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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...
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When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.Positive Frequency-Dependent SelectionIn positive...
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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.The structures that arise from convergent evolution are called analogous structures. They are similar in function even if they are dissimilar in structure. Further, structures can be analogous while also...
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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: Jun 12, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

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Published on: February 10, 2023

JCoDA: a tool for detecting evolutionary selection.

Steven N Steinway1, Ruth Dannenfelser, Christopher D Laucius

  • 1Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA.

BMC Bioinformatics
|May 29, 2010
PubMed
Summary

JCoDA is a user-friendly tool for evolutionary analysis of homologous coding sequences. It helps detect sites and regions under selection, aiding evolutionary relationship studies.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Databases now contain vast amounts of annotated sequence data from multiple species.
  • This data offers significant potential for evaluating evolutionary relationships.
  • Existing tools require improvement for efficient analysis of evolutionary selection.

Purpose of the Study:

  • To develop JCoDA (Java Codon Delimited Alignment), a visualization tool for detecting evolutionary selection.
  • To provide a user-friendly platform for analyzing homologous coding sequences.
  • To facilitate the identification of site-specific and regional evolutionary selection.

Main Methods:

  • JCoDA performs codon-delimited alignment using ClustalW.
  • It calculates dN/dS ratios using PAML (yn00 and codeml) to identify selection.
  • Includes graphical interfaces for Phylip tree generation and manages data flow between programs.

Main Results:

  • JCoDA visualizes pairwise and gene family comparisons using configurable graphs with sliding windows.
  • Output includes codon-delimited alignments in common formats and dN/dS calculations in CSV.
  • Demonstrated JCoDA's utility by analyzing nematode sex determination genes for positive selection.

Conclusions:

  • JCoDA is an open-source, configurable, and user-friendly tool for evolutionary analysis.
  • It enables rapid screening of genes and gene regions under selection using PAML.
  • The software is freely available for download.