2009

Burns, K. J. and R. A. Racicot*. 2009. Molecular phylogenetics of a clade of lowland tanagers: Implications for avian participation in the Great American Interchange. The Auk 126: 635-648.

Hedin M. and S. Thomas*. 2009. Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves. Molecular Phylogenetics and Evolution. In Press.

Hedin M., S. Derkarabetian*, M. McCormack*, C. Richart*, J.W. Shultz. 2009. The phylogenetic utility of the nuclear protein-coding gene EF-1a for resolving recent divergences in Opiliones, emphasizing intron evolution. Journal of Arachnology. In Press.

Holzman, J. P.*, A. J. Bohonak, L. R. Kirkendall, D. Gottlieb, A. R. Harari, and S. T. Kelley. 2009. Inbreeding variability and population structure in the invasive haplodiploid palm-seed borer (Coccotrypes dactyliperda). Journal of Evolutionary Biology 22: 1076-1087.

Mauck, W. M.* and K. J. Burns. 2009. Phylogeny, biogeography, and recurrent evolution of divergent bill types in the nectar-stealing flowerpiercers (Thraupini: Diglossa and Diglossopis). Biological Journal of the Linnean Society 98: 14-28.

Pierce, N. and M. G. Simpson. 2009. Polyaperturate pollen types and ratios of heteromorphism in the monocot genus Conostylis R. Br. (Haemodoraceae). Australian Systematic Botany 22: 16-30.

Reeder, T. W., and J. D. Reichert*.  Phylogenetic relationships within the Australian limb-reduced lizard genus Hemiergis (Scincidae; Squamata) based on mitochondrial rRNA gene sequences.  Copeia, in press.

Sedano, R. E.* and Burns, K. J. in press. Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini). Journal of Biogeography.

Simpson, M. G. and K. E. Hasenstab*. 2009. Cryptantha of Southern California. Crossosoma 35: 1-59.

Snowman, C.V., K.S. Zigler, M. Hedin. 2009. Caves as Islands: Mitochondrial phylogeography of the cave-obligate spider species Nesticus barri (Araneae: Nesticidae). Journal of Arachnology. In Press.

Steele, A. N.*, M. A. Simovich, D. Pepino, K. McNamara Schroeder, A. G. Vandergast and A. J. Bohonak. In press. Optimized DNA extraction methods for encysted embryos of the endangered fairy shrimp, Branchinecta sandiegonensis. Conservation Genetics.

Turner, J. L., S. T. Kelley, J. S. Otto, F. Valafar and A. J. Bohonak. 2009. Parallelization and optimization of genetic analyses in Isolation by Distance Web Service. BMC Genetics 10: 29.

Vandergast, A. G., D. Wood, M. A. Simovich and A. J. Bohonak. 2009. Identification of co-occurring Branchinecta fairy shrimp species from encysted embryos using multiplex PCR. Molecular Ecology Resources 9: 767-770.

Vandergast, A. G., *E. A. Lewallen, **J. Deas, A. J. Bohonak, D. B. Weissman, and R. N. Fisher. 2009. Loss of genetic connectivity and diversity in urban microreserves in a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus “santa monica”). Journal of Insect Conservation 13: 329-345.

Wiens, J. J., C. A. Kuczynski, S. Arif, and T. W. Reeder.  Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial DNA, and a revised phylogeny of Sceloporus.  Molecular Phylogenetics and Evolution, in press.

2008

Aevermann B.D*. and Waters E.R.  2008. The duplication and retention of the small heat shock protein gene family in Caenorhabditis elegans and Caenorhabditis briggsae.  Genetica. Oct 17 2007; [Epub ahead of print]. Print publication expected Summer 2008.

Archibald, J. D.  2008.  Edward Hitchcock's pre-Darwin (1840) "Tree of life."  Journal of the History of Biology. Online First.

