Bacterial Sex Has Scrambled the Tree of Life

Scientist now agree that the horizontal flow of genes is a part of the story of life.

Vertical inheritance, “descent with modification”, is a fundamental concept of Darwinian inheritance. You pass your genes to your children: that’s heredity, in a ‘downward’ direction. However, your children do not get a complete copy of your genes–they are not clones of you, or your mate. Rather, your genes combine with your partner’s genes, and there is a uniquely different mix in each child, and gradually, over many generations, evolution takes place.

Now, consider bacteria (and archaea, the other Domain of one-celled prokaryotes): they reproduce by fission, essentially cloning, where the daughter cells are exact copies of the parent. But then, how do bacteria evolve over time, if reproduction results in exact copies? Some variation can result from mutations, and if the mutations enhance survival, then those mutated traits are naturally selected. Naturally. But, now (as Ed Yong supposes in his book, I Contain Multitudes: The Microbes Within Us and a Grander View of Life):

“imagine a different world where friends and colleagues can swap genes at will. If your

“imagine a different world where friends and colleagues can swap genes at will. If your boss has a gene that makes her resistant to various viruses, you can borrow it.  If your child has a gene that puts him at risk of disease, you can swap it out for your healthier version. If distant relatives have a gene that allows them to better digest certain foods, it’s yours. In this world, genes aren’t just heirlooms to be passed on vertically from one generation to the next, but commodities to be traded horizontally, from one individual to another.”That is how bacteria can rapidly adapt to environmental challenges, by borrowing ready-made genes, acquired through horizontal gene transfer, HGT.

David Quammen observes in his new book, The Tangled Tree: A Radical New History of Life:

“Evolution is trickier, far more intricate, than we had realized. The tree of life is more tangled. Genes don’t move just vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms  of life, and some have come sideways into our own lineage from unsuspected,  nonprimate sources. It’s the genetic equivalent of a blood transfusion or (a different metaphor, preferred by some scientists) an infection that transforms identity.

Infective heredity was first discovered by Esther and Joshua Lederberg, and their colleagues, Luigi Cavalli-Sforza and William Hayes. These scientists discovered the F-factor (F for fertility), the first bacterial plasmid to be identified. The F-factor is a small circular piece of DNA, containing only a few genes, that can transform recipients into fertile bacteria, that are then able to transfer genes via bacterial sex.

Several years later, in the aftermath of a dysentery epidemic in Japan, Tsutomu Watanabe reported that clinical researchers had identified multiple-drug resistant Shigella pathogens, that had acquired resistance genes from E. coli, present in the normal intestinal flora of patients.

The implications of such cross-species gene transfer for bacterial evolution have only recently come to light, with the availability of genome sequencing.

Twenty years ago, Elizabeth Pennisi commented in Science, “New genome sequences are mystifying evolutionary biologists by revealing unexpected connections between microbes thought to have diverged hundreds of millions of years ago. The newly unveiled genomes often contain a mix of DNAs, some seeming to come from the archaea and others from bacteria.” Indeed, as Francesco de la Cruz and Julian Davies wrote in 2000, “more candidates for horizontally transferred genes [were] identified: among prokaryotes; from bacteria to eukaryotes; from bacteria to archaea; from animals to bacteria; and so on.”

About 17% of the genomes of Salmonella or E. coli “appear to have been acquired by HGT during the past 100 million years,” note de la Cruz and Davies, “a significant proportion of the genome of any strain of a single bacterial species comprises fragments of DNA from various origins which, properly ‘nurtured’, can give rise to new bacterial species. . . .It would therefore appear that much of the speciation and sub-speciation in bacteria can be explained as the result of macroevolution events mediated by HGT, an alternative to fixation of point mutations.”

Microbiologists now regard HGT as major driver of evolutionary novelty among bacteria and archaea.

Michael Syvanen, the UC Davis microbiologist who has been writing about the subject for over thirty years, recently concluded, “We now know that the ability of genes to function perfectly well across species boundaries has resulted in a significant horizontal flow of genes. Whether the genes are transferred by transposons, viruses bacteria or other vectors, . . . . the horizontal flow of genes is a part of the story of life.”



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