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    Gecko Genome Size And Cell Size
    By T. Ryan Gregory | July 5th 2008 10:12 AM | 2 comments | Print | E-mail | Track Comments
    About T. Ryan

    I am an evolutionary biologist specializing in genome size evolution at the University of Guelph in Guelph, Ontario, Canada. Be sure to visit

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    One of the many aggravations I encounter when reviewing manuscripts is that some authors greatly overstate the applicability of statistically significant patterns they report. For example, a statistically significant pattern in a small comparison of a few animals may be extrapolated in the discussion to the kingdom at large.

    Today I was disappointed to see a paper that is soon to come out in Zoology that does the opposite -- i.e. takes a non-significant relationship in a handful of species and pretends that it challenges the importance of broad relationships that have been considered important for decades.

    The paper in question is:

    Starostova, Z., L. Kratochvil, and M. Flajshans. 2008. Cell size does not always correspond to genome size: phylogenetic analysis in geckos questions optimal DNA theories of genome size evolution. Zoology, in press.

    They compared genome size and cell size across 15 geckos and found no correlation. From this, they went on to argue that genome size does not causally influence cell size and that genome size is not under selection due to cell size impacts.

    First, let me point out that strong, positive correlations between genome size and cell size have been reported within and across all vertebrate classes including reptiles. So, on a broad scale, the relationship is clear.

    Genome size and cell size in reptiles.  From Gregory (2001), based on data from Olmo and Odierna (1982).

    Second, let me say that I have issues with their methods. For example, they used DAPI as the fluorochrome, which is base-pair specific and can give biased determinations (they recognize this but assume the species are all the same in AT content). Second, they produced fairly substantial error ranges in their measurements given that these were all raised in the lab or obtained from pet shops and not taken from different wild populations (i.e., the variability between conspecifics is probably artifact). Third, they counted "forms" of the same species from different places as being independent in their analyses -- so it wasn't 15 species, rather it was 12 species with several represented by multiple points.

    These are not the main problems, though.  The first is that they clearly had outliers in the dataset.  In particular, Coleomyx brevis (CB) and Coleomyx variegatus (CV) have "large" (~2pg) genomes but comparatively small cells.  I don't think I even need to draw the line through the remaining points, but in case eyeball statistics don't do it, the correlation is highly significant without them (r = 0.74, p < 0.006) (they recognize this, too, but note the title they chose for the paper nonetheless). 

    From Starostova et al. (2008). 

    So, how can this be explained?  Well, you have to know something about nucleotypic theory, which these authors actually did mention.  It's not genome size all alone that is the determining factor -- nucleus size is critical.  The "nucleotype" is defined as "that condition of the nucleus that affects the phenotype independently of the informational content of the DNA” (Bennett 1971).  As has been pointed out repeatedly (e.g., by me, Cavalier-Smith, Bennett, and others), the compaction level of DNA in the nucleus adds a second dimension to the relationship.  More DNA is one thing, but if it is compressed into a tightly packed, reduced nucleus, then cell size may still be small.  

    That leads to the second major problem.  Looking at the data reported in a previous study (Starostova et al 2005), there is no correlation between genome size and nucleus size.  There is, however, a positive correlation between nucleus size and cell size across these reptiles. 

    Based on databy Starostova et al. (2005).


    The two outliers in the genome size vs cell size comparison have more compact nuclei and this allows smaller cell sizes with larger genome size. Cell size is correlated with body size in these geckos, and these two species are "dwarfs" (~4.5g) relative to other species (as big as ~90g).  So, there could very easily be selection for reduced cell size which, in this narrow range in DNA amount, was met by a compaction of the nucleus rather than a loss of DNA.

    This actually reinforces the strength of nucleotypic theory.

     

    ______

    Bennett, M.D. 1971. The duration of meiosis. Proceedings of the Royal Society of London B 178: 277-299.

    Gregory, T.R. 2001. The bigger the C-value, the larger the cell: genome size and red blood cell size in vertebrates. Blood Cells, Molecules, and Diseases 27: 830-843.

    Olmo, E. and G. Odierna. 1982. Relationships between DNA content and cell morphometric parameters in reptiles. Basic and Applied Histochemistry 26: 27-34.

    Starostova, Z., L. Kratchovil, and D. Frynta. 2005. Dwarf and giant geckos from the cellular perspective: the bigger the animal, the bigger its erythrocytes? Functional Ecology 19: 744-749.


    Comments

    As the authors of the criticized paper, we were rather disappointed by several misinterpretations T. Ryan Gregory made in his comment. We decided to clarify some of them (although we recommend an interested reader to study our original work):

    1) We have never doubt the positive correlation between cell size (better to say size of red blood cells) and genome size on a BROAD taxonomic scale (across and within the whole vertebrate classes). Nevertheless, we stress that although that the pattern is clear, it is much less obvious which processes shape it. The nucleotypic theory is just one possibility and it gives clear predictions about the polarity and direction of evolutionary changes on the smaller taxonomic scales as well. We decided to test them in an explicit phylogenetic framework among several closely related forms of a single lizard family.

