, R.A., Costantino, R.F., Cushing, J.M., Henson, S.M., Dennis, B, and King, A.A. 2006. Experimental support for the scaling rule of demographic stochasticity. Ecology Letters 9: 537-547.
Reuman, D.C., Desharnais, R.A., Costantino, R.F., Ahmad, O.S., and Cohen, J.E. 2006. Power spectra reveal the influence of stochasticity on nonlinear population dynamics. Proceedings of the National Academy of Sciences USA 103: 18860-18865.
Desharnais, R.A., Dennis, B., Cushing, J.M., Henson, S.M., and Costantino, R.F. 2001. Chaos and population control of insect outbreaks. Ecology Letters 4: 229-235.

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Bryophyte Ecology and Evolution

Tropical moss with asexual propagules     Contact:  Kirsten Fisher, Ph.D.
Office:  ASCL 393, ext: 3-2089
Laboratory:  ASCL 351, ext: 3-2085
E-mail:  kfisher2@calstatela.edu
Web:  http://instructional1.calstatela.edu/kfisher2
Tropical moss, Calymperes tenerum, with asexual propagules.

Research Summary
Our research interests include plant molecular systematics, phylogeography, and the use of phylogenetic trees for exploring evolutionary questions in general. In particular, we apply molecular phylogenetic methods to understanding cryptic diversity in mosses. We are investigating the potential link between physiological specialization and cryptic diversification in this group of plants, focusing on the desiccation tolerant model moss Syntrichia ruralis.

Representative Publications
Fisher, K. 2011. Sex on the edge: reproductive patterns across the geographic range of the Syrrhopodon involutus (Calymperaceae) complex. The Bryologist 114: 674-685.
Fisher, K. 2008. Bayesian reconstruction of ancestral gene expression in the LEA families reveals propagule-derived desiccation tolerance in resurrection plants. American Journal of Botany 95: 506-515.
Fisher, K., Wall, D.P., Yip, K.L., and Mishler, B.D. 2007. Phylogeny of the Calymperaceae, with a rank-free systematic treatment. The Bryologist 110: 43-73.
Fisher, K. 2006. Rank-free monography: a practical example from the moss clade Leucophanella. Systematic Botany 31: 13-30.
La Farge, C., Mishler, B.D., Wheeler, J.A., Wall, D.P., Johannes, K., Schaffer, S., and Shaw, A.J. 2000. Phylogenetic relationships of the Haplolepideous mosses. The Bryologist 103: 257-276.

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Evolutionary Ecology of Marine Invertebrates

Caribbean sea slug     Contact:  Patrick Krug, Ph.D.
Office:  ASCL 314, ext: 3-2076
Laboratory:  ASCL 325, ext: 3-2098
E-mail:  pkrug@calstatela.edu
Web:  http://instructional1.calstatela.edu/pkrug/lab
The Caribbean sea slug Elysia crispata stores chloroplasts from the algae it eats and can go months between meals, living off of photosynthesis performed by the hijacked plastids.

Research Summary
Our lab studies the evolution of dispersal and habitat colonization by planktonic larvae of marine animals, aiming to identify factors that limit gene flow, set range limits, and promote local adaptation. We use herbivorous sea slugs as a model system to investigate the evolution of alternative larval strategies, and to study ecological speciation in the sea. Field studies focus on a dynamic range boundary in San Francisco Bay, examining physical and biological forces that allow two species to cyclically displace each other every year. We are also building a molecular phylogeny, or family tree, of algae-eating sea slugs to study the evolution of traits such as larval type and host use.

