In this first systematic book-length examination of the organism-environment relationship in the life sciences, Alejandro Fábregas-Tejeda addresses a crucia...

Interview with Cassandra Extavour, who studies the evolution of the genetic mechanisms employed during early animal embryogenesis to specify cell fate, development, and differentiation at Harvard Univ...

Rubisco is the main gateway through which inorganic carbon enters the biosphere, catalyzing the vast majority of carbon fixation on Earth. This piv...

AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

The department of Biology is a large, unified department with strong undergraduate degrees, nationally-ranked graduate programs, and world-class research spanning the breadth of biological questions a...

Genomic and evolutionary research has transformed our understanding of how biological interactions shape life’s diversity. From symbiosis and host–pathogen relationships to competition, cooperation, …

Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

Diatoms dominate the oceans, yet sexual reproduction - key to bloom dynamics and species evolvability - is rarely observed. Using a lab-to-field approach, this study presents conserved markers applica...

It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

Selecting an appropriate statistical method is a challenge frequently encountered by applied researchers, especially if assumptions for classical, parametric approaches are violated. To provide some guidelines and support, we compared classical hypothesis tests with their typical distributional assumptions of normality and homoskedasticity with common and easily accessible alternative inference methods (HC3, HC4, and six bootstrap methods) in the framework of ordinary least squares (OLS) regression. The method’s performance was assessed for four different regression models with varying levels of non-normality and heteroskedasticity of errors, and for five different sample sizes ranging from 25 to 500 cases. For each scenario, 10,000 samples of observations were generated. Type I error and coverage rates, power, and standard error bias were examined to assess the methods’ performance. No method considered here performed satisfactorily on all accounts. Using HC3 or HC4 standard errors, or a wild bootstrap procedure with percentile confidence intervals, could yield reliable results in many, but not all, scenarios. We suppose that, in the case of assumption violations, researchers might refer to a method that performed best in a scenario most similar to their data situation. To aid the selection of an appropriate method, we provide tables comparing relative performances in all considered scenarios.

Marker genes used in microbial phylogenomics are limited to fixed gene sets selected from complete genomes. TMarSel is a flexible yet robust method for selecting any number of markers from genomes or ...