The Y‐STR landscape of coastal southeastern han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics

2021 ◽  
Author(s):  
Haoliang Fan ◽  
Ying Zeng ◽  
Weiwei Wu ◽  
Hong Liu ◽  
Quyi Xu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Mutation Rates

scholarly journals Likelihoods and Simulation Methods for a Class of Nonneutral Population Genetics Models

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 853-867 ◽  
Author(s):  
Peter Donnelly ◽  
Magnus Nordborg ◽  
Paul Joyce
Keyword(s):  
Population Genetics ◽  
Population Size ◽  
Mutant Allele ◽  
Mutation Rates ◽  
Simulation Methods ◽  
Large Populations ◽  
Selection Intensities ◽  
Infinite Alleles Model

Abstract Methods for simulating samples and sample statistics, under mutation-selection-drift equilibrium for a class of nonneutral population genetics models, and for evaluating the likelihood surface, in selection and mutation parameters, are developed and applied for observed data. The methods apply to large populations in settings in which selection is weak, in the sense that selection intensities, like mutation rates, are of the order of the inverse of the population size. General diploid selection is allowed, but the approach is currently restricted to models, such as the infinite alleles model and certain K-models, in which the type of a mutant allele does not depend on the type of its progenitor allele. The simulation methods have considerable advantages over available alternatives. No other methods currently seem practicable for approximating likelihood surfaces.

scholarly journals Inferring biophysical models of evolution from genome-wide patterns of codon usage

2019 ◽  
Author(s):  
Willow B. Kion-Crosby ◽  
Michael Manhart ◽  
Alexandre V. Morozov
Keyword(s):  
Population Genetics ◽  
Codon Usage ◽  
Codon Bias ◽  
Purifying Selection ◽  
Mutation Rates ◽  
Nucleotide Position ◽  
Mutational Robustness ◽  
Translation Speed ◽  
Genome Wide ◽  
Speed And Accuracy

AbstractFrequencies of synonymous codons are typically non-uniform, despite the fact that such codons correspond to the same amino acid in the genetic code. This phenomenon, known as codon bias, is broadly believed to be due to a combination of factors including genetic drift, mutational biases, and selection for speed and accuracy of codon translation; however, quantitative modeling of codon bias has been elusive. We have developed a biophysical population genetics model which explains genome-wide codon frequencies observed across 20 organisms. We assume that codons evolve independently of each other under the influence of mutation and selection forces, and that the codon population has reached evolutionary steady state. Our model implements codon-level treatment of mutations with transition/transversion biases, and includes two contributions to codon fitness which describe codon translation speed and accuracy. Furthermore, our model includes wobble pairing – the possibility of codon-anticodon base pairing mismatches at the 3’ nucleotide position of the codon. We find that the observed patterns of genome-wide codon usage are consistent with a strong selective penalty for mistranslated amino acids. Thus codons undergo purifying selection and their relative frequencies are affected in part by mutational robustness. We find that the dependence of codon fitness on translation speed is weaker on average compared to the strength of selection against mistranslation. Although no constraints on codon-anticodon pairing are imposed a priori, a reasonable hierarchy of pairing rates, which conforms to the wobble hypothesis and is consistent with available structural evidence, emerges spontaneously as a model prediction. Finally, treating the translation process explicitly in the context of a finite ribosomal pool has allowed us to estimate mutation rates per nucleotide directly from the coding sequences. Reminiscent of Drake’s observation that mutation rates are inversely correlated with the genome size, we predict that mutation rates are inversely proportional to the number of genes. Overall, our approach offers a unified biophysical and population genetics framework for studying codon bias across all domains of life.

scholarly journals Widespread selection against deleterious mutations in the Drosophila genome

2020 ◽  
Author(s):  
Pavel Khromov ◽  
Alexandre V. Morozov
Keyword(s):  
Population Genetics ◽  
Steady State ◽  
Genomic Sequences ◽  
Mutation Rates ◽  
Drosophila Genome ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Ewens Sampling Formula ◽  
Selective Constraints ◽  
Sampling Formula

