Related papers: The driving force behind genomic diversity
Evolution depends on the fitness of organisms, the expected rate of reproducing. Directly getting offspring is the most basic form of fitness, but fitness can also be increased indirectly by helping genetically related individuals (such as…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
Developmental bias plays a major role in phenotypic evolution. Some researchers have argued that phenotypes, regulated by development, can only evolve along restricted trajectory under certain scenarios, such as the case for mammalian molar…
Evolution by Natural Selection is a process by which progeny inherit some properties from their progenitors with small variation. These properties are subject to Natural Selection and are called adaptive traits and carriers of the latter…
One essential ingredient of evolutionary theory is the concept of fitness as a measure for a species' success in its living conditions. Here, we quantify the effect of environmental fluctuations onto fitness by analytical calculations on a…
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…
Current analyses of genomes from numerous species show that the diversity of organism's functional and behavioral characters is not proportional to the number of genes that encode the organism. We investigate the hypothesis that the…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
A variety of genome transformations can occur as a microbial population adapts to a large environmental change. In particular, genomic surveys indicate that, following the transition to an obligate, host-dependent symbiont, the density of…
The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
It is widely acknowledged that there is a diversity problem in genomics stemming from the vast underrepresentation of non-European genetic ancestry populations. While many challenges exist to address this gap, a major complicating factor is…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…
Explaining biodiversity is a central focus in theoretical ecology. A significant obstacle arises from the Competitive Exclusion Principle (CEP), which states that two species competing for the same type of resources cannot coexist at…
A central biological question is how natural organisms are so evolvable (capable of quickly adapting to new environments). A key driver of evolvability is the widespread modularity of biological networks--their organization as functional,…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of…