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A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom‐up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying...
On the origin and structure of haplotype blocksNARA Subscribed
The term “haplotype block” is commonly used in the developing field of haplotype‐based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochastici...
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severityNARA Subscribed
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the pr...
Summary A caryochloris marina is a symbiotic species of cyanobacteria that is capable of utilizing far‐red light. We report the characterization of the phages A ‐ HIS 1 and A ‐ HIS 2, capable of infecting A caryochloris . Morphological characterization of these phages places them in the family S iphoviridae . However, molecular characterization reveals that they do not show genetic similarity with any known siphoviruses. While...
Summary A bacterium in the genus Halomonas that grew on dimethylsulfoniopropionate (DMSP) or acrylate as sole carbon sources and that liberated the climate‐changing gas dimethyl sulfide in media containing DMSP was obtained from the phylloplane of the macroalga Ulva. We identified a cluster that contains genes specifically involved in DMSP catabolism ( dddD, dddT ) or in degrading acrylate ( acuN , acuK ) or that are required...