scholarly journals Direct estimation of mutations in great apes reveals significant recent human slowdown in the yearly mutation rate

2018 ◽  
Author(s):  
Søren Besenbacher ◽  
Christina Hvilsom ◽  
Tomas Marques-Bonet ◽  
Thomas Mailund ◽  
Mikkel Heide Schierup
Keyword(s):  
Linear Relationship ◽  
Mutation Rate ◽  
Fossil Record ◽  
Great Apes ◽  
Mutation Rates ◽  
Rate Estimate ◽  
The Past ◽  
Divergence Estimates ◽  
Human Mutation ◽  
Mutation Rate Estimate

AbstractThe human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother. The yearly trio-based mutation rate estimate of ~0.43×10−9 is markedly lower than prior indirect estimates of ~1×10−9 per year from phylogenetic comparisons of the great apes. This suggests either a slowdown over the past 10 million years or an inaccurate interpretation of the fossil record. Here we use sequencing of chimpanzee, gorilla and orangutan trios and find that each species has higher estimated mutation rates per year by factors of 1.67+/− 0.22, 1.54+/− 0.2 and 1.84+/− 0.19, respectively. These estimates suggest a very recent and appreciable slowdown in human mutation rate, and, if extrapolated over the great apes phylogeny, yields divergence estimates much more in line with the fossil record and the biogeography.

scholarly journals The Distribution of Bacterial Doubling Times in the Wild

2017 ◽  
Author(s):  
Beth Gibson ◽  
Daniel Wilson ◽  
Edward Feil ◽  
Adam Eyre-Walker
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
Generation Time ◽  
Doubling Time ◽  
Mutation Rates ◽  
Substantial Fraction ◽  
Rate Estimate ◽  
In The Wild ◽  
Doubling Times ◽  
Mutation Rate Estimate

AbstractGeneration time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT), has been estimated for many bacteria in the lab, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the lab. If we assume the mutation rate per generation is the same in the wild and in the lab, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for four species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the lab, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.

scholarly journals The distribution of bacterial doubling times in the wild

2018 ◽  
Vol 285 (1880) ◽  
pp. 20180789 ◽  
Author(s):  
Beth Gibson ◽  
Daniel J. Wilson ◽  
Edward Feil ◽  
Adam Eyre-Walker
Keyword(s):  
Life History ◽  
Mutation Rate ◽  
Generation Time ◽  
Doubling Time ◽  
Mutation Rates ◽  
Substantial Fraction ◽  
Rate Estimate ◽  
In The Wild ◽  
Doubling Times ◽  
Mutation Rate Estimate

Generation time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT) has been estimated for many bacteria in the laboratory, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the laboratory. If we assume the mutation rate per generation is the same in the wild and in the laboratory, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.

scholarly journals Rapid evolution of the human mutation spectrum

2016 ◽  
Author(s):  
Kelley Harris ◽  
Jonathan K. Pritchard
Keyword(s):  
Mutation Rate ◽  
Genetic Modifier ◽  
Rapid Evolution ◽  
Biological Information ◽  
Mutation Rates ◽  
Specific Sequence ◽  
Mutational Spectra ◽  
Damage Repair ◽  
Human Mutation ◽  
System Selection

AbstractDNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely-related populations. Close examination of one signal, an increased TCC→TTC mutation rate in Europeans, indicates a burst of mutations from about 15,000 to 2,000 years ago, perhaps due to the appearance, drift, and ultimate elimination of a genetic modifier of mutation rate. Our results suggest that mutation rates can evolve markedly over short evolutionary timescales and suggest the possibility of mapping mutational modifiers.

scholarly journals Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

2015 ◽  
Author(s):  
Mark Lipson ◽  
Po-Ru Loh ◽  
Sriram Sankararaman ◽  
Nick Patterson ◽  
Bonnie Berger ◽  
...  
Keyword(s):  
Mutation Rate ◽  
De Novo ◽  
Sequence Divergence ◽  
Great Apes ◽  
Human Populations ◽  
De Novo Mutations ◽  
Essential Parameter ◽  
Human Mutation ◽  
Rate Of Accumulation

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Most notably, recent approaches based on counting de novo mutations in family pedigrees have yielded significantly smaller values than classical methods based on sequence divergence. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.61 +/- 0.13 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.

