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Molecular and Phylogenetic Analyses Suggest an Additional Hepatitis B Virus Genotype “I”  [PDF]
Hai Yu,Quan Yuan,Sheng-Xiang Ge,Hurng-Yi Wang,Ya-Li Zhang,Qing-Rui Chen,Jun Zhang,Pei-Jer Chen,Ning-Shao Xia
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009297
Abstract: A novel hepatitis B virus (HBV) strain (W29) was isolated from serum samples in the northwest of China. Phylogenetic and distance analyses indicate that this strain is grouped with a series of distinct strains discovered in Vietnam and Laos that have been proposed to be a new genotype I. TreeOrderScan and GroupScan methods were used to study the intergenotype recombination of this special group. Recombination plots and tree maps of W29 and these putative genotype I strains exhibit distinct characteristics that are unexpected in typical genotype C strains of HBV. The amino acids of P gene, S gene, X gene, and C gene of all genotypes (including subtypes) were compared, and eight unique sites were found in genotype I. In vitro and in vivo experiments were also conducted to determine phenotypic characteristics between W29 and other representative strains of different genotypes obtained from China. Secretion of HBsAg in Huh7 cells is uniformly abundant among genotypes A, B, C, and I (W29), but not genotype D. HBeAg secretion is low in genotype I (W29), whose level is close to genotype A and much lower than genotypes B, C, and D. Results from the acute hydrodynamic injection mouse model also exhibit a similar pattern. From an overview of the results, the viral markers of W29 (I1) in Huh7 cells and mice had a more similar level to genotype A than genotype C, although the latter was closer to W29 in distance analysis. All evidence suggests that W29, together with other related strains found in Vietnam and Laos, should be classified into a new genotype.
Dissection of the Possible Routes on Porcine Circoviruses Infecting Human
Shao-Lun Zhai,Sheng-Nan Chen,Jian-Wu Zhang,Zu-Zhang Wei,Jin-Xue Long,Shi-Shan Yuan,Wen-Kang Wei,Qin-Ling Chen,Hua Xuan,Da-Cheng Wu
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2012.1281.1286
Abstract: In 10 years recently whether porcine circoviruses infect human is in dispute. Previous studies reported DNAs of porcine circovirus type 1 and porcine circovirus type 2 were detected in pigs, cattle, pepsin and rodents. However, the latest published article in the well-known journals also showed that porcine circovirus type 2 existed in the human stools, human vaccines and beef. This review dissected of the possible routes on porcine circoviruses infecting human such as foodborne infection, vaccination infection, xenotransplantation infection, airborne infection and vector infection based on some published literatures in order to cause some concerns in public health and cross-species transmission. Moreover, to better understand phylogenetic analysis of porcine circoviruses isolated from different origins (swine, bovine, human and pepsin), researchers constructed the phylogenetic tree based on its complete genome. This study systematically reviewed the possible routes on porcine circoviruses infecting human.
Dispersal Routes and Habitat Utilization of Juvenile Atlantic Bluefin Tuna, Thunnus thynnus, Tracked with Mini PSAT and Archival Tags  [PDF]
Benjamin Galuardi, Molly Lutcavage
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037829
Abstract: Between 2005 and 2009, we deployed 58 miniature pop-up satellite archival tags (PSAT) and 132 implanted archival tags on juvenile Atlantic bluefin tuna (age 2–5) in the northwest Atlantic Ocean. Data returned from these efforts (n = 26 PSATs, 1 archival tag) revealed their dispersal routes, horizontal and vertical movements and habitat utilization. All of the tagged bluefin tuna remained in the northwest Atlantic for the duration observed, and in summer months exhibited core-use of coastal seas extending from Maryland to Cape Cod, MA, (USA) out to the shelf break. Their winter distributions were more spatially disaggregated, ranging south to the South Atlantic Bight, northern Bahamas and Gulf Stream. Vertical habitat patterns showed that juvenile bluefin tuna mainly occupied shallow depths (mean = 5–12 m, sd = 15–23.7 m) and relatively warm water masses in summer (mean = 17.9–20.9°C, sd = 4.2–2.6°C) and had deeper and more variable depth patterns in winter (mean = 41–58 m, sd = 48.9–62.2 m). Our tagging results reveal annual dispersal patterns, behavior and oceanographic associations of juvenile Atlantic bluefin tuna that were only surmised in earlier studies. Fishery independent profiling from electronic tagging also provide spatially and temporally explicit information for evaluating dispersals rates, population structure and fisheries catch patterns.
Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus
David S Horner, Konstantinos Lefkimmiatis, Aurelio Reyes, Carmela Gissi, Cecilia Saccone, Graziano Pesole
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-16
Abstract: We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago.Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.Phylogenetic relationships and divergence times within the superorder Glires (Rodentia, and Lagomorpha) remain controversial, with many discrepancies between estimates from morphological, molecular and fossil data. The problem is exacerbated both by the fact that Rodentia represents the most abundant and diversified order of living mammals and by variations in molecular evolutionary rate and mode in some families. For example, several molecular studies have suggested paraphyly of Rodentia or Glires [1-3], while others (and the majority of morphological data) support the monophyly of both groups [4-6]. Both molecular approaches and morphological analyses have their limitations. Critics of conclusions based on molecular characters cite the limited number of sequences considered and the apparent dependence of conclusions on the analytical methodologies employed, while adherents of mo
Phylogenetic Analysis and Molecular Dating Suggest That Hemidactylus anamallensis Is Not a Member of the Hemidactylus Radiation and Has an Ancient Late Cretaceous Origin  [PDF]
Rohini Bansal, K. Praveen Karanth
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060615
Abstract: Background of the Work The phylogenetic position and evolution of Hemidactylus anamallensis (family Gekkonidae) has been much debated in recent times. In the past it has been variously assigned to genus Hoplodactylus (Diplodactylidae) as well as a monotypic genus ‘Dravidogecko’ (Gekkonidae). Since 1995, this species has been assigned to Hemidactylus, but there is much disagreement between authors regarding its phylogenetic position within this genus. In a recent molecular study H. anamallensis was sister to Hemidactylus but appeared distinct from it in both mitochondrial and nuclear markers. However, this study did not include genera closely allied to Hemidactylus, thus a robust evaluation of this hypothesis was not undertaken. Methods The objective of this study was to investigate the phylogenetic position of H. anamallensis within the gekkonid radiation. To this end, several nuclear and mitochondrial markers were sequenced from H. anamallensis, selected members of the Hemidactylus radiation and genera closely allied to Hemidactylus. These sequences in conjunction with published sequences were subjected to multiple phylogenetic analyses. Furthermore the nuclear dataset was also subjected to molecular dating analysis to ascertain the divergence between H. anamallensis and related genera. Results and Conclusion Results showed that H. anamallensis lineage was indeed sister to Hemidactylus group but was separated from the rest of the Hemidactylus by a long branch. The divergence estimates supported a scenario wherein H. anamallensis dispersed across a marine barrier to the drifting peninsular Indian plate in the late Cretaceous whereas Hemidactylus arrived on the peninsular India after the Indian plate collided with the Eurasian plate. Based on these molecular evidence and biogeographical scenario we suggest that the genus Dravidogecko should be resurrected.
Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers  [PDF]
Antoni Fernàndez-Guerra, Emilio O. Casamayor
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047330
Abstract: Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γAOA > γAOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged picture of AOB and AOA distribution in different habitats provides a new view to understand the ecophysiology of ammonia oxidizers on Earth.
Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family
Jari Intra, Giulio Pavesi, David S Horner
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-214
Abstract: Careful phylogenetic analyses of 233 inferred protein sequences from eukaryotes and prokaryotes reveal a complex history for the GH20 family. In bacteria, multiple gene duplications and lineage specific gene loss (and/or horizontal gene transfer) are required to explain the observed taxonomic distribution. The last common ancestor of extant eukaryotes is likely to have possessed at least one GH20 family member. At least one gene duplication before the divergence of animals, plants and fungi as well as other lineage specific duplication events have given rise to multiple paralogous subfamilies in eukaryotes. Phylogenetic analyses also suggest that a second, divergent subfamily of GH20 family genes present in animals derive from an independent prokaryotic source. Our data suggest multiple convergent changes of functional roles of GH20 family members in eukaryotes.This study represents the first detailed evolutionary analysis of the glycosyl hydrolase GH20 family. Mapping of data concerning physiological function of GH20 family members onto the phylogenetic tree reveals that apparently convergent and highly lineage specific changes in substrate specificity have occurred in multiple GH20 subfamilies.Carbohydrates are involved in many biological functions including maintenance of cell structural integrity, energy storage, pathogen defence, viral penetration, cellular signalling and fertilization. Enzymes specifically responsible for carbohydrate hydrolysis have been classified in 111 families of glycosyl hydrolases (GH) on the basis of amino acid sequence similarity [1,2]. Hexosaminidases belong to families GH3, GH20 and GH84 [2]. Among these, family 20 is of particular interest, and includes β-N-acetylhexosaminidases (β-hexosaminidase) (EC 3.2.1.52), enzymes that hydrolyze non-reducing terminal β-1,4 linked N-acetylglucosamine (GlcNAc) or β-N-acetylgalactosamine (GalNAc) residues of oligosaccharides and their conjugates, bacterial chitobiases (EC 3.2.1.30) and lacto-N-b
Roots and Routes
Ann-Dorte Christensen, Sune Qvotrup Jensen
Nordic Journal of Migration Research , 2011, DOI: 10.2478/v10202-011-0013-1
Abstract: This article is about transnational migrants, how they construct belonging to ‘new’ places where they have arrived, and how the feelings of belonging to their places of origin change when they go back. The theoretical part of the article outlines the relationship between migration and belonging arguing that there is a dynamic interplay between roots and routes in people's lives. The empirical point of departure is narratives about roots and routes by ethnic minorities settled in Aalborg East, an underprivileged neighbourhood in northern Denmark. One of the main findings is a gap between the national exclusion of transnational migrants marked as ‘strangers’ and border figures of the nation and a relatively high degree of local belonging to the neighbourhood. This is followed by an in-depth empirical analysis inspired by Alfred Schutz's distinction between the stranger and the homecomer. A somewhat paradoxical finding is that it appears to be more difficult for transnational migrants to maintain their roots in the country of origin when they go back than it was to establish new roots in the host country.
