Evolution__3rd_Edition

..
Summary
1 Phylogenies show the ancestral relations between
species. For each species, a phylogeny shows which
other species (or group of species) it shares its most
recent common ancestor with.
2 Phylogenetic relations are inferred using the shared
characters of species. The characters can be morphological,
in living and fossil species, or molecular.
3 When different characters imply the same phylogeny,
phylogenetic inference is easy; when they do not, other
methods are needed to unravel the disagreement.
4 Theoretical arguments suggest that some kinds
of shared characters indicate phylogenetic relations
reliably, whereas others do not. Homoplasies and
ancestral homologies do not reliably indicate phylogenetic
groups. Derived homologies do. Phylogenetic
inference should be based on derived homologies.
5 Techniques exist to distinguish homologies from
homoplasies, and ancestral homologies from derived
homologies.
6 Character polarities can be inferred, with varying
degrees of certainty, by outgroup comparison, the
fossil record, and other criteria, including paralog
rooting.
7 For molecular characters, the kinds of character
analysis used with morphology are often inapplicable.
Further reading
CHAPTER 15 / The Reconstruction of Phylogeny 467
Phylogenies are usually inferred by statistical techniques.
The three main classes of techniques are distance
methods, parsimony, and maximum likelihood.
8 Distance methods group species according to their
molecular similarity. With parsimony, the best estimate
of the tree for a group of species is the tree that
requires the fewest evolutionary changes. With maximum
likelihood, the best estimate of the tree is the
one that is most probable, given a model of sequence
evolution.
9 Molecular evidence is often used to infer the phylogeny
in the form of an unrooted tree. An unrooted tree
specifies the branching relations among species, but
not the direction of evolution.
10 Molecular phylogenetics is used in medical
research to identify the source of emerging diseases.
11 Molecular phylogenetic inference encounters problems
with sequence alignment, the large number of
possible trees, multiple hits, inadequate data, unequal
rates of evolution, and confusions between paralogous
and orthologous genes.
12 The unrooted tree of the Hawaiian fruitflies is the
most firmly established phylogeny of any large group
of species. It has been reconstructed using chromosomal
inversions.
Felsenstein (2003) is an authoritative book about phylogenetic inference. However, for
most of the further reading it makes sense to distinguish between cladistic references, in
which rooted trees are inferred using character polarities, often with morphological
evidence, and molecular references, in which unrooted trees are inferred by some statistical
method.
Cladistics. For the cladistic method, see Wiley et al. (1991) and Kitching et al. (1998);
references can be traced from these sources. Kemp (1999) concentrates on fossils, but
introduce cladistics generally. Hennig (1966) is the classic reference. Sober (1989) is a
philosophical discussion of most of the main methods, and he has also edited an
anthology (Sober 1994) that reprints a number of relevant papers. Another philosophical
question, not covered in this chapter, is whether phylogenetic reconstruction