FIGURE 20.21 Unusual Lipids of Archaea

The archaebacteria have lipid chains made of five carbon isoprenoid units rather than two carbon units as seen in eubacteria. The isoprenoid chains are linked to a glycerol via an ether link rather than an ester link. In some instances the isoprenoid lipid chains may contain 40 carbons (bacterioruberin, for example). These longer lipids span the whole membrane of the archaea.

quantitative measurements of genetic relatedness. Even if we cannot unambiguously define a species, we can be consistent in how much sequence divergence is needed to allocate organisms to different species or families.

Originally ribosomal RNA sequences were used for classification. However as ever more sequence data is obtained, including whole genomes, it is possible to take an increasing number of other genes into account. Computer programs exist for calculating the relative divergence of the sequences and can generate trees such as that in Figure 20.22. Here we have four bacteria, all in different genera but belonging to the same family, the Enterobacteria. To root such a tree correctly we also need the sequence from an organism in an "out-group;" in this case we have used the bacterium Pseudomonas, which is only distantly related to enteric bacteria. The nodes in Figure 20.22 represent the deduced common ancestors. The branch lengths are often scaled to represent the number of mutations needed and the numbers indicate how many base changes are needed to convert the sequence at each branch point into the next. (The total length of the 16s rRNA of Enteric bacteria is 1542 bases.)

As discussed in Ch. 19, parasites have many adaptations and quirks that developed due to the unusual environment they inhabit. Establishing phylogenetic relationships among parasites is very difficult based on simple trait analysis. Fortunately, gene sequences can often be used to trace the ancestry of parasitic or aberrant life forms. Aberrant development due to unusual environments is not only seen in parasites. Animals such as moles have adapted to living underground or in caves, and have lost their eyes in the process since these organs are not useful. Sometimes vestigial remnants of structures remain even though the animal has no use for the structure.Whales have the atrophied remains of hind limbs, which implies that whales are not real fish, but mammals that have become fish-like in general form as they have adapted to life in the ocean. Until gene sequencing emerged, it remained unknown which mammals are the whale's closest relatives. It now appears that whales are related to the artio-dactyls, hoofed mammals such as hippos, giraffes, pigs and camels.

One major problem with sequence comparison is that base changes can revert. Although statistical comparison of multiple sequences with many altered sites is often sufficient to establish a lineage, ambiguity sometimes remains. A useful way to help resolve ambiguities is by using conserved insertions or deletions—known as signature sequences or "indels". Although a single base insertion or deletion might possible revert, the likelihood that an insertion or deletion of several bases might revert so as

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