Homoplastic microinversions and the avian tree of life

Authors

Edward L. Braun, University of FloridaFollow
Rebecca T. Kimball, University of FloridaFollow
Kin-Lan Han, University of FloridaFollow
Naomi R. Iuhasz-Velez, University of FloridaFollow
Amber J. Bonilla, University of FloridaFollow
Jena L. Chojnowski, University of FloridaFollow
Jordan V. Smith, University of FloridaFollow
Rauri CK Bowie, Field Museum of Natural History, ChicagoFollow
Michael J. Braun, Smithsonian InstitutionFollow
Shannon J. Hackett, Field Museum of Natural History, ChicagoFollow
John Harshman, Field Museum of Natural History, ChicagoFollow
Christopher J. Huddleston, Smithsonian InstitutionFollow
Ben D. Marks, Louisiana State UniversityFollow
Kathleen J. Miglia, Wayne State UniversityFollow
William S. Moore, Wayne State UniversityFollow
Sushma Reddy, Field Museum of Natural History, ChicagoFollow
Frederick H. Sheldon, Louisiana State UniversityFollow
Christopher C. Witt, Louisiana State UniversityFollow
Tamaki Yuri, University of FloridaFollow

Document Type

Article

Abstract

Abstract

Background

Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution.

Results

We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots.

Conclusions

Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies.

Disciplines

Poultry or Avian Science

Recommended Citation

Braun et al.: Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology 2011 11:141.