PHylogENy: THE UNITy ANd dIvERSITy of lIfE 421
that the ancestors of insects had appendages not only on the thorax
but also on the abdomen.
Ancestral state reconstruction is being used to estimate and then
synthesize ancestral DNA sequences. The function of the encoded
proteins is analyzed, as well as that of proteins that differ by one or
more amino acid changes, in order to infer how the function evolved
[16]. One example comes from research on opsins, which are proteins
involved in vision [38–40]. Vertebrates have several opsins that differ
in the wavelength to which they are most sensitive, λmax. Many spe-
cies, such as the conger eel (Conger myriaster), have adapted to dim
light, such as in deep water, by substitutions in the opsin genes that
shift λmax toward absorption of blue (shorter wavelengths). Some of
the same amino acid substitutions, such as A292S (denoting a change
from alanine to serine at position 292 in the protein) and D83N (a
change from aspartic acid to asparagine at position 83), have repeat-
edly contributed to this shift (FIGURE 16.20). A292S is one of the
substitutions in an opsin in the conger eel, with λmax = 486 nano-
meters (nm). Shozo Yokoyama and colleagues inferred and synthe-
sized the sequence of the ancestral gene, expressed the opsin protein
it encoded, and found that the opsin’s maximal absorption was at a
longer wavelength (λmax = 501 nm). By introducing the mutations
in this ancestral sequence to match the conger eel opsin gene, the
researchers found that they could recreate the same function (λmax =
486 nm), but only by combining A292S with two other substitutions
that also occurred in the conger eel; by themselves, these changes did
not change λmax. Apparently, the conger eel’s adaptation to dim light
is based on epistasis, or synergism, among the three amino acid sub-
stitutions. This important conclusion would be difficult to discover
except by reconstructing the history of evolution.
The geographic distribution of a population or species can be con-
sidered a characteristic, and ancestral state reconstruction can thus
trace evolutionary changes in geographic distribution. We will plumb
this topic more deeply in Chapter 18. Here we recall an important
example with which we began this book: tracing the spread of the
deadly Ebola virus. The virus was first described in 1975, in the Democratic Republic
of Congo. Twenty-four localized outbreaks occurred during the next 37 years. Then
in 2014, a devastating outbreak ravaged West Africa: among more than 26,000 cases,
there were more than 11,000 deaths. Viral gene sequences were obtained from the
new infections and from samples that had been preserved from earlier outbreaks.
By September 2014, evolutionary biologists and epidemiologists had estimated a
gene tree of the virus (FIGURE 16.21). Most of the West Africa samples were traced
to a single common ancestral sequence that was introduced into Sierra Leone from
Guinea. This, in turn, was derived from Congo and nearby Gabon.
The key insight was that all the epidemics resulted from a single human infec-
tion. This shows that the virus is not easily acquired from the environment, unlike
other viruses (such as influenza) that frequently jump between species. That find-
ing, based on a phylogenetic analysis, has dramatic implications for how we might
prevent future epidemics.Studying adaptations: The comparative method
Evidence of convergent evolution has long been seen as a clue to how natural
selection has shaped an organism’s characteristics. For example, Bergmann’s
rule is the tendency for populations of many species of mammals and birds in
colder climates to have a larger body size than populations of the same speciesFutuyma Kirkpatrick Evolution, 4e
Sinauer Associates
Troutt Visual Services
Evolution4e_16.20.ai Date 01-25-2017P194R, N195A, A292SD83ND83N, A292SD83N, A292S
D83N, A292SY96V, Y102FE122QA292SE122I, F261YF261YConger A
Eel A
Eel B
Conger B
Cave sh
Zebra sh
Medaka
Thornyhead
Lamp sh
Scabbard A
Scabbard B
Viper sh502501501
501501502501501500503507489496492481485
482479486483FIGURE 16.20 Evolutionary changes in one of the verte-
brate rhodopsins (visual pigments), mapped onto a gene
tree. These pigments are adapted for surface, interme-
diate, or deep-sea light environments, shown by the
white, light gray, and dark gray ovals. The number in each
oval is the wavelength of maximal absorption, which has
been reconstructed for common ancestors, shown at the
internal nodes. The wavelength of maximal absorption has
become lower in species shown by blue branches. The
amino acid substitutions that have occurred along each
branch are indicated above the branch. Adaptation of
these pigments for vision in dim light has evolved repeat-
edly, and certain amino acid substitutions have repeatedly
played a role. For example, the substitution D83N has
occurred on several of the blue branches, and A292S has
occurred on all of the branches leading to the dark gray
ovals. The A and B pigments of conger and eel are prod-
ucts of paralogous genes. (After [38].)16_EVOL4E_CH16.indd 421 3/22/17 1:33 PM