Related papers: Late-replicating CNVs as a source of new genes
Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
Commonly recognized evolutionarily relevant effects of sexual reproduction include increased diversity, accelerated adaptation, and constrained accumulation of deleterious mutations, along with a secondary effect of species genotype…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
Consider a branching process with a homogeneous reproduction law. Sampling a single cell uniformly from the population at a time $T > 0$ and looking along the sampled cell's ancestral lineage, we find that the reproduction law is…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
We present a genetic algorithm which is distributed in two novel ways: along genotype and temporal axes. Our algorithm first distributes, for every member of the population, a subset of the genotype to each network node, rather than a…
Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
In both natural and artificial studies, evolution is often seen as synonymous to natural selection. Individuals evolve under pressures set by environments that are either reset or do not carry over significant changes from previous…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the…