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  • The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution 

    Ryan, Joseph F.; Pang, Kevin; Schnitzler, Christine E.; Nguyen, Anh-Dao; Moreland, R. Travis; Simmons, David K.; Koch, Bernard J.; Francis, Warren R.; Havlak, Paul; NISC Comparative Sequencing Program; Smith, Stephen A.; Putnam, Nicholas H.; Haddock, Steven H.D.; Dunn, Casey W.; Wolfsberg, Tyra G.; Mullikin, James C.; Martindale, Mark Q.; Baxevanis, Andreas D. (2013)
    An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis ...
  • Balancing anti-herbivore benefits and anti-pollinator costs of defensive mutualists 

    Ohm, Johanna R.; Miller, Tom E.X. (2014)
    Quantifying costs and benefits of ostensibly mutualistic interactions is an important step toward understanding their evolutionary trajectories. In food-for-protection interactions between ants and extrafloral nectar ...
  • Intraspecific priority effects and disease interact to alter population growth 

    Dibble, Christopher J.; Hall, Spencer R.; Rudolf, Volker H.W. (2014)
    Intraspecific variation may shape colonization of new habitat patches through a variety of mechanisms. In particular, trait variation among colonizing individuals can produce intraspecific priority effects (IPEs), where ...
  • Climate warming increases biological control agent impact on a non-target species 

    Lu, Xinmin; Siemann, Evan; He, Minyan; Wei, Hui; Shao, Xu; Ding, Jianqing (2015)
    Climate change may shift interactions of invasive plants, herbivorous insects and native plants, potentially affecting biological control efficacy and non-target effects on native species. Here, we show how climate warming ...
  • The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 

    Chipman, Ariel D.; Ferrier, David E.K.; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S.T.; Schrӧder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C.; Alonso, Claudio R.; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C.J.; Blankenburg, Kerstin P.; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K.; Du Pasquier, Louis; Duncan, Elizabeth J.; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D.; Extavour, Cassandra G.; Francisco, Liezl; Gabaldón, Toni; Gillis, William J.; Goodwin-Horn, Elizabeth A.; Green, Jack E.; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J.P.; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H.L.; Hunn, Julia P.; Hunnekuhl, Vera S.; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N.; Jiggins, Francis M.; Jones, Tamsin E.; Kaiser, Tobias S.; Kalra, Divya; Kenny, Nathan J.; Korchina, Viktoriya; Kovar, Christie L.; Kraus, F. Bernhard; Lapraz, François; Lee, Sandra L.; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N.; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J.; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H.; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C.; Robertson, Helen E.; Robertson, Hugh M.; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E.; Schurko, Andrew M.; Siggens, Kenneth W.; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J.; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M.; Willis, Judith H.; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M.; Worley, Kim C.; Gibbs, Richard A.; Akam, Michael; Richards, Stephen (2014)
    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...
  • Computational approaches to species phylogeny inference and gene tree reconciliation 

    Nakhleh, Luay (2013)
    An intricate relationship exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene ...
  • Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above-belowground herbivore interactions 

    Huang, Wei; Siemann, Evan; Xiao, Li; Yang, Xuefang; Ding, Jianqing (2014)
    Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of ...
  • Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication 

    Nossa, Carlos W.; Havlak, Paul; Yue, Jia-Xing; Lv, Jie; Vincent, Kimberly Y.; Brockmann, H. Jane; Putnam, Nicholas H. (2014)
    Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral ...
  • An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes 

    Liu, Kevin J.; Dai, Jingxuan; Truong, Kathy; Song, Ying; Kohn, Michael H.; Nakhleh, Luay (2014-06-12)
    One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. ...
  • Adaptation of Enterococcus faecalis to Daptomycin Reveals an Ordered Progression to Resistance 

    Miller, Corwin; Kong, Jiayi; Tran, Truc T.; Arias, Cesar A.; Saxer, Gerda; Shamoo, Yousif (2013)
    With increasing numbers of hospital-acquired antibiotic resistant infections each year and staggering health care costs, there is a clear need for new antimicrobial agents, as well as novel strategies to extend their ...
  • Total Synthesis of Viridicatumtoxin B and Analogues Thereof: Strategy Evolution, Structural Revision, and Biological Evaluation 

