Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes
Reconstructing the Ancestral Relationships Between Bacterial Pathogen Genomes
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DOI：
10.1007/978-1-4939-6673-8_8
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发表时间：
2017-01-01
期刊：
影响因子：
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通讯作者：
Didelot, Xavier
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文献类型：
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作者：
Collins, Caitlin;Didelot, Xavier
随着DNA测序技术的最新发展，现在可以以相对较低的成本对数百个细菌分离株的全基因组进行测序。从祖先关系的角度分析这些日益丰富的基因组数据，可以揭示细菌病原体的进化、生态学和流行病学的许多有趣方面。然而，重建细菌样本的祖先仍然具有挑战性，特别是对于大多数重组频繁的物种。在这里，我们回顾和描述了目前可用于推断祖先关系的计算技术，包括系统发育方法，忽略或考虑重组的影响，以及基于模型和无模型的同源性独立方法。
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches.