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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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The evolution of phylogeographic data sets.

Ryan C Garrick1, Isabel A S Bonatelli, Chaz Hyseni

  • 1Department of Biology, University of Mississippi, Oxford, MS, 38677, USA.

Molecular Ecology
|February 14, 2015
PubMed
Summary

Phylogeographic studies increasingly use more genetic data, with significant growth in single nucleotide polymorphisms (SNPs) over the past five years. Future research requires advanced methods to analyze these large genetic datasets.

Keywords:
DNA sequencesinformation contentphylogeographysamplingsingle nucleotide polymorphismstemporal trends

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Area of Science:

  • Evolutionary Biology
  • Genetics
  • Ecology

Background:

  • Phylogeographic studies aim to understand organismal history and population genetics.
  • Theoretical work suggests more genetic loci improve demographic parameter estimates.
  • Next-generation sequencing offers potential for revolutionizing phylogeographic data collection.

Purpose of the Study:

  • To systematically assess changes in phylogeographic data set size and content over the last 20 years.
  • To identify trends in the evolution of genetic data used in phylogeography.
  • To forecast future data set sizes and analytical needs.

Main Methods:

  • Quantitative analysis of phylogeographic studies published in "Molecular Ecology" over two decades.
  • Focus on the number of independent loci, alleles, and single nucleotide polymorphisms (SNPs).
  • Trend analysis and forecast modeling based on observed data growth.

Main Results:

  • Significant increases in the number of loci, alleles, and SNPs per data set over time.
  • Accelerated growth in data set size observed in the last five years.
  • Uniparentally inherited markers (mitochondrial, chloroplast DNA) remain important.
  • Single-species studies on vertebrates, especially fish and birds, are prominent.
  • Forecast suggests median SNPs per data set may reach ~20,000 by 2016.

Conclusions:

  • Phylogeographic data sets have grown substantially in size and information content.
  • The increasing volume of genetic data necessitates the development of advanced analytical methods.
  • Organellar DNA and vertebrate studies continue to be key components of phylogeography.