@article{jenny_shapiro_davis_davies_pierce_meineke_2023, title={Herbarium specimens reveal herbivory patterns across the genus Cucurbita}, ISSN={["1537-2197"]}, DOI={10.1002/ajb2.16126}, abstractNote={Abstract}, journal={AMERICAN JOURNAL OF BOTANY}, author={Jenny, Laura A. A. and Shapiro, Lori R. R. and Davis, Charles C. C. and Davies, T. Jonathan and Pierce, Naomi E. E. and Meineke, Emily}, year={2023}, month={Feb} }
 @article{landis_oliverio_mckenney_nichols_kfoury_biango-daniels_shell_madden_shapiro_sakunala_et al._2021, title={The diversity and function of sourdough starter microbiomes}, volume={10}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.61644}, DOI={10.7554/eLife.61644}, abstractNote={Humans have relied on sourdough starter microbial communities to make leavened bread for thousands of years, but only a small fraction of global sourdough biodiversity has been characterized. Working with a community-scientist network of bread bakers, we determined the microbial diversity of 500 sourdough starters from four continents. In sharp contrast with widespread assumptions, we found little evidence for biogeographic patterns in starter communities. Strong co-occurrence patterns observed in situ and recreated in vitro demonstrate that microbial interactions shape sourdough community structure. Variation in dough rise rates and aromas were largely explained by acetic acid bacteria, a mostly overlooked group of sourdough microbes. Our study reveals the extent of microbial diversity in an ancient fermented food across diverse cultural and geographic backgrounds.}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Landis, Elizabeth A and Oliverio, Angela M and McKenney, Erin A and Nichols, Lauren M and Kfoury, Nicole and Biango-Daniels, Megan and Shell, Leonora K and Madden, Anne A and Shapiro, Lori and Sakunala, Shravya and et al.}, year={2021}, month={Jan} }
 @article{chase_zhaxybayeva_rocha_cosgrove_shapiro_2020, title={Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution}, volume={226}, ISSN={["1469-8137"]}, DOI={10.1111/nph.16428}, abstractNote={Summary}, number={3}, journal={NEW PHYTOLOGIST}, author={Chase, William R. and Zhaxybayeva, Olga and Rocha, Jorge and Cosgrove, Daniel J. and Shapiro, Lori R.}, year={2020}, month={May}, pages={921–938} }
 @article{shapiro_paulson_arnold_scully_zhaxybayeva_pierce_rocha_klepac-ceraj_holton_kolter_2018, title={An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila}, volume={9}, ISSN={["2150-7511"]}, DOI={10.1128/mBio.01307-18}, abstractNote={
            Erwinia tracheiphila
            is a virulent phytopathogen that infects two genera of cucurbit crop plants,
            Cucurbita
            spp. (pumpkin and squash) and
            Cucumis
            spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an
            E. tracheiphila
            isolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introduced
            Cucumis
            spp. crop plants are driving the diversification of
            E. tracheiphila
            into multiple lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.
          }, number={5}, journal={MBIO}, author={Shapiro, Lori R. and Paulson, Joseph N. and Arnold, Brian J. and Scully, Erin D. and Zhaxybayeva, Olga and Pierce, Naomi E. and Rocha, Jorge and Klepac-Ceraj, Vanja and Holton, Kristina and Kolter, Roberto}, year={2018} }
 @article{andrade-dominguez_kolte_shapiro_2018, title={Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila}, volume={6}, ISSN={["2169-8287"]}, DOI={10.1128/genomeA.00127-18}, abstractNote={ABSTRACT}, number={8}, journal={GENOME ANNOUNCEMENTS}, author={Andrade-Dominguez, Andres and Kolte, Roberto and Shapiro, Lori R.}, year={2018}, month={Feb} }
 @article{shapiro_andrade_scully_rocha_paulson_kolter_2018, title={Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo)}, volume={7}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.01058-18}, abstractNote={
            Erwinia tracheiphila
            is a bacterial plant pathogen emerging in eastern North America. To aid in understanding genetic variation within
            E. tracheiphila
            , here we sequence the first reference genome of an infected muskmelon (
            Cucumis melo
            ).
          }, number={17}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Shapiro, Lori R. and Andrade, Andres and Scully, Erin D. and Rocha, Jorge and Paulson, Joseph N. and Kolter, Roberto}, year={2018}, month={Nov} }
 @article{mauck_chesnais_shapiro_2018, title={Evolutionary Determinants of Host and Vector Manipulation by Plant Viruses}, volume={101}, ISSN={["0065-3527"]}, DOI={10.1016/bs.aivir.2018.02.007}, abstractNote={Plant viruses possess adaptations for facilitating acquisition, retention, and inoculation by vectors. Until recently, it was hypothesized that these adaptations are limited to virus proteins that enable virions to bind to vector mouthparts or invade their internal tissues. However, increasing evidence suggests that viruses can also manipulate host plant phenotypes and vector behaviors in ways that enhance their own transmission. Manipulation of vector-host interactions occurs through virus effects on host cues that mediate vector orientation, feeding, and dispersal behaviors, and thereby, the probability of virus transmission. Effects on host phenotypes vary by pathosystem but show a remarkable degree of convergence among unrelated viruses whose transmission is favored by the same vector behaviors. Convergence based on transmission mechanism, rather than phylogeny, supports the hypothesis that virus effects are adaptive and not just by-products of infection. Based on this, it has been proposed that viruses manipulate hosts through multifunctional proteins that facilitate exploitation of host resources and elicitation of specific changes in host phenotypes. But this proposition is rarely discussed in the context of the numerous constraints on virus evolution imposed by molecular and environmental factors, which figure prominently in research on virus-host interactions not dealing with host manipulation. To explore the implications of this oversight, we synthesized available literature to identify patterns in virus effects among pathogens with shared transmission mechanisms and discussed the results of this synthesis in the context of molecular and environmental constraints on virus evolution, limitations of existing studies, and prospects for future research.}, journal={ENVIRONMENTAL VIROLOGY AND VIRUS ECOLOGY}, author={Mauck, Kerry E. and Chesnais, Quentin and Shapiro, Lori R.}, year={2018}, pages={189–250} }
 @article{haney_wiesmann_shapiro_melnyk_lucy r. o'sullivan_khorasani_xiao_han_bush_carrillo_et al._2018, title={Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens}, volume={27}, ISSN={["1365-294X"]}, DOI={10.1111/mec.14400}, abstractNote={Abstract}, number={8}, journal={MOLECULAR ECOLOGY}, author={Haney, Cara H. and Wiesmann, Christina L. and Shapiro, Lori R. and Melnyk, Ryan A. and Lucy R. O'Sullivan and Khorasani, Sophie and Xiao, Li and Han, Jiatong and Bush, Jenifer and Carrillo, Juli and et al.}, year={2018}, month={Apr}, pages={1833–1847} }