Arenas-Mena, C. 2008. HeBlimp and HeT-Brain expression in an indirectly developing polychaete correlates with endodermal and neural precursors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution.  (In press)

Bohonak, A. J. 2008. Genetic drift in human populations. in Encyclopedia of Life Sciences, cross-listed in Handbook of Human Molecular Evolution. John Wiley and Sons, Ltd. http://www.els.net/

Clark, R. W., Brown W. S., Stechert, R., and K. W. Zamudio. 2008. Integrating individual behavior and landscape genetics: the population structure of timber rattlesnake hibernacula. Molecular Ecology 17:719-730.

Crawford, N. G.*, J. Zalidvar-Rae, C. Hagen, A. Schable, E. B. Rosenblum, M. G. Ritchie, T. W. Reeder, J. A. Graves, and T. C. Glenn.  2008.  Thirteen polymorphic microsatellite DNA loci from whiptails of the genus Aspidoscelis and related cnemidophorine lizards.  Molecular Ecology Resources 8:219-223.

Deméré, T.A., M. R. McGowen*, A. Berta. and J. Gatesy. 2008. Morphological and molecular evidence for step-wise evolutionary transition from teeth to baleen in mysticete whales. Systematic Biology 57:15-37.

Deméré, T.A. and A. Berta. 2008. Cranial anatomy of the toothed mysticete Aetiocetus weltoni and its implications for aetiocetid phylogeny. Zoological Journal of Linnean Society 154(2): 308-352.

de Quieroz, K. and T. W. Reeder.  2008.  Squamata – Lizards. In B. I. Crother (ed.), Scientific and Standard English Names of Amphibians and Reptiles of North America North of Mexico, pp. 24–45. SSAR Herpetological Circular No. 37.

Desnues C.G., B. Rodriguez-Brito*, S. Rayhawk*, S. Kelley, T. Tran*, M. Haynes, H. Liu, D. Hall*, F.E. Angly*, R.A. Edwards, R.B. Thurber, P. Reid, J. Siefert, V. Souza, D.L. Valentine, B.K. Swan, M. Breitbart, F. Rohwer. 2008 (in press). Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature.

Dinsdale E.A., R.A. Edwards, D. Hall*, F. Angly*, M. Breitbart, J.M. Brulc, M. Furlan*, C. Desnues, M. Haynes, L. Li, L. McDaniel, M.A. Moran , K.E. Nelson, C. Nilsson, R. Olson, J. Paul, B. Rodriguez-Brito*, Y. Ruan, B.K. Swan, R. Stevens, D.L. Valentine, R.V. Thurber, L. Wegley*, B.A. White, and F. Rohwer. 2008 (in press). Functional metagenomic profiling of nine biomes. Nature.

Ellis, D.*, R.W. Bizzoco, and S.T. Kelley. 2008. Halophilic Archaea identified in fumarole steam vapor from vents around the world.  Environmental Microbiology 10: 1582-1590.

Kunin, V., S. He, F. Warnecke, S.B. Peterson, H.G. Martin, M. Haynes, N. Ivanova, L.L. Blackall, M. Breitbart, F. Rohwer, K.D. McMahon, P. Hugenholtz (2008, in press). A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research.

Lutz, K., N. Diaz, R.A. Edwards, F. Rohwer, S.T. Kelley, and J. Stoye. 2008. Taxonomic classification of short environmental DNA fragments. Nucleic Acids Research E-Pub.

Paquin, P., N. Dupérré, J.C. Cokendolpher, K. White, and M. Hedin. 2008. The fundamental importance of taxonomy in conservation biology: the case of the eyeless Cicurina bandida (Araneae: Dictynidae) of Central Texas, including new synonyms and the description of the male of the species.  Invertebrate Systematics 22: 1-11.

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T **, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL. 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008 Jan 4; 319(5859): 64-9.

Thomas, S.M.* and M. Hedin. 2008. Multigenic phylogeographic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae). Molecular Phylogenetics & Evolution 46: 645-658.

Townsend T.M., E.R. Alegre*, S.T. Kelley, J.J. Wiens, T.W. Reeder. 2008. Rapid Development of Multiple Nuclear Loci for Phylogenetic Analysis Using Genomic Resources. Molecular Phylogenetics and Evolution 47: 129-142.

