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Plant Chromosome Structures Challenge Biological Evolution

Researchers from France recently examined the structure of the coffee tree, tomato, and grapevine genomes. Surprisingly, the results of their work fail to satisfy a key prediction of the evolutionary paradigm—namely, that the ordering of genes along chromosomes (called synteny) should reflect the evolutionary relatedness of these plants. Instead these investigators found that the synteny of these genomes does not vary with phylogenetic distance.

It has been said, “time heals all wounds.” I do not agree. The wounds remain. In time, the mind, protecting its sanity, covers them with scar tissue and the pain lessens. But it is never gone.

— Rose Kennedy (1890–1995), mother of President John F. Kennedy and US senators Robert F. Kennedy and Edward “Ted” Kennedy

As time goes by, past events become a distant memory—at least in some cases. Evolutionary biologists make use of this principle when they analyze and compare the genomes of organisms.

The idea is pretty straightforward. If evolutionary processes generated life’s diversity, then closely related organisms should have highly similar genomes. Likewise, distantly related organisms should have disparate genomes.

The similarities (and differences) not only include gene types and sequences, but also the physical arrangement, or ordering, of genes (and other DNA elements) along a chromosome. The ordering of genes along a chromosome is called synteny.

According to the evolutionary paradigm, at the time two species diverge from each other to form distinct evolutionary lineages, their genomes would be nearly identical. The genomes of the two species change over time. Processes like mutations and recombination alter the genomes’ DNA sequences and the genes’ synteny, respectively. The genome of each species will accrue different changes. As time goes on, the number of changes, and consequently, the extent of the differences between the two genomes will become greater and greater. The prediction, then, is that genomic features (like synteny) will reflect the evolutionary relationships of a particular collection of organisms. (Go here for a well-written article by Dennis Venema that describes this relationship.)

However, new work by French researchers fails to satisfy this prediction.1 The investigators characterized the large-scale and small-scale arrangement (synteny) of genes and DNA elements in the genomes of the coffee tree, tomato, and grapevine. The coffee tree and tomato belong to the same biological group (asterids), whereas the grapevine is part of a separate group (rosids).

From an evolutionary perspective, the asterids diverged from the rosids about 125 million years ago. The tomato and the coffee tree then diverged from each other around 85 million years ago. Based on these evolutionary relationships, the researchers expected that the grapevine genome structure would be distinct from those of the coffee tree and tomato. As it turns out, a higher level of synteny for some regions was observed between the coffee tree and grapevine than between the coffee tree and tomato. In other cases, the synteny was the same for all three plants. In other words, synteny did not decrease as the plants became more distantly related from an evolutionary perspective.

This is not the first time that evolutionary biologists have been confronted with this problem. Still, many proponents of the evolutionary paradigm maintain that the relationship between synteny and evolutionary history is a compelling reason to accept biological evolution as a fact. Yet, if this relationship doesn’t hold, then it should form the basis for skepticism about biological evolution.