Browsing by Author "Kellogg, Elizabeth A."

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    Continued Adaptation of C-4 Photosynthesis After an Initial Burst of Changes in the Andropogoneae Grasses
    (Oxford University Press, 2020) Bianconi, Matheus E.; Hackel, Jan; Vorontsova, Maria S.; Alberti, Adriana; Arthan, Watchara; Burke, Sean V.; Duvall, Melvin R.; Kellogg, Elizabeth A.; Lavergne, Sebastien; McKain, Michael R.; Meunier, Alexandre; Osborne, Colin P.; Traiperm, Paweena; Christin, Pascal-Antoine; Besnard, Guillaume; University of Sheffield; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute of Ecology & Environment (INEE); Universite de Toulouse; Universite Federale Toulouse Midi-Pyrenees (ComUE); Universite Toulouse III - Paul Sabatier; Ecole Nationale Formation Agronomique (ENSFEA); Institut de Recherche pour le Developpement (IRD); Royal Botanic Gardens, Kew; CEA; UDICE-French Research Universities; Universite Paris Saclay; University of Reading; Northern Illinois University; Donald Danforth Plant Science Center; Communaute Universite Grenoble Alpes; Universite Grenoble Alpes (UGA); Universite de Savoie; University of Alabama Tuscaloosa; Mahidol University
    C-4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C lineages is Andropogoneae, a group of 1200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C evolution in the group have compared a few model C plants to distantly related C species so that changes directly responsible for the transition to C could not be distinguished from those that preceded or followed it. In this study, we analyze the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C origin gave birth to a diversity of C phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state.
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    Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae
    (Oxford University Press, 2020) Ramachandran, Dhanushya; McKain, Michael R.; Kellogg, Elizabeth A.; Hawkins, Jennifer S.; West Virginia University; Donald Danforth Plant Science Center; University of Alabama Tuscaloosa
    Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.
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    Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium
    (Royal Society of London, 2019) McAllister, Christine A.; McKain, Michael R.; Li, Mao; Bookout, Bess; Kellogg, Elizabeth A.; Donald Danforth Plant Science Center; University of Alabama Tuscaloosa
    Herbaria contain a cumulative sample of the world's flora, assembled by thousands of people over centuries. To capitalize on this resource, we conducted a specimen-based analysis of a major clade in the grass tribe Andropogoneae, including the dominant species of the world's grasslands in the genera Andropogon, Schizachyrium, Hyparrhenia and several others. We imaged 186 of the 250 named species of the clade, georeferenced the specimens and extracted climatic variables for each. Using semi- and fully automated image analysis techniques, we extracted spikelet morphological characters and correlated these with environmental variables. We generated chloroplast genome sequences to correct for phylogenetic covariance and here present a new phylogeny for 81 of the species. We confirm and extend earlier studies to show that Andropogon and Schizachyrium are not monophyletic. In addition, we find all morphological and ecological characters are homoplasious but variable among clades. For example, sessile spikelet length is positively correlated with awn length when all accessions are considered, but when separated by clade, the relationship is positive for three sub-clades and negative for three others. Climate variables showed no correlation with morphological variation in the spikelet pair; only very weak effects of temperature and precipitation were detected on macrohair density. This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.