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Related Concept Videos

Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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 characterized.
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
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...
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...

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Related Experiment Video

Updated: May 21, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.

Mukul S Bansal1, Eric J Alm, Manolis Kellis

  • 1Computer Science and Artificial Intelligence Laboratory, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. mukul@csail.mit.edu

Bioinformatics (Oxford, England)
|June 13, 2012
PubMed
Summary

New algorithms significantly accelerate gene family evolution analysis by improving duplication-transfer-loss (DTL) reconciliation. This advancement enables more robust evolutionary genomics and tree reconstruction for large gene families.

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Related Experiment Videos

Last Updated: May 21, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

  • Comparative genomics
  • Evolutionary genomics
  • Bioinformatics

Background:

  • Gene family evolution is shaped by speciation, duplication, horizontal gene transfer, and gene loss.
  • Reconciling gene and species phylogenies (duplication-transfer-loss or DTL reconciliation) is crucial for understanding evolutionary events.
  • Existing DTL reconciliation algorithms are computationally intensive, limiting their application to large gene families.

Purpose of the Study:

  • To develop significantly faster algorithms for DTL reconciliation.
  • To extend the DTL reconciliation model with distance-dependent transfer costs for improved accuracy.
  • To enable rigorous evolutionary analyses of large gene families and advanced tree reconstruction methods.

Main Methods:

  • Development of two novel, asymptotically and practically faster algorithms for DTL reconciliation.
  • Extension of the standard DTL model to incorporate distance-dependent transfer costs.
  • Implementation and evaluation of new algorithms on simulated and biological datasets.

Main Results:

  • Achieved up to 100,000-fold speed-up compared to existing DTL reconciliation methods.
  • Demonstrated the efficiency and accuracy of the new algorithms in practical applications.
  • Enabled DTL reconciliation for large gene families, previously computationally prohibitive.

Conclusions:

  • The new algorithms provide a dramatic improvement in speed and efficiency for DTL reconciliation.
  • The extended DTL model with distance-dependent costs enhances reconciliation accuracy.
  • These advancements facilitate advanced evolutionary analyses and tree reconstruction in genomics.