Tag Archives: genes

The bigger the genome, the less efficient?

Researchers at Kew Gardens’ Jodrell Laboratory*  have identified the largest genome so far discovered. It belongs to the Paris japonica, a slow-growing herb native to the mountains of  the Japanese island of Honshu and  to the chagrin of many a frustrated gardener trying to cultivate in gardens , a very difficult plant to grow.  The difficulty in reproduction is probably related to the size of the genome,  for the larger the genome , the greater the difficulty in reproducing because every time a cell divides it has to reproduce the DNA. The more DNA, the longer that process takes and the more resources it requires. 

Homo sapiens has a measly three billion base pairs in its genome. (Two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair.  Adenine (A) forms a base pair with thymine (T) and guanine (G) with cytosine (C). In RNA, thymine is replaced by uracil (U)). Paris japonica has  150 billion base pairs.  Paris japonica replaces the previous record holder for the largest genome ,  the marbled catfish (Protopterus aethiopicus), which had 130 billion base pairs. At the other end of the genome size scale there is a bacterium called Carsonella ruddii, which has fewer than 160,000 base pairs.

This  immense disparity in genome size raises an interesting question. Why should genomes in general vary so widely and why does homo sapiens, indubitably the organism which has the most varied behaviour by far of any animal (arguably the best benchmark to judge the sophistication and capacities of an organism)(  should have a genome so much smaller than a plant or a fish? Efficiency is a plausible reason.

Efficiency improves with fewer components. Take the analogy of  written languages. Ideographic languages such as Chinese have  thousands of characters to do the same job that the alphabet does with 26 letters. If you set a dullard and a genius the task of devising a form of writing the dullard would produce Chinese characters and the genius the alphabet.  Another analogy. The more exotic versions of the Swiss Army knife have  several dozen implements, most of which are never used. The Swiss Army knife would be a much more efficient item if it had far fewer implements which were designed to be dual purpose, for example, a double edged blade with different types of edge on the two edges or a blade  with a file on its non-cutting surfaces.

Those two analogies  could explain why homo sapiens has such a small genome. Our genome may be comparatively small because it has reduced the number of components in the cause of efficiency.  The question then arises why would natural selection work to make some genomes more efficient than others.  Three likely candidates put themselves forward. The first is the innate capacities of the ancestral organism, the second, the environment in which an organism evolves. The third, the existential imperative to pass on the organism’s genes.

It is noticeable that the largest genomes are attached to organisms which are relatively low on the evolutionary scale.  It could be that they simply do not have the capacity to refine their genomes to become more efficient while  those higher up the evolutionary scale have the capacity in varying degrees. (I would bet that mammals have smaller genomes on average  than reptiles and amphibians).  This would mean that instead of refining their genomes towards efficiency every time a favourable or at least non-harmful mutation occurs this gets added to the genome which gets ever larger.   

As for environment, it is noticeable that the organisms which have the very large genomes tend to be in environments which have probably  been stable.  Paris japonica comes from a very restricted  mountain landscape which was on an island ; catfish wallow around in murky water.  Natural selection would not be directed towards improving genetic efficiency because the organisms were doing very nicely thank you.  Conversely, homo sapiens and his evolutionary forebears had immense selection pressure on them to survive because they were widespread enough to experience a  considerable range of environments both geographical and over time.  It may also be that living on land is a more demanding environment than water.  To that can be added the high intelligence, self-awareness  and language  of  homo sapiens which produces unique  selective choices because the mental environment is rich and varied in a way that it cannot be for any other animal.  Such environmental pressures were  probably the prime or sole  driver  for greater efficiency, although of course the flexibility of the genome could be dependent on mutations which were independent of environment.    If so, then the efficiency of our genomes is simply a lucky chance.  

If the prime directive of existence is to pass on genes, there would be a strong selective pressure to reduce the size of the genome to increase  reproductive capacity.  For such a large animal  (we are in the top 5% of land animals by size) homo sapiens has become a most fantastically successful breeder, no other animal of comparable size comes close to our breeding success.  A very large genome would have greatly  restricted such reproduction both in terms of time taken to reproduce and the increased likelihood of genetic defects (more genes, more potential  defects).  

* The team’s findings are already available online and will be printed in an upcoming issue of the Botanical Journal of the Linnean Society. The paper can be downloaded from

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8339.2010.01072.x/abstract

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