| Item type |
学術雑誌論文 / Journal Article(1) |
| 公開日 |
2012-12-18 |
| タイトル |
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タイトル |
Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions |
| タイトル |
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タイトル |
Confounding factors in HGT detection: Statistical error, coalescent effects, and multiple solutions |
|
言語 |
en |
| 言語 |
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|
言語 |
eng |
| 資源タイプ |
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資源タイプ識別子 |
http://purl.org/coar/resource_type/c_6501 |
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資源タイプ |
journal article |
| 著者 |
THAN, Cuong
RUTHS, Derek
INNAN, Hideki
NAKHLEH, Luay
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| 著者別名 |
印南, 秀樹
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| 抄録 |
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内容記述タイプ |
Abstract |
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内容記述 |
Prokaryotic organisms share genetic material across species boundaries by means of a process known as horizontal gene transfer (HGT). This process has great significance for understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used methods for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with the species phylogeny. Using these methods, we can compare gene and species trees, and infer a set of HGT events to reconcile the differences among these trees. In this paper, we address three factors that confound the detection of the true HGT events, including the donors and recipients of horizontally transferred genes. First, we study experimentally the effects of error in the estimated gene trees (statistical error) on the accuracy of inferred HGT events. Our results indicate that statistical error leads to overestimation of the number of HGT events, and that HGT detection methods should be designed with unresolved gene trees in mind. Second, we demonstrate, both theoretically and empirically, that based on topological comparison alone, the number of HGT scenarios that reconcile a pair of species/gene trees may be exponential. This number may be reduced when branch lengths in both trees are estimated correctly. This set of results implies that in the absence of additional biological information, and/or a biological model of how HGT occurs, multiple HGT scenarios must be sought, and efficient strategies for how to enumerate such solutions must be developed. Third, we address the issue of lineage sorting, how it confounds HGT detection, and how to incorporate it with HGT into a single stochastic framework that distinguishes between the two events by extending population genetics theories. This result is very important, particularly when analyzing closely related organisms, where coalescent effects may not be ignored when reconciling gene trees. In addition to these three confounding factors, we consider the problem of enumerating all valid coalescent scenarios that constitute plausible species/gene tree reconciliations, and develop a polynomial-time dynamic programming algorithm for solving it. This result bears great significance on reducing the search space for heuristics that seek reconciliation scenarios. Finally, we show, empirically, that the locality of incongruence between a pair of trees has an impact on the numbers of HGT and coalescent reconciliation scenarios. |
| 書誌情報 |
Journal of Computational Biology
en : Journal of Computational Biology
巻 14,
号 4,
p. 517-535,
発行日 2007-06-15
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| 出版者 |
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出版者 |
Mary Ann Liebert |
| ISSN |
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収録物識別子タイプ |
ISSN |
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収録物識別子 |
10665277 |
| PubMed番号 |
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関連タイプ |
isIdenticalTo |
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識別子タイプ |
PMID |
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関連識別子 |
17572027 |
| DOI |
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関連タイプ |
isIdenticalTo |
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識別子タイプ |
DOI |
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関連識別子 |
https://doi.org/10.1089/cmb.2007.A010 |
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関連名称 |
10.1089/cmb.2007.A010 |
| 権利 |
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|
権利情報 |
© Mary Ann Liebert, Inc. |
| 関連サイト |
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識別子タイプ |
URI |
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関連識別子 |
http://www.liebertpub.com/media/content/transfer_of_copyright.pdf |
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関連名称 |
Copyright |
| フォーマット |
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内容記述タイプ |
Other |
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内容記述 |
application/pdf |
| 著者版フラグ |
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出版タイプ |
VoR |
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出版タイプResource |
http://purl.org/coar/version/c_970fb48d4fbd8a85 |
cmb.2007 (1.6 MB)
