The fossil record over the last half a billion years shows biodiversity as a zigzagging pattern of species births and extinctions. For decades scientist have attempted to answer the question: Which rules supreme – life or the environment? To explain this macroevolution, scientists have used two opposing theories: the Red Queen versus the Court Jester theory, inspired by the story Alice in Wonderland. New research by McGill University and Vilnius University puts these two theories to the test.

The latest Virtual Issue from Genome Biology and Evolution highlights articles that provide new insight into the deep evolutionary relationships among extant organisms and the origin of eukaryotes from among archaeal lineages. All cellular organisms are descended from a shared ancestor, often referred to as LUCA—the last universal common ancestor. Relationships among these organisms can be depicted by an evolutionary network known as the “tree of life”, which for the past few decades has included three major forms of life—bacteria, archaea, and eukaryotes. Evolutionary biologists have long sought to understand the placement of LUCA within this framework, as well as the origin of LECA—the last eukaryotic common ancestor. Unfortunately, accurately inferring relationships among microbial lineages presents a major challenge due to the vast evolutionary distances involved, as well as the frequent lateral transfer of genetic material between lineages. Recently, however, new data and methods have resulted in profound changes to our understanding of the tree of life.

Researchers from Karolinska Institutet identify an epigenetic regulator controlling the very first cell type specification in the human embryo. The study is published in Nature Cell Biology.

Industry produces acetone and isopropanol using processes that release carbon dioxide and other greenhouse gases. Researchers have now developed a new fermentation process that efficiently converts waste carbon oxide gases into acetone and isopropanol. This use of engineered bacteria advances progress on “carbon-negative” biomanufacturing for more sustainable industrial production and reduced greenhouse gas emissions.

A research team at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Massachusetts Institute of Technology (MIT), using a synthetic biology approach, has developed an engineered live biotherapeutic product (eLBP) that, when given together with commonly used antibiotics known as beta-lactams (which includes the well-known antibiotic penicillin), protects the gut microbiome from dysbiosis. The study is published in Nature Biomedical Engineering.

Machine-learning algorithms for protein structure prediction can now generate models directly from sequences. However, photosynthetic assemblies represent a challenge due to additional levels of complexity arising from their multi-protein nature and presence of cofactors.