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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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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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Branching-Process Modeling of Homology Distribution in Salmonid Genomes.

Yue Zhang1, David Sankoff2

  • 1Department of Mathematics and Statistics, Thompson Rivers University, Kamloops, BC, Canada.

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|March 28, 2026
PubMed
Summary

Salmonid evolution involves whole-genome duplication (WGD) and speciation, challenging gene family modeling. A new framework quantifies gene loss rates after WGD, revealing conserved dynamics and lineage-specific retention patterns.

Keywords:
Salmonidaebranching processgene retention dynamicssequence similarity distributionsynteny losswhole-genome duplication

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Area of Science:

  • Evolutionary genomics
  • Bioinformatics
  • Population genetics

Background:

  • Whole-genome duplication (WGD) events and rapid speciation in Salmonidae complicate the study of gene family evolution.
  • Understanding gene retention and sequence divergence is crucial for reconstructing evolutionary histories.
  • Existing models struggle to accurately capture the complex dynamics of gene loss following WGD in species-rich lineages.

Purpose of the Study:

  • To develop a novel stochastic branching-process framework for modeling sequence similarity decay and gene fractionation rates.
  • To quantify gene retention patterns and evolutionary dynamics across multiple salmonid species.
  • To investigate the factors influencing duplicate gene retention, distinguishing between loss rates and temporal gaps.

Main Methods:

  • Development of a stochastic branching-process model to simulate sequence similarity decay over evolutionary time.
  • Derivation of moment-generating functions for pairwise similarity scores.
  • Application of the model to salmonid genomes (Atlantic salmon, rainbow trout, Chinook salmon) and simulation-based validation.

Main Results:

  • The model successfully recapitulates observed bimodal sequence similarity distributions in salmonids.
  • Estimated fractionation rates for the two WGDs are consistent across species (~0.0009-0.0013 per Myr) and independent of synteny block size.
  • Lineage-specific differences in duplicate retention are primarily attributed to the timing of duplication events, not instantaneous loss rates.

Conclusions:

  • Fractionation dynamics following WGD are highly conserved across salmonid species, indicating stable gene loss mechanisms.
  • The temporal spacing between WGD events plays a critical role in shaping lineage-specific gene retention patterns.
  • Structural genome decay significantly influences retention patterns, providing insights into salmonid and sucker fish evolution.