Phylogenetic Analysis Workflows - User-Level Workflow Design: A Bioinformatics Perspective - page 64

different members of a family, they depict the phylogenetic evolution of living
organismsand the originof species overthe courseof time. The exemplary “uni-
versal tree of life” depicted in Figure 3.1 shows a phylogenetic tree that visual-
izes the separation of the realms of bacteria, archaea, and eukaryotes [346]. As
it was inferredfrom comparativeanalysis of ribosomalRNA (rRNA) sequences,
it differs in details such as exact branching points and the exact position of the
root (the suspected common ancestor) from trees that have been constructed
based on other genes. The general picture, however, remains the same. Note
that humankind is located within the “Animals” branch of the eukaryotes (in
the upper right corner of the figure), and that the vast majority of species are
microorganisms that are too small to be seen by the naked eye.
In the daily routine of molecular biology research, however, the phyloge-
netic relationships between different strains of particular organisms play a
more important role than the universal tree of life. During the 2011 EHEC
outbreak in Germany, for instance, phylogenetic methods were applied to an-
alyze the E. coli strains that caused the severe hemolytic-uremic syndrome
(HUS) [21]: Samples of the infectious variant of the normally harmless and
vital intestinal bacteria were isolated and their genomes sequenced. A phy-
longetic analysis (incorporating a phylogenetic tree constructed from known
E. coli strains and the newly sequenced ones) revealed that the new strains
were in fact closely related to a known pathogenic strain. Subsequently, addi-
tional knowledge about the new strain could be derived from more detailed
comparisons with the closely related strains. Collecting such comprehensive
knowledge about the biological characteristics of a pathogenic organism is of
course of academic interest, but furthermore essential for the development of
effective treatments and medication.

3.1.2 Sequence Alignments

Sequence alignments (cf., e.g., [254, Chapter 6]) try to establish correspon-
dences between the bases or codons of DNA, RNA, or amino acid sequences.
They are used in phylogenetics to identify similarities between sequences which
result from the existence of a common ancestor. Other applications of align-
ments are the matching of sequences against databases, the detection of over-
laps and subsequences, the prediction of secondary and tertiary structures of
proteins, as well as the prediction of active or functionally important sites of
proteins.

Fig. 3.2 Simple pairwise nucleotide sequence alignment

Figure 3.2 shows a possible alignment for the nucleotide sequences TG-
GACCATTT ( s 1 ) and TGCACGCATAT ( s 2 ). The asterisks indicate exact