Research article

BMC Evolutionary Biology

, 11:141

Open Access This content is freely available online to anyone, anywhere at any time.

Homoplastic microinversions and the avian tree of life

  • Edward L BraunAffiliated withDepartment of Biology, University of Florida Email author 
  • , Rebecca T KimballAffiliated withDepartment of Biology, University of Florida
  • , Kin-Lan HanAffiliated withDepartment of Biology, University of Florida
  • , Naomi R Iuhasz-VelezAffiliated withDepartment of Mathematics, University of Florida
  • , Amber J BonillaAffiliated withDepartment of Biology, University of Florida
  • , Jena L ChojnowskiAffiliated withDepartment of Biology, University of Florida
  • , Jordan V SmithAffiliated withDepartment of Biology, University of Florida
  • , Rauri CK BowieAffiliated withZoology Department, Field Museum of Natural HistoryMuseum of Vertebrate Zoology and Department of Integrative Biology, University of California
  • , Michael J BraunAffiliated withDepartment of Vertebrate Zoology, Smithsonian InstitutionBehavior, Ecology, Evolution, and Systematics Program, University of Maryland
    • , Shannon J HackettAffiliated withZoology Department, Field Museum of Natural History
    • , John HarshmanAffiliated withZoology Department, Field Museum of Natural History
    • , Christopher J HuddlestonAffiliated withDepartment of Vertebrate Zoology, Smithsonian Institution
    • , Ben D MarksAffiliated withMuseum of Natural Science and Department of Biological Sciences, Louisiana State University
    • , Kathleen J MigliaAffiliated withDepartment of Biological Sciences, Wayne State University
    • , William S MooreAffiliated withDepartment of Biological Sciences, Wayne State University
    • , Sushma ReddyAffiliated withZoology Department, Field Museum of Natural HistoryBiology Department, Loyola University Chicago
    • , Frederick H SheldonAffiliated withMuseum of Natural Science and Department of Biological Sciences, Louisiana State University
    • , Christopher C WittAffiliated withMuseum of Natural Science and Department of Biological Sciences, Louisiana State UniversityDepartment of Biology and Museum of Southwestern Biology, University of New Mexico
    • , Tamaki YuriAffiliated withDepartment of Biology, University of FloridaDepartment of Vertebrate Zoology, Smithsonian InstitutionSam Noble Oklahoma Museum of Natural History, University of Oklahoma

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.