Evolution__3rd_Edition

558 PART 5 / Macroevolution
Some human genes date back to
early cellular life ...
. . . and other genes were added
later
In this chapter, I have mainly picked examples that use the human genome, not least
because the human genome has been so intensively studied, since its partial publication
in 2001. However, the field of evolutionary genomics is not limited to understanding
the human genome, and aims to understand genome evolution in all life.
19.2 The human genome documents the history of the
human gene set since early life
We can begin by looking at the part of the human genome that codes for genes. The
two papers published in February 2001 (Celera 2001; International Human Genome
Sequencing Consortium 2001) suggested that the human genome contains about
30,000 genes. (And the figure has been little changed in subsequent research.) The data
can be refined further by concentrating on genes that code for proteins. Some genes
code for RNA molecules, such as ribosomal RNA, that are not translated into protein,
and these genes are excluded from the following analysis. We are concentrating on the
proteome a the full set of proteins in an organism. Because most genes code for proteins,
results for the proteome will be similar to results for the genome.
Figure 19.1 shows the percentage of human protein-coding genes that are homologous
with genes in a range of other organisms. Humans share 21% of their genes with
all cellular life forms. These are the “housekeeping” genes of each cell, the genes that
regulate basic cellular machinery. The oldest fossil cells are 3,000–3,500 million years
old (Section 18.3.1, p. 530). At least some, maybe all, the cellular housekeeping genes
had evolved by then. Most housekeeping genes evolve slowly and have been copied
with little change for billions of years. Our DNA has probably been copied 10–100
times a year on average since our bacterial ancestors. If a basic cellular gene such as a
histone gene existed 3.5 billion years ago, then it would have been copied about 10 11
times through a line of ancestors leading to each of us, with little change. The cellular
housekeeping genes reverberate with “deep time” in all our DNA molecules.
Another 32% of our genes are homologous with genes in all eukaryotes, but not with
bacteria. Those too are cellular housekeeping genes, reflecting the greater complexity of
cellular metabolism in eukaryotes. The next stage for which we can make an inference
is the origin of animals. About 24% of our genes are shared with other animals, but not
with single-celled eukaryotes or prokaryotes. These “animal” genes include the genes
such as Hox genes that control development. We look at these genes further in Chapter
20. Another 22% of our genes are shared only with vertebrates. These genes are 500
or more million years old. They include genes that operate in the immune system and
the nervous system. Human beings, for example, have about 100 genes coding for the
immune system, compared with more like 10 in the worm and the fly. The number of
genes concerned with the nervous system has also expanded in the vertebrates, perhaps
associated with the relatively complex vertebrate brain. Only 1%, or less, of human
genes are “unique”’ to humans, having no homologs with other vertebrates. (I put
“unique” in quotes because the main other vertebrate for which we have data is the
mouse. The 1% of genes we do not share with mice could well be shared with closer
relatives, such as monkeys; the genes would then not be unique to us.)
..