Taxonomy Red in Tooth and Claw 19

and Woese 2007). Microbial taxonomists have traditionally been much

more concerned with phenotypic characters than with phylogenetic
relationships (Goodfellow et al. 1997, 26). This is due in part to con-
jugation, a process in which bacteria are able to pass genetic material
(and thus ultimately phenotypic traits) to other individuals that are not
their own offspring. Such “cross-borrowing” tends to decrease the ex-
planatory utility of cladistic analysis to the extent that these represent
lineages of evolving populations of organisms.
There are many cladistic analyses of prokaryotic life; indeed, the idea
that the tree of life is organized into three ancient domains, the archaea,
the eubacteria, and the eukaryotes, is based on the discovery of an an-
cient split among the prokaryotes. But there is an important sense in
which these trees are histories of gene lineages rather than organisms.9
For one thing, these phylogenies are based on genetic data: the compari-
son of homologous genes. But more importantly, if cross-borrowing is
a regular feature of bacterial life, we cannot assume that closely related
genes—genes dating back to a recent common ancestor—are parts of
the genome of closely related organisms. Among the eukaryotes, gene
histories and organism histories are typically (though not universally)
concordant. When two versions of a gene complex begin accumulating
changes independently of each other, it will be because those genes’ lin-
eages are contributing to two organism lineages evolving independently
of each other. If genes are often transferred laterally, that is an assump-
tion we can no longer make. We cannot treat the branching pattern of
gene evolution as a proxy for the branching pattern of the organism
lineages of which they are a part.
Moreover, there is a set of technical challenges to the tractability of
their approach. Parsimony analysis is computationally intensive. Find-
ing the most likely phylogeny is made difficult by the fact that the num-
ber of possible “trees” increases exponentially as more taxa are added to
the analysis. Three taxa can be arranged in only three different rooted
tree topologies (ones that show both phylogenetic relationships be-
tween taxa and also pick out a particular taxon as being the ancestor of
all the others). Five can be arranged in 105. Ten can be arranged in 3.4
× 107, while twenty can be arranged in 8.2 × 1021 (Quicke 1993, 59). It is
true that there are algorithms to find the most parsimonious tree that
do not involve exhaustively searching all the possible tree topologies.
Even so, in practice computation tractability will always be an issue for
cladistic analysis.
In short, cladistics is explanatorily powerful, with a well-defined ra-
tionale. These are great virtues in a taxonomic system. But it purchases
these virtues at the cost of abandoning an explicit representation of