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Related Concept Videos

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...
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...
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.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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...

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding

Guy Baele1, Yves Van de Peer, Stijn Vansteelandt

  • 1Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. gubae@psb.vib-ugent.be

Journal of Molecular Evolution
|July 13, 2010
PubMed
Summary
This summary is machine-generated.

Non-reversible evolutionary models significantly improve accuracy in analyzing context-dependent DNA changes, especially for mammalian evolution. These models offer better parameter estimation for processes like CpG-methylation-deamination.

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Last Updated: Jun 11, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Published on: February 3, 2023

Novel Sequence Discovery by Subtractive Genomics
09:40

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Published on: January 25, 2019

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

  • Evolutionary Biology
  • Genomics
  • Computational Biology

Background:

  • Context-dependent evolutionary processes, such as CpG-methylation-deamination in mammals, are inherently non-reversible.
  • Existing evolutionary models often assume reversibility, potentially limiting accuracy in modeling complex biological processes.
  • Accurate modeling of DNA sequence evolution is crucial for understanding genomic changes and evolutionary history.

Purpose of the Study:

  • To investigate the utility of non-reversible, context-dependent evolutionary models for analyzing genomic data.
  • To assess whether these advanced models improve the accuracy of estimating substitution parameters compared to independent models.
  • To explore parameter clustering as a method for further enhancing model performance.

Main Methods:

  • Development of time-homogeneous, context-dependent evolutionary models.
  • Analysis of a large genomic dataset of primate ancestral repeats.
  • Comparison of model fit using Bayes Factors derived from thermodynamic integration.

Main Results:

  • Non-reversible context-dependent models demonstrated a drastic increase in model fit compared to independent models on primate non-coding datasets.
  • The flexibility of non-reversible models allows for more accurate estimation of context-dependent substitution parameters.
  • Clustering similar parameters across different contexts further improved model performance.

Conclusions:

  • Non-reversible context-dependent evolutionary models are essential for accurately analyzing processes with inherent directionality, like CpG-methylation-deamination.
  • These models provide a more robust framework for evolutionary genomic studies, particularly in non-coding regions.
  • The findings advocate for the adoption of non-reversible models to enhance the precision of evolutionary inference.