Evolution, 4th Edition

in the 1960s. Since then, a much-tempered

version has become woven into the fabric of

modern evolutionary biology. Accounts of

our understanding of molecular evolution in

the age of genomics can be found in “The

neutral theory of molecular evolution in the

genomic era” by M. Nei and colleagues (Annu.

Rev. Genomics Hum. Genet. 11: 265–289, 2010)

and Molecular and Genome Evolution by d.

grauer (Sinauer, Sunderland, MA, 2016).

The development of methods for making infer-

ences about evolution from dNA sequences

is an exciting and rapidly changing field of re-

search. Introductions to how different kinds of

selection are detected are “Molecular signa-

tures of natural selection” by R. Nielsen (Annu.

Rev. Genet. 39: 197–218, 2005), An Introduction

to Population Genetics: Theory and Applica-

tions by R. Nielsen and M. Slatkin (Sinauer,

Sunderland, MA, 2013), “Population genetic

inference from genomic sequence variation”

by J. E. Pool and colleagues (Genome Res. 20:

291–300, 2010), and “detecting natural selec-

tion in genomic data” by J. J. vitti and col-

leagues (Annu. Rev. Genet. 47: 97–120, 2013).

H. Ellegren and N. galtier review variation be-

tween species in levels of dNA polymorphism

in “determinants of genetic diversity” (Nat.

Rev. Genet. 17: 422–433, 2016).

PRoBlEMS ANd dISCUSSIoN ToPICS

1. Imagine that you have the dNA sequences from
   the intron of a gene in three species called A, B,
   and C. Species A and B are most closely related,
   while C is more distantly related. The sequences
   of A and B differ by 18 base pairs, A and C differ
   by 26 base pairs, and B and C differ by 28 base
   pairs. fossils show that species A and B diverged
   about 1.2 Mya, but there is no fossil evidence as
   to when the most recent common ancestor of
   all three species lived. Use the genetic data to
   estimate that date. What assumptions are you
   making to get this estimate?


2. In a population of 10^5 rabbits that has equal
   numbers of males and females, how many cop-
   ies of a gene are there at a locus that is carried on
   an autosome, at a locus on the X chromosome,
   and at a locus on the y chromosome? If all else is
   equal, which loci do you expect to be the most
   polymorphic, and which the least? Justify your
   response. How would your answers change if
   mutation rates were much higher in males than in
   females (which is the case in many species)?


3. Consider a species of sparrow that originally
   lived only in Alaska but recently expanded its
   range through North America, then Central
   America, and finally South America. How would
   you expect heterozygosity for most loci to differ
   among populations in North America, Central
   America, and South America? Why? Which of
   those three regions would you expect to have
   the most genetically similar populations, and
   which the most different?


4. The logic of the MK test mentioned in the text is
   based on the ratio of the number of sites that are
   different between two species and the number
   of sites that are polymorphic within one of those

species. This ratio is expected to be the same for

synonymous and nonsynonymous changes in a

locus that is evolving neutrally. A study of a locus

in two species of fishes called A and B obtained

the following results:

Nonsynonymous

Synonymous changes changes

Sites different in A and B 13 10

Polymorphic sites in A 11 2

Polymorphic sites in B 7 1

Calculate the ratios of polymorphic sites within

a species and the differences between species

for synonymous and nonsynonymous changes.

What do your results suggest about how this

locus is evolving?

5. Two populations of a fly are isolated from all
   other populations. Population S lives on a very
   small island and has a population size of 10^3
   individuals. Population l lives on a continent and
   has a population size of 10^8 individuals. There
   is a beneficial mutation that increases fitness by
   1 percent, but initially neither population has a
   copy of that allele. The mutation rate from the
   current allele to the beneficial mutation is 5 ×
   10 –7. Approximately how likely is it that the ben-
   eficial mutation will be common in each popula-
   tion after 1000 generations?


6. In Chapter 6 you saw how quantitative traits
   evolve in response to selection. Quantitative
   traits can also evolve by random genetic drift.
   discuss how you expect the population size
   might affect the additive genetic variance within
   a population and the divergence between pop-
   ulations for a quantitative trait.

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