Evolution__3rd_Edition

570 PART 5 / Macroevolution
Summary
1 Genome sequencing and development genetics
are two areas of molecular genetics that are adding
to our understanding of evolution, in particular
macroevolution.
2 The protein-coding genes of the human genome can
be compared with genes in prokaryotes, unicellular
eukaryotics, invertebrate animals, and vertebrates.
About 20% of our genes are shared with all life; a further
32% originated in single-celled eukaryotes; 24%
were evolved before the origin of animals; and 22%
near the origin of vertebrates. The human genome can
be used to study the history of human DNA.
3 A genome sequence contains duplicated regions,
and (using a molecular clock) the history of duplications
has been inferred in the flower plant Arabidopsis.
The evolutionary rate of gene duplication and loss in
Arabidopsis is about as high as the rate of nucleotide
substitution.
Further reading
4 The history of duplication can be studied in the
shape of the gene tree for paralogous genes in a
modern genome. The evidence does not support the
hypothesis that the genome was duplicated twice near
the origin of vertebrates.
5 The genomes of intracellular parasites and symbionts
tend to shrink, by gene loss, over evolutionary time.
6 The genomes of eukaryotes contain a compound
gene set, descended from the symbiotic merger event
that led to the evolution of the eukarotic cell.
7 The mammalian sex chromosomes seem to have
evolved in four (dateable) stages, perhaps corresponding
to four inversions that prevented gene exchange.
8 The history of non-coding DNA can be inferred
using a molecular clock on regions of the genome
that derive from transposition. Transposable elements
may have become exceptionally immobile in the past
25 million years of human evolution.
On evolutionary genomics in general, molecular evolution texts such as Page & Holmes
(1998) and Graur & Li (2000) contain much material, as does Hughes (1999). The special
issues of Nature and Science about the genome of particular species are informative.
Bennetzen (2002) discusses another topic, the rice genome.
King & Wilson (1975) provide a classic view on regulatory genes a discussed in the
evo-devo section of this chapter.
Ohno’s (1970) “2R” hypothesis is the subject of a newspiece in Science December 21,
2001, pp. 2458–60. Lynch & Conery (2000) estimate the rate of duplications, and find it
is about the same as the rate of base substitutions. A further topic is whether one gene in
a newly duplicated pair experiences relaxed selection and evolves fast to a new function.
This is a further example of the “valley crossing” theory of evolution. Hughes (1999)
provides evidence against, but see also Lynch & Conery (2000).
Ochman & Moran (2001) review gene loss, in parasites and elsewhere. Nature
May 23, 2002, pp. 374–6 contains a newspiece on genome size. For gene loss and gene
transfers following symbiotic mergers, see Blanchard & Lynch (2000), and Martin
et al. (1998) for chloroplasts. I discuss gene transfers and mergers in Ridley (2001).
On the general topic of chromososmes, and particularly sex chromosomes, see
O’Brien et al. (1998) and O’Brien & Stanyon (1999). For the three phases of
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