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Open Access Publications from the University of California

Quantitative analysis of phylogenetic informativeness, signal and noise in ultraconserved elements within Percomorpha and Neoaves

  • Author(s): Gilbert, Princess Scheran
  • Advisor(s): Alfaro, Michael E
  • et al.

The work described herein explores the ability of UCEs to resolve clade relationships within the vertebrate tree of life, specifically percomorph fishes and neoaves birds. To do so, I used Phylogenetic Informativeness and the phylogenetic signal to noise ratios in order to calculate the ability of a marker to resolve deep clade relationships, I also developed an automated pipeline in order to calculate these statistical measures for each of the nucleotides in thousands of UCEs. UCE cores and their respective flanking regions are large and spread out across the entire genome. Thus the approaches and findings described here are the first to analyze UCEs at a fine scale (per nucleotide) and the first to assess this phylogenetic marker type using these methods. Chapter 2 has been previously published as Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes. (2015) Gilbert PS, Chang J, Pan C, Sobel EM, Sinsheimer JS, Faircloth BC, Alfaro ME. Mol Phylogenet Evol. 2015 Nov;92:140-6. doi: 10.1016/j.ympev.2015.05.027.) Chapter 3 is in preparation for submission.

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