The Origin and Evolution of Mammals - Moodle

een a more fundamental impact than on mammalian
systematics. It began with the now very primitivelooking
immunological techniques generating such
radical proposals as the close relationship of humans
to the African apes (Sarich and Wilson 1967), and the
monophyly of the Australian marsupials (Kirsch
1977). With the increased availability of comparative
sequence, initially of proteins and subsequently
nucleic acids, unfamiliar new hypotheses arrived,
like the monophyly of Afrotheria, a morphologically
very mixed bag of placental orders with no evident
morphological characters in common at all, and the
improbable-looking sister-group relationship of
whales to hippos. However, both these are now
widely, if not universally agreed upon by palaeontologists,
who indeed have found support from fossils.
In fairness of course, other early molecular
proposals have disappeared without trace, such as
guinea pigs not being rodents. In equal fairness,
though, rejection of the latter was due primarily to
further molecular evidence, rather than morphological
evidence. The present position is that relatively
enormous volumes of sequence data are already
available across virtually the whole of living mammal
diversity at the level of orders, and increasingly
of families and lower taxa. This includes a mixture of
sources. Many, and increasing numbers of complete
mitochondrial genomes have been sequenced, along
with a variety of nuclear genes. Databases for analysis
are already ten to twenty thousand nucleotides
long (10–20 kb), with presumably vastly increased
potential resolving power. Nucleotide sequences
have several advantages over morphological
descriptions besides the more or less limitless
amount of information available. It is easy in principle
to recognise a single nucleotide as a unit character.
It is also possible to have estimates of differential
probabilities of different kinds of nucleotide substitutions,
depending, for example, on whether it is a
transition or a transversion, or first, second, or third
placed position in the codon. Therefore, more realistic
models of the evolutionary process are possible
for inferring relationships from the data, with the
help of suitably sophisticated methods such as maximum
likelihood, and Bayesian inference. Again this
subject is extensively discussed in several texts such
as Salemi and Vandamme (2003).
A few years ago, it was legitimate to question
whether molecular phylogeny was more reliable
than morphological, and consequently whether it
should be allowed to overrule the latter in cases of
conflicting hypotheses of relationships. A common
reaction was that molecular and morphological
data should be combined to produce a compromise
phylogeny. This was always a conceptually difficult
thing to achieve, and all too often simply resulted in
a very poorly resolved cladogram instead. However,
the increasing number of occasions on which newer
palaeontological evidence, both morphological and
biogeographical, has tended to support, or at least
be compatible with the molecular evidence suggests
that with a careful enough analysis, molecular
data is perfectly capable of resolving the interrelationships
of mammalian groups that have living
members. Indeed, it is heralding an exciting new
phase in mammalian palaeobiology. With much
more strongly supported and widely agreed phylogenies
to hand, the fossil record is open to a whole
new set of improved interpretations about the complex
interplay between phylogenesis, biogeography,
and palaeoecology that constitutes the history
of mammals.
A classification of Synapsida
TIME AND CLASSIFICATION 11
The classifications in Tables 2.1–2.4 are designed for
general reference. All the formally expressed groups
are monophyletic clades, but not all relationships
between them are fully resolved to dichotomies.
In the classifications of the Synapsida and the
Mammalia, certain ancestral, or paraphyletic group
names are included but in quotation marks, either
because they are so familiar from the literature that
they remain useful nomenclatural handles, or because
the relationships of their constituent subgroups are
inadequately known. Monophyletic groups whose
cladistic position is relatively uncertain are indicated
by a query.
These classifications are designed for the relatively
uninitiated in the field of synapsid systematics. They
are therefore a compromise between a fully cladistic
classification that would be overly name-bound,
and would tend to convey overconfidence in the
expressed relationships, and an ‘evolutionary’ classification
with undeclared paraphyletic groups and
the consequent loss of genealogical information. For
more detail and discussion, the appropriate chapters
should be consulted.