Related papers: Expected Anomalies in the Fossil Record
The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification…
Delayed processes are ubiquitous in biological systems and are often characterized by delay differential equations (DDEs) and their extension to include stochastic effects. DDEs do not explicitly incorporate intermediate states associated…
We consider the adiabatic regime of two parameters evolution semigroups generated by linear operators that are analytic in time and satisfy the following gap condition for all times: the spectrum of the generator consists in finitely many…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
In 1957, Lindley published "A statistical paradox" in Biometrika, revealing a fundamental conflict between frequentist and Bayesian inference as sample size approaches infinity. We present a new paradox of a different kind: a conflict…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Joint species distribution models are popular in ecology for modeling covariate effects on species occurrence, while characterizing cross-species dependence. Data consist of multivariate binary indicators of the occurrences of different…
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"…
We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of…
In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the…
The question of what determines genetic diversity both between and within species has long remained unsolved by the modern evolutionary theory (MET). However, it has not deterred researchers from producing interpretations of genetic…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Empirical observations in marine ecosystems have suggested a balance of biological and advection time scales as a possible explanation of species coexistence. To characterise this scenario, we measure the time to fixation in neutrally…
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the…
The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species' reaction to climate change. One of the frequently observed features at range…
We consider branching process evolving in i.i.d. random environment. It is assumed that the process is intermediately subcritical. We investigate the initial stage of the evolution of the process given its survival for a long time.
In making models for biological systems one expects to grasp the biology and be able to use ones intuition to predict the outcome. This paper is about the discrepancy between what is expected and what is the outcome of the analysis of the…
We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors…