Biology subjects

Azevedo, R. B. R.

Publications and source records attributed to Azevedo, R. B. R..

3 recordsLinked to original sources

bioRxiv2018

Muller’s Ratchet in Asexual Populations Doomed to Extinction

Asexual populations are expected to accumulate deleterious mutations through a process known as Mullers ratchet. Lynch and colleagues proposed that the ratchet eventually results in a vicious cycle of mutation accumulation and population decline that drives populations to extinction. They called this phenomenon mutational meltdown. Here, we analyze mutational meltdown using a multi-type branching process model where, in the presence of mutation, populations are doomed to extinction. We analyse the change in size and composition of the population and the time of extinction under this model.

evolutionary biology↗

bioRxiv2017

Correlated selection on amino acid deletion and replacement in mammalian protein sequences

A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is a sign of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. Oddly, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8,595 protein coding-region sequences from 9 mammalian species to examine the relationship between deletion rate and dN/dS. We found significant positive correlations at both the level of sites and genes. We compared our data against controls consisting of simulated coding sequences evolving along identical phylogenetic trees, where the correlation is not included in the model a priori. A much weaker correlation was found in the corresponding simulated sequences, which is probably caused by alignment errors. In the real data, the correlations cannot be explained by alignment errors. Separate investigations on nonsynonymous (dN) and synonymous (dS) substitution rates indicate that the correlation is most likely due to a similarity in patterns of selection rather than mutation rates.

evolutionary biology↗

bioRxiv2017

The Evolution Of Small RNA-Mediated Silencing Of An Invading Transposable Element

Transposable elements (TEs) are genomic parasites that impose fitness costs on their hosts by producing deleterious mutations and disrupting gametogenesis. Host genomes avoid these costs by regulating TE activity, particularly in germline cells where new insertions are heritable and TEs are exceptionally active. However, the capacity of different TE-associated fitness costs to select for repression in the host, and the role of selection in the evolution of TE regulation more generally, remain controversial. In this study, we use forward, individual-based simulations to examine the evolution of small-RNA-mediated TE regulation, a conserved mechanism for TE repression that is employed by both prokaryotes and eukaryotes. To design and parameterize a biologically realistic model, we drew on an extensive survey of empirical studies of the transposition and regulation of P-element DNA transposons in Drosophila melanogaster. We observed that even under conservative assumptions, where small-RNA-mediated regulation reduces transposition only, repression evolves rapidly and adaptively after the genome is invaded by a new TE. We further show that the spread of repressor alleles is greatly enhanced by two additional TE-imposed fitness costs: dysgenic sterility and ectopic recombination. Finally, we demonstrate that the mutation rate to repression (i.e., the size of the mutational target) is a critical parameter that influences both the evolutionary trajectory of host repression and the associated proliferation of TEs after invasion. Our findings suggest that adaptive evolution of TE regulation may be stronger and more prevalent than previously appreciated, and provide a framework for evaluating empirical data.

evolutionary biology↗