Ecological and Evolutionary Science
- Letter to the Editor | Ecological and Evolutionary ScienceNew Phylogenetic Grouping of Positive-Sense RNA Viruses Is Concordant with Replication Complex Morphology
- Research Article | Ecological and Evolutionary ScienceLinking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter
Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a...
- Research Article | Ecological and Evolutionary ScienceA Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
Understanding the evolution of traits across technologically and medically significant fungi requires a robust phylogeny. Even though species in the Aspergillus and Penicillium genera (family Aspergillaceae, class Eurotiomycetes) are some of the most significant technologically and medically relevant fungi, we still lack a genome-scale phylogeny of...
- Commentary | Ecological and Evolutionary ScienceEarly Cyanobacteria and the Innovation of Microbial Sunscreens
Metabolism drives life; thus, understanding how and when various branches of metabolism evolved provides a critical piece to understanding how life has integrated itself into the geochemical cycles of our planet over billions of years.
- Research Article | Ecological and Evolutionary ScienceTransient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element
Bacterial evolution is driven to a large extent by horizontal gene transfer (HGT)—the processes that distribute genetic material between species rather than by vertical descent. The different elements and processes mediating HGT have been characterized in great molecular detail. In contrast, very little is known on adaptive features selecting HGT evolvability and fitness optimization. By studying the molecular behavior of an integrated...
- Research Article | Ecological and Evolutionary ScienceHigh-Throughput Analysis of Gene Function in the Bacterial Predator Bdellovibrio bacteriovorus
Bdellovibrio bacteriovorus is a predatory bacterium that can kill a wide range of Gram-negative bacteria, including many human pathogens. Given the global rise of antibiotic resistance and dearth of new antibiotics discovered in the past 30 years, this predator has potential as an alternative to traditional antibiotics. For many years,...
- Research Article | Ecological and Evolutionary ScienceGenetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens
The evolutionary drivers of speciation are critical to our understanding of how new pathogens arise from nonpathogenic lineages and adapt to new environments. Here we focus on the Cryptococcus amylolentus species complex, a nonpathogenic fungal lineage closely related to the human-pathogenic Cryptococcus...
- Editor's Pick Research Article | Ecological and Evolutionary ScienceDe Novo Emergence of Peptides That Confer Antibiotic Resistance
De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel...
- Research Article | Ecological and Evolutionary ScienceCodon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry
Bacterial genomes usually include many thousands of genes which are expressed with diverse spatial-temporal patterns and intensities. A well-known evidence is that highly expressed genes, such as the ribosomal and other translation-related proteins (RTRPs), have accommodated their codon usage to optimize translation efficiency and accuracy. Using a bioinformatic approach, we identify core-genes sets with different ancestries, and...
- Editor's Pick Research Article | Ecological and Evolutionary ScienceTiming the Evolutionary Advent of Cyanobacteria and the Later Great Oxidation Event Using Gene Phylogenies of a Sunscreen
The advent of cyanobacteria, with their invention of oxygenic photosynthesis, and the Great Oxidation Event are arguably among the most important events in the evolutionary history of life on Earth. Oxygen is a significant toxicant to all life, but its accumulation in the atmosphere also enabled the successful development and proliferation of many aerobic organisms, especially metazoans. The currently favored dating of the Great...