Section edited by Laura Kubatko and Arne Traulsen
This section considers studies in mathematical modeling of evolutionary processes and research into theoretical areas.
Section edited by Laura Kubatko and Arne Traulsen
This section considers studies in mathematical modeling of evolutionary processes and research into theoretical areas.
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The glucose effect is a well known phenomenon whereby cells, when presented with two different nutrients, show a diauxic growth pattern, i.e. an episode of exponential growth followed by a lag phase of reduced...
Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the s...
The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master...
The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have rec...
The value of a continuous character evolving on a phylogenetic tree is commonly modelled as the location of a particle moving under one-dimensional Brownian motion with constant rate. The Brownian motion model...
RNA or RNA-like polymers are the most likely candidates for having played the lead roles on the stage of the origin of life. RNA is known to feature two of the three essential functions of living entities (met...
Brain signaling requires energy. The cost of maintaining and supporting energetically demanding neurons is the key constraint on brain size. The dramatic increase in brain size among mammals and birds cannot b...
Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is known that thousands of isoforms bind themselves through specific homophilic interact...
The relationship between allopolyploidy and plant virus resistance is poorly understood. To determine the relationship of plant evolutionary history and basal virus resistance, a panel of Nicotiana species from d...
Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is kno...
Some species of water frogs originated from hybridization between different species. Such hybrid populations have a particular reproduction system called hybridogenesis. In this paper we consider the two species
Transgenic constructs intended to be stably established at high frequencies in wild populations have been demonstrated to “drive” from low frequencies in experimental insect populations. Linking such populatio...
Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Access...
As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many metho...
Host-parasite coevolution is generally believed to follow Red Queen dynamics consisting of ongoing oscillations in the frequencies of interacting host and parasite alleles. This belief is founded on previous t...
A major goal of molecular evolution is to determine how natural selection has shaped the evolution of a gene. One approach taken by methods such as K A /K ...
We wish to understand how sex and recombination affect endogenous retroviral insertion and deletion. While theory suggests that the risk of ectopic recombination will limit the accumulation of repetitive DNA i...
It is often assumed that evolution takes place on very large timescales. Countering this assumption, rapid evolutionary dynamics are increasingly documented in biological systems, e.g. in the context of predat...
Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded th...
Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted...
The coexistence of macromolecular replicators and thus the stability of presumed prebiotic replicator communities have been shown to critically depend on spatially constrained catalytic cooperation among RNA-l...
Sex in higher diploids carries a two-fold cost of males that should reduce its fitness relative to cloning, and result in its extinction. Instead, sex is widespread and clonal species face early obsolescence. ...
Niche construction has received increasing attention in recent years as a vital force in evolution and examples of niche construction have been identified in a wide variety of taxa, but viruses are conspicuous...
Dispersal is a major factor in ecological and evolutionary dynamics. Although empirical evidence shows that the tendency to disperse varies among individuals in many organisms, the evolution of dispersal patte...
Cryptic genetic variation (CGV) is considered to facilitate phenotypic evolution by producing visible variations in response to changes in the internal and/or external environment. Several mechanisms enabling ...
Most eukaryotic genes are interrupted by spliceosomal introns. The evolution of exon-intron structure remains mysterious despite rapid advance in genome sequencing technique. In this work, a novel approach is ...
The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to inv...
The multispecies coalescent model has become popular in recent years as a framework to infer a species phylogeny from multilocus genetic data collected from multiple individuals. The model assumes that speciat...
There has been a considerable increase in studies investigating rates of diversification and character evolution, with one of the promising techniques being the BiSSE method (binary state speciation and extinc...
Bacteriophage (viruses that infect bacteria) are of key importance in ecological processes at scales from biofilms to biogeochemical cycles. Close interaction can lead to antagonistic coevolution of phage and ...
Indirect reciprocity is a mechanism for cooperation in social dilemma situations. In indirect reciprocity, an individual is motivated to help another to acquire a good reputation and receive help from others a...
Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge ...
Changes in gene regulatory networks drive the evolution of phenotypic diversity both within and between species. Rewiring of transcriptional networks is achieved either by changes to transcription factor bindi...
Sex-ratio distorting parasites are of interest due to their effects upon host population dynamics and their potential to influence the evolution of host sex determination systems. In theory, the ability to dis...
Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evol...
The human mating system is characterized by bi-parental care and faithful monogamy is highly valued in most cultures. Marriage has evolved as a social institution and punishment for extra pair mating (EPM) or ...
Many animals live in groups. One proposed reason is that grouping allows cooperative food finding. Group foraging models suggest that grouping could increase food finding rates, but that such group processes c...
The emergence of organismal complexity has been a difficult subject for researchers because it is not readily amenable to investigation by experimental approaches. Complexity has a myriad of untested definitio...
Homing endonucleases (HEases) are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases h...
Genomic and pathology analysis has revealed enormous diversity in genes involved in disease, including those encoding host resistance and parasite effectors (also known in plant pathology as avirulence genes)....
Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades....
A well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility...
The evolutionary success of Wolbachia bacteria, infections of which are widespread in invertebrates, is largely attributed to an ability to manipulate host reproduction without imposing substantial fitness costs....
The ability to predict the function and structure of complex molecular mechanisms underlying cellular behaviour is one of the main aims of systems biology. To achieve it, we need to understand the evolutionary...
Anopheles gambiae mates in flight at particular mating sites over specific landmarks known as swarm markers. The swarms are composed of males; females typically approach a swarm, and leave in copula. This mating ...
One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth sca...
Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a...
Hepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular ...
Phylogenetic analyses strongly associate nonsocial ancestors of cooperatively-breeding or eusocial species with monogamy. Because monogamy creates high-relatedness family groups, kin selection has been conclud...
Characterization of robustness and plasticity of phenotypes is a basic issue in evolutionary and developmental biology. The robustness and plasticity are concerned with changeability of a biological system aga...
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