scholarly journals Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkleMelarhaphe neritoides(Mollusca: Gastropoda)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2549 ◽  
Author(s):  
Séverine Fourdrilis ◽  
Patrick Mardulyn ◽  
Olivier J. Hardy ◽  
Kurt Jordaens ◽  
António Manuel de Frias Martins ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Spatial Scales ◽  
Haplotype Diversity ◽  
Mtdna Mutation ◽  
Effective Population ◽  
Marine Gastropods

We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkleMelarhaphe neritoides(Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytbgene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity inM. neritoidesis characterized by extremely high haplotype diversity (Hd= 0.999 ± 0.001), high nucleotide diversity (π= 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn= 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identifyM. neritoides. The mtDNA hyperdiversity inM. neritoidesis best explained by the remarkably high mutation rate at the COI locus (μ= 5.82 × 10−5per site per yearorμ= 1.99 × 10−4mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne= 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to highμvalues and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.

scholarly journals Somatic drift and rapid loss of heterozygosity suggest small effective population size of stem cells and high somatic mutation rate in asexual planaria

2019 ◽  
Author(s):  
Hosseinali Asgharian ◽  
Joseph Dunham ◽  
Paul Marjoram ◽  
Sergey V. Nuzhdin
Keyword(s):  
Stem Cells ◽  
Population Size ◽  
Effective Population Size ◽  
Somatic Mutation ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Genetic Model ◽  
Neutral Evolution ◽  
Multiple Time ◽  
Effective Population

AbstractPlanarian flatworms have emerged as highly promising models of body regeneration due to the many stem cells scattered through their bodies. Currently, there is no consensus as to the number of stem cells active in each cycle of regeneration or the equality of their relative contributions. We approached this problem with a population genetic model of somatic genetic drift. We modeled the fissiparous life cycle of asexual planarians as an asexual population of cells that goes through repeated events of splitting into two subpopulations followed by population growth to restore the original size. We sampled a pedigree of obligate asexual clones of Girardia cf. tigrina at multiple time points encompassing 14 generations. Effective population size of stem cells was inferred from the magnitude of temporal fluctuations in the frequency of somatic variants and under most of the examined scenarios was estimated to be in the range of a few hundreds. Average genomic nucleotide diversity was 0.00398. Assuming neutral evolution and mutation-drift equilibrium, the somatic mutation rate was estimated in the 10−5 − 10−7 range. Alternatively, we estimated Ne and somatic μ from temporal changes in nucleotide diversity π without the assumption of equilibrium. This second method suggested even smaller Ne and larger μ. A key unknown parameter in our model on which estimates of Ne and μ depend is g, the ratio of cellular to organismal generations determined by tissue turnover rate. Small effective number of propagating stem cells might contribute to reducing reproductive conflicts in clonal organisms.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

scholarly journals Coalescent Theory for a Partially Selfing Population

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1489-1499 ◽  
Author(s):  
Yun-Xin Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
Coalescent Theory ◽  
Selfing Rate ◽  
Effective Population ◽  
Diploid Population ◽  
Approximate Formulas ◽  
Segregating Sites

A coalescent theory for a sample of DNA sequences from a partially selfing diploid population and an algorithm for simulating such samples are developed in this article. Approximate formulas are given for the expectation and the variance of the number of segregating sites in a sample of k sequences from n individuals. Several new estimators of the important parameters θ = 4Nμ and the selfing rate s, where N and μ are, respectively, the effective population size and the mutation rate per sequence per generation, are proposed and their sampling properties are studied.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, neutral diversity depends upon the product of the effective population size and mutation rate there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest dataset to date from 639 mammalian species. In a multiple regression we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of non-synonymous to synonymous diversity, is also significantly negatively correlated to both range and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

scholarly journals Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

2021 ◽  
Author(s):  
Irene Novo ◽  
Armando Caballero ◽  
Enrique Santiago
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Loss Of Function ◽  
Effective Population ◽  
Genomic Regions ◽  
The Relationship ◽  
Key Parameter

The effective population size ( N e ) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in N e across time using measures of genome diversity or linkage disequilibrium between markers. Selection is expected to reduce diversity and N e , and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and of recombination rate heterogeneity in the estimation of historical N e . We also investigate the relationship between diversity parameters and N e across the different regions of the genome using human marker data. We show that the estimates of historical N e obtained from linkage disequilibrium between markers ( N e LD ) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, what could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of N e LD obtained for particular genomic regions do not correlate with recombination rate, nucleotide diversity, polymorphism, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that N e LD measures are merely indicative of demographic changes in population size across generations.

scholarly journals DISTRIBUTION OF NUCLEOTIDE DIFFERENCES BETWEEN TWO RANDOMLY CHOSEN CISTRONS IN A FINITE POPULATION

Genetics ◽  
1977 ◽  
Vol 85 (2) ◽  
pp. 331-337
Author(s):  
Wen-Hsiung Li
Keyword(s):  
Steady State ◽  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Finite Population ◽  
Effective Population ◽  
Steady State Distribution ◽  
State Distribution ◽  
Simple Estimate ◽  
The Mean

ABSTRACT Watterson's (1975) formula for the steady-state distribution of the number of nucleotide differences between two randomly chosen cistrons in a finite population has been extended to transient states. The rate for the mean of this distribution to approach its equilibrium value is 1/2 N and independent of mutation rate, but that for the variance is dependent on mutation rate, where N denotes the effective population size. Numerical computations show that if the heterozygosity (i.e., the probability that two cistrons are different) is low, say of the order of 0.1 or less, the probability that two cistrons differ at two or more nucleotide sites is less than 10 percent of the heterozygosity, whereas this probability may be as high as 50 percent of the heterozygosity if the heterozygosity is 0.5. A simple estimate for the mean number (d) of site differences between cistrons is d = h/(1 - h) where h is the heterozygosity. At equilibrium, the probability that two cistrons differ by more than one site is equal to h  2, the square of heterozygosity.

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