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Evolution__3rd_Edition

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558 PART 5 / Macroevolution<br />

Some human genes date back to<br />

early cellular life ...<br />

. . . and other genes were added<br />

later<br />

In this chapter, I have mainly picked examples that use the human genome, not least<br />

because the human genome has been so intensively studied, since its partial publication<br />

in 2001. However, the field of evolutionary genomics is not limited to understanding<br />

the human genome, and aims to understand genome evolution in all life.<br />

19.2 The human genome documents the history of the<br />

human gene set since early life<br />

We can begin by looking at the part of the human genome that codes for genes. The<br />

two papers published in February 2001 (Celera 2001; International Human Genome<br />

Sequencing Consortium 2001) suggested that the human genome contains about<br />

30,000 genes. (And the figure has been little changed in subsequent research.) The data<br />

can be refined further by concentrating on genes that code for proteins. Some genes<br />

code for RNA molecules, such as ribosomal RNA, that are not translated into protein,<br />

and these genes are excluded from the following analysis. We are concentrating on the<br />

proteome a the full set of proteins in an organism. Because most genes code for proteins,<br />

results for the proteome will be similar to results for the genome.<br />

Figure 19.1 shows the percentage of human protein-coding genes that are homologous<br />

with genes in a range of other organisms. Humans share 21% of their genes with<br />

all cellular life forms. These are the “housekeeping” genes of each cell, the genes that<br />

regulate basic cellular machinery. The oldest fossil cells are 3,000–3,500 million years<br />

old (Section 18.3.1, p. 530). At least some, maybe all, the cellular housekeeping genes<br />

had evolved by then. Most housekeeping genes evolve slowly and have been copied<br />

with little change for billions of years. Our DNA has probably been copied 10–100<br />

times a year on average since our bacterial ancestors. If a basic cellular gene such as a<br />

histone gene existed 3.5 billion years ago, then it would have been copied about 10 11<br />

times through a line of ancestors leading to each of us, with little change. The cellular<br />

housekeeping genes reverberate with “deep time” in all our DNA molecules.<br />

Another 32% of our genes are homologous with genes in all eukaryotes, but not with<br />

bacteria. Those too are cellular housekeeping genes, reflecting the greater complexity of<br />

cellular metabolism in eukaryotes. The next stage for which we can make an inference<br />

is the origin of animals. About 24% of our genes are shared with other animals, but not<br />

with single-celled eukaryotes or prokaryotes. These “animal” genes include the genes<br />

such as Hox genes that control development. We look at these genes further in Chapter<br />

20. Another 22% of our genes are shared only with vertebrates. These genes are 500<br />

or more million years old. They include genes that operate in the immune system and<br />

the nervous system. Human beings, for example, have about 100 genes coding for the<br />

immune system, compared with more like 10 in the worm and the fly. The number of<br />

genes concerned with the nervous system has also expanded in the vertebrates, perhaps<br />

associated with the relatively complex vertebrate brain. Only 1%, or less, of human<br />

genes are “unique”’ to humans, having no homologs with other vertebrates. (I put<br />

“unique” in quotes because the main other vertebrate for which we have data is the<br />

mouse. The 1% of genes we do not share with mice could well be shared with closer<br />

relatives, such as monkeys; the genes would then not be unique to us.)<br />

..

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