Evolution, 4th Edition

neutral theory

of molecular

evolution

operon

overlapping gene

paralog

pseudogene

purifying selection

retrotransposition

subfunctionalization

transposable

element (TE)

whole genome

duplication

suGGEsTions foR fuRTHER REAdinG

d an Graur’s Molecular and Genome Evolution

(sinauer, sunderland, mA, 2016) gives an

authoritative perspective on the topics cov-

ered by this chapter (and much more). michael

lynch’s The Origins of Genome Architecture

(sinauer, sunderland, mA, 2007) is another

valuable reference. lynch argues that several

key aspects of the genome are consequences

of random genetic drift.

T. Ryan Gregory’s website (http://www.grego-

rylab.org/research/) and his Animal Genome

size database (http://www.genomesize.com)

are fonts of information about genome size.

PRoBlEms And disCussion ToPiCs

1. The origin of genes that have new func-
   tions often involves the divergence of gene
   duplicates. duplicates can arise via several
   mechanisms.
   a. one mechanism of gene duplication is ret-
   rotransposition, the insertion into the genome
   of dnA produced by reverse transcription of
   a messenger RnA. These gene duplicates are
   often dead on arrival: they are pseudogenes
   as soon as they are formed. Why are such
   duplicates so often dead on arrival?
   b. A second mechanism of gene duplication
   occurs via unequal crossing over during
   meiosis. Gene duplicates formed this way are
   functional more often than when they arise by
   reverse transcription. Why is that?
   c. if a gene duplicate is initially functional, what
   are its possible ultimate fates? Which is most
   likely, and why?


2. The ratio of nonsynonymous differences per
   nonsynonymous site, dn, to synonymous dif-
   ferences per synonymous site, ds, can be used
   to test for positive selection (see Chapter 7).
   imagine that in a duplicate pair of loci, one
   paralog is evolving neutrally while the other is
   evolving under strong positive selection. What
   specific data are needed to detect that situation
   using the dn/ds ratio, and what pattern do you
   expect to see?
   3. The human genome contains more than a mil-
   lion copies of the Alu transposable element.
   Comparative genomics reveals that the Alu ele-
   ment is found only in the clade of mammals that
   includes primates, tree shrews, rodents, and
   rabbits.
   a. What does the observation that the Alu trans-
   poson is limited to this clade reveal about its
   origin and method of spread among species?
   b. At many sites in the genome, an Alu element is
   present in humans but absent in chimpanzees,
   while at many other sites an Alu element is
   present in chimpanzees but absent in humans.
   What are two hypotheses that could explain
   this situation? for any particular site, how could
   the hypotheses be distinguished?
   4. Gene trafficking is the movement of loci from
   one region of the genome to another. You saw
   that gene trafficking in Drosophila has caused
   many loci that were formerly on the X chromo-
   some to move to the autosomes. suggest a
   hypothesis for that observation.
   5. imagine that you have a device that can accu-
   rately measure the dnA content of individual
   cells of living yeast. This device enables you to
   do artificial selection on the genome size of the
   yeast. Propose an experiment using artificial
   selection that could test the hypothesis that the
   yeast genome size is optimal for yeast fitness
   versus the alternative hypothesis that transpo-
   sons have caused the genome to evolve to a size
   that is larger than what maximizes yeast fitness.

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