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Dmitri A Petrov

Publications and source records attributed to Dmitri A Petrov.

2 recordsLinked to original sources

Ploidy and the Predictability of Evolution in Fishers Geometric Model

Predicting adaptive evolutionary trajectories is a primary goal of evolutionary biology. One can differentiate between forward and backward predictability, where forward predictability measures the likelihood of the same adaptive trajectory occurring in independent evolutions and backward predictability measures the likelihood of a particular adaptive path given the knowledge of starting and final states. Recent studies have attempted to measure both forward and backward predictability using experimental evolution in asexual haploid microorganisms. Similar experiments in diploid organisms have not been conducted. Here we simulate adaptive walks using Fisher's Geometric Model in haploids and diploids and find that adaptive walks in diploids are less forward- and more backward-predictable than adaptive walks in haploids. We argue that the difference is due to the ability of diploids in our simulations to generate transiently stable polymorphisms and to allow adaptive mutations of larger phenotypic effect. As stable polymorphisms can be generated in both haploid and diploid natural populations through a number of mechanisms, we argue that inferences based on experiments in which adaptive walks proceed through succession of monomorphic states might miss many of the key features of adaptation.

q-bio.PE↗

Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects

This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since the mammalian radiation, yielding a number of results that would have been difficult to obtain using the more conventional comparative method of analysis. This analysis revealed substantial and consistent variability of rates of substitution, with the variability ranging up to 2-fold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the reverse rates suggesting that much of that variation is due to differences in mutation rates rather than in the probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all types of substitution we observe substantially more hotspots than coldspots, with hotspots showing substantial clustering over tens of Mbp's. Our analysis revealed that GC-content of surrounding sequences is the best predictor of the rates of substitution. The pattern of substitution appears very different near telomeres compared to the rest of the genome and cannot be explained by the genome-wide correlations of the substitution rates with GC content or exon density. The telomere pattern of substitution is consistent with natural selection or biased gene conversion acting to increase the GC-content of the sequences that are within 10-15 Mbp away from the telomere.

q-bio.GN↗