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.

Meristic Differences between Spring- and Autumn-Spawning Atlantic Herring (Clupea harengus harengus) from Southwestern Newfoundland

1971 ◽  
Vol 28 (4) ◽  
pp. 553-558 ◽  
Author(s):  
L. S. Parsons ◽  
V. M. Hodder
Keyword(s):  
Clupea Harengus ◽  
Atlantic Herring ◽  
Gill Rakers ◽  
Dorsal Fin ◽  
Fin Ray ◽  
Significant Difference ◽  
Fin Rays ◽  
Developmental Rates ◽  
Clupea Harengus Harengus ◽  
Gill Raker

Numbers of vertebrae, gill rakers, and of pectoral, anal, and dorsal fin rays of spring- and autumn-spawning Atlantic herring (Clupea harengus harengus Linnaeus) in 10 samples from the coastal waters of southwestern Newfoundland were compared. There was no significant difference (P > 0.05) between mean vertebral numbers of spring and autumn spawners. Mean numbers of gill rakers and of pectoral, anal, and dorsal fin rays were all higher (P < 0.01) for autumn spawners than for spring spawners with gill-raker and pectoral fin-ray numbers exhibiting the greatest degree of difference. It is suggested that the differences in fin-ray numbers between spring and autumn spawners are related to water temperatures during larval development and to differences in developmental rates of spring- and autumn-hatched larvae.

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 Low genetic variation is associated with low mutation rate in the giant duckweed

2018 ◽  
Author(s):  
Shuqing Xu ◽  
Jessica Stapley ◽  
Saskia Gablenz ◽  
Justin Boyer ◽  
Klaus J. Appenroth ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Mutation Rate ◽  
Spontaneous Mutation ◽  
Effective Population ◽  
Spontaneous Mutation Rate ◽  
Low Genetic Diversity ◽  
Genome Wide ◽  
Census Population Size

AbstractMutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. We investigate genetic diversity, spontaneous mutation rate andNein the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals revealed extremely low within-species genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereasNeis large. These results demonstrate that low genetic diversity can be associated with large-Nespecies, where selection can reduce mutation rates to very low levels, and accurate estimates of mutation rate can help to explain seemingly counterintuitive patterns of genome-wide variation.One Sentence SummaryThe low-down on a tiny plant: extremely low genetic diversity in an aquatic plant is associated with its exceptionally low mutation rate.

scholarly journals Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sunnvør í Kongsstovu ◽  
Svein-Ole Mikalsen ◽  
Eydna í Homrum ◽  
Jan Arge Jacobsen ◽  
Paul Flicek ◽  
...  
Keyword(s):  
North Atlantic ◽  
Genome Assembly ◽  
De Novo ◽  
Clupea Harengus ◽  
Atlantic Herring ◽  
The North ◽  
Long Reads ◽  
Mate Pair ◽  
The World ◽  
Crucial Part

AbstractAtlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.

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 De Novo Mutation Rate Estimation in Wolves of Known Pedigree

2019 ◽  
Vol 36 (11) ◽  
pp. 2536-2547 ◽  
Author(s):  
Evan M Koch ◽  
Rena M Schweizer ◽  
Teia M Schweizer ◽  
Daniel R Stahler ◽  
Douglas W Smith ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Demographic History ◽  
Full Range ◽  
False Negative ◽  
False Negative Rate ◽  
De Novo Mutation ◽  
Mutation Rates ◽  
Point Estimate ◽  
De Novo Mutations

Abstract Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in a pedigree of seven wolves. Putative de novo mutations were discovered by whole-genome sequencing and were verified by Sanger sequencing of parents and offspring. Using stringent filters and an estimate of the false negative rate in the remaining observable genome, we obtain an estimate of ∼4.5 × 10−9 per base pair per generation and provide conservative bounds between 2.6 × 10−9 and 7.1 × 10−9. Although our estimate is consistent with recent mutation rate estimates from ancient DNA (4.0 × 10−9 and 3.0–4.5 × 10−9), it suggests a wider possible range. We also examined the consequences of our rate and the accompanying interval for dating several critical events in canid demographic history. For example, applying our full range of rates to coalescent models of dog and wolf demographic history implies a wide set of possible divergence times between the ancestral populations of dogs and extant Eurasian wolves (16,000–64,000 years ago) although our point estimate indicates a date between 25,000 and 33,000 years ago. Aside from one study in mice, ours provides the only direct mammalian mutation rate outside of primates and is likely to be vital to future investigations of mutation rate evolution.

scholarly journals Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1511-1518 ◽  
Author(s):  
Ning Yu ◽  
Michael I Jensen-Seaman ◽  
Leona Chemnick ◽  
Judith R Kidd ◽  
Amos S Deinard ◽  
...  
Keyword(s):  
Nucleotide Diversity ◽  
Nuclear Dna ◽  
Demographic History ◽  
Nuclear Genome ◽  
Limited Data ◽  
Effective Population ◽  
East Central ◽  
Dna Diversity ◽  
History Of ◽  
Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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