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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...
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...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
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...

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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

Pawel Górecki1, Oliver Eulenstein

  • 1Institute of Informatics, University of Warsaw, Warsaw, 02-097, Poland. gorecki@mimuw.edu.pl

BMC Bioinformatics
|July 5, 2012
PubMed
Summary

This study presents a new method to correct errors in gene trees, improving the accuracy of evolutionary analyses and species tree inference. The approach handles unrooted and erroneous gene trees, making phylogenetic studies more reliable.

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Area of Science:

  • Phylogenetics and Evolutionary Biology
  • Bioinformatics and Computational Biology
  • Genomic Sequence Analysis

Background:

  • Genomic data growth challenges traditional evolutionary methods.
  • Gene duplication, loss, and coalescence cause incongruence between gene and species trees.
  • Current gene tree reconciliation is limited by sensitivity to gene tree errors and rooting.

Purpose of the Study:

  • To address the limitations of gene tree reconciliation with erroneous and unrooted gene trees.
  • To develop an efficient error-correction method for gene tree reconciliation.
  • To improve the accuracy of gene duplication problem applications.

Main Methods:

  • Introduced a novel problem of reconciling unrooted and erroneous gene trees.
  • Developed an efficient algorithm for simultaneous rooting and error-correction.
  • Proposed an error-corrected heuristic for the gene duplication problem.

Main Results:

  • The error-correcting approach significantly improves gene tree reconciliation accuracy.
  • Species tree inference accuracy is enhanced using the new method.
  • The algorithm demonstrates efficiency for large-scale phylogenetic studies.

Conclusions:

  • The error-correction approach enhances the robustness of gene tree reconciliation.
  • This advancement improves the accuracy of downstream applications like gene-duplication supertree inference.
  • The method is crucial for reliable evolutionary analyses in the genomic era.