Related papers: Comparable system-level organization of Archaea an…

Evolution is often understood through genetic mutations driving changes in an organism's fitness, but there is potential to extend this understanding beyond the genetic code. We propose that natural products - complex molecules central to…

The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this…

Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…

Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in…

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…

A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…

Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…

The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…

Hierarchical organization -- the recursive composition of sub-modules -- is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations…

Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…

Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here…

Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…

Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…

The species-area relationship is one of the central generalizations in ecology however its origin has remained a puzzle. Since ecosystems are understood as energy transduction systems, the regularities in species richness are considered to…

Bacteria and their bacteriophages are the most abundant, widespread and diverse groups of biological entities on the planet. In an attempt to understand how the interactions between bacteria, virulent phages and temperate phages might…

Bioconvection, a phenomenon arising from the collective motion of motile microorganisms, plays a crucial role in shaping microbial distributions, fluid dynamics, and bloom formation in aquatic environments. While extensive research has…

The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c)…