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Benjamin E Carter, Juan Larraín, Alžběta Manukjanová, Blanka Shaw, A Jonathan Shaw, Jochen Heinrichs, Peter de Lange, Monica Suleiman, Louis Thouvenot, Matt von Konrat
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere...
October 12, 2016: Molecular Phylogenetics and Evolution
K Yoshizawa, M Souza-Silva, R L Ferreira
A new barklouse species belonging to the Trichadenotecnum s.str. clade (Psocodea: "Psocoptera": Psocidae) was described from southeastern Brazil (Minas Gerais state). This locality is highly isolated (about 3400 km) from the closest known distributional range of this clade. It also represents the southernmost distributional record of Trichadenotecnum s.str. Phylogenetic placement of the species and biogeography of Neotropical Trichadenotecnum were briefly discussed. Trichadenotecnum punctipenne New, 1972 described from Brazil was synonymized with Trichadenotecnum pardus Badonnel, 1955...
October 14, 2016: Neotropical Entomology
Daniel Poveda-Martínez, Chrystian C Sosa, Katherine Chacón-Vargas, Víctor Hugo García-Merchán
Characidium is a Neotropical fish genus. Its distribution ranges from eastern Panama to northern Argentina, and it is an important component of the Neotropical ichthyofauna present in the major rivers of South America. We here provide an approximation to the dispersal and historical distributions of Characidium. The biogeographic history of five species of the genus was analyzed through nuclear RAG-2 and mitochondrial 16S genes and a time-calibrated phylogenetic analysis using three outgroup species. A biogeographical reconstruction was performed to estimate ancestral geographic ranges and infer the historical events that impacted the geographic distributions of Characidium species...
2016: PloS One
P Kumudha, R Venkatesan
Effective prediction of software modules, those that are prone to defects, will enable software developers to achieve efficient allocation of resources and to concentrate on quality assurance activities. The process of software development life cycle basically includes design, analysis, implementation, testing, and release phases. Generally, software testing is a critical task in the software development process wherein it is to save time and budget by detecting defects at the earliest and deliver a product without defects to the customers...
2016: TheScientificWorldJournal
William G R Crampton, Carlos David de Santana, Joseph C Waddell, Nathan R Lovejoy
A species-level phylogenetic reconstruction of the Neotropical bluntnose knifefish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) is presented, based on 60 morphological characters, approximately 1100 base pairs of the mitochondrial cytb gene, and approximately 1000 base pairs of the nuclear rag2 gene. The phylogeny includes 28 species of Brachyhypopomus and nine outgroup species from nine other gymnotiform genera, including seven in the superfamily Rhamphichthyoidea (Hypopomidae and Rhamphichthyidae). Parsimony and Bayesian total evidence phylogenetic analyses confirm the monophyly of the genus, and identify nine robust species groups...
2016: PloS One
Erin M Eggleston, Ian Hewson
This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10 N-40 S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 × 10(7) virus like particles (VLPs) in surface waters, decreasing to an average of 6.50 ± 2.26 × 10(5) VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance...
2016: Frontiers in Microbiology
F Sara Ceccarelli, Brent D Opell, Charles R Haddad, Robert J Raven, Eduardo M Soto, Martín J Ramírez
Closely related organisms with transoceanic distributions have long been the focus of historical biogeography, prompting the question of whether long-distance dispersal, or tectonic-driven vicariance shaped their current distribution. Regarding the Southern Hemisphere continents, this question deals with the break-up of the Gondwanan landmass, which has also affected global wind and oceanic current patterns since the Miocene. With the advent of phylogenetic node age estimation and parametric bioinformatic advances, researchers have been able to disentangle historical evolutionary processes of taxa with greater accuracy...
2016: PloS One
L Patrick Schenck, Michael G Surette, Dawn M E Bowdish
The intestinal microbiota is essential for nutrient acquisition, immune development, and exclusion of invading pathogens. The upper respiratory tract (URT) microbiota is less well studied and does not appear to abide by many of the paradigms of the gastrointestinal tract. Decades of carriage studies in children have demonstrated that microbe-microbe competition and collusion occurs in the URT. Whether colonization with common pathogens (e.g. Staphylococcus aureus and Streptococcus pneumoniae) alters immune development or susceptibility to respiratory conditions is just beginning to be understood...
October 12, 2016: FEBS Letters
Daniela Keilberg, Yana Zavros, Benjamin Shepherd, Nina R Salama, Karen M Ottemann
: Gland colonization may be one crucial route for bacteria to maintain chronic gastrointestinal infection. We developed a quantitative gland isolation method to allow robust bacterial population analysis and applied it to the gastric pathobiont Helicobacter pylori After infections in the murine model system, H. pylori populations multiply both inside and outside glands in a manner that requires the bacteria to be motile and chemotactic. H. pylori is able to achieve gland densities averaging 25 to 40 bacteria/gland after 2 to 4 weeks of infection...
