Genome-wide detection of selection and other evolutionary forces

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

Genome-wide detection of selection and other evolutionary forces. / Xu, Zhuofei; Zhou, Rui.

Bacterial pangenomics: methods and protocols. ed. / Alessio Mengoni; Marco Galardini; Marco Fondi . Springer, 2015. p. 271-287 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Xu, Z & Zhou, R 2015, Genome-wide detection of selection and other evolutionary forces. in A Mengoni, M Galardini & M Fondi (eds), Bacterial pangenomics: methods and protocols. Springer, Methods in Molecular Biology, pp. 271-287. https://doi.org/10.1007/978-1-4939-1720-4_17

APA

Xu, Z., & Zhou, R. (2015). Genome-wide detection of selection and other evolutionary forces. In A. Mengoni, M. Galardini, & M. Fondi (Eds.), Bacterial pangenomics: methods and protocols (pp. 271-287). Springer. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-1720-4_17

Vancouver

Xu Z, Zhou R. Genome-wide detection of selection and other evolutionary forces. In Mengoni A, Galardini M, Fondi M, editors, Bacterial pangenomics: methods and protocols. Springer. 2015. p. 271-287. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-1720-4_17

Author

Xu, Zhuofei ; Zhou, Rui. / Genome-wide detection of selection and other evolutionary forces. Bacterial pangenomics: methods and protocols. editor / Alessio Mengoni ; Marco Galardini ; Marco Fondi . Springer, 2015. pp. 271-287 (Methods in Molecular Biology).

Bibtex

@inbook{00540047326945f18b95a96327263a9d,
title = "Genome-wide detection of selection and other evolutionary forces",
abstract = "As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed preferentially. Many recent comparative genomics studies have pointed out the importance of selective forces in the molecular evolution of bacterial pathogens. The public availability of large-scale next-generation sequencing data and many state-of-the-art statistical methods of molecular evolution enable us to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome of an animal pathogen. The evolutionary analysis of the protein-coding part of the genomes will provide a wide spectrum oof genetic variations that play potential roles in adaptive evolution of bacteria.",
keywords = "Adaptive evolution, Bacteria, Intragenic homologous recombination, Positive selection, Sequence alignment",
author = "Zhuofei Xu and Rui Zhou",
year = "2015",
doi = "10.1007/978-1-4939-1720-4_17",
language = "English",
isbn = "978-1-4939-1719-8",
series = "Methods in Molecular Biology",
publisher = "Springer",
pages = "271--287",
editor = "Mengoni, {Alessio } and Galardini, {Marco } and {Fondi }, {Marco }",
booktitle = "Bacterial pangenomics",
address = "Switzerland",

}

RIS

TY - CHAP

T1 - Genome-wide detection of selection and other evolutionary forces

AU - Xu, Zhuofei

AU - Zhou, Rui

PY - 2015

Y1 - 2015

N2 - As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed preferentially. Many recent comparative genomics studies have pointed out the importance of selective forces in the molecular evolution of bacterial pathogens. The public availability of large-scale next-generation sequencing data and many state-of-the-art statistical methods of molecular evolution enable us to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome of an animal pathogen. The evolutionary analysis of the protein-coding part of the genomes will provide a wide spectrum oof genetic variations that play potential roles in adaptive evolution of bacteria.

AB - As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed preferentially. Many recent comparative genomics studies have pointed out the importance of selective forces in the molecular evolution of bacterial pathogens. The public availability of large-scale next-generation sequencing data and many state-of-the-art statistical methods of molecular evolution enable us to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome of an animal pathogen. The evolutionary analysis of the protein-coding part of the genomes will provide a wide spectrum oof genetic variations that play potential roles in adaptive evolution of bacteria.

KW - Adaptive evolution

KW - Bacteria

KW - Intragenic homologous recombination

KW - Positive selection

KW - Sequence alignment

U2 - 10.1007/978-1-4939-1720-4_17

DO - 10.1007/978-1-4939-1720-4_17

M3 - Book chapter

C2 - 25343871

AN - SCOPUS:84914141701

SN - 978-1-4939-1719-8

T3 - Methods in Molecular Biology

SP - 271

EP - 287

BT - Bacterial pangenomics

A2 - Mengoni, Alessio

A2 - Galardini, Marco

A2 - Fondi , Marco

PB - Springer

ER -

ID: 153604954