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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

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).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...
Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Related Experiment Video

Updated: Jun 4, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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Published on: August 14, 2018

Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian

Peter D Keightley1, Lél Eöry, Daniel L Halligan

  • 1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom. keightley.genetics2011@gmail.com

Genetics
|February 4, 2011
PubMed
Summary

We developed a new method to estimate genetic mutation and selection parameters by analyzing DNA sequence differences. This approach reveals significant differences in mutation rates and selective pressures across primate, murid, and carnivore genomes.

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Last Updated: Jun 4, 2026

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Computational biology

Background:

  • Estimating molecular evolutionary parameters like mutation rates and selection pressures is crucial for understanding genome evolution.
  • Existing methods may not fully account for complex factors such as CpG hypermutability, varying base substitution biases, and different selective pressures on synonymous and nonsynonymous sites.

Purpose of the Study:

  • To develop and validate a novel inference method using approximate Bayesian computation (ABC) for simultaneously estimating mutational parameters and selective constraint.
  • To apply this method to analyze protein-coding genes across primate, murid, and carnivore genomes.

Main Methods:

  • Developed an ABC-based inference method incorporating explicit modeling of CpG hypermutability, transition/transversion biases, and selection on synonymous/nonsynonymous sites.
  • Evaluated method performance through simulations, comparing linear, quadratic, and weighted regression within the ABC framework.
  • Applied the validated method to analyze genomic data from primates, murids, and carnivores.

Main Results:

  • The ABC method provides reasonably unbiased parameter estimates for non-short sequences and sufficient divergence.
  • Quadratic regression within ABC improves efficiency over linear regression; weighted regression has minimal impact.
  • CpG hypermutability is higher in primates than murids/carnivores; nonsynonymous constraint is higher in murids/carnivores than primates.
  • Autosomal sites show higher nonsynonymous constraint than X-chromosome sites across all taxa.
  • Significant synonymous site constraint detected in primates, carnivores, and murids, but weakest in murids despite larger effective population sizes.

Conclusions:

  • The developed ABC method is a robust tool for inferring complex molecular evolutionary parameters.
  • Comparative genomic analyses reveal distinct patterns of mutation and selection across major mammalian clades.
  • The findings highlight significant differences in evolutionary pressures, particularly concerning CpG hypermutability and selective constraint on coding sites, with surprising results for synonymous site constraint in murids.