Vandergast, A. G., A. J. Bohonak, S. A. Hathaway, J. Boys** and R. N. Fisher. 2008. Are hotspots of evolutionary potential adequately protected in southern California? Biological Conservation 141: 1648-1664.

Viaud-Martinez, K. A.*, R. L. Brownell, Jr., A. Komnenou and A. J. Bohonak. 2008. Genetic isolation and morphological divergence of Black Sea bottlenose dolphins. Biological Conservation 141: 1600-1611.

Vink, C.J., M. Hedin, M.R. Bodner, W.P. Maddison, C.Y. Hayashi, and J.E. Garb. 2008. Actin 5C, a promising nuclear gene for spider phylogenetics. Molecular Phylogenetics & Evolution 48: 377-382.

Waters E.R., B. D. Aevermann*, Z. Sanders-Reed**. 2008. Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns. Cell Stress and Chaperones  Published OnLine First.  Print publication expected Summer 2008.

Waters, E.R., S. Nguyen**, R. Eskandar**, J. Behan**, and Z. Sanders-Reed**. 2008. The recent evolution of a pseudogene: diversity and divergence of a mitochondrial-localized small heat shock protein in Arabidopsis thaliana. Genome 51:177-86.

Wiens, J. J., C. A. Kuczynski, S. A. Smith, D. Mulcahy, J. W. Sites, Jr., T. M. Townsend, and T. W. Reeder. 2008. Branch length, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes. Systematic Biology 57: 420-431.

2007

Archibald, J. D. and MacLeod, N. 2007. Dinosaurs, extinction theories for. In, Encyclopedia of Biodiversity, Elsevier, p. 1-9.

Arenas-Mena, C. 2007. Developmental transcriptional-competence model for a histone variant and a unicellular origin scenario for transcriptional-multipotency mechanisms. Evolution & Development. 9: 208-211.

Arenas-Mena, C. 2007. Embryonic expression of HeFoxA1 and HeFoxA2 in an indirectly developing polychaete. Development Genes and Evolution 216: 727-736.

Arenas-Mena, C. 2007. Sinistral equal-size spiral cleavage of the indirectly developing polychaete Hydroides elegans. Developmental Dynamics 236: 1611-1622.

Arenas-Mena, C. and K. S-Y. Wong.  2007.  HeOtx expression in an indirectly developing polychaete correlates with gastrulation by invagination.  Development, Genes and Evolution. May; 217(5):373-384.

Arenas-Mena C., Wong, K. S. Y., and N. R. Arandi-Foroshani. 2007. Histone H2A.Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells. Evolution & Development 9: 231-243.

Arenas-Mena, C., Wong, K. S. Y. and N. Arandi-Forosani. 2007. Ciliary band gene expression patterns in the embryo and trochophore larva of an indirectly developing polychaete. Gene Expression Patterns 7: 544-549.

Ayoub N.A., J.E. Garb, M. Hedin and C.Y. Hayashi. 2007. Utility of the nuclear protein-coding gene, elongation factor-1 gamma (EF-1g) for spider systematics, emphasizing family level relationships of tarantulas and their kin (Aranaea: Mygalomorphae). Molecular Phylogenetics and Evolution 42: 394-409.

Burns, K. J., M. P. Alexander*, D. N. Barhoum*, and E. A. Sgariglia*. 2007. A statistical assessment of congruence among phylogeographic histories of three avian species in the California Floristic Province. Pages 96-109 in Festschrift for Ned K. Johnson: Geographic Variation and Evolution in Birds (C. Cicero and J. V. Remsen, Jr., Eds.). Ornithological Monographs, no. 63.

Clark, R. W. 2007. Public information for solitary foragers: timber rattlesnakes use conspecific chemical cues to select ambush sites. Behavioral Ecology 18:487-490.