Representative Publications
Krug, P.J., Asif, J.H.*, Baeza, I.*, Morley, M., Blom, W. and Gosliner, T. 2012. Molecular identification of two species of the carnivorous sea slug Philine, invaders of the U.S. west coast. Biological Invasions, in press.
Asif, J.H.*, and Krug, P.J. 2012. Lineage distribution and barriers to gene flow among populations of a globally invasive marine mollusc. Biological Invasions 14: 1431-1444.
Krug, P.J., Gordon, D.*, and M. Romero*. 2012. Seasonal polyphenism in larval type: Rearing environment influences the development mode expressed by adults in the sea slug Alderia willowi. Integrative & Comparative Biology 52: 161-172.
Vendetti, J.E., Trowbridge, C.D., and P. J. Krug. 2012. Poecilogony and population genetic structure in Elysia pusilla (Heterobranchia: Sacoglossa), and reproductive data for five sacoglossans that express dimorphisms in larval development. Integrative & Comparative Biology 52: 138-150.
Smolensky, N.*, Romero, M.*, and Krug, P.J. 2009. Evidence for costs of mating and self-fertilization in a simultaneous hermaphrodite with hypodermic insemination, the opisthobranch Alderia willowi. Biological Bulletin 216: 188-199.

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Conservation Biology and Ecology of Tree Squirrels

Western Gray Squirrel     Contact:  Alan Muchlinski, Ph.D.
Office:  ADM 710, ext: 3-3826
E-mail:  amuchli@calstatela.edu
Web:  http://instructional1.calstatela.edu/amuchli
Western gray squirrel, Sciurus griseus. The distribution of this species in Southern California is threatened by the expansion of the introduced eastern fox squirrel, Sciurus niger.

Research Summary
We focus on the ecological and behavioral aspects of the interactions between the native western gray squirrel and the introduced eastern fox squirrel. Current projects involve the use of field studies along with Geographic Information System (GIS) software to develop Habitat Suitability Models for the two species.

Representative Publications
King, J.L.*, Sue, M.C., and Muchlinski, A.E. 2010. Distribution of the eastern fox squirrel (Sciurus niger) in southern California. The Southwestern Naturalist 55:42-49.
Muchlinski, A.E., Stewart, G.R., King, J.L.*, and Lewis, S.A.* 2009. Documentation of replacement of native western gray squirrels by introduced eastern fox squirrels. Bulletin Southern California Academy of Sciences 108:160-162.
Muchlinski, A.E., Baldwin, B.C., and Gramajo, R. 2000. Endotoxin elicits a febrile response in laboratory-maintained but not free-living California ground squirrels. Journal of Mammalogy, 81: 701-708.
Lee, B.Y., Padick, D.A., and Muchlinski, A.E. 2000. Season influences the magnitude of stress fever in the California ground squirrel. Comparative Biochemistry and Physiology - Part A 125: 325-330.
Muchlinski, A.E., Gramajo, R., and Garcia, C. 1999. Pre-existing bacterial infections, not stress fever, influenced previous studies which labeled Gerrhosaurus major an afebrile lizard species. Comparative Biochemistry and Physiology - Part A 124: 353-357.

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Benthic Marine Ecology

Sea star attacking a mussel     Contact:  Carlos Robles, Ph.D.
Office:  ASCB 323E, ext: 3-2067
Laboratory:  ASCB 346, ext: 3-5661
E-mail:  crobles@calstatela.edu
Web:  http://cea-crest.calstatela.edu/crobleswebsite2.htm
Sea star, Pisaster ochraceus, attacking a marine mussel, Mytilus californianus. Size-dependent predator-prey interactions between these organisms lead to intertidal zonation.

Research Summary
Our current work emphasizes experimental investigations of the mechanisms of intertidal zonation. We proposed that the lower boundary of a mussel bed falls at a shore level corresponding to an abrupt shift in equilibria—from an equilibrium maintaining a sparse population of small individuals below to a second maintaining a dense population of larger individuals above. The equilibria are a dynamic balance between rates of size-dependant predation and prey production (recruitment and growth). The shift from one equilibrium to another is forced by spatial variation in tidal submergence and wave energy, and as a result prey population structure (boundaries and size structure) varies greatly over large spatial scales in the intertidal landscape. This adjusted equilibrium hypothesis was expressed in a computer simulation model which allows us to consider other spatially structured mechanisms. The model stands as an alternative to the widely-held refuge theory, which maintains that dense zones of invertebrate prey form only on shore levels above the effective foraging range of the predators. Our on-going projects are field studies that address either the testing or further development of spatially explicit population models.

