T HE TREE of LifE 43
among groups of organisms, especially distantly related taxa: there is not a universal
molecular clock. For example, sequence evolution among hominoid primates (apes,
including humans) has been slower than among other primates and mammals (see
Figure 2.17). Differences in generation time and in mutation rate are among the fac-
tors that have been proposed to explain why rates of sequence evolution vary among
taxa [8, 9, 23].Patterns of evolution
Data on morphological and other characteristics of organisms were used to infer
phylogenetic inferences before DNA sequences were available, and these charac-
teristics are still used in some studies. A phylogenetic perspective on the diversity of
organisms and their characteristics enables biologists to trace patterns of evolution of
various characteristics. The inferred patterns provide massive evidence that species
have evolved from common organisms; that is, they are very strong evidence for the
fact of evolution (BOX 2B).MoST fEATURES of oRGANiSMS HAVE BEEN MoDifiED fRoM PRE-EXiSTiNG fEA-
TURES Phylogenetic analysis is based on homologous features, those derived from
common ancestors. It is made possible by one of the most important principles of
evolution: the features of organisms almost always evolve from pre-existing features
of their ancestors; they do not arise de novo, from nothing. By analyzing homologous
characters, biologists have documented many fascinating evolutionary changes in
form and function. The middle-ear bones of mammals evolved from jaw bones of
reptiles (see Chapter 20). The wings of birds, bats, and pterosaurs are highly modi-
fied forelimbs (see Figure 2.9); they do not arise from the shoulders (as in angels
and dragons), presumably because the ancestors of these animals had no shoulder
structures that could be modified for flight. Homologous morphological characters in
different species generally have similar genetic and developmental underpinnings,
but these foundations have sometimes undergone greater divergence than have the
finished products. Likewise, existing proteins have been modified from ancestral
proteins and have new functions (see C hapter 14).
A character may be homologous among species (e.g., toes), but a given character
state may not be (e.g., a certain number of toes). The pentadactyl (five-toed) state is
homologous in humans and crocodiles (both have an unbroken history of pentadac-
tyly as far back as their common ancestor), but the three-toed state in guinea pigs
and rhinoceroses is not homologous, for this condition has evolved independently in
these animals by modification from a five-toed ancestral state.
Determining whether or not characters of two species are homologous can
be difficult. The most common criteria for hypothesizing homology of anatomical
characters are correspondence of position relative to other parts of the body and
correspondence of structure (the parts of which a complex feature is composed).
Correspondence of shape or of function is not a useful criterion for homology
(consider the forelimbs of a horse and an eagle). Embryological studies are
often important for hypothesizing homology. For example, the structural cor-
respondence between the hindlimbs of birds and crocodiles is more evident in
the embryo than in the adult because many of the bird’s bones become fused
as development proceeds. Homology between DNA sequences is determined by
finding an alignment that maximizes the match between nucleotides; often there
are “gaps,” caused by past deletions or duplications (see Chapter 16).RATES of CHARACTER EVoLUTioN DiffER Like DNA sequences, different phe-
notypic characters evolve at different rates, as is evident from the simple observation
that any two species differ in some features but not in others. Some characters, often02_EVOL4E_CH02.indd 43 3/23/17 8:59 AM