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James A. Shapiro

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More Evidence on the Real Nature of Evolutionary DNA Change

Posted: 01/06/12 11:15 AM ET

"Scientific development depends in part on a process of non-incremental or revolutionary change...The usual prelude to changes of this sort is...the awareness of anomaly, of an occurrence or set of occurrences that does not fit existing ways of ordering phenomena. The changes that result therefore require 'putting on a different kind of thinking-cap'..." -- Thomas Kuhn

Conventional wisdom has it that the genetic changes underlying evolution are random accidents, each having a small chance of making incremental improvements in fitness. These ideas came about before we knew about DNA. Now that we have almost 60 years of DNA-based molecular genetics and genome sequencing behind us, a different picture has emerged. As I argue in my June 2011 book, molecular science reveals built-in cell systems for restructuring genomes in times of stress and challenge. The mobile genetic elements first discovered by Barbara McClintock have proved to be everywhere. Sometimes these are also called transposable elements (TEs) because they move ("transpose") from one site in the genome to new sites. They are part of an elaborate set of biochemical functions essential for making changes in DNA sequences (which do not happen without these functions). But the question still remains: does the evidence exist that these same functions are responsible for actual evolutionary change? A recent Nature paper (Lindblad-Toh, Garber et al. 2011) provides some answers.

Investigators from Harvard and MIT's Broad Institute carried out an exhaustive comparison of the human genome sequence with the sequences of 29 other eutherian mammals (the ones that have placenta and diverged from Marsupials). Using state-of-the-art bioinformatic tools, they searched for positively selected features in the human and other 29 genomes. The search identified genetic loci encoding approximately 4,400 out of 13,000 protein families as falling into the positively selected category and are, therefore, presumed adaptively useful throughout eutherian mammals' evolution. While this result was consistent with conventional expectations, the big surprise came when the researchers looked at so-called "non-coding" regions of the genome. These regions contain DNA sequence signals for essential functions, such as packaging the DNA within the nucleus, copying DNA into RNA, replicating the genome, and distributing the two genome copies equally to daughter cells at cell division. "Our data revealed >280,000 mobile element exaptations common to mammalian genomes covering ~7 Mb..., a considerable expansion from the ~10,000 previously recognized cases. Of the ~1.1 million constrained elements that arose during the 90 million years between the divergence from marsupials and the eutherian radiation, we can trace >19% to mobile element exaptations."

A detour will probably be helpful here to explain the term "exaptation" for readers not familiar with it. The word "exaptation" was invented by the late Stephen J. Gould and fellow paleontologist Elisabeth Vrba in 1982 to describe inherited adaptations that have acquired new functions in the course of evolutionary change (Gould and Vrba 1982). It denotes a fundamental aspect of evolution where the jobs encoded by one component of the genome can undergo alteration so that they meet a new adaptive need. Exaptations can occur at all levels of genome encoding, from essential recognition sites to protein coding sequences to entire networks of proteins and the DNA signals they recognize. For example, the same signaling cascade of proteins is used in various organisms to communicate information to the genome about oxidative stress, osmotic pressure, and the presence of suitable sex partners.

As the Broad Institute authors note, "Mobile elements provide an elegant mechanism for distributing a common sequence across the genome, which can then be retained in locations where it confers advantageous regulatory functions to the host -- a process termed exaptation." In other words, new DNA signals in the genome do not need to evolve independently by random mutation at each site where they play an important role. Different DNA signals can be distributed to many sites by the biochemical systems that mobilize defined segments of DNA (mobile genetic elements) to new locations. In this way, evolution of the DNA signals embedded in the genome resembles genetic engineering more than a mutational random walk. The fact is that only fairly recent exaptations can be identified because the traces of the original mobile genetic elements tend to disappear with sequence changes over time. Thus, the >280,000 cases of mobile genetic element exaptation identified in the Lindblad-Toh et al. paper represent the lower limit of genome formatting by a process I dubbed "natural genetic engineering" twenty years ago (Shapiro 1992). Although conventional evolutionists have tended to ignore the importance of mobile genetic elements in evolution -- calling them "junk DNA" (Orgel 1980) -- and treat the well-documented cases of mobile genetic element exaptation as minor and accidental exceptions, the weight of evidence revealed by this article cannot be dismissed so easily.

The idea that mobile genetic elements and natural genetic engineering are fundamental to genome evolution dates back to Barbara McClintock's work on what she called "controlling elements" (McClintock 1987). When she compared controlling elements to the recently discovered repressor-operator system of E. coli (McClintock 1961), her interpretation was widely rejected because DNA mobility was not considered important to the short-term regulation of protein synthesis and genome expression. This rejection notwithstanding, her "controlling elements" terminology now appears prescient in light of recent genomic discoveries. She considered mobile genetic elements as "controlling" elements in the genome because they altered the expression patterns of a particular genetic locus when they inserted into it. This is just what evolution needs to rewire genomic networks at times of evolutionary challenge, especially when similar changes have to occur at more than one locus (McClintock 1956).

There are many eye-opening consequences of the basic role that natural genetic engineering plays in the evolutionary process. We will explore these conceptual changes in future blogs. For the moment, it is deeply satisfying to note that intense genome sequence analysis has validated the work of McClintock and her many followers in the field of mobile genetic elements.


REFERENCES

Gould, S. J. and E. S. Vrba (1982). "Exaptation--a missing term in the science of form." Paleobiology 8(1): 4-15. http://www.jstor.org/stable/2400563 .
Lindblad-Toh, K., M. Garber, et al. (2011). "A high-resolution map of human evolutionary constraint using 29 mammals." Nature 478(7370): 476-482. http://www.ncbi.nlm.nih.gov/pubmed/21993624.
McClintock, B. (1956). "Intranuclear systems controlling gene action and mutation." Brookhaven Symp Biol(8): 58-74. http://www.ncbi.nlm.nih.gov/pubmed/13293421.
McClintock, B. (1961). "Some parallels between gene control systems in maize and in bacteria." American Naturalist 95: 265-277. http://www.jstor.org/stable/2458651.
McClintock, B. (1987). Discovery And Characterization of Transposable Elements: The Collected Papers of Barbara McClintock New York, Garland. ISBN 978-0824013912.
Orgel, L., Crick, FH (1980). "Selfish DNA: the ultimate parasite." Nature 284: 604-607. http://www.ncbi.nlm.nih.gov/pubmed/7366731.
Shapiro, J. A. (1992). "Natural genetic engineering in evolution." Genetica 86(1-3): 99-111. http://www.ncbi.nlm.nih.gov/pubmed/1334920.