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Ecological and Evolutionary Science

  • Open Access
    A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera <em>Aspergillus</em> and <em>Penicillium</em>
    Research Article | Ecological and Evolutionary Science
    A 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...

    Jacob L. Steenwyk, Xing-Xing Shen, Abigail L. Lind, Gustavo H. Goldman, Antonis Rokas
  • Open Access
    Early Cyanobacteria and the Innovation of Microbial Sunscreens
    Commentary | Ecological and Evolutionary Science
    Early 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.

    Patrick M. Shih
  • Open Access
    Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element
    Research Article | Ecological and Evolutionary Science
    Transient 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...

    François Delavat, Roxane Moritz, Jan Roelof van der Meer
  • Open Access
    High-Throughput Analysis of Gene Function in the Bacterial Predator <span class="named-content genus-species" id="named-content-1">Bdellovibrio bacteriovorus</span>
    Research Article | Ecological and Evolutionary Science
    High-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,...

    Miles C. Duncan, Rebecca K. Gillette, Micah A. Maglasang, Elizabeth A. Corn, Albert K. Tai, David W. Lazinski, Robert M. Q. Shanks, Daniel E. Kadouri, Andrew Camilli
  • Open Access
    Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to <em>Cryptococcus</em> Pathogens
    Research Article | Ecological and Evolutionary Science
    Genetic 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...

    Andrew Ryan Passer, Marco A. Coelho, Robert Blake Billmyre, Minou Nowrousian, Moritz Mittelbach, Andrey M. Yurkov, Anna Floyd Averette, Christina A. Cuomo, Sheng Sun, Joseph Heitman
  • Open Access
    <em>De Novo</em> Emergence of Peptides That Confer Antibiotic Resistance
    Editor's Pick Research Article | Ecological and Evolutionary Science
    De 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...

    Michael Knopp, Jonina S. Gudmundsdottir, Tobias Nilsson, Finja König, Omar Warsi, Fredrika Rajer, Pia Ädelroth, Dan I. Andersson
  • Open Access
    Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry
    Research Article | Ecological and Evolutionary Science
    Codon 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...

    J. L. López, M. J. Lozano, A. Lagares, M. L. Fabre, W. O. Draghi, M. F. Del Papa, M. Pistorio, A. Becker, D. Wibberg, A. Schlüter, A. Pühler, J. Blom, A. Goesmann, A. Lagares
  • Open Access
    Timing the Evolutionary Advent of Cyanobacteria and the Later Great Oxidation Event Using Gene Phylogenies of a Sunscreen
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Timing 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...

    Ferran Garcia-Pichel, Jonathan Lombard, Tanya Soule, Sean Dunaj, Steven H. Wu, Martin F. Wojciechowski
  • Open Access
    Nonrandom Distribution of Azole Resistance across the Global Population of <span class="named-content genus-species" id="named-content-1">Aspergillus fumigatus</span>
    Research Article | Ecological and Evolutionary Science
    Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus

    Azole drug resistance in the human-pathogenic fungus Aspergillus fumigatus continues to emerge, potentially leading to untreatable aspergillosis in immunosuppressed hosts. Two dominant, environmentally associated resistance mechanisms, which are thought to have evolved through selection by the agricultural application of azole fungicides, are now distributed globally...

    Thomas R. Sewell, Jianing Zhu, Johanna Rhodes, Ferry Hagen, Jacques F. Meis, Matthew C. Fisher, Thibaut Jombart
  • Open Access
    Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Morphological Plasticity in a Sulfur-Oxidizing Marine Bacterium from the SUP05 Clade Enhances Dark Carbon Fixation

    Identifying shifts in microbial metabolism across redox gradients will improve efforts to model marine oxygen minimum zone (OMZ) ecosystems. Here, we show that aerobic morphology and metabolism increase cell size, sulfur storage capacity, and carbon fixation rates in “Ca. Thioglobus autotrophicus,” a chemosynthetic bacterium from the SUP05 clade that crosses oxic-anoxic boundaries.

    Vega Shah, Xiaowei Zhao, Rachel A. Lundeen, Anitra E. Ingalls, Daniela Nicastro, Robert M. Morris

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