<%BANNER%>

Homoplastic microinversions and the avian tree of life

PRIVATE ITEM Digitization of this item is currently in progress.
  • STANDARD VIEW
  • MARC VIEW

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:

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

  • STANDARD VIEW
  • MARC VIEW

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:

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