Clark, R. W., Brown W. S., Stechert, R., and K. W. Zamudio. In Press. Integrating individual behavior and landscape genetics: the population structure of timber rattlesnake hibernacula. Molecular Ecology.

Cooper, L. N.*, A. Berta, J. Reidenberg, and S.D. Dawson. 2007a. Hyperphalangy and digit reduction: evolution of the cetacean manus. Anatomical Record 290: 654-673.

Cooper, L.N.*, S.D. Dawson, J. Reidenberg and A. Berta. 2007b. Neuromuscular anatomy and the evolution of the cetacean forelimb. Anatomical Record 290: 1121-1137.

Fierer, N., M. Breitbart, J. Nulton, P. Salamon, C. Lozupone, R. Jones, M. Robeson, R. Edwards, B. Felts, S. Rayhawk*, R. Knight, F. Rohwer, and RB Jackson. 2007. Metagenomic and small-subunit rRNA analyses of the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and Environmental Microbiology 73(21):7059-7066.

Klicka, J., K. J. Burns, and G. M. Spellman. 2007. Defining a monophyletic Cardinalini: a molecular perspective. Molecular Phylogenetics and Evolution 45:1014-1032.

Lee, U., I. Rioflorido*, S.W. Hong, J. Larkindale, E. Waters, and E. Vierling. 2007 The Arabidopsis ClpB/HSP100 family of proteins: Chaperones for stress and chloroplast development. The Plant Journal 49:115-127.

Lewallen, E. A.*, T. W. Anderson and A. J. Bohonak. 2007. Genetic structure of leopard shark (Triakis semifasciata) populations in California waters. Marine Biology 152: 599-609.

Mathur*, J., R.W. Bizzoco, D.G. Ellis*, D.A. Lipson, A. Poole*, R. Levine and S.T. Kelley. 2007. Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs. Applied and Environmental Microbiology 73: 2612-2623.

Renner, T.** and E.R. Waters. 2007 Comparative genomic analysis of the HSP70s in five diverse algal species. Cell Stress & Chaperones 12:172-185.

Shepherd, T. M.* and K. J. Burns. 2007. Intraspecific genetic analysis of the Summer Tanager (Piranga rubra): Implications for species limits and conservation. Journal of Avian Biology 38: 13-27.

Smith, S. A., A. Nieto Montes de Oca, T. W. Reeder, and J. J. Wiens. 2007. A phylogenetic perspective on elevational species richness patterns in Middle American treefrogs: why so few species in lowland tropical rainforests? Evolution 61:1188-1207.

Starrett, J.* and M. Hedin. 2007. Multilocus genealogies reveal multiple cryptic species and biogeographic complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodieatidae). Molecular Ecology 16, 583-604.

Starrett J. * and Waters E.R. 2007. Positive natural selection has driven the evolution of the Hsp70s in Diguetia spiders. Biology Letters 3:439-444.

Vandergast, A. G., A. J. Bohonak, D. B. Weissman and R. N. Fisher. 2007. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Molecular Ecology 16: 977-992.

Viaud-Martinez, K. A.*, M. Martinez Vergara*, P. E. Gol’din, V. Ridoux, A. A. Öztürk, B. Öztürk, P. E. Rosel, A. Frantzis, A. Komnenou and A. J. Bohonak. 2007. Morphological and genetic differentiation of the Black Sea harbour porpoise Phocoena phocoena. Marine Ecology Progress Series 338: 281–294.

Waters, E.R. and I. Rioflorido**. 2007 Evolutionary analysis of the small heat shock proteins in five complete algal genomes. Journal of Molecular Evolution 65:162-174.

Wegley, L*, R Edwards, B Rodriguez-Brito*, Hong Liu, and F Rohwer. 2007. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental Microbiology 9 (11):2707-2719.

Wiens, J. J., C. A. Kuczynski, W. E. Duellman, and T. W. Reeder. 2007. Loss and re-evolution of complex life cycles in marsupial frogs: Does ancestral trait reconstruction mislead? Evolution 61:1886-1899.

