Evolving Darwinian Evolution: Mutation Preselection Theory and the Selective Advantage of a High Male to Female Mutation Rate Ratio: Testing Mutations Before Spending a Life

2021 ◽  
Author(s):  
Alex Bäcker
Keyword(s):  
Mutation Rate ◽  
Rate Ratio ◽  
Selective Advantage ◽  
Darwinian Evolution ◽  
Male To Female

scholarly journals The Causes of Synonymous Rate Variation in the Rodent Genome: Can Substitution Rates Be Used to Estimate the Sex Bias in Mutation Rate?

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 661-673 ◽  
Author(s):  
Nick G C Smith ◽  
Laurence D Hurst
Keyword(s):  
Mutation Rate ◽  
Rate Ratio ◽  
Synonymous Substitution ◽  
Sex Bias ◽  
Imprinted Genes ◽  
Rate Variation ◽  
Substitution Rates ◽  
Synonymous Substitution Rates ◽  
Male To Female ◽  
Different Parts

Abstract Miyata et al. have suggested that the male-to-female mutation rate ratio (α) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of α. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of α are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of α, obtained using this method, need to be treated with caution.

scholarly journals Meiotic recombination counteracts male-biased mutation (male-driven evolution)

2016 ◽  
Vol 283 (1823) ◽  
pp. 20152691 ◽  
Author(s):  
Shuuji Mawaribuchi ◽  
Michihiko Ito ◽  
Mitsuaki Ogata ◽  
Hiroki Oota ◽  
Takafumi Katsumura ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Meiotic Recombination ◽  
Rate Ratio ◽  
Molecular Evidence ◽  
Nucleotide Substitution Rate ◽  
Type Group ◽  
Replication Errors ◽  
Two Factors ◽  
Dna Replication Errors ◽  
Male To Female

Meiotic recombination is believed to produce greater genetic variation despite the fact that deoxyribonucleic acid (DNA)-replication errors are a major source of mutations. In some vertebrates, mutation rates are higher in males than in females, which developed the theory of male-driven evolution (male-biased mutation). However, there is little molecular evidence regarding the relationships between meiotic recombination and male-biased mutation. Here we tested the theory using the frog Rana rugosa, which has both XX/XY- and ZZ/ZW-type sex-determining systems within the species. The male-to-female mutation-rate ratio ( α ) was calculated from homologous sequences on the X/Y or Z/W sex chromosomes, which supported male-driven evolution. Surprisingly, each α value was notably higher in the XX/XY-type group than in the ZZ/ZW-type group, although α should have similar values within a species. Interestingly, meiotic recombination between homologous chromosomes did not occur except at terminal regions in males of this species. Then, by subdividing α into two new factors, a replication-based male-to-female mutation-rate ratio ( β ) and a meiotic recombination-based XX-to-XY/ZZ-to-ZW mutation-rate ratio ( γ ), we constructed a formula describing the relationship among a nucleotide-substitution rate and the two factors, β and γ . Intriguingly, the β - and γ -values were larger and smaller than 1, respectively, indicating that meiotic recombination might reduce male-biased mutations.

Potential problems in estimating the male-to-female mutation rate ratio from DNA sequence data

1993 ◽  
Vol 37 (2) ◽  
pp. 160-166 ◽  
Author(s):  
Lawrence C. Shimmin ◽  
Benny Hung-Junn Chang ◽  
David Hewett-Emmett ◽  
Wen-Hsiung Li
Keyword(s):  
Dna Sequence ◽  
Mutation Rate ◽  
Rate Ratio ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Potential Problems ◽  
Male To Female

scholarly journals A Branching Process Model of Evolutionary Rescue

2021 ◽  
Author(s):  
Peter Olofsson ◽  
Ricardo B. R. Azevedo
Keyword(s):  
Population Growth ◽  
Mutation Rate ◽  
Discrete Time ◽  
Growth Curve ◽  
Process Model ◽  
Branching Process ◽  
Selective Advantage ◽  
Population Declines ◽  
Beneficial Mutations ◽  
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 beneficial 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.

Population genomic analyses confirm male-biased mutation rates in snakes

2021 ◽  
Author(s):  
Drew R Schield ◽  
Blair W Perry ◽  
Zachary L Nikolakis ◽  
Stephen P Mackessy ◽  
Todd A Castoe
Keyword(s):  
Sex Determination ◽  
Mutation Rate ◽  
Mutation Rates ◽  
Unbiased Estimation ◽  
Z Chromosome ◽  
Summary Statistics ◽  
Genomic Dataset ◽  
Population Genomic ◽  
Genomic Analyses ◽  
Male To Female

