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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.
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...
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Gene Families01:57

Gene Families

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.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Mutation, Gene Flow, and Genetic Drift01:09

Mutation, Gene Flow, and Genetic Drift

In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).Mechanisms of Genetic VariationThe original sources of genetic variation are mutations,...
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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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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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Published on: August 14, 2018

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

Pawel Górecki1, Gordon J Burleigh, Oliver Eulenstein

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

BMC Bioinformatics
|February 24, 2011
PubMed
Summary

This study introduces DrML, a new maximum likelihood model and efficient algorithm for mapping gene duplication and loss events on species phylogenies. DrML provides a practical statistical framework, offering different results than parsimony methods.

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Phylogenetics

Background:

  • Genomic data enables mapping of gene duplication and loss events on species phylogenies.
  • Early methods relied on parsimony, minimizing duplication/loss events.
  • Probabilistic modeling, often using birth-death processes, is a newer approach.

Purpose of the Study:

  • To introduce a novel maximum likelihood model for estimating gene duplication and loss events within a species tree.
  • To develop an efficient algorithm for computing optimal evolutionary scenarios under this model.
  • To implement the algorithm in a practical software tool (DrML).

Main Methods:

  • Developed a maximum likelihood model for gene duplication and loss inference.
  • Created an efficient algorithm to compute optimal evolutionary scenarios.
  • Implemented the algorithm in the DrML program.
  • Validated performance using empirical and simulated data.

Main Results:

  • The DrML program efficiently computes optimal gene duplication and loss scenarios in minutes, even for large gene trees.
  • Optimal scenarios identified by DrML often differ from those obtained using parsimony-based least common ancestor (LCA) mapping.
  • The model accurately estimates speciation and gene duplication/loss events.

Conclusions:

  • DrML offers a new, practical statistical framework for studying gene duplication.
  • The tool is efficient and handles large datasets.
  • Findings highlight the limitations of parsimony-based methods and the utility of probabilistic approaches.