Related Experiment Video
Updated: Oct 16, 2025
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
1.1K
Studying mutation rate evolution in primates-the effects of computational pipelines and parameter choices
Susanne P Pfeifer1,2,3
1School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
Gigascience
|October 21, 2021
Summary
Computational pipelines and parameter choices significantly impact mutation rate estimation. This commentary uses a rhesus macaque study to highlight these critical factors in genetic analysis.
Area of Science:
- Genetics
- Bioinformatics
- Evolutionary Biology
Background:
- Mutation rate estimation is crucial for understanding evolutionary processes.
- Accurate estimation relies heavily on the chosen computational methods and parameters.
- Previous studies may have variations due to differing analytical pipelines.
Purpose of the Study:
- To investigate the influence of computational pipeline and parameter selection on mutation rate estimation.
- To use the Bergeron et al. study on rhesus macaque germline mutations as a case example.
- To emphasize the importance of methodological transparency in genetic research.
Main Methods:
- Review and analysis of computational approaches for mutation rate estimation.
- Examination of parameter settings commonly used in phylogenetic and genetic studies.
- Comparative assessment of potential impacts of different pipelines on results.
Main Results:
- The choice of computational pipeline and parameters can lead to substantial variations in estimated mutation rates.
- Specific parameter choices can affect the interpretation of evolutionary timescales.
- Methodological differences can explain discrepancies in mutation rate estimates across studies.
Conclusions:
- Careful consideration and reporting of computational pipelines and parameters are essential for reliable mutation rate estimation.
- Standardization or clear documentation of methods is needed to ensure reproducibility and comparability.
- Understanding these factors is vital for accurate phylogenetic dating and evolutionary inference.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
6.5K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.5K
00:36Viral Mutations
35.0K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
35.0K
01:09Mutation, Gene Flow, and Genetic Drift
60.1K
In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
60.1K
02:05Gene Evolution - Fast or Slow?
7.6K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.6K
01:18Mutations in Microorganisms
182
Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
182
01:30Point and Frameshift Mutations
268
Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
268