    Nicolaou, K.C.; Hale, Christopher R.H.; Nilewski, Christian; Ioannidou, Heraklidia A.; ElMarrouni, Abdelatif; Nilewski, Lizanne G.; Beabout, Kathryn; Wang, Tim T.; Shamoo, Yousif (2014)
    The details of the total synthesis of viridicatumtoxin B (1) are described. Initial synthetic strategies toward this intriguing tetracycline antibiotic resulted in the development of key alkylation and Lewis acid-mediated ...
  • Decomposition of Phragmites australis litter retarded by invasive Solidago canadensis in mixtures: an antagonistic non-additive effect 

    Zhang, Ling; Zhang, Yaojun; Zou, Jianwen; Siemann, Evan (2014)
    Solidago canadensis is an aggressive invader in China. Solidago invasion success is partially attributed to allelopathic compounds release and more benefits fromAMfungi, which potentially makes the properties of Solidago ...
  • Nitrogen, biochar, and mycorrhizae: Alteration of the symbiosis and oxidation of the char surface 

    LeCroy, Chase; Masiello, Caroline A.; Rudgers, Jennifer A.; Hockaday, William C.; Silberg, Jonathan J. (2014)
    In some cases amending soil with biochar improves fertility, although the exact mechanisms through which biochar alters soil processes are not well understood. In other cases, however, biochar amendment can have no effect ...
  • Resolving the roles of body size and species identity in driving functional diversity 

    Rudolf, Volker H.W.; Rasmussen, Nick L.; Dibble, Christopher J.; Van Allen, Benjamin G. (2014)
    Efforts to characterize food webs have generated two influential approaches that reduce the complexity of natural communities. The traditional approach groups individuals based on their species identity, while recently ...
  • Linking phenological shifts to species interactions through size-mediated priority effects 

    Rasmussen, Nick L.; Van Allen, Benjamin G.; Rudolf, Volker H.W. (2014)
    Interannual variation in seasonal weather patterns causes shifts in the relative timing of phenological events of species within communities, but we currently lack a mechanistic understanding of how these phenological ...
  • Non-Native Plant Litter Enhances Soil Carbon Dioxide Emissions in an Invaded Annual Grassland 

    Zhang, Ling; Wang, Hong; Zou, Jianwen; Rogers, William E.; Siemann, Evan (2014-03-19)
    Litter decomposition is a fundamental ecosystem process in which breakdown and decay of plant detritus releases carbon and nutrients. Invasive exotic plants may produce litter that differs from native plant litter in quality ...
  • Niche Differentiation in the Dynamics of Host-Symbiont Interactions: Symbiont Prevalence as a Coexistence Problem 

    Miller, Tom E.X.; Rudgers, Jennifer A. (2014-04)
    Heritable symbioses can have important ecological effects and have triggered important evolutionary innovations. Current predictions for long-term symbiont prevalence are based on their fitness benefits and vertical ...
  • Plant size and reproductive state affect the quantity and quality of rewards to animal mutualists 

    Miller, Tom E.X. (2014)
    Many plants engage ants in defensive mutualisms by offering extrafloral nectar (EFN). Identifying sources of variation in EFN quantity (amount) and quality (composition) is important because they can affect ant visitation ...
  • Mitochondrial DNA Phylogeography of the Norway Rat 

    Song, Ying; Lan, Zhenjiang; Kohn, Michael H. (2014-02-28)
    Central Eastern Asia, foremost the area bordering northern China and Mongolia, has been thought to be the geographic region where Norway rats (Rattus norvegicus) have originated. However recent fossil analyses pointed to ...
  • Consequences of sex-selective harvesting and harvest refuges in experimental meta-populations 

    Snyder, Kate T.; Freidenfelds, Nicole A.; Miller, Tom E.X. (2013)
    Harvesting for food or sport is often non-random with respect to demographic state, such as size or life stage. The population- level consequences of such selective harvesting depend upon which states are harvested and ...

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