- Dugong dugon

- Procavia capensis

Figure 5.11 Relationships of the woolly mammoth based on mitochondrial DNA (mtDNA). This analysis (Rogaev et al. 2006) places the mammoth Mammuthus primigenius closest to the Asiatic elephant Elephas maximus, while other analyses of mammoth mtDNA place the mammoth closer to the African elephant Loxodonta africana. Either way, the relationship to the modern elephants is close, suggesting all three species diverged in the last 5-6 myr. Two samples of mtDNA for the two modern elephants are included, and the outgroups are the sea cow Dugong dugon and the hyrax Procavia capensis. The sets of digits at each branching point are various measures of robustness: values range from 0 to 1 and 0 to 100, with 1.0 and 100% indicating maximum robustness of the node. Scale bar is 0.1 base-pair substitutions per site. (Courtesy of Evgeny Rogaev.)

The vast numbers of DNA and RNA sequences that are generated daily from the whole diversity of life are stored as letter codes in open-access databases. Any investigator may download the sequences of any particular gene or chromosome for as many species as are available. There are then two key processes in extracting a phylogenetic tree from such data. First, the nucleic acid sequences must be aligned, that is matched, so that the code of a particular gene in one species is lined up with the same sequence in another species. Alignment can be difficult because species do not differ only in the placement of particular base pairs, but sometimes gaps in the sequence are introduced, or whole sections may be repeated. Once the sequences of a number of species are satisfactorily aligned, the phylogenetic analysis is carried out. The base-pair codes are treated like the presence/absence (1/0) codes in a morphological data matrix, and a variety of algorithms are applied to extract the most likely tree that explains the data.

The tree of life

Paleontologists and biologists are using morphology and molecules to put together ever-larger sectors of the tree of life. Desktop computers are exploding in labs around the world as analysts ask them to crank out ever-larger trees. Bear in mind that the number of possible trees is N = (2n - 3)!/(2n-2(n - 2)!). So for three species, there are three possible unique trees. For four species, there are 15 possible trees (Fig. 5.12), for eight species 168,210 possible trees, and for 50 species about the same number as there are atoms in the universe. You can do these calculations in table 1.3.1 at http://www.talkorigins.org/faqs/ comdesc/section1.html.

And yet 50 species is not a demanding number. Systematists want to know the complete tree for all 240 species of primates, all 4500 species of mammals (now available: Bininda-Emonds et al. 2007), and so on. Mathematicians tinker with the tree-finding software so it finds clever ways to find the best-fitting tree quickly, even though many millions or billions of potential trees are considered and rejected. Another approach is to link existing trees for parts of the group of interest to create a supertree that summarizes

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