Homoplastic microinversions and the avian tree of life
<p>Abstract</p> <p>Background</p> <p>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 charac...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-05-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://www.biomedcentral.com/1471-2148/11/141 |
| _version_ | 1818887323169849344 |
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| author | Marks Ben D Huddleston Christopher J Harshman John Hackett Shannon J Braun Michael J Smith Jordan V Bowie Rauri CK Chojnowski Jena L Bonilla Amber J Iuhasz-Velez Naomi R Han Kin-Lan Kimball Rebecca T Braun Edward L Miglia Kathleen J Moore William S Reddy Sushma Sheldon Frederick H Witt Christopher C Yuri Tamaki |
| author_facet | Marks Ben D Huddleston Christopher J Harshman John Hackett Shannon J Braun Michael J Smith Jordan V Bowie Rauri CK Chojnowski Jena L Bonilla Amber J Iuhasz-Velez Naomi R Han Kin-Lan Kimball Rebecca T Braun Edward L Miglia Kathleen J Moore William S Reddy Sushma Sheldon Frederick H Witt Christopher C Yuri Tamaki |
| author_sort | Marks Ben D |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> |
| first_indexed | 2024-12-19T16:35:24Z |
| format | Article |
| id | doaj.art-1deda5f968d8425a9ed554f5b6e15c96 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-19T16:35:24Z |
| publishDate | 2011-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-1deda5f968d8425a9ed554f5b6e15c962022-12-21T20:13:58ZengBMCBMC Evolutionary Biology1471-21482011-05-0111114110.1186/1471-2148-11-141Homoplastic microinversions and the avian tree of lifeMarks Ben DHuddleston Christopher JHarshman JohnHackett Shannon JBraun Michael JSmith Jordan VBowie Rauri CKChojnowski Jena LBonilla Amber JIuhasz-Velez Naomi RHan Kin-LanKimball Rebecca TBraun Edward LMiglia Kathleen JMoore William SReddy SushmaSheldon Frederick HWitt Christopher CYuri Tamaki<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2148/11/141 |
| spellingShingle | Marks Ben D Huddleston Christopher J Harshman John Hackett Shannon J Braun Michael J Smith Jordan V Bowie Rauri CK Chojnowski Jena L Bonilla Amber J Iuhasz-Velez Naomi R Han Kin-Lan Kimball Rebecca T Braun Edward L Miglia Kathleen J Moore William S Reddy Sushma Sheldon Frederick H Witt Christopher C Yuri Tamaki Homoplastic microinversions and the avian tree of life BMC Evolutionary Biology |
| title | Homoplastic microinversions and the avian tree of life |
| title_full | Homoplastic microinversions and the avian tree of life |
| title_fullStr | Homoplastic microinversions and the avian tree of life |
| title_full_unstemmed | Homoplastic microinversions and the avian tree of life |
| title_short | Homoplastic microinversions and the avian tree of life |
| title_sort | homoplastic microinversions and the avian tree of life |
| url | http://www.biomedcentral.com/1471-2148/11/141 |
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