Ecological and Evolutionary Science
Research Article | Ecological and Evolutionary ScienceEnvironmental Viral Genomes Shed New Light on Virus-Host Interactions in the OceanViruses are diverse and play significant ecological roles in marine ecosystems. However, our knowledge of genome-level diversity in viruses is biased toward those isolated from few culturable hosts. Here, we determined 1,352 nonredundant complete viral genomes from marine environments. Lifting the uncertainty that clouds short incomplete sequences, whole-genome-wide analysis suggests that these environmental genomes represent hundreds...
Research Article | Ecological and Evolutionary ScienceUnexplored Archaeal Diversity in the Great Ape Gut MicrobiomeOur findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast...
Research Article | Ecological and Evolutionary ScienceGlobal Population Genetic Analysis of Aspergillus fumigatusThe genetic diversity and geographic structure of the human fungal pathogen A. fumigatus have been the subject of many studies. However, most previous studies had relatively limited sample ranges and sizes and/or used genetic markers with low-level polymorphisms. In this paper, we characterize a global collection of strains of...
Research Article | Ecological and Evolutionary ScienceEffects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile VirusesMosquito microbiota provide important physiological and ecological attributes to mosquitoes, including an impact on their susceptibility to pathogens, fitness, and sensitivity to mosquito control agents. Culex nigripalpus mosquito populations transmit various pathogens, including the Saint Louis and West Nile viruses, and proliferate in nutrient-rich environments,...
Editor's Pick Research Article | Ecological and Evolutionary ScienceDe Novo Generation of a Unique Cervid Prion Strain Using Protein Misfolding Cyclic AmplificationCWD is the only known TSE that affects free-ranging wildlife, specifically cervids such as elk, deer, moose, caribou, and reindeer. CWD has become endemic in both free-ranging and captive herds in North America, South Korea, and, most recently, northern Europe. The prion research community continues to debate the origins of CWD. Original foci of CWD emergence in Colorado and Wyoming coincident with the sheep TSE scrapie suggest that...
Research Article | Ecological and Evolutionary ScienceHost Range Restriction of Insect-Specific Flaviviruses Occurs at Several Levels of the Viral Life CycleMost viruses of the genus Flavivirus, e.g., YFV and dengue virus, are mosquito borne and transmitted to vertebrates during blood feeding of mosquitoes. Within the last decade, an increasing number of viruses with a host range exclusively restricted to insects in close relationship to the vertebrate-pathogenic flaviviruses were discovered in mosquitoes. To identify barriers that could block the arboviral vertebrate tropism, we...
Research Article | Ecological and Evolutionary ScienceGut Microbiome of the Canadian Arctic InuitNon-Western populations have been shown to have distinct gut microbial communities shaped by traditional diets. The hitherto-uncharacterized microbiome of the Inuit may help us to better understand health risks specific to this population such as diabetes and obesity, which increase in prevalence as many Inuit transition to a Western diet. Here we show that even Inuit consuming a mostly traditional diet have a broadly Western-like...
Research Article | Ecological and Evolutionary ScienceSpecies in the Cryptococcus gattii Complex Differ in Capsule and Cell Size following Growth under Capsule-Inducing ConditionsInfections with the fungal pathogen Cryptococcus gattii have been increasing in recent years. Recently, four different species have been described within C. gattii, which correspond to four previously known molecular genotypes (VGI to VGIV). Examining traits related to infection and disease is...
Research Article | Ecological and Evolutionary ScienceA Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A VirusesA fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with...
Resource Report | Ecological and Evolutionary ScienceDNA from Dust: Comparative Genomics of Large DNA Viruses in Field Surveillance SamplesDespite both clinical and laboratory data that show increased virulence in field isolates of MDV-1 over the last half century, we do not yet understand the genetic basis of its pathogenicity. Our knowledge of genome-wide variation between strains of this virus comes exclusively from isolates that have been cultured in the laboratory. MDV-1 isolates tend to lose virulence during repeated cycles of replication in the laboratory, raising...