Potential DNA methods for measuring the human heritable mutation rate

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 860-863 ◽  
Author(s):  
Mortimer L. Mendelsohn
Keyword(s):  
Mutation Rate ◽  
Human Sperm ◽  
Mutation Rates ◽  
Practical Implementation ◽  
Dna Technology ◽  
Heritable Mutation ◽  
Human Mutation ◽  
Potential Methods

Potential methods are reviewed for estimating human heritable mutation rates by comparing the DNA of parents and offspring. In the 4 years since the Alta Workshop on this subject, information has accumulated on several of the six methods detailed in that meeting. Some of the methods now appear to be infeasible, and all continue to be too inefficient for practical implementation. Newer DNA approaches are discussed, including several that could become practical enough for implementation. Finally, DNA-oriented methods using human sperm are considered as possible alternatives to the heritable approaches.Key words: human heritable mutation, human mutation rate, DNA method – DNA technology, radiation.

scholarly journals Rapid evolution of the human mutation spectrum

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Kelley Harris ◽  
Jonathan K Pritchard
Keyword(s):  
Mutation Rate ◽  
Genetic Modifier ◽  
Rapid Evolution ◽  
Biological Information ◽  
Mutation Rates ◽  
Specific Sequence ◽  
Mutational Spectra ◽  
Damage Repair ◽  
Human Mutation ◽  
System Selection

DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely related populations. Close examination of one signal, an increased TCC→TTC mutation rate in Europeans, indicates a burst of mutations from about 15,000 to 2000 years ago, perhaps due to the appearance, drift, and ultimate elimination of a genetic modifier of mutation rate. Our results suggest that mutation rates can evolve markedly over short evolutionary timescales and suggest the possibility of mapping mutational modifiers.

Intrinsic versus extrinsic biases in the fossil record: contrasting the fossil record of echinoids in the Triassic and early Jurassic using sampling data, phylogenetic analysis, and molecular clocks

Paleobiology ◽  
2007 ◽  
Vol 33 (2) ◽  
pp. 310-323 ◽  
Author(s):  
Andrew B. Smith
Keyword(s):  
Fossil Record ◽  
Critical Time ◽  
Lower Jurassic ◽  
Time Interval ◽  
Molecular Clocks ◽  
The Past ◽  
Consistent Feature ◽  
Divergence Estimates ◽  
Lineage Analysis

Four independent lines of evidence, (1) the quality of specimen preservation, (2) taxonomic collection curves, (3) molecular divergence estimates, and (4) ghost lineage analysis of a genus-level cladogram, point to echinoids having a much poorer fossil record in the Triassic than in the Lower Jurassic. Furthermore, preservational differences between Triassic and Lower Jurassic echinoids have remained a consistent feature over 160 years of discovery. Differences exist in how effectively paleontologists have collected the fauna from available outcrops in the Triassic and Lower Jurassic. Collection curves suggest that rocks have been more efficiently searched for their fossils in Europe than elsewhere in the world, and that Lower Jurassic faunas are better sampled from available outcrop than Triassic faunas. The discovery of Triassic taxa has quickened in pace over the past 4 decades (though largely driven by a single Lagerstätte—the St. Cassian beds) while discoveries of new taxa from the Lower Jurassic have slowed. Molecular analysis of extant families and ghost lineage analysis of Triassic and Lower Jurassic genera both point to poorer sampling of Triassic faunas. This difference in the quality of the fossil record may be partially explained by differences in rock outcrop area, as marine sedimentary rocks are much less common in the Triassic than in the Lower Jurassic. However, improving biomechanical design of the echinoid test over this critical time interval was probably as important, and better explains observed preservational trends. Changes in the quality of the echinoid fossil record were thus driven as much by intrinsic biological factors as by sampling patterns.

Did Ground Cover Change Over Geologic Time?

2000 ◽  
Vol 6 ◽  
pp. 171-182 ◽  
Author(s):  
Ben A. LePage ◽  
Hermann W. Pfefferkorn
Keyword(s):  
Fossil Record ◽  
Ground Cover ◽  
The Other ◽  
Detailed Account ◽  
Geologic Time ◽  
The Past ◽  
Other Hand ◽  
Plant Fossil

When one hears the term “ground cover,” one immediately thinks of “grasses.” This perception is so deep-seated that paleobotanists even have been overheard to proclaim that “there was no ground cover before grasses.” Today grasses are so predominant in many environments that this perception is perpetuated easily. On the other hand, it is difficult to imagine the absence or lack of ground cover prior to the mid-Tertiary. We tested the hypothesis that different forms of ground cover existed in the past against examples from the Recent and the fossil record (Table 1). The Recent data were obtained from a large number of sources including those in the ecological, horticultural, and microbiological literature. Other data were derived from our knowledge of Precambrian life, sedimentology and paleosols, and the plant fossil record, especially in situ floras and fossil “monocultures.” Some of the data are original observations, but many others are from the literature. A detailed account of these results will be presented elsewhere (Pfefferkorn and LePage, in preparation).

Sign in / Sign up

Export Citation Format

Share Document