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Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs.

Daniel M Portik1,2, Jeffrey W Streicher3, David C Blackburn4

  • 1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.

Molecular Biology and Evolution
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Summary

Integrating phylogenomic and supermatrix data is possible, even with extensive missing data. This approach successfully reconstructs frog evolutionary relationships, demonstrating a method for combining gene and taxon sampling.

Keywords:
amphibiansmissing dataphylogenomicsphylogenysupermatrix

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Area of Science:

  • Evolutionary Biology
  • Genomics
  • Bioinformatics

Background:

  • Reconstructing molecular phylogenies faces challenges due to disparate data availability, ranging from thousands of genetic markers for a few species to few genes for many taxa.
  • Integrating these diverse data types is crucial for a comprehensive understanding of evolutionary relationships across a broad range of species and genetic markers.

Purpose of the Study:

  • To investigate the feasibility of combining large phylogenomic datasets (thousands of markers) with supermatrix datasets (many taxa, fewer genes) to reconstruct evolutionary history.
  • To assess whether high levels of missing data impede the successful integration of these datasets and the resolution of phylogenetic relationships.

Main Methods:

  • Generated a phylogenomic dataset of 3,784 nuclear markers (ultraconserved elements [UCEs]) for 138 frog species.
  • Assembled a supermatrix dataset including 441 frog genera (97% of known genera) with 1-307 genes per taxon.
  • Combined these datasets into a 'gigamatrix' of 4,091 markers and 441 taxa, characterized by 86% missing data, and performed likelihood analysis.

Main Results:

  • The combined gigamatrix analysis yielded a well-supported phylogenetic tree among frog families, consistent with phylogenomic data alone.
  • All terminal taxa were correctly placed within their expected families, despite a significant proportion (42.5%) having >99.5% missing data.

Conclusions:

  • Missing data do not necessarily hinder the successful integration of large phylogenomic and supermatrix datasets.
  • This study demonstrates a viable method for simultaneously maximizing gene and taxon sampling in phylogenetic reconstructions, opening new avenues for evolutionary studies.