Determinants of Plant Community Assembly in a Mosaic of Landscape Units in Central Amazonia: Ecological and Phylogenetic Perspectives  [PDF]
María Natalia Uma?a, Natalia Norden, ángela Cano, Pablo R. Stevenson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0045199
Abstract: The Amazon harbours one of the richest ecosystems on Earth. Such diversity is likely to be promoted by plant specialization, associated with the occurrence of a mosaic of landscape units. Here, we integrate ecological and phylogenetic data at different spatial scales to assess the importance of habitat specialization in driving compositional and phylogenetic variation across the Amazonian forest. To do so, we evaluated patterns of floristic dissimilarity and phylogenetic turnover, habitat association and phylogenetic structure in three different landscape units occurring in terra firme (Hilly and Terrace) and flooded forests (Igapó). We established two 1-ha tree plots in each of these landscape units at the Caparú Biological Station, SW Colombia, and measured edaphic, topographic and light variables. At large spatial scales, terra firme forests exhibited higher levels of species diversity and phylodiversity than flooded forests. These two types of forests showed conspicuous differences in species and phylogenetic composition, suggesting that environmental sorting due to flood is important, and can go beyond the species level. At a local level, landscape units showed floristic divergence, driven both by geographical distance and by edaphic specialization. In terms of phylogenetic structure, Igapó forests showed phylogenetic clustering, whereas Hilly and Terrace forests showed phylogenetic evenness. Within plots, however, local communities did not show any particular trend. Overall, our findings suggest that flooded forests, characterized by stressful environments, impose limits to species occurrence, whereas terra firme forests, more environmentally heterogeneous, are likely to provide a wider range of ecological conditions and therefore to bear higher diversity. Thus, Amazonia should be considered as a mosaic of landscape units, where the strength of habitat association depends upon their environmental properties.
Testing Phylogenetic Hypotheses of the Subgenera of the Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)  [PDF]
Jesse W. Breinholt, Megan L. Porter, Keith A. Crandall
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046105
Abstract: Background The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression. Methodology/Principal Findings We use three mitochondrial and one nuclear gene regions to estimate the phylogenetic relationships for species within the genus Cambarus and test evolutionary hypotheses of relationships and associated morphological and biogeographical hypotheses. Our resulting phylogeny indicates that the genus Cambarus is polyphyletic, however we fail to reject the monophyly of Cambarus with a topology test. The majority of the Cambarus subgenera are rejected as monophyletic, suggesting the morphological characters used to define those taxa are subject to convergent evolution. While we found incongruence between taxonomy and estimated phylogenetic relationships, a multiple model regression analysis indicates that taxonomy had more explanatory power of genetic relationships than either habitat or geographic distance. Conclusions We find convergent evolution has impacted the morphological features used to delimit Cambarus subgenera. Studies of the crayfish genus Orconectes have shown gonopod morphology used to delimit subgenera is also affected by convergent evolution. This suggests that morphological diagnoses based on traditional crayfish taxonomy might be confounded by convergent evolution across the cambarids and has little utility in diagnosing relationships or defining natural groups. We further suggest that convergent morphological evolution appears to be a common occurrence in invertebrates suggesting the need for careful phylogenetically based interpretations of morphological evolution in invertebrate systematics.
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