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Open Access Highly Accessed Research article

Homoplastic microinversions and the avian tree of life

Edward L Braun1*, Rebecca T Kimball1, Kin-Lan Han1, Naomi R Iuhasz-Velez2, Amber J Bonilla1, Jena L Chojnowski1, Jordan V Smith1, Rauri CK Bowie34, Michael J Braun56, Shannon J Hackett3, John Harshman37, Christopher J Huddleston5, Ben D Marks8, Kathleen J Miglia9, William S Moore9, Sushma Reddy103, Frederick H Sheldon8, Christopher C Witt118 and Tamaki Yuri1125

Author Affiliations

1 Department of Biology, University of Florida, Gainesville, FL 32611, USA

2 Department of Mathematics, University of Florida, Gainesville, FL 32611, USA

3 Zoology Department, Field Museum of Natural History, 1400 S. Lakeshore Drive, Chicago, IL 60605, USA

4 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA

5 Department of Vertebrate Zoology, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA

6 Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD 20742, USA

7 4869 Pepperwood Way, San Jose, CA 95124, USA

8 Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA

9 Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA

10 Biology Department, Loyola University Chicago, Chicago, IL 60626, USA

11 Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA

12 Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA

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BMC Evolutionary Biology 2011, 11:141  doi:10.1186/1471-2148-11-141

Published: 25 May 2011

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.