Thursday, August 29, 2013

What is the survival advantage of a larger genome?

The huge variation in genome sizes.  (Note that the X-axis
 is logirithmic.) Source: Wikimedia.
The amount of genomic DNA varies at least 40000-fold across eukaryotic species. But species with a lot of nuclear DNA content do not necessarily seem more complex than those with a small genome-- for example, amoebas have genomes much larger than those of humans. What's more, sequencing data show that the DNA of organisms with large genomes does not include large numbers of "extra" protein coding genes absent in their relatives with small genomes.  Instead, the difference among closely related species is made up chiefly by DNA sequences which do not code for proteins. 

 The high degree of variability  in genome sizes among closely related species is an instance of "the C-value enigma."  It costs a lot of energy to maintain DNA, to repair it when it's damaged, and to handle it accurately during cell division and sexual reproduction, and these costs would be expected to translate into a survival disadvantage, driving species over time toward very compact genomes. And there are real costs to having large genomes. Among plants, for example, there is a strong correlation between the size of the genome and the duration of meiosis. Plants with larger genomes are also more sensitive, in aggregate, to DNA damage via radiation, and they do less well in ecosystems with heavy metal pollution.  Is there some type of counterbalancing survival advantage to having and maintaining all that extra DNA? If so, what is it?

An 2009 paper by Leitch et al.  illustrates this enigma with respect to orchids. Genome sizes in this plant family vary more than 150-fold. (For comparision, genome size variation across all mammals is about 4 fold.) Leitch et al gathered data from 300 different orchid species and crunched the numbers to see if they could discern correlations between genome size and other traits of the plants.  The first trend that Leitch et al noticed was that the genome sizes of most orchid species, across all subfamilies, clustered at a fairly small size, comparable to the sizes observed for mammals. Larger genomes were much rarer.

Genome size (reported as 1C,  or the 
DNA content of unfertilized seeds) of
orchids, separated by lifestyle:
 terrestrial (top) or epiphytic (bottom).  
Genomes larger than 15 ph are observed 
exclusively in land-dwelling orchids.
Next, Leitch et al. noticed a striking difference when genome sizes were plotted according to the plant lifestyle. All of the large genomes they observed belonged  to ground-dwelling orchids.  Epiphyte orchids in this study (which grow  on other plants for physical support) exclusively had genomes at the small end of the range for all species. This pattern held even within orchid subfamilies containing species with both lifestyles. This difference in size distributions suggests that either a large genome is selected against in plants with an ephiphytic lifestyle, or that some advantage might be available for plants with large genomes and terrestrial lifestyle. 
Referring to data from other plant studies, Leitch et al. hypothesize that having a larger genome is disadvantageous for epiphytic orchids. One possible disadvantage that they consider is the known correlation between larger genome sizes and larger plant cell sizes.  Larger cells-- specifically, larger guard cells forming the pores on the bottom of leaves-- would make larger air pores, leading to more rapid exchange of gas but also to increased water loss. Perhaps epiphytic orchids, which must conserve water, have undergone selection for smaller guard cells and thus smaller genomes. Alternatively, phosphorous-- a key component of DNA-- is scarce in the epiphytic niche, and could become a source of selective pressure. Thus the study of Leitch et al. ends up by documenting a specific instance in which larger DNA genomic content appears to be a survival disadvantage. 

The model of Frank et al. Increases
 in atmospheric CO2 levels would
 tend to favor plants with larger guard cells
on their leaves. 
Another approach to understanding the relationship between genome sizes to evolutionary processes is to examine the fossil record. There is a really fascinating example of this in a 2012 paper by  Frank et al.  Frank et al speculated that larger guard cells, by promoting gas exchange,  would be advantageous during evolutionary intervals in which atmospheric carbon dioxide was high. To evaluate this, they collected measurements of guard cell volumes from 400 million years of the fossil record, and remarkably did find a correlation between this simple geometric measure and measures of atmospheric CO2.  Since genome size correlates with guard cell size, its possible that genomic size contributed to evolutionary processes on this longer time scale.
Frank et al. are careful to add this disclaimer to their work: "Our goal is not to identify, nor does it require, a mechanism for change in or evolution of plant genome size. However, an understanding of the selective forces involved requires a model that tells us what to expect from a given set of assumptions, so to this end, we describe a simple model to accompany our findings." With this caveat, their paper provides conceptual support for large genomes as a structural, rather than strictly genetic, trait. 


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