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Title: | 藉由保存式反轉機制來推測親緣關係 The Phylogeny Inference by Preserving Inversion |
Authors: | Chun-Wei Kao 高峻偉 |
Advisor: | 趙坤茂(Kun-Mao Chao) |
Keyword: | 親緣關係學,基因序列,基因重組,中位數網路,有號排列,保存式反轉, Phylogeny,Gene order,Genome rearrangement,Median network,Signed permutation,Preserving inversion, |
Publication Year : | 2011 |
Degree: | 碩士 |
Abstract: | 在親緣關係學 (phylogeny) 裡,親緣關係樹 (phylogenetic trees) 可用以表現不同物種之間的演化關係,它是相當實用的工具。然而,近年來發現親緣關係網路 (phylogenetic networks) 在當演化過程中可能包含如非同源相似 (homoplasy)、重組 (recombination)、雜交 (hybridization) 等網狀演化機制 (reticulate evolution) 時,相較於親緣關係樹可以保存更豐富的資訊。過去,親緣關係網路或親緣關係樹多半是由核甘酸 (nucleotide)、單倍群 (halpotype) 或 DNA 等資料建構而成。隨著基因組的定序 (genome sequencing) 以及比較基因組學 (comparative genomics) 的研究漸趨完善,愈來愈多的研究以基因組間的基因重組 (genome rearrangement) 為基礎來推測物種間的親緣關係。另外,研究發現,某些固定排列在一起的基因組 (gene groups) 不斷的在演化過程中被保存下來。若能在推測物種間親緣關係的過程中,同時將這些基因組保存下來,應能獲得更貼近物種間實際演化過程的推論結果。然而,目前與基因重組理論相關的研究多半致力於建構親緣關係樹,並且未考慮將某些特定的基因組保存下來。在這個研究裡,我們以保存式反轉機制 (preserving inversion) 為基礎來建構中位數網路 (median network)。保存式反轉機制為基因重組中的一種機制,且具有保存某些特定基因組的特性,而中位數網路亦是親緣關係網路中的一種。除此之外,我們也設計一個演算法可用來決定在特定的樹的拓樸結構中,該拓樸所能包含的基因重組之最低數目。當我們針對給定的一組物種,列舉所有可能的樹的拓樸結構,這個演算法為我們尋找親緣關係樹提供了非常實用的功能。 In the context of phylogeny, phylogenetic trees are widely used to describe the evolutionary relationships between species. In recent years, it is proven that phylogenetic networks can bring more information than phylogenetic trees when the underlying evolutionary history involves reticulate events, e.g. homoplasy, recombination and hybridization. In the past, phylogenetic trees (networks) are usually constructed from gene-scale dataset, e.g. nucleotide, haplotype or DNA. With the advance in genome sequencing and comparative genomics, more and more works on phylogeny inference are based on genome rearrangements. Moreover, it is observed that certain gene groups are preserved during evolution. That is, it is more plausible to assume that gene groups exist in both contemporary species and hypothetical ancestors. However, at present, previous works based on genome rearrangement were most dedicated to constructing phylogenetic trees without regard to conserving gene groups in the evolutionary scenarios. In this work, we construct a phylogenetic network, i.e. median network, based on genome rearrangement that conserves gene groups, i.e. preserving inversion. In addition, as far as phylogenetic tree is concerned, we provide an algorithm to decide the minimum number of rearrangement operations on a given tree topology. It is useful for finding phylogenetic trees when we enumerate all possible tree topologies for a set of species. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/39552 |
Fulltext Rights: | 有償授權 |
Appears in Collections: | 資訊工程學系 |
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