Winner, A. and M. G. Simpson. 2007. A new subspecies of Pentagramma triangularis (Pteridaceae). Madroño 54:345-353.

Zickovich, J. M.* and A. J. Bohonak. 2007. Dispersal ability and genetic structure in aquatic invertebrates: a comparative study in southern California streams and reservoirs. Freshwater Biology 52: 1982-1996.

2006

Alexander, M. P.* and K. J. Burns. 2006. Intraspecific phylogeography and adaptive divergence in the White-headed Woodpecker. The Condor 108:489-518.

Angly F., B. Felts, M. Breitbart, P. Salamon, R.A. Edwards, C. Carlson, A.M. Chan, M. Haynes, S. Kelley, H. Liu, J. Mahaffy, J.E. Mueller, J. Nulton, R. Olson, R. Parsons, S. Rayhawk, C.A. Suttle, F. Rohwer. 2006. The marine viromes of four oceanic regions. PLoS Biology 4(11):2121-2131.

Archibald, J. D. 2006. A cacophony of causes. Review of Extinction: How Life Nearly Ended 250 Million Years Ago by Douglas H. Erwin. Trends in Ecology and Evolution 21:428.

Archibald, J. D. 2006. Review of Mammals from the Age of Dinosaurs: Origins, Evolution, and Structure. by Zofia Kielan-Jaworowska, Richard L. Cifelli, and Zhe-Xi Luo. Journal of Mammal Evolution 13:147-149.

Archibald, J. D. and Averianov, A. O. 2006. Late Cretaceous asioryctitherian eutherian mammals from Uzbekistan and phylogentic analysis of Asioryctitheria. Acta Palaeontologca Polonica 51:351-376.

Arenas-Mena, C., Cameron, R. A., and E. H. Davidson. 2006. Hindgut specification and cell-adhesion functions of Sphox11/13b in the endoderm of the sea urchin embryo. Development Growth & Differentiation 48: 463-472.

Averianov, A. O. and Archibald, J. D. 2006. Further data on the multituberculate mammal Uzbekbaatar from the Late Cretaceous of Uzbekistan Acta Palaeontologca Polonica. 51:377-380.

Berta, A., J.L. Sumich, and K. Kovacs. 2006. Marine Mammals: Evolutionary Biology. 2nd ed. Elsevier, 547 pp.

Bohonak, A. J., M. D. Holland, B. Santer, M. Zeller, C. M. Kearns and N. G. Hairston, Jr. 2006. The population genetic consequences of diapause in Eudiaptomus copepods. Archiv für Hydrobiologie 167: 183-202.

Bond, J.E. and M. Hedin. 2006. A total evidence assessment of the phylogeny of North American euctenizine trapdoor spiders Euctenizinae (Araneae, Mygalomorphae, Cyrtaucheniidae) using Bayesian inference. Molecular Phylogenetics and Evolution 41: 70-85.

Bond, J.E., D.A. Beamer, T. Lamb and M. Hedin. 2006. Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region. Animal Conservation 9: 145-157.

Burns, K. J. and D. N. Barhoum*. 2006. Population-level history of the Wrentit (Chamaea fasciata): Implications for comparative phylogeography in the California Floristic Province. Molecular Phylogenetics and Evolution 38: 117-129.

Casas V., J. Miyake, H. Balsley, J. Roarke, S. Telles, S. Leeds, I. Zurita, M. Breitbart, D. Bartlett, F. Azam, F. Rohwer. 2006. Detection of phage-encoded exotoxins in the environment. FEM Microbiology Letters 261:141-149.

Clark R. W. 2006. Fixed videography to study predation behavior of an ambush foraging snake, Crotalus horridus. Copeia 2006:181-187.

Clark R. W. 2006. Strike-induced chemosensory searching by timber rattlesnakes during natural predation events. Ethology 112:1089-1094.

Crews, S.C.* and M. Hedin. 2006. Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula. Molecular Phylogenetics and Evolution 38: 470-487.

