The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

/pdf/the-global-distribution-and-burden-of-dengue-4d1crnic4u.pdf

The global distribution and burden of dengue

Identification of the selective forces on plant dispersal engenders theoretical argument, empirical study, and speculation. We separate evidence, testable hypotheses, and conjecture surrounding two major questions in dispersal ecology. The first asks what ecological, and ultimately evolutionary, advantages exist in seed dispersal. Astonishingly little is known about the advantages to a parent plant that are actually conferred by investment in dispersal structures. Does dispersal enable seeds and ultimately seedlings to escape mortality near the parent? Is continual recolonization of unstable habitats the primary advantage? Must seeds find rare microhabitats suitable for reestablishment? Such issues are addressed through joint consideration of dispersal and establishment-those stages both mediated by parental provisioning and subject to the highest mortality in the life of a plant. The second broad question asks what general and explicit environmental forces influence the timing and mode of dispersal. Do climates or seasons favor one dispersal mode over another? Do differences in number, size, morphology, or nutritional quality of fruits influence frugivore choice, and consequently differential dispersal of species or individuals within species? Studies of dispersal process and mode should be intimately connected. A general objective of this paper is to explore the degree to which they are integrated and, in so doing, to catalyze their union. We emphasize topics most in need of critical attention: the evolutionary ecology of dispersal process and mode. Excellent recent reviews consider such related topics as dispersal mechanism (131, 184), seed dormancy (1, 30), phytogeography (11, 115, 146), masting and predator satiation (105, 156), and succession (68, 69, 189).

https://www.jstor.org/stable/info/2097067

Ecology of Seed Dispersal

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

Rates of herbivory and defensive characteristics of young and mature leaves were measured for saplings of 46 canopy tree species in a lowland tropical rain forest (Barro Colorado Island, Panama). Grazing rates were determined in the field for sample periods in the early wet, late wet, and dry seasons. Leaf properties such as pubescence, toughness, water, protein, fiber, and phenolic contents explained over 70W% of the variation among plant species in the rates of herbivory on mature leaves. Leaf toughness was most highly correlated with levels of herbivory, followed by fiber content and nutritive value. Phenol content and phenol: protein ratios were not significantly correlated with damage. Mature leaves of gap-colonizing species were grazed six times more rapidly than leaves of shade- tolerant species. Gap-colonizers have less tough leaves, lower concentrations of fiber and phenolics, higher levels of nitrogen and water, shorter leaf lifetimes, and faster growth rates than do shade- tolerant species. Gap-colonizers did not escape discovery by herbivores to any greater extent than shade-tolerant species, as measured by the spatial distribution of plants or by the intraspecific dis- tribution of herbivore damage under natural or experimentally manipulated conditions. In 70W% of the species, young leaves suffered higher damage levels than mature leaves. Although young leaves are more nutritious and less tough and fibrous, they have two to three times the con- centrations of phenols. The temporal appearance of young leaves was not correlated with the distri- bution of herbivory among individuals of a species. Interspecific patterns of defense mechanisms are discussed in terms of current theories of plant apparency, and an alternative model for the evolution of plant defenses is presented.

Herbivory and defensive characteristics of tree species in a lowland tropical forest

Flora of Barro Colorado Island

Aim The presence-only data stored in natural history collections is the most important source of information available regarding the distribution of organisms These data and profile techniques can be used to generate species distribution models (SDMs), but pseudo-absences must be generated to use group discriminative techniques In this study, we evaluated whether the SDMs generated with pseudo-absences are reliable and also if there are differences in the results obtained with profile and group discriminative techniques

Location  Ecuador, South America

Methods  The SDMs were generated with a training data set for each of the five species of Anthurium and six different methods: two profile techniques (BIOCLIM and Gower’s distance index), three group discriminative techniques [logistic multiple regression (LMR), multivariate adaptative regression splines (MARS) and Maxent] and a mixed modelling approach genetic algorithm for rule-set production (GARP), which employs a combination of profile and group discriminative techniques and generates its own pseudo-absences For LMR, MARS and Maxent, three types of absences were generated: (1) random pseudo-absences in equal number to presences and excluding a buffer area around presences (except for Maxent, which assumes that this background sample includes presences), (2) a large number (10,000) of random pseudo-absences, also excluding a buffer area around each presence and (3) ‘target-group absences’ (TGA), consisting of sites where other species of the group have been collected by the specialist, but not the species being modelled To compare the predictive performance of the SDMs, the area under the curve statistic was calculated using an independent testing data set for each species

Results  MARS, Maxent and LMR produce better results than the profile techniques The models created with TGA are generally more accurate than those generated with pseudo-absences

Main conclusions  The advantages and disadvantages of different options for using pseudo-absences and TGA with profile and group discriminative modelling techniques are explained and recommendations are made for the future

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1472-4642.2009.00617.x

Profile or group discriminative techniques? Generating reliable species distribution models using pseudo‐absences and target‐group absences from natural history collections

A Revision of Philodendron Subgenus Philodendron (Araceae) for Mexico and Central America

INTRODUCTION Araceae, a family of herbaceous monocotyledons with 106 genera, is a complex group in terms of life form and ecology. The family is widespread, with almost an equal number of genera in both the Old and New Worlds, but with the majority of species occurring in the New World tropics. A few genera range into north temperate regions with one species ranging to at least 63 degrees north latitude. Few aroids range into temperate regions of the southern hemisphere; the most southernly being Pistia stratiotes L., which can be found through 36 degrees south latitude in Argentina. The family occupies a wide variety of life zones and habitats throughout its range, extending from tropical dry to pluvial rainforest, but also ranges into subarctic marshes, tropical swamps, cloud forests, cold windswept montane plains and semi-arid to arid coastal plains. The family has many species which will not tolerate any degree of frost or cold such as Anthurium brownei Masters, as well as some, like Symplocarpus foetidus (L.) Nutt., which actually emerge from snowcovered ground. The most interesting aspect of the family's ecology is the diversity of adaptive life forms. These range from submerged to free-floating, and emergent aquatics to terrestrial plants and to epilithic or epiphytic forms which may be true epiphytes or hemiepiphytic (growing on trees but rooted in soil). Hemiepiphytism is diverse itself, with some species beginning their lives as terrestrial seedlings, then growing skototropically (toward darkness) until they arrive at the nearest suitable tree ( usually a relatively large one which casts a darker shadow) where a physiological change takes place allowing them to grow toward light (Strong & Ray, 1975). They grow as appressed epiphytes on trees or as vines in the canopy. Others begin their lives as true epiphytes, some reconverting to hemiepiphytes by producing long, dangling roots contacting the forest floor below.

Thomas B. Croat

Papers

Flora of Barro Colorado Island

Profile or group discriminative techniques? Generating reliable species distribution models using pseudo‐absences and target‐group absences from natural history collections

A Revision of Philodendron Subgenus Philodendron (Araceae) for Mexico and Central America

Ecology and life forms of Araceae

Phylogenomics of the plant family Araceae