PHylogENy: THE UNITy ANd dIvERSITy of lIfE 417
Two major tests for constancy have been used. One is to plot sequence differences
between pairs of species (e.g., human, mouse) against the time since the lineages
(primate, rodent) diverged (see Fig ure 2.17). The earliest fossil member of either of
the two lineages gives the minimal divergence time. (The lineages are almost cer-
tainly older than their earliest fossil.) It may also be possible to determine whether
sequence evolution is fairly constant even without information on divergence time.
Walter Fitch suggested a second method for determining constancy, called the
relative rate test [11]. We know that the time that has elapsed from any common
ancestor (i.e., any branch point on a phylogenetic tree) to each of the living species
derived from that ancestor is exactly the same. Therefore, if lineages have diverged
at a constant rate, the number of changes along all paths of the phylogenetic tree
from one descendant species to another through their common ancestor should be
about the same (FIGURE 16.16).
Fossil-based tests and relative rate tests, when applied to DNA sequence data
from various organisms, have shown that rates of sequence evolution of a given
gene are often quite similar among taxa, especially if they are fairly closely related,
but sometimes they do differ considerably [13, 21]. For example, sequence evolu-
tion has been slower in hominoid primates (apes, including humans) than in other
primates, in primates than in rodents, and in trees and shrubs than in herbaceous
plants. Why do their rates differ? One hypothesis is that sequence evolution is
faster in species with short generation times, and therefore more generations per
unit of time. This hypothesis assumes that inherited mutations occur in cells des-
tined to give rise to gametes (i.e., the germ line) only during DNA replication. This
idea applies to animals, which have a distinct germ line, but might not apply to
plants, which may produce flowers from various somatic tissues in which muta-
tions may accumulate with cell division [13].
Despite these complications, divergence times in phylogenies can be reason-
ably well estimated, given enough sequence data. One study of divergence times
was based on a DNA sequence of 59,764 base pairs in 13 species of primates and 6
other (outgroup) mammals, and the rate of sequence evolution was calibrated by
four fossil-based divergence times [33]. This analysis suggested that the human-
chimpanzee divergence was about 6.6 Mya (range 7.0–6.0), and that this branch
diverged from gorilla about 8.6 Mya (range 9.2–7.7) (FIGURE 16.17). A more recent
study was based on vastly more data—whole-genome sequences—and it used data
on human mutation rates to estimate divergence time. (Recall from Chapter 7 that
neutral mutations, occurring at a rate μn per site, are expected to generate a dif-
ference in DNA sequence equal to 2μnt for two lineages that separated from their
common ancestor t generations ago.) These authors estimated divergence at about
6 Mya for human and chimpanzee and at 10 Mya for divergence of these from
gorilla [30]. The two estimates of divergence time use independent methods, and
given all the room for error, they are quite close.Discovering the history of genes and cultures
Almost anything that has the properties of inheritance and variation can be stud-
ied with phylogenetic methods. Gene trees can be used to address a wide range
of evolutionary questions. For example, an important question is how often adap-
tation is based on a supply of new mutations (and may therefore be limited by
that supply), versus being based on standing genetic variation [1]. If a mutation is
beneficial when it first appears and then sweeps rapidly through a population, it
generates shallow gene trees in a large region of the chromosome that hitchhikes
along with the mutation. Because fewer mutations have had time to accumulate
on shallow gene trees, shallow gene trees are visible because they have reduced
polymorphism. An example is shown in Fig ure 5.16. Other mutations are notFutuyma Kirkpatrick Evolution, 4e
Sinauer Associates
Troutt Visual Services
Evolution4e_16.16.ai Date 01-02-2017Sp 1 Sp 2
A
B
515Sp 3FIGURE 16.16 The relative rate test for the
constancy of molecular evolution. Sup-
pose we are confident in the phylogeny of
three species, and we compare differences
among their DNA sequences. Say that spe-
cies 1 and species 3 differ by 15 mutations,
but species 2 and species 3 differ by only
5 mutations. Then species 1 must have
accumulated 10 more mutations along
branch A than species 2 did along branch
B, because the path between these two
species and species 3 is identical except
for their separate paths since their common
ancestor. Therefore, the rate of molecular
evolution was faster in the species 1 lineage
than in the species 2 lineage. We can reject
the hypothesis of a molecular clock for this
gene in these species.16_EVOL4E_CH16.indd 417 3/22/17 1:33 PM