Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.
Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
Methods Mol Biol. 2022;2569:283-303. doi: 10.1007/978-1-0716-2691-7_14.
The reconstruction of genetic material of ancestral organisms constitutes a powerful application of evolutionary biology. A fundamental step in this inference is the ancestral sequence reconstruction (ASR), which can be performed with diverse methodologies implemented in computer frameworks. However, most of these methodologies ignore evolutionary properties frequently observed in microbes, such as genetic recombination and complex selection processes, that can bias the traditional ASR. From a practical perspective, here I review methodologies for the reconstruction of ancestral DNA and protein sequences, with particular focus on microbes, and including biases, recommendations, and software implementations. I conclude that microbial ASR is a complex analysis that should be carefully performed and that there is a need for methods to infer more realistic ancestral microbial sequences.
对远古生物遗传物质的重建构成了进化生物学的一项强大应用。该推断的一个基本步骤是祖先序列重建（ASR），它可以通过计算机框架中实现的各种方法来完成。然而，这些方法大多忽略了微生物中经常观察到的进化特性，例如遗传重组和复杂的选择过程，这可能会使传统的 ASR 产生偏差。从实际的角度来看，在这里我回顾了重建祖先 DNA 和蛋白质序列的方法，特别关注微生物，并包括了偏差、建议和软件实现。我得出结论，微生物的 ASR 是一项复杂的分析，应该谨慎进行，并且需要有方法来推断更现实的远古微生物序列。
