Evolution__3rd_Edition

466 PART 4 / Evolution and Diversity
Molecular evidence has revived
phylogenetics
Some phylogenies are frustratingly
uncertain ...
. . . others are satisfyingly solid
15.15 Conclusion
Phylogenetic research has been transformed in two ways in recent years, one being
purely scientific. Biologists have been trying to infer the tree of life since Darwin’s time.
Much progress was made with morphological evidence from living and fossil species,
but some problems were insoluble with this kind of evidence alone and the pace of scientific
progress had slowed by the 1960s and 1970s. Since then, increasing quantities of
molecular evidence have become available. The next generation of biologists can hope
to know what biologists of all past generations have wanted to know: the complete tree
of life.
The second transformation has come from the same source a the huge quantity of
molecular data. Phylogenetics has grown into a kind of applied evolutionary biology,
and is used to solve forensic and medical problems. In all, phylogenetics has moved
from being an unfashionable, slightly dusty topic to become one of the two or three
hottest go-go areas of evolutionary biology.
Phylogenetic inference draws on all kinds of evidence, from molecular sequences, to
chromosomal inversions, to morphology in modern and fossil forms. With morphological
evolution, the commonest (though not universal) course of research is to distinguish
homoplasies from homologies, and then infer the polarity of the homologous
characters. The conflict between the characters shared among the species may be
reduced (ideally to zero) during this analysis. A residue of reliable derived homologies
may be left, and can be used to infer the (rooted) tree. With molecules, individual characters
are analyzed less and a statistical method such as “distance,” parsimony, or maximum
likelihood is used to infer the unrooted tree. The location of the root can then be
inferred by other evidence.
Phylogenetic inference can sometimes seem to be an exceptionally uncertain, shaky
kind of science. In a full discussion of an unsolved and controversial problem, an endless
series of pieces of evidence may seem to support first one phylogeny, and then
another. One student (of Professor C.F.A. Pantin of Cambridge University, England),
when confronted with a classically recalcitrant problem in phylogenetic inference a
the origin of the chordates a summed it up as “paleontology is mute, comparative
anatomy meaningless, and embryology lies.”
That impression could be misleading. Discussion (as well as research) naturally
focuses on unsolved problems a and the unsolved problems tend to be the difficult
ones. Many phylogenetic problems have been solved, so one can have reasonable certainty
in a case such as the human–chimp–amoeba example, while reserving opinion in
more slippery cases such as the relations between Eukarya, Archaea, and Bacteria. In
addition, in the phylogeny of the picture-winged fruitflies of Hawaii, deduced from 214
conflict-free, multiply overlapping chromosomal inversions, the phylogenetic inference
has a level of certainty that compares favorably with most of the facts known in the
natural sciences.
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