40 CHAPTER 2to haplotypes in birds from the United States. For several reasons (such
as HGT), different genes sometimes have had different phylogenetic
histories—different gene trees (see Chapter 16). Thus, a gene tree can
differ from the species tree, the phylogeny of the species from which
the genes are sampled.
Organisms vary greatly in the number of functional genes in
their genome; for example, eukaryotes usually have far more genes
than prokaryotes (see C hapter 14). One of the most important pro-
cesses by which genomes have increased in size is gene duplica-
tion (see Chapter 8). A new copy of a locus (say, β) arises by dupli-
cation of a pre-existing gene (α), so that a single gene locus in an
ancestor is represented by two loci in the descendant. These two
genes will subsequently undergo different evolutionary changes in
sequence and can therefore be distinguished. If two species (1 and
2) both inherit the duplicated pair α, β from their common ancestor,
the relationships among the genes represent two forms of homol-
ogy, and so warrant different terms. The genes that originate from
an ancestral gene duplication are paralogous, whereas the genes
that diverge from a common ancestral gene by phylogenetic split-
ting at the organismal level are orthologous (i.e., homologous in
the usual sense) (FIGURE 2.14). This process may occur repeatedly
over evolutionary time, generating a gene family. The history of
gene duplication and sequence divergence—the relationships
among the orthologous and paralogous genes in two or more spe-
cies—can be determined by standard phylogenetic methods. In the
human genome, for example, the 12 members of the globin gene
family include genes that encode myoglobin and several α- and
β-hemoglobin chains (FIGURE 2.15). The origin of myoglobin and
hemoglobin by duplication of an ancestral globin gene occurredFutuyma Kirkpatrick Evolution, 4e
Sinauer Associates
Troutt Visual Services
Evolution4e_02.14.ai Date 12-12-2016Species 1 Species 2Duplication
αβα 1 β 1 α 2 β 2SpeciationαFIGURE 2.14 When gene duplication is followed by spe-
ciation, two types of relationship exist among the four cop-
ies of the locus. The loci in different species that descend-
ed from the same locus in their most recent ancestor (α 1
and α2, shown in red, or β1 and β2, shown in green) are
called orthologous. Loci in the same species or in different
species that descended from different duplicate genes in
the ancestral species are shown as differing in color, such
as α1 and β2. They are called paralogous genes. Homolo-
gous loci in different species are more closely related than
are paralogous loci within the same species.Futuyma Kirkpatrick Evolution, 4e
Sinauer Associates
Troutt Visual Services
Evolution4e_02.15.ai Date 12-12-2016Placental
mammalsHemoglobin β subfamily Hemoglobin α subfamilyβ Subfamilyδβ ψβ 1 Aγ Gγ ε ζ ψζ 1 ψα 1 α 2 α (^1) (active in muscle)Myoglobin
α Subfamily
Common ancestor
of α and β hemoglobin
subfamilies Common ancestor of hemoglobin
and myoglobin, 600–800 Mya
Primates
100–140
Mya
100–140 Mya 40–50 Mya
150–200 Mya
300 Mya
Jawed
vertebrates
FIGURE 2.15 Phylogeny of genes in the globin
family in the human genome. Myoglobin con-
sists of a single protein unit, whereas mamma-
lian hemoglobins consist of four subunits, two
each from the α and β subfamilies. Each branch
point on the tree denotes a gene duplication
event; some of these events are marked with
estimates of when the duplication occurred. The
origin of hemoglobin and myoglobin from a
common ancestral gene occurred in the ances-
tor of all vertebrates, but the α and β hemoglo-
bin subfamilies originated by duplication in an
ancestor of the jawed vertebrates. The dupli-
cation of the β-hemoglobin into two genes
occurred in the ancestor of placental mammals,
since the Aγ, Gγ, and ε genes are lacking in
monotremes and marsupials. In some instances,
one of the pairs of genes formed by duplication
became a nonfunctional pseudogene, symbol-
ized by ψ. (After [13, 22].)
02_EVOL4E_CH02.indd 40 3/23/17 8:59 AM