The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

/pdf/analysis-of-the-genome-sequence-of-the-flowering-plant-3vizsb52m2.pdf

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

/pdf/genome-sequencing-and-analysis-of-the-model-grass-5dln1jkes2.pdf

Genome sequencing and analysis of the model grass Brachypodium distachyon

/pdf/genome-sequencing-and-analysis-of-themodel-grass-3hu9hqmqqm.pdf

Genome sequencing and analysis of themodel grass Brachypodium distachyon

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

Polyploidy and angiosperm diversification

Contents

Summary 341

I.  Introduction 342
II.  What is C4 photosynthesis? 343
III.  Why did C4 photosynthesis evolve? 347
IV.  Evolutionary lineages of C4 photosynthesis 348
V.  Where did C4 photosynthesis evolve? 350
VI.  How did C4 photosynthesis evolve? 352
VII.  Molecular evolution of C4 photosynthesis 361
VIII. When did C4 photosynthesis evolve 362
IX.  The rise of C4 photosynthesis in relation to climate and CO2 363
X.  Final thoughts: the future evolution of C4 photosynthesis 365

Acknowledgements 365


References 365



Summary
C4 photosynthesis is a series of anatomical and biochemical modifications that concentrate CO2 around the carboxylating enzyme Rubisco, thereby increasing photosynthetic efficiency in conditions promoting high rates of photorespiration. The C4 pathway independently evolved over 45 times in 19 families of angiosperms, and thus represents one of the most convergent of evolutionary phenomena. Most origins of C4 photosynthesis occurred in the dicots, with at least 30 lineages. C4 photosynthesis first arose in grasses, probably during the Oligocene epoch (24–35 million yr ago). The earliest C4 dicots are likely members of the Chenopodiaceae dating back 15–21 million yr; however, most C4 dicot lineages are estimated to have appeared relatively recently, perhaps less than 5 million yr ago. C4 photosynthesis in the dicots originated in arid regions of low latitude, implicating combined effects of heat, drought and/or salinity as important conditions promoting C4 evolution. Low atmospheric CO2 is a significant contributing factor, because it is required for high rates of photorespiration. Consistently, the appearance of C4 plants in the evolutionary record coincides with periods of increasing global aridification and declining atmospheric CO2. Gene duplication followed by neo- and nonfunctionalization are the leading mechanisms for creating C4 genomes, with selection for carbon conservation traits under conditions promoting high photorespiration being the ultimate factor behind the origin of C4 photosynthesis.

The evolution of C4 photosynthesis

Caminhamento-Um metodo expedito para levantamentos floristicos qualitativos

\n Information on where species occur is an important component of conservation and management decisions, but knowledge of distributions is often coarse or incomplete. Species distribution models provide a tool for mapping habitat and can produce credible, defensible, and repeatable information with which to inform decisions. However, these models are sensitive to data inputs and methodological choices, making it important to assess the reliability and utility of model predictions. We provide a rubric that model developers can use to communicate a model's attributes and its appropriate uses. We emphasize the importance of tailoring model development and delivery to the species of interest and the intended use and the advantages of iterative modeling and validation. We highlight how species distribution models have been used to design surveys for new populations, inform spatial prioritization decisions for management actions, and support regulatory decision-making and compliance, tying these examples back to our model assessment rubric.

/pdf/development-and-delivery-of-species-distribution-models-to-2qeh9re6lt.pdf

Development and Delivery of Species Distribution Models to Inform Decision-Making

The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

/pdf/the-importance-of-species-name-synonyms-in-literature-dxl7mfcf1x.pdf

The Importance of Species Name Synonyms in Literature Searches.

Andropogon crispifolius a new species from the environs of the Parque Nacional das Emas (in the states of Goias and Mato Grosso do Sul) in central Brazil is here described, illustrated and compared with A. pohlianus Hack. It is a large, perennial, coarse grass characterized primarily by its strongly crispate older leaves. This new species is placed in sect. Notosolen Stapf, previously represented in South America by a single species, A. pohlianus.

Andropogon crispifolius (Poaceae: Andropogoneae): a new species from the cerrado of central Brazil

Summary. Recent biodiversity surveys in the Cayman Islands have generated several new records for the reasonably be attributed to recent introduction. Exotics not clearly spreading, but known to be weedy elsewhere, were often seen in planted lawns and in landscape situations. Notable among these were Hydrocotyle umbellata L. and Polypremum procumbens L. found apparently as accidental introductions in recent landscaping at the Queen Elizabeth II Botanic Park and several large fruiting specimens of Melaleuca quinquenervia (Cav.) S. T. Blake in a landscape planting on Cayman Brac. Also, several grasses previously unknown in the Cayman Islands were observed in cultivation in Georgetown and environs. The species observed included Cymbopogon citratus (DC.) Stapf, Pennisetum setaceum (Forssk.) Chiov., Pennisetum macrostachyum (Brogn.) Trin., Phyllostachys sp., Pogonatherum paniceum (Lam.) Hack., Tripsacum floridanum Porter ex Vasey, and Tripsacum dactyloides (L.) L. The flora of the Cayman Islands is dynamic and work continues on cataloguing and conserving the biodiversity of the islands. There will certainly be more species found (e.g. an as yet undetermined Drypetes found recently in the Mastic area) and some will certainly disappear. We will continue to report on the developments. Photographs of most (and eventually all) collections at CAYM and FTG can be seen

Additions to the flora of the Cayman Islands.

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