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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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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.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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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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Synteny and Evolution02:31

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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Exon Recombination02:32

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Convergent Evolution01:54

Convergent Evolution

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Evolution shapes the features of organisms over time, ensuring that they are suited for the environments in which they live. Sometimes, selection pressure leads to the rise of similar but unrelated adaptations in organisms with no recent common ancestors, a process known as convergent evolution.
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Gene Evolution - Fast or Slow?02:05

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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.
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Related Experiment Video

Updated: Dec 19, 2025

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Evolution through segmental duplications and losses: a Super-Reconciliation approach.

Mattéo Delabre1, Nadia El-Mabrouk1, Katharina T Huber2

  • 1Département d'informatique (DIRO), Université de Montréal, Québec, Canada.

Algorithms for Molecular Biology : AMB
|June 9, 2020
PubMed
Summary

We introduce Super-Reconciliation to study concerted gene evolution, inferring segmental duplication and loss events for gene families within syntenic blocks. This extends traditional gene family evolution models by considering linked gene histories.

Keywords:
DuplicationGene treeLossReconciliationSynteny

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Area of Science:

  • Computational Biology
  • Evolutionary Genetics
  • Bioinformatics

Background:

  • Classical gene and species tree reconciliation assumes independent gene family evolution.
  • This assumption is inadequate for genes in syntenic blocks, which evolve concertedly.
  • Syntenic blocks suggest a history of segmental duplication and loss events.

Purpose of the Study:

  • Introduce the Super-Reconciliation problem to model concerted evolution of neighboring genes.
  • Extend traditional Duplication-Loss reconciliation to handle sets of gene trees within syntenic blocks.
  • Infer evolutionary histories involving segmental duplications and losses for linked genes.

Main Methods:

  • Define the Super-Reconciliation problem for inferring segmental duplication and loss events.
  • Develop an exact exponential-time algorithm for reconstructing the most parsimonious Super-Reconciliation.
  • Propose a polynomial-time algorithm when accounting for genomic rearrangements alongside duplications and losses.

Main Results:

  • The problem of reconstructing a most parsimonious Super-Reconciliation is NP-hard.
  • An exact exponential-time algorithm was developed for the Duplication-Loss model.
  • A polynomial-time algorithm was derived by incorporating rearrangements into the evolutionary model.

Conclusions:

  • Super-Reconciliation provides a framework for understanding the concerted evolution of gene families in syntenic blocks.
  • The computational complexity of Super-Reconciliation depends on the inclusion of genomic rearrangements.
  • The proposed methods were validated on simulated data and a case study of opioid receptor genes.