Biology subjects

Azevedo, R. B. R.

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

7 recordsLinked to original sources

bioRxiv2022

Genetic drift promotes and recombination hinders speciation on a holey fitness landscape

Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation. Author summaryAs geographically isolated populations evolve, genetic incompatibilities accumulate between them. Eventually, these incompatibilities may cause the populations to become different species. What determines how quickly species are formed in this way remains unclear. We investigate this question using computer simulations and find that genetic incompatibilities accumulate more slowly among populations with individuals that are robust to genetic perturbations. We identify two factors that influence the accumulation rate via their effects on genetic robustness: the size of the populations and how much recombination takes place in them. Small populations with rare recombination accumulate incompatibilities more quickly.

evolutionary biology↗

bioRxiv2021

A Branching Process Model of Evolutionary Rescue

Evolutionary rescue is the process whereby a declining population may start growing again, thus avoiding extinction, via an increase in the frequency of fitter genotypes. These genotypes may either already be present in the population in small numbers, or arise by mutation as the population declines. We present a simple two-type discrete-time branching process model and use it to obtain results such as the probability of rescue, the shape of the population growth curve of a rescued population, and the time until the first rescuing mutation occurs. Comparisons are made to existing results in the literature in cases where both the mutation rate and the selective advantage of the beneficial mutations are small.

evolutionary biology↗

bioRxiv2021

Sea Turtle Facial Recognition Using Map Graphs of Scales

O_LIIndividual identification of sea turtles is important to study their biology and aide in conservation efforts. Traditional methods for identifying sea turtles that rely on physical or GPS tags can be expensive, and difficult to implement. Alternatively, the scale structure on the side of a turtles head has been shown to be specific to the individual and stable over its lifetime, and therefore can be used as the individuals "fingerprint". C_LIO_LIHere we propose a novel facial recognition method where an image of a sea turtle is converted into a graph (network) with nodes representing scales, and edges connecting two scales that share a border. The topology of the graph is used to differentiate species. C_LIO_LIWe additionally develop a robust metric to compare turtles based on a correspondence between nodes generated by a coherent point drift algorithm and computing a graph edit distance to identify individual turtles with over 94% accuracy. C_LIO_LIBy representing the special and topological features of sea turtle scales as a graph, we perform more accurate individual identification which is robust under different imaging conditions and may be adapted for a wider number of species. C_LI

ecology↗

bioRxiv2019

Amitosis confers benefits of sex in the absence of sex to Tetrahymena

Sex appears to be the most successful reproductive strategy in eukaryotes despite its many costs. While a complete explanation for sexs success remains elusive, several evolutionary benefits of sex have been identified. It is predicted that, by forgoing these benefits, asexual lineages are evolutionary dead-ends. Consistent with this prediction, many asexual lineages show signs of accelerated accumulation of deleterious mutations compared to their sexual relatives. Despite these low expectations, some asexual eukaryotic lineages appear to be successful, including the ciliate Tetrahymena. Here, we show that the mechanism of somatic nuclear division in Tetrahymena, known as amitosis, provides benefits similar to sex, allowing for the long-term success of asexual lineages. We found that, when compared to mitosis, amitosis with chromosome copy number control reduces mutation load deterministically, slows the accumulation of deleterious mutations under genetic drift, and accelerates adaptation. These benefits arise because, like sex, amitosis can generate substantial genetic variation in fitness among (asexual) progeny. Our results indicate that the ability of Tetrahymena to persist in the absence of sex may depend on non-sexual genetic mechanisms conferring benefits typically provided by sex, as has been found in other asexual lineages.

evolutionary biology↗

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↗