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Chapter 36 : Reconstructing and Interpreting Evolutionary Relationships

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Abstract:

Phylogenetics is the study of evolutionary relationships among organisms or genes, and phylogenetic analyses aim at estimating or reconstructing the evolutionary relationships among such “operational taxonomic units” (OTUs). These relationships are usually visualized as a phylogenetic tree, which portrays the evolutionary history of the OTUs. In this chapter the OTUs of interest are represented either by DNA or amino acid sequences. A reader with little or no prior experience, however, should be able to use the chapter as a guide to the options available for different types of data as well as to software available for doing the analysis. Importantly, if the rooting aspect of a tree is crucial to resolve a question, it is also likely to be the most unreliable part of the analysis. Halobacteria would remain monophyletic but the would become paraphyletic. With the increasing amount of sequences available, mainly from the genome-sequencing projects, it has become increasingly evident that many genes from prokaryotic genomes have different evolutionary relationships due to transfer of genes between lineages or species, a phenomenon termed lateral or horizontal gene transfer (LGT). It is apparent that the range of phylogenetic techniques is considerable, as are the questions that can be addressed using these techniques. It is also clear that phylogenetic analysis cannot be regarded as a "black box" and that each analysis will be "custom made".

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36

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Figures

Image of FIGURE 1
FIGURE 1

Three possible alignments between the same two sequences, showing the compromises between the number of gaps and the number of mismatches. Positions in bold indicate matching sites.

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36
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Image of FIGURE 2
FIGURE 2

Sequences in FASTA format. Each sequence is composed of two parts. The first part includes the first line only, which always starts with a “greater than” sign (>) and is a more or less complex description of the sequence. To avoid any downstream problems, we recommend using a nine-character descriptor with spaces represented by an underscore sign (e.g., the last sequence). The second part is the actual string of nucleotides or amino acids. By default this part will start after the descriptor paragraph mark and will end just before the next “greater than” sign.

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36
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Image of FIGURE 3
FIGURE 3

Unrooted (A) versus rooted (B and C) trees. Ovals enclose monophyletic groups and rectangles enclose paraphyletic groups. Underlined taxa are members of a polyphyletic group. The black dots on the tree represent each group's ancestor. Note that when the outgroup is changed, some monophyletic groups may become paraphyletic (e.g., the are monophyletic in tree B but not in C). The scale bar represents substitutions per 100 sites.

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36
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References

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Tables

Generic image for table
TABLE 1

Useful software

This list is far from being exhaustive, but presents a few of the most widely used software packages. A more complete list can be found at Joe Felsenstein's web page (http://evolution.genetics.washington.edu/phylip/software.html).

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36
Generic image for table
TABLE 2

Function implemented in some of the most common phylogenetic software

Absence of a check mark does not mean that the given software cannot perform the task, but that we do not find it advisable to carry out the task. When between parentheses, a check mark indicates a weak possibility. *, via other software. nt, nucleotides; aa, amino acids.

Citation: Douady C, Nesbø C. 2007. Reconstructing and Interpreting Evolutionary Relationships, p 856-868. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch36

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