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Evolutionary Relationships through Genome Comparisons02:54

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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...
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Genome Divergence Based on Entropic Segmentation of DNA.

Pedro A Bernaola-Galván1,2, Pedro Carpena1,2, Cristina Gómez-Martín3,4,5

  • 1Department of Applied Physics II, University of Málaga, 29071 Málaga, Spain.

Entropy (Basel, Switzerland)
|October 28, 2025
PubMed
Summary

We developed a new genome signature using DNA composition to compare species. This Segment Compositional Distance metric correlates with evolutionary divergence and phylogenetic relationships.

Keywords:
Jensen-Shannon divergencecomparative genomicsentropic segmentationgenome compositional evolutiongenome signatureslarge-scale evolutionary patterns

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Genome signatures are DNA patterns used for species identification and comparison.
  • Current methods often rely on sequence alignment or specific mutations.
  • Phylogenetic analysis requires understanding evolutionary relationships reflected in DNA.

Purpose of the Study:

  • To introduce a novel genome signature based on DNA compositional structure.
  • To quantify species divergence using a new distance metric.
  • To assess the phylogenetic signal captured by this compositional approach.

Main Methods:

  • Utilized entropic segmentation to divide DNA into segments.
  • Analyzed distributions of DNA base ratios (strong/weak, purine/pyrimidine, keto/amino).
  • Applied Jensen-Shannon distance to calculate Segment Compositional Distance (D) between genomes.

Main Results:

  • DNA ratio distributions showed similarity in related species and divergence in distant ones.
  • Segment Compositional Distance (D) demonstrated a clear correlation with species divergence times.
  • The metric effectively captured significant phylogenetic signals.

Conclusions:

  • The proposed genome signature and Segment Compositional Distance (D) offer a robust method for comparative genomics.
  • This genome-wide, compositional approach provides insights into genome evolution and the molecular clock hypothesis.
  • The method is applicable to identifying species and understanding evolutionary history without sequence alignment.