Abstract
Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite–host or parasite–vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.
| Original language | English |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc |
| Pages | 9-68 |
| Number of pages | 60 |
| DOIs | |
| Publication status | Published - 15 Apr 2019 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1971 |
| ISSN (Print) | 1064-3745 |
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Keywords
- DNA sequence analysis
- Genetic markers
- Leishmania
- Multilocus approaches
- Phylogenetic inference methods
- Phylogenetic inference software
- Phylogenetics
- Single locus approaches
- Taxonomic levels
Cite this
}
Phylogenetic Studies. / Kuhls, Katrin; Mauricio, Isabel.
Methods in Molecular Biology. Humana Press Inc, 2019. p. 9-68 (Methods in Molecular Biology; Vol. 1971).Research output: Chapter in Book/Report/Conference proceeding › Chapter
TY - CHAP
T1 - Phylogenetic Studies
AU - Kuhls, Katrin
AU - Mauricio, Isabel
PY - 2019/4/15
Y1 - 2019/4/15
N2 - Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite–host or parasite–vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.
AB - Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite–host or parasite–vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.
KW - DNA sequence analysis
KW - Genetic markers
KW - Leishmania
KW - Multilocus approaches
KW - Phylogenetic inference methods
KW - Phylogenetic inference software
KW - Phylogenetics
KW - Single locus approaches
KW - Taxonomic levels
UR - http://www.scopus.com/inward/record.url?scp=85064757056&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-9210-2_2
DO - 10.1007/978-1-4939-9210-2_2
M3 - Chapter
T3 - Methods in Molecular Biology
SP - 9
EP - 68
BT - Methods in Molecular Biology
PB - Humana Press Inc
ER -