AbstractWe have developed a computational approach to simultaneous genome-wide inference of key population genetics parameters: selection strengths, mutation rates rescaled by the effective population size and the fraction of viable genotypes, solely from an alignment of genomic sequences sampled from the same population. Our approach is based on a generalization of the Ewens sampling formula, used to compute steady-state probabilities of allelic counts in a neutrally evolving population, to populations subjected to selective constraints. Patterns of polymorphisms observed in alignments of genomic sequences are used as input to Approximate Bayesian Computation, which employs the generalized Ewens sampling formula to infer the distributions of population genetics parameters. After carrying out extensive validation of our approach on synthetic data, we have applied it to the evolution of the Drosophila melanogaster genome, where an alignment of 197 genomic sequences is available for a single ancestral-range population from Zambia, Africa. We have divided the Drosophila genome into 100-bp windows and assumed that sequences in each window can exist in either low- or high-fitness state. Thus, the steady-state population in our model is subject to a constant influx of deleterious mutations, which shape the observed frequencies of allelic counts in each window. Our approach, which focuses on deleterious mutations and accounts for intra-window linkage and epistasis, provides an alternative description of background selection. We find that most of the Drosophila genome evolves under selective constraints imposed by deleterious mutations. These constraints are not confined to known functional regions of the genome such as coding sequences and may reflect global biological processes such as the necessity to maintain chromatin structure. Furthermore, we find that inference of mutation rates in the presence of selection leads to mutation rate estimates that are several-fold higher than neutral estimates widely used in the literature. Our computational pipeline can be used in any organism for which a sample of genomic sequences from the same population is available.

scholarly journals The population genetics of mutations: good, bad and indifferent

2010 ◽  
Vol 365 (1544) ◽  
pp. 1153-1167 ◽  
Author(s):  
Laurence Loewe ◽  
William G. Hill
Keyword(s):  
Population Genetics ◽  
Dna Sequences ◽  
Quantitative Traits ◽  
Current Knowledge ◽  
Raw Materials ◽  
Mutation Rates ◽  
Beneficial Effects ◽  
Changing Environments ◽  
The Past ◽  
Review Current

Population genetics is fundamental to our understanding of evolution, and mutations are essential raw materials for evolution. In this introduction to more detailed papers that follow, we aim to provide an oversight of the field. We review current knowledge on mutation rates and their harmful and beneficial effects on fitness and then consider theories that predict the fate of individual mutations or the consequences of mutation accumulation for quantitative traits. Many advances in the past built on models that treat the evolution of mutations at each DNA site independently, neglecting linkage of sites on chromosomes and interactions of effects between sites (epistasis). We review work that addresses these limitations, to predict how mutations interfere with each other. An understanding of the population genetics of mutations of individual loci and of traits affected by many loci helps in addressing many fundamental and applied questions: for example, how do organisms adapt to changing environments, how did sex evolve, which DNA sequences are medically important, why do we age, which genetic processes can generate new species or drive endangered species to extinction, and how should policy on levels of potentially harmful mutagens introduced into the environment by humans be determined?

scholarly journals The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR

2020 ◽  
Author(s):  
Jinding Liu ◽  
Rongshuai Wang ◽  
Jie Shi ◽  
Xiaojuan Cheng ◽  
Ting Hao ◽  
...  
Keyword(s):  
Population Genetics ◽  
Dna Analysis ◽  
Cost Effective ◽  
Forensic Identification ◽  
Mutation Rates ◽  
Discrimination Power ◽  
Fluorescent Pcr ◽  
High Discrimination ◽  
Male Specific ◽  
Str System

AbstractY-chromosomal short tandem repeat (Y-STR) polymorphisms are useful in forensic identification, population genetics and human structures. However, the current Y-STR systems are limited in discriminating distant relatives in a family with a low discrimination power. Increasing the capacity of detecting Y chromosomal polymorphisms will drastically narrow down the matching number of genealogy populations or pedigrees. In this study, we developed a system containing 17 Y-STRs that are complementary to the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected sizes of 126-400 bp labeled by different fluorescence molecules (DYS715, DYS709, DYS716, DYS713 and DYS607 labeled by FAM; DYS718, DYS723, DYS708 and DYS714 labeled by JOE; DYS712, DYS717, DYS721 and DYS605 labeled by TAMRA; and DYS719, DYS726, DYS598 and DYS722 labeled by ROX). The system was extensively tested for sensitivity, male specificity, species specificity, mixture, population genetics and mutation rates following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The genetic data were obtained from eight populations with a total of 1260 individuals. Our results showed that all the 17 Y-STRs are human- and male-specific and include only one copy of the Y-chromosome. The 17 Y-STR system detects 143 alleles and has a high discrimination power (0.996031746). Mutation rates were different among the 17 Y-STRs, ranging from 0.30% to 3.03%. In conclusion, our study provides a robust, sensitive and cost-effective genotyping method for human identification, which will be beneficial for narrowing the search scope when applied to genealogy searching with the Y-STR DNA databank.