Abstract Male-biased mutation rates occur in a diverse array of organisms. The ratio of male-to-female mutation rate may have major ramifications for evolution across the genome, and for sex-linked genes in particular. In ZW species, the Z chromosome is carried by males two-thirds of the time, leading to the prediction that male-biased mutation rates will have a disproportionate effect on the evolution of Z-linked genes relative to autosomes and the W chromosome. Colubroid snakes (including colubrids, elapids, and viperids) have ZW sex determination, yet male-biased mutation rates have not been well studied in this group. Here we analyze a population genomic dataset from rattlesnakes to quantify genetic variation within and genetic divergence between species. We use a new method for unbiased estimation of population genetic summary statistics to compare variation between the Z chromosome and autosomes and to calculate net nucleotide differentiation between species. We find evidence for a 2.03-fold greater mutation rate in male rattlesnakes relative to females, corresponding to an average μZ/μA ratio of 1.1. Our results from snakes are quantitatively similar to birds, suggesting that male-biased mutation rates may be a common feature across vertebrate lineages with ZW sex determination.

scholarly journals Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

2021 ◽  
Vol 118 (50) ◽  
pp. e2111193118
Author(s):  
Feng Zhou ◽  
Ruojie Sha ◽  
Heng Ni ◽  
Nadrian Seeman ◽  
Paul Chaikin
Keyword(s):  
Growth Rate ◽  
Mutation Rate ◽  
Exponential Growth ◽  
Dna Origami ◽  
Darwinian Evolution ◽  
Similar Species ◽  
Controlled Growth ◽  
New Materials ◽  
Self Replication ◽  
Cd Species

Artificial self-replication and exponential growth holds the promise of gaining a better understanding of fundamental processes in nature but also of evolving new materials and devices with useful properties. A system of DNA origami dimers has been shown to exhibit exponential growth and selection. Here we introduce mutation and growth advantages to study the possibility of Darwinian-like evolution. We seed and grow one dimer species, AB, from A and B monomers that doubles in each cycle. A similar species from C and D monomers can replicate at a controlled growth rate of two or four per cycle but is unseeded. Introducing a small mutation rate so that AB parents infrequently template CD offspring we show experimentally that the CD species can take over the system in approximately six generations in an advantageous environment. This demonstration opens the door to the use of evolution in materials design.

scholarly journals Do ΔF508 heterozygotes have a selective advantage?

2001 ◽  
Vol 78 (1) ◽  
pp. 41-47 ◽  
Author(s):  
CARSTEN WIUF
Keyword(s):  
Mutation Rate ◽  
Microsatellite Loci ◽  
Demographic History ◽  
Selective Advantage ◽  
European Population ◽  
Microsatellite Mutation Rate ◽  
Order Of Magnitude ◽  
History Of ◽  
Microsatellite Mutation ◽  
Selection Of

In this paper the fitness of the ΔF508 heterozygote is assessed and the age of the ΔF508 mutation in the cystic fibrosis locus is estimated. Data from three microsatellite loci are applied. The analysis is performed conditional on the present-day frequency of the ΔF508 mutation and based on assumptions about the demographic history of the European population and the mutation rate in the three microsatellite loci. It is shown that the data gives evidence of positive selection (up to 2–3% per ΔF508 heterozygote), but also that data could be explained by negative selection of roughly the same order of magnitude. The age of the ΔF508 mutation is subsequently estimated; it is found that the mutation is at least 580 generations old, but could be much older depending on the microsatellite mutation rate and the exact number of substitutions experienced in the history of the three microsatellite loci.

scholarly journals Dynamics and fate of beneficial mutations under lineage contamination by linked deleterious mutations

2016 ◽  
Author(s):  
Sophie Pénisson ◽  
Tanya Singh ◽  
Paul Sniegowski ◽  
Philip Gerrish
Keyword(s):  
Mutation Rate ◽  
Branching Process ◽  
Deleterious Mutation ◽  
Selective Advantage ◽  
Single Type ◽  
Deleterious Mutations ◽  
Beneficial Mutations ◽  
Multitype Branching Process ◽  
Fitness Effects ◽  
Adaptive Substitution

ABSTRACTBeneficial mutations drive adaptive evolution, yet their selective advantage does not ensure their fixation. Haldane’s application of single-type branching process theory showed that genetic drift alone could cause the extinction of newly-arising beneficial mutations with high probability. With linkage, deleterious mutations will affect the dynamics of beneficial mutations and might further increase their extinction probability. Here, we model the lineage dynamics of a newly-arising beneficial mutation as a multitype branching process; this approach allows us to account for the combined effects of drift and the stochastic accumulation of linked deleterious mutations, which we call lineage contamination. We first study the lineage contamination phenomenon in isolation, deriving extinction times and probabilities of beneficial lineages. We then put the lineage contamination phenomenon into the context of an evolving population by incorporating the effects of background selection. We find that the survival probability of beneficial mutations is simply Haldane’s classical formula multiplied by the correction factor , where U is deleterious mutation rate, is mean selective advantage of beneficial mutations, κ ∈ (1, ε], and ε = 2 – e−1. We also find there exists a genomic deleterious mutation rate, , that maximizes the rate of production of surviving beneficial mutations, and that . Both of these results, and others, are curiously independent of the fitness effects of deleterious mutations. We derive critical mutation rates above which: 1) lineage contamination alleviates competition among beneficial mutations, and 2) the adaptive substitution process all but shuts down.

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