October 11, 2016: MBio
Martin R Smith
The present-day distribution of velvet worms corresponds neatly to the ancient supercontinent Gondwana - except for a puzzling outpost in southeast Asia. Jaw-dropping new fossil material now establishes when and how peripatid onychophorans reached this isolated spot.
October 10, 2016: Current Biology: CB
Tianle Xu, Stavros D Veresoglou, Yongliang Chen, Matthias C Rillig, Dan Xiang, Daniel Ondrej, Zhipeng Hao, Lei Liu, Ye Deng, Yajun Hu, Weiping Chen, Juntao Wang, Jizheng He, Baodong Chen
Arbuscular mycorrhizal fungi (AMF) are ubiquitous mutualists of terrestrial plants and play key roles in regulating various ecosystem processes, but little is known about AMF biogeography at regional scale. This study aims at exploring the key predictors of AMF communities across a 5000-km transect in northern China. We determined the soil AMF species richness and community composition at 47 sites representative of four vegetation types (meadow steppe, typical steppe, desert steppe and desert) and related them to plant community characteristics, abiotic factors and geographic distance...
October 7, 2016: Environmental Microbiology Reports
Jani Heino, Janne Soininen, Janne Alahuhta, Jyrki Lappalainen, Risto Virtanen
Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity...
October 6, 2016: Oecologia
M Romina Schiaffino, Enrique Lara, Leonardo D Fernández, Vanessa Balagué, David Singer, Christophe C W Seppey, Ramon Massana, Irina Izaguirre
Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (IlluminaHiSeq)...
October 6, 2016: Environmental Microbiology
Walter G Joyce, Tyler R Lyson, James I Kirkland
BACKGROUND: Bothremydidae is a clade of extinct pleurodiran turtles known from the Cretaceous to Paleogene of Africa, Europe, India, Madagascar, and North and South America. The group is most diverse during the Late Cretaceous to Paleogene of Africa. Little is known, however, about the early evolution of the group. METHODS: We here figure and describe a fossil turtle from early Late Cretaceous deposits exposed at MacFarlane Mine in Cedar Canyon, southwestern Utah, USA...
2016: PeerJ
Matthew G Girard, W Leo Smith
The marine sculpins (Psychrolutidae) are a diverse percomorph family with notable morphological variation and repeated biogeographic patterns within the group. The psychrolutid genus Icelinus is unusual because it is one of the few near-shore members of the family that exhibits a trans-Pacific distribution; it has two species in the western Pacific and nine species in the eastern Pacific. Furthermore, the placement of Icelinus has been more inconsistent across molecular and morphological analyses than many genera...
September 29, 2016: Zootaxa
Daniel Edler, Thaís Guedes, Alexander Zizka, Martin Rosvall, Alexandre Antonelli
Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps...
October 1, 2016: Systematic Biology
Liming Cai, Zhenxiang Xi, Kylee Peterson, Catherine Rushworth, Jeremy Beaulieu, Charles C Davis
The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family...
2016: PloS One
Jie Song, Jia-Jia Chen, Min Wang, Yuan-Yuan Chen, Bao-Kai Cui
Bondarzewia is a conspicuous and widely distributed mushroom genus, but little is known about its origin and biogeography. Here, we investigated the systematics and biogeography of Bondarzewia species using multi-locus phylogenetic analysis. Four genetic markers, including the internal transcribed spacer (ITS), large nuclear ribosomal RNA subunit (nLSU), elongation factor 1-α (tef1) and mitochondrial small subunit rDNA (mtSSU), were used to infer the phylogenetic relationships of Bondarzewia. We performed Bayesian evolutionary analysis on the gene datasets of the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2)...
September 29, 2016: Scientific Reports
William H DePas, Ruth Starwalt-Lee, Lindsey Van Sambeek, Sripriya Ravindra Kumar, Viviana Gradinaru, Dianne K Newman
: Physiological resistance to antibiotics confounds the treatment of many chronic bacterial infections, motivating researchers to identify novel therapeutic approaches. To do this effectively, an understanding of how microbes survive in vivo is needed. Though much can be inferred from bulk approaches to characterizing complex environments, essential information can be lost if spatial organization is not preserved. Here, we introduce a tissue-clearing technique, termed MiPACT, designed to retain and visualize bacteria with associated proteins and nucleic acids in situ on various spatial scales...
September 27, 2016: MBio
Felix May, Thorsten Wiegand, Sebastian Lehmann, Andreas Huth, Marie-Josée Fortin
AIM: It has been recently suggested that different 'unified theories of biodiversity and biogeography' can be characterized by three common 'minimal sufficient rules': (1) species abundance distributions follow a hollow curve, (2) species show intraspecific aggregation, and (3) species are independently placed with respect to other species. Here, we translate these qualitative rules into a quantitative framework and assess if these minimal rules are indeed sufficient to predict multiple macroecological biodiversity patterns simultaneously...
May 2016: Global Ecology and Biogeography: a Journal of Macroecology
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