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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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A phylogenomic analysis of turtles.

Nicholas G Crawford1, James F Parham2, Anna B Sellas3

  • 1Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA.

Molecular Phylogenetics and Evolution
|December 3, 2014
PubMed
Summary

This study presents the first genome-scale analysis of turtle phylogeny, revealing a robust evolutionary tree. This new molecular phylogeny clarifies turtle relationships and provides a framework for future research.

Keywords:
BiogeographyPhylogeographySystematicsTurtlesUltraconserved elements

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Area of Science:

  • Herpetology
  • Evolutionary Biology
  • Genomics

Background:

  • Morphological studies have historically shaped turtle taxonomy.
  • Recent molecular analyses have challenged existing hypotheses on turtle evolutionary relationships.
  • A comprehensive, genome-scale phylogenetic analysis is needed to resolve discrepancies.

Purpose of the Study:

  • To conduct the first genome-scale analysis of turtle phylogeny.
  • To establish a robust evolutionary framework for all recognized turtle families.
  • To reconcile molecular data with existing taxonomic and paleontological evidence.

Main Methods:

  • Sequencing of 2381 ultraconserved element (UCE) loci.
  • Analysis of over 1.7 million base pairs of aligned sequence data.
  • Phylogenetic reconstruction using maximum likelihood, Bayesian, and species tree methods with 32 turtle taxa and six outgroups.

Main Results:

  • A single, well-resolved phylogeny for turtles was consistently produced across multiple analytical methods.
  • The resolved phylogeny supports previously proposed phylogenetic names and well-defined clades.
  • The resulting topology aligns better with the temporal distribution of turtle clades and paleobiogeographical data.

Conclusions:

  • This genome-scale phylogeny provides a robust scaffold for understanding turtle evolution.
  • The findings support a new taxonomy based on molecular data, overturning previous morphological hypotheses.
  • Future studies on fossil turtles should utilize this molecular topology as a basis for morphological phylogenetic analyses.