Representative Publications
Robles, C.D., Desharnais, R.A., Garza, C., Donahue, M.J., and Martinez, C.A.* 2009. Complex equilibria in the maintenance of boundaries: experiments with mussel beds. Ecology 90: 985-995.
Robles, C.D. 2007. Lobsters. In: Encyclopedia of Tide Pools and Rocky Shores. M.W. Denny and S.D. Gaines (eds), University of California Press, Berkeley. Pages 333-335.
Blakeway, D., Robles, C.D., Fuentes, D., and Qiu, H.L. 2004. Spatially extensive, high-resolution images of rocky shore communities. In Handbook of Scaling in Aquatic Ecology: Measurement, Analysis and Simulation, P. Strutton and L. Seuront (eds), CRC Press. Pages 109-124.
Donalson, D., Desharnais, R.A., Robles, C.D., and Nisbet, R. 2004. Spatial dynamics of a benthic community: applying multiple models to a single system. In Handbook of Scaling in Aquatic Ecology: Measurement, Analysis and Simulation, P. Strutton and L. Seuront (eds), CRC Press. Pages 429-444.
Robles, C. D. and R. A. Desharnais. 2002. History and current development of a paradigm of predation in rocky intertidal communities. Ecology 82: 1521-1536.

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Taxonomy & Evolution of Marine Ostracodes

Ostracod crustacean that lives off of the Pacific Coast     Contact:  Elizabeth Torres, Ph.D.
Office:  ASCL 313, ext: 3-2179
Laboratory:  ASCL 311, ext: 3-5856
E-mail:  etorre11@calstatela.edu
Web:  http://www.calstatela.edu/faculty/etorre11/etorre11.htm
Vargula tsujii is a cypridinid ostracod crustacean that lives off of the Pacific Coast of North America. It secretes a bright blue luminescence produced in the light organ (yellow vertical bar just below the compound eye).

Research Summary
We use molecular methods and classic taxonomic approaches to understand phylogeny, diversity, and speciation in Caribbean cypridinid ostracode crustaceans. We are especially interested in the evolution of bioluminescence in cypridinids. Our genetic data have revealed several new species in the Caribbean, which we are in the process of describing. Students in our lab have also worked on other taxa, such as butterflies, Channel Island foxes, fox squirrels, marine snails, and bioluminescent fish.

Representative Publications
Torres, E., and Morin, J.G. 2007. Vargula annecohenae, a new species of bioluminescent ostracode (Myodocopida: Cypridinidae) from Belize. Journal of Crustacean Biology 27: 649-659.
Torres, E., and Gonzalez, V.L. 2007. Molecular phylogeny of cypridinid ostracodes and the evolution of bioluminescence. In Proceedings of the 14th International Symposium on Bioluminescence and Chemiluminescence: Chemistry, Biology, and Applications. A.A. Szalay, P.J. Hill, L.J. Kricka, and P.E. Stanley (eds). New Jersey: World Scientific Publishing Company, pgs. 269-272.
Torres, E., and Cohen. A.C. 2005. Vargula morini, a new species of bioluminescent ostracode (Myodocopida: Cypridinidae) from Belize and an associated copepod (Copepoda:Siphonostomatoida:Nicothoidae). Journal of Crustacean Biology 2: 11-24.
Torres, E., Lees, D.C., Vane-Wright, R.I., Kremen, C., Leonard, J.A., and Wayne, R.K. 2001. Testing monophyly in a large radiation of Madagascan butterflies (Lepidoptera: Satyrinae: Mycalesidina) based on mitochondrial DNA data. Molecular Phylogenetics and Evolution 20: 460-473.

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Note: ADM = Administration Building, ASCL = Wallis Annenberg Integrated Science Complex-Wing A (La Kretz Hall), ASCB = Wallis Annenberg Integrated Science Complex-Wing B. When calling from off-campus, the area code and prefix for all telephone extensions is (323) 34X-XXXX.

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Last Update: 04/2/2013