Edwards R.A., B. Rodriguez-Brito, L. Wegley, M. Haynes, M. Breitbart, D.M. Peterson, M.O. Saar, S. Alexander, E.C. Alexander, Jr, and F. Rohwer. 2006. Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeological conditions. BMC Genomics 7(57):1-13.

Fajardo-Mellor, L.*, A. Berta, R.L. Brownell, Jr., C. Boy and N. Goodall. 2006. The phylogenetic relationships and biogeography of true porpoises (Mammalia: Phocoenidae) based on morphological data. Marine Mammal Science 22: 910-932.

Hedin, M. and J.E. Bond. 2006. Molecular phylogenetics of the spider Infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): Conflict and agreement with the current system of classification. Molecular Phylogenetics and Evolution 41: 454-471.

Hemila, S., S. Nummela, A. Berta, and T. Reuter. 2006. High-frequency hearing in phocid and otariid pinnipeds: an interpretation based on inertial and cochlear constraints. Journal of the Acoustical Society of America, 120(6): 3463-3466.

Kelley S.T., E.F. Cassirer, G.C. Weiser and S. Safaee*. 2006. Phylogenetic Diversity of Pasteurellaceae and Horizontal Gene Transfer of Leukotoxin in Wild and Domestic Sheep. Infection, Genetics and Evolution 7: 13-23.

Nguyen, T.X., E.R. Alegre** and S.T. Kelley. 2006. Analysis of General Bacterial Porins: A Phylogenomic Case Study. Journal of Molecular Microbiology and Biotechnology 11: 291-301.

Rebman, J. P. and Simpson, M. G. 2006. Checklist of the Vascular Plants of San Diego County. 4th edition. San Diego Natural History Museum, San Diego, California.

Rodriguez-Brito B., F. Rohwer, R. Edwards. 2006. A statistical approach to compare metagenomes. BMC Bioinformatics 7(162):1-11.

Safaee*, S., G.C. Weiser, E.F. Cassirer, R.R. Ramey and S.T. Kelley. 2006. Microbial diversity in bighorn sheep revealed by culture-independent methods. Journal of Wildlife Diseases 42: 545-555.

Sharp, B. L.* and B. E. Kus. 2006. Factors influencing the incidence of cowbird parasitism of Least Bell’s Vireo. The Journal of Wildlife Management 70: 682-690.

Simpson, M. G. 2006. Plant Systematics. Elsevier-Academic Press. 

Simpson, M. G. and D. H. Burton*. 2006. Floral anatomy of the Pontederiaceae and its systematic significance. In: Columbus, J. T., E. A. Friar, J. M. Porter, L. M. Prince, and M. G. Simpson [eds.]. Monocots: Comparative biology and evolution. 2 vols. Rancho Santa Ana Botanic Garden, Claremont, California, U. S. A.

Smith J.E., M. Shaw, R.A. Edwards, M. Hatay, D. Obura, O. Pantos, E. Sala, S.A. Sandin, S. Smriga, F. Rohwer. 2006. Effects of algae on coral: Algal-mediated, microbe-induced coral mortality. Ecology Letters 9 (7):835-845.

Thomas, S.M.* and M. Hedin. 2006. Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation. Zootaxa 1242: 21-36.

Wiens, J. J., C. H. Graham, D. S. Moen, S. A. Smith, and T. W. Reeder.  2006.  Evolutionary and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog trees unearth the roots of high tropical diversity. American Naturalist 168:579-596.

Wiens, J. J., M. C. Brandley*, and T. W. Reeder.  2006.  Why does a trait evolve multiple times within a clade?  Repeated evolution of snake-like body form in squamate reptiles. Evolution 60:123-141.

Yu, Y., M. Breitbart, F. Rohwer. 2006. FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 7(57):1-9.

Zhang, T., M. Breitbart, W.H. Lee, J. Run, C.L. Wei, S.W.L. Soh, M.L. Hibberd, E.T. Liu, F. Rohwer, and Y. Ruan. 2006. RNA viral community in the human gut: Prevalence of plant pathogenic viruses. PLoS Biology 4(1):1-11.