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Updated: May 9, 2026
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Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time
Shannon M Hedtke1, Matthew J Morgan, David C Cannatella
1Department of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas at Austin, Austin, Texas, United States of America. shannon.hedtke@gmail.com
Plos One
|July 12, 2013
Summary
Phylogenetic analysis using hybridization-based exon enrichment can resolve deep evolutionary frog relationships. This method is practical for non-model organisms despite challenges with divergent species and missing data.
Area of Science:
- Evolutionary biology
- Genomics
- Phylogenetics
Background:
- Accurate evolutionary phylogenies require extensive genomic data across many species.
- Sequencing whole genomes for non-model organisms is resource-intensive.
- Resolving deep evolutionary divergences remains a challenge.
Purpose of the Study:
- To test the efficacy of hybridization-based exon enrichment for inferring phylogenies of diverse frog species.
- To assess the impact of evolutionary divergence time on enrichment success.
- To determine the feasibility of this method for deep evolutionary time.
Main Methods:
- Utilized genomic data from a single reference species for probe design.
- Employed hybridization-based enrichment to capture hundreds of exons across various frog species.
- Analyzed sequence data to construct phylogenetic trees, accounting for missing data.
Main Results:
- Enrichment success was inversely correlated with species divergence time from the reference.
- Resulting alignments contained a notable proportion of missing data.
- A well-supported phylogeny of frogs was successfully generated.
Conclusions:
- Hybridization-based exon enrichment is a practical approach for resolving deep evolutionary relationships.
- This technique offers a viable solution for phylogenetic inference in non-model organisms.
- The method facilitates the reconstruction of evolutionary history across significant time scales.
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