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Related Concept Videos

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 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...
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.
Synteny and Evolution02:31

Synteny and Evolution

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.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral chromosome underwent...

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Related Experiment Video

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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Distance-based genome rearrangement phylogeny.

Li-San Wang1, Tandy Warnow, Bernard M E Moret

  • 1Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA. lswang@mail.upenn.edu

Journal of Molecular Evolution
|October 6, 2006
PubMed
Summary

This study introduces the empirically derived estimator (EDE) for whole genome phylogeny reconstruction. EDE significantly improves the accuracy of phylogenetic trees when analyzing gene content evolution.

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Whole genome evolution involves gene rearrangements and content changes.
  • Gene order data can resolve ancient evolutionary relationships.
  • Accurate phylogenetic reconstruction is crucial for understanding life's history.

Purpose of the Study:

  • To develop improved distance correction methods for whole genome phylogeny.
  • To address the challenge of estimating evolutionary histories from genomes with equal gene content.

Main Methods:

  • Development and application of the empirically derived estimator (EDE).
  • Inference of phylogenies using Neighbor-Joining and Minimum Evolution methods with EDE distances.
  • Evaluation under diverse model conditions for whole genomes with identical gene content.

Main Results:

  • The empirically derived estimator (EDE) provides accurate distance corrections for whole genome phylogeny.
  • Phylogenetic trees reconstructed using EDE distances show significantly higher accuracy.
  • EDE-based distances outperform previously suggested methods for whole genome analysis.

Conclusions:

  • The empirically derived estimator (EDE) is a powerful tool for whole genome phylogenetic reconstruction.
  • Accurate phylogenetic inference is enhanced by incorporating gene content evolution.
  • This method offers a computationally efficient approach to robust evolutionary history estimation.