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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Homoplastic microinversions and the avian tree of life
BMC Evolutionary Biology, Volume 11, No. 1, Article 141, Year 2011
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Description
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. © 2011 Braun et al; licensee BioMed Central Ltd.
Authors & Co-Authors
Braun, Edward L.
United States, Gainesville
University of Florida
Kimball, Rebecca T.
United States, Gainesville
University of Florida
Han, Kin Lan
United States, Gainesville
University of Florida
Chojnowski, Jena L.
United States, Gainesville
University of Florida
Smith, Jordan V.
United States, Gainesville
University of Florida
Bowie, Rauri C. K.
United States, Chicago
Field Museum of Natural History
United States, Berkeley
University of California, Berkeley
Braun, Michael J.
United States, Washington, D.c.
Smithsonian Institution
United States, College Park
University of Maryland, College Park
Hackett, Shannon J.
United States, Chicago
Field Museum of Natural History
Harshman, John
United States, Chicago
Field Museum of Natural History
Huddleston, Christopher J.
United States, Washington, D.c.
Smithsonian Institution
Marks, Ben D.
United States, Baton Rouge
Louisiana State University
Miglia, Kathleen J.
United States, Detroit
Wayne State University
Moore, William Samuel
United States, Detroit
Wayne State University
Reddy, Sushma
United States, Chicago
Field Museum of Natural History
United States, Chicago
Loyola University Chicago
Sheldon, Frederick H.
United States, Baton Rouge
Louisiana State University
Witt, Christopher C.
United States, Baton Rouge
Louisiana State University
United States, Albuquerque
The University of new Mexico
Yuri, Tamaki
United States, Gainesville
University of Florida
United States, Washington, D.c.
Smithsonian Institution
United States, Norman
The University of Oklahoma
Statistics
Citations: 29
Authors: 17
Affiliations: 10
Identifiers
Doi:
10.1186/1471-2148-11-141
ISSN:
14712148
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study