Material Information
- Title:
- Homoplastic microinversions and the avian tree of life
- Physical Description:
- Mixed Material
- Language:
- English
- Creator:
- Braun, Edward L.
Kimball, Rebecca T.
Han, Kin-Lan
Iuhasz-Velez, Naomi R.
Bonilla, Amber
Chojnowski, Jena L.
Smith, Jordan V.
- Publisher:
- Bio-Med Central (BMC Evolutionary Biology)
- Publication Date:
- 2011
Notes
- 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 homoplasyfree
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.
- General Note:
- Braun et al. BMC Evolutionary Biology 2011, 11:141
http://www.biomedcentral.com/1471-2148/11/141; Pages 1-10
- General Note:
- doi:10.1186/1471-2148-11-141
Cite this article as: Braun et al.: Homoplastic microinversions and the
avian tree of life. BMC Evolutionary Biology 2011 11:141.
Record Information
- Source Institution:
- University of Florida
- Holding Location:
- University of Florida
- Rights Management:
- All rights reserved by the source institution.
- Resource Identifier:
- oclc -
- System ID:
- AA00019191:00001
|
Material Information
- Title:
- Homoplastic microinversions and the avian tree of life
- Physical Description:
- Mixed Material
- Language:
- English
- Creator:
- Braun, Edward L.
Kimball, Rebecca T.
Han, Kin-Lan
Iuhasz-Velez, Naomi R.
Bonilla, Amber
Chojnowski, Jena L.
Smith, Jordan V.
- Publisher:
- Bio-Med Central (BMC Evolutionary Biology)
- Publication Date:
- 2011
Notes
- 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 homoplasyfree
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.
- General Note:
- Braun et al. BMC Evolutionary Biology 2011, 11:141
http://www.biomedcentral.com/1471-2148/11/141; Pages 1-10
- General Note:
- doi:10.1186/1471-2148-11-141
Cite this article as: Braun et al.: Homoplastic microinversions and the
avian tree of life. BMC Evolutionary Biology 2011 11:141.
Record Information
- Source Institution:
- University of Florida
- Holding Location:
- University of Florida
- Rights Management:
- All rights reserved by the source institution.
- Resource Identifier:
- oclc -
- System ID:
- AA00019191:00001
|