scholarly journals Complexities of Viral Mutation Rates

2018 ◽  
Vol 92 (14) ◽  
Author(s):  
Kayla M. Peck ◽  
Adam S. Lauring
Keyword(s):  
Population Genetics ◽  
Mutation Rate ◽  
Mutation Rates ◽  
Rate Estimation ◽  
Viral Mutation ◽  
Context Dependent ◽  
Mutation Rate Estimation

ABSTRACT Many viruses evolve rapidly. This is due, in part, to their high mutation rates. Mutation rate estimates for over 25 viruses are currently available. Here, we review the population genetics of virus mutation rates. We specifically cover the topics of mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent.

scholarly journals On the evolutionary adjustment of spontaneous mutation rates

1967 ◽  
Vol 9 (1) ◽  
pp. 23-34 ◽  
Author(s):  
Motoo Kimura
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Genetic Material ◽  
Genetic Load ◽  
Mutation Rates ◽  
Spontaneous Mutation Rate ◽  
Physiological Limit ◽  
Present Mode

Evolutionary factors which tend to decrease the mutation rate through natural selection and those which tend to increase the mutation rate are discussed from the standpoint of population genetics. The author's theory of optimum mutation rate based on the principle of minimum genetic load is re-examined, assuming that mutation rate is adjusted in the course of evolution in such a way that the sum of mutational and substitutional load is minimized. Another hypothesis is also examined that only selection toward lowering the mutation rate is effective and the present mutation rate in each organism represents the physical or physiological limit that may be attained by natural selection.The possibility cannot be excluded that the spontaneous mutation rate is near the minimum that may be attained under the present mode of organization of the genetic material, and at the same time is not very far from the optimum in the sense of minimizing the genetic load.

scholarly journals Mutation rate estimation for 15 autosomal STR loci in a large population from Mainland China

2015 ◽  
Author(s):  
Zhuo Zhao ◽  
Hua Wang ◽  
Jie Zhang ◽  
Zhi-Peng Liu ◽  
Ming Liu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Mutation Rate ◽  
Large Population ◽  
Mainland China ◽  
Mutation Rates ◽  
Str Analysis ◽  
Str Loci ◽  
Autosomal Str ◽  
Parents And Children ◽  
Genetic Assessment

STR, short trandem repeats, is well known as a type of powerful genetic marker and widely used in studying human population genetics. Compared with the conventional genetic markers, the mutation rate of STR is higher. Additionally, the mutations of STR loci do not lead to genetic inconsistencies between the genotypes of parents and children; therefore, the analysis of STR mutation is more suited to assess the population mutation. In this study, we focused on 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA). DNA samples from a total of 42416 unrelated healthy individuals (19037 trios) from the population of Mainland China collected between Jan 2012 and May 2014 were successfully investigated. In our study, the allele frequencies, paternal mutation rates, maternal mutation rates and average mutation rates were detected in the 15 STR loci. Furthermore, we also investigated the relationship between paternal ages, maternal ages, pregnant time, area and average mutation rate. We found that paternal mutation rate is higher than maternal mutation rate and the paternal, maternal, and average mutation rates have a positive correlation with paternal ages, maternal ages and times respectively. Additionally, the average mutation rates of coastal areas are higher than that of inland areas. Overall, these results suggest that the 15 autosomal STR loci can provide highly informative polymorphic data for population genetic assessment in Mainland China, as well as confirm and extend the application of STR analysis in population genetics.

Do Mutation Rates Match the Kelly Criterion?

2020 ◽  
Vol 2 (1) ◽  
pp. 31
Author(s):  
Jonathan Bartlett
Keyword(s):  
Mutation Rates ◽  
Kelly Criterion

The Kelly Criterion defines an optimal betting strategy for games that have a defined risk and payoff. This letter explores the question of if this can be used as a methodology for analyzing mutation rates.

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