scholarly journals Author response: Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

2017 ◽  
Author(s):  
Chungang Feng ◽  
Mats Pettersson ◽  
Sangeet Lamichhaney ◽  
Carl-Johan Rubin ◽  
Nima Rafati ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Author Response ◽  
Atlantic Herring

scholarly journals Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

2017 ◽  
Author(s):  
Chungang Feng ◽  
Mats Pettersson ◽  
Sangeet Lamichhaney ◽  
Carl-Johan Rubin ◽  
Nima Rafati ◽  
...  
Keyword(s):  
Population Size ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
De Novo ◽  
Demographic History ◽  
Large Fraction ◽  
Clupea Harengus ◽  
Atlantic Herring ◽  
Significant Difference ◽  
Census Population Size

AbstractThe Atlantic herring (Clupea harengus) is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π=0.3%), only three-fold higher than in human. The expected nucleotide diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 × 10−9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate – the lowest among vertebrates analyzed to date – partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size (>1011). But our analysis indicates that a species like the herring will never reach its expected nucleotide diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high nucleotide diversity. In addition, background selection and selective sweeps lead to reductions in nucleotide diversity at linked neutral sites.

scholarly journals Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Chungang Feng ◽  
Mats Pettersson ◽  
Sangeet Lamichhaney ◽  
Carl-Johan Rubin ◽  
Nima Rafati ◽  
...  
Keyword(s):  
Population Size ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
De Novo ◽  
Large Fraction ◽  
Atlantic Herring ◽  
De Novo Mutations ◽  
High Nucleotide Diversity ◽  
Census Population Size ◽  
High Degree

The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 × 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate – the lowest among vertebrates analyzed to date – partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.

scholarly journals Author response: Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci

2020 ◽  
Author(s):  
Fan Han ◽  
Minal Jamsandekar ◽  
Mats E Pettersson ◽  
Leyi Su ◽  
Angela P Fuentes-Pardo ◽  
...  
Keyword(s):  
Allele Frequencies ◽  
Ecological Adaptation ◽  
Author Response ◽  
Atlantic Herring

scholarly journals Author response: Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

2017 ◽  
Author(s):  
Malene Juul ◽  
Johanna Bertl ◽  
Qianyun Guo ◽  
Morten Muhlig Nielsen ◽  
Michał Świtnicki ◽  
...  
Keyword(s):  
Somatic Mutation ◽  
Mutation Rate ◽  
Specific Model ◽  
Author Response ◽  
Cancer Driver

Deleterious background selection with recombination.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1605-1617 ◽  
Author(s):  
R R Hudson ◽  
N L Kaplan
Keyword(s):  
Drosophila Melanogaster ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Deleterious Mutation ◽  
Selection Model ◽  
Background Selection ◽  
The Third ◽  
Neutral Locus ◽  
Analytic Expression ◽  
Low Levels

Abstract An analytic expression for the expected nucleotide diversity is obtained for a neutral locus in a region with deleterious mutation and recombination. Our analytic results are used to predict levels of variation for the entire third chromosome of Drosophila melanogaster. The predictions are consistent with the low levels of variation that have been observed at loci near the centromeres of the third chromosome of D. melanogaster. However, the low levels of variation observed near the tips of this chromosome are not predicted using currently available estimates of the deleterious mutation rate and of selection coefficients. If considerably smaller selection coefficients are assumed, the low observed levels of variation at the tips of the third chromosome are consistent with the background selection model.

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 Author response: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

2016 ◽  
Author(s):  
Alvaro Martinez Barrio ◽  
Sangeet Lamichhaney ◽  
Guangyi Fan ◽  
Nima Rafati ◽  
Mats Pettersson ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genetic Basis ◽  
Ecological Adaptation ◽  
Author Response ◽  
Atlantic Herring

scholarly journals Mutation rate variation shapes genome-wide diversity in Drosophila melanogaster

2021 ◽  
Author(s):  
Gustavo Valadares Barroso ◽  
Julien Y Dutheil
Keyword(s):  
Drosophila Melanogaster ◽  
Molecular Evolution ◽  
Mutation Rate ◽  
Nucleotide Diversity ◽  
Population Genomics ◽  
Genomic Variation ◽  
Mutation Rates ◽  
Rate Variation ◽  
Evolutionary Forces ◽  
Mutation Rate Variation

What shapes the distribution of nucleotide diversity along the genome? Attempts to answer this question have sparked debate about the roles of neutral stochastic processes and natural selection in molecular evolution. However, the mechanisms of evolution do not act in isolation, and integrative models that simultaneously consider the influence of multiple factors on diversity are lacking; without them, confounding factors lurk in the estimates. Here we present a new statistical method that jointly infers the genomic landscapes of genealogies, recombination rates and mutation rates. In doing so, our model captures the effects of genetic drift, linked selection and local mutation rates on patterns of genomic variation. Guided by our causal model, we use linear regression to estimate the individual contributions of these micro-evolutionary forces to levels of nucleotide diversity. Our analyses reveal the signature of selection in Drosophila melanogaster, but we estimate that the mutation landscape is the major driver of the distribution of diversity in this species. Furthermore, our simulation study suggests that in many evolutionary scenarios the mutation landscape will be a crucial force shaping diversity, depending notably on the genomic window size used in the analysis. We argue that incorporating mutation rate variation into the null model of molecular evolution will lead to more realistic inference in population genomics.

Sign in / Sign up

Export Citation Format

Share Document