Evolution__3rd_Edition

..
Shared characters are used to infer
phylogenies
Cladism uses morphological
characters ...
. . . divided into discrete states
CHAPTER 15 / The Reconstruction of Phylogeny 425
Phylogenies are inferred using characters that are shared between species. The characters
may be at the level of gross morphology. For instance, humans and chimpanzees
share such vertebrate characters as brains and backbones, mammalian characters such
as lactation, and great ape characters such as their distinctive molar teeth and absence
of a tail. Or the characters used may be at the level of chromosomes, such as the number
or structure of the chromosomes in the species under study. Much phylogenetic inference
in biology today uses molecular sequences, particularly the nucleotide sequence of
DNA in different species. In this chapter we shall look first at how phylogenies are
inferred with morphological evidence, and then move on to molecular evidence. The
methods used for morphology and molecules both rely, at an abstract level, on the same
logic. However, the detailed implementation of that logic differs so much between
morphological and molecular evidence that it is convenient to look at them separately.
We can also look at some examples where the two kinds of evidence have come into
conflict.
15.2 Phylogenies are inferred from morphological
characters using cladistic techniques
Phylogenetic inference using morphological characters proceeds in the same way with
both living and fossil species. For fossil species, we usually have evidence only from
hard parts, such as bones in vertebrates or shells in mollusks. For living species, we have
further evidence from the soft parts. We also have evidence from characters that are not
morphological in a narrow sense, but can be included with morphological characters in
phylogenetic research. For instance, mammals are viviparous (produce live young) and
lactate, whereas birds are oviparous (lay eggs). Reproductive and physiological characters
of this kind are all good evidence for phylogenetic inference. In this chapter, “morphological”
evidence refers to all observable characters in the whole organism, as
distinct from molecular characters.
The techniques used with morphological characters are called cladistic techniques.
(The word cladistics comes from the Greek word for a branch.) The techniques were
mainly formalized in a book, Phylogenetic Systematics, by the German entomologist
Willi Hennig (1966). The book is not an easy read, but has been highly influential, with
good reason. Hennig had thought through the problem of phylogenetic inference more
thoroughly than most of his predescessors. Subsequent work (with morphological
characters) mainly follows on Hennig’s lead.
For cladistic analysis, the evidence consists of a number of characters, each with a
number of discrete character states. For example, one character might be “mode of
reproduction” and it might have the states “viviparity” or “oviparity.” Another character
might be “structure of forelimb,” and its states might be “wing” and “arm.” The particular
characters and character states will depend on the species that are being studied.
They may also be revised during research: the character state “wing” might have to be
replaced by “bird wing” and “bat wing” if both birds and bats were included in the
study. The division of an organism’s morphology into characters, and the division of
characters into discrete states, can itself be problematic. However, in this chapter we