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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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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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Published on: August 14, 2018

Choosing and using introns in molecular phylogenetics.

Simon Creer1

  • 1School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom. s.creer@bangor.ac.uk

Evolutionary Bioinformatics Online
|May 23, 2009
PubMed
Summary

This review details using introns for molecular phylogenetics, covering locus selection, paralogy, recombination, and analytical methods for accurate species tree reconstruction using non-coding nuclear data.

Keywords:
EPIC primersalignmentindelintronslength variant heterozygote (LVH)recombination

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Introns are increasingly utilized in molecular phylogenetics to infer species trees.
  • Empirical studies often overlook crucial genomic, logistical, and analytical considerations for intron data.

Purpose of the Study:

  • To provide a comprehensive guide for using intron data in contemporary phylogenetics.
  • To address frequently overlooked aspects of intron data generation and analysis.

Main Methods:

  • Outlines strategies for locus selection and managing paralogy.
  • Describes methods for recombination detection and identifying lineage-specific introns (LVHs).
  • Reviews parsimony and Bayesian approaches for sequence alignment and indel treatment.

Main Results:

  • Offers practical solutions for common challenges in intron-based phylogenetics.
  • Highlights various analytical techniques applicable to intron sequence data.
  • Emphasizes the importance of addressing specific analytical considerations for robust phylogenetic inference.

Conclusions:

  • This review serves as an introduction to using introns and other non-coding nuclear data for phylogenetic studies.
  • Provides a framework for researchers to effectively utilize intron data for accurate evolutionary analyses.