The hypothesis explains a mysterious genetic difference between bacteria and eukaryotes, a giant group of organisms that includes animals, plants, fungi and algae. Bacteria tend to have extremely lean genomes; their genes barely fit into them, without much genetic material left over. Eukaryotic genomes are a complex mixture of useful genes and useless (“junk”) DNA jammed haphazardly between genes and even within them.

“The evolution of genomic complexity is inevitable,” said IUB biologist Michael Lynch, who led the study. “It’s just that in bacteria, there is a pressure against it—natural selection—which works more efficiently when population sizes are big. Eukaryotes have much smaller population sizes compared to bacteria, and we believe this is the main reason junk DNA sequences are still with us.”

Junk DNA dominates eukaryotic chromosomes. The chromosomal space taken up by just 30 human genes and the DNA within and between those genes could easily accommodate whole bacterial genomes containing 3,000 or 4,000 genes, Lynch said. While some of what geneticists have called “junk DNA” is turning out to be not so junky after all, Lynch said a substantial fraction of such genetic material probably deserves the name.

Genetic mutations occur in all organisms. But since large-scale mutations—such as the random insertion of large DNA sequences within or between genes—are almost always bad for an organism, Lynch and University of Oregon computer scientist John Conery suggest the only way junk DNA can survive the streamlining force of natural selection is if natural selection’s potency is weakened.

When populations get small, Lynch explained, natural selection becomes less efficient, which makes it possible for extraneous genetic sequences to creep into populations by mutation and stay there. In larger populations, disadvantageous mutations vanish quickly.

Most experts believe that the first eukaryotes, which were probably single celled, appeared on Earth 2.5 billion years ago. Multicellular eukaryotes are generally believed to have evolved 700 million years ago. If Lynch’s and Conery’s explanation of why bacterial and eukaryotic genomes are so different is true, it provides new insights into the genomic characteristics of Earth’s first single-celled and multicellular eukaryotes.

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