    2) Our paper is not based on “a non-significant relationship in a handful of species”. We are far from doing interpretations from non-detection of statistically significant correlation. One of the major messages of our paper is that the cladistic analysis of character states can reveal the directions of evolutionary changes and thus it is much more powerful tool than simple search for statistical correlation between several variables (let say genome and cell size). We tried to exemplify such careful comparative phylogenetic analysis in the case of our geckos – and we reconstructed the sequence of evolutionary changes at variance with the predictions of the nucleotypic theory.

    3) The nucleotypic theory tries to explain the empirically observed correlations between genome size and cell size via the expected correlation between genome size and nucleus size. It is clear that in the case of our geckos, the nucleus size and cell size are in good agreement. But we stress that cell size does not always correspond to GENOME size, not NUCLEUS size. In our paper, we present several other important examples documented that genome size and cell size are not so tightly linked as the proponents of the nucleotypic theory often claim: individual alleles of a single gene can dramatically alter cell size clearly without any change in genome size, cell size is often phenotypically plastic, i.e. single genome size can “create” rather wide range of cell sizes etc.

    4) Based on these examples and our results concerning lower taxonomic scales, we think that there is no need to expect a direct causative link between genome size and cell size to explain the correlation between genome size and cell size at higher taxonomic levels. We suggest that we could explain this pattern non-adaptively when 1) we assume a simple mechanistic constraints of nucleus size on genome size, i.e. large nuclei can be present only in large cells, and 2) we connect the well-known negative relationship between cell size and metabolic size (Goniakowska 1973; Mongold and Lenski 1996) with the recetly documented link between metabolic rate and the rate of evolution (Gillooly et al. 2005) and the recent admiring progress in the population-genetic model of genome complexity (Lynch 2002, 2006).

    In summary, we predict that the research on genome size – cell size relationship will shift from testing the correlations at broad scales (where the patterns are clear) to careful, cladistic analyses on lower taxonomic scales. We expect that other future studies on cell size and genome size will also find mismatch between evolutionary changes in these two characteristics, although such nice correlations between them exist on broad taxonomic scales. Even if not, it is always useful to try to rethink our old, favorite theories and do not totally dismiss their alternatives.

    Lukas Kratochvil and Zuzana Starostova

    T Ryan Gregory
    I have already explained the misconceptions in your paper, and I will simply quote from one of mine about the ones repeated in your response.



    Gregory 2001:



    Genes affecting cell volume have long been known to exist (e.g. Nurse, 1985). This fact has been enlisted by various authors as a primary argument against the nucleotypic theory (most notably Cavalier-Smith, 1985b, 1991). Because cell volume can be regulated genically, they argue, there is little room for bulk DNA content as a mechanism of cell size determination. This either-or (mis)interpretation of the nucleotypic theory rings of the outmoded “nature vs. nurture” debate in psychology, and is fallacious for the same reasons. In reality, the nucleotypic theory has always been one of joint action between the genotype and the nucleotype; as Bennett (1972) describes, “while it has been thought that the phenotype is the product of an interaction between the genotype and the environment alone, it now seems that a third factor affecting the phenotype must be recognized, namely the nucleotype. [This] should not be interpreted as indicating that the role of the genotype is secondary to that of the nucleotype. [T]he nucleotype provides a coarse control which may be modified by the much finer control of gene action. An important property of the nucleotype is that it can sometimes limit the phenotypic expressions which can be achieved by gene action”. Similarly, Karp, Rees&Jewell (1982) stress that “the nucleotype imposes certain regulations and constraints upon cell growth and development but regulations and constraints which are subject to modification and elaboration by the genotype”. Again, the primary role of bulk DNA content may be in setting the minimum size attainable by a cell. Cell size may be modified greatly by the action of genic regions above this minimum, but short of ejecting DNA* the cell may be incapable of reaching a smaller size (Bennett, 1987; Figure 3). For this reason, correlations between C-value and the volumes of differentiated cells such as erythrocytes, and the maintenance of this correlation following reductions in DNA content, are problematic for all theories except the nucleotypic.



    ...



    Additionally, some authors argue that the imperfect nature of the relationship between genome size and cellular parameters within eukaryotes speaks against the nucleotypic theory. However, numerous reasons are available to explain the noise observed in the cell size relationship, including the size and presence of vacuoles in plants and protists, nutritional and temperature conditions, phylogenetic considerations, and the additional action of modifying genes, to name but a few. Cell division rates can similarly be subject to numerous extraneous influences.



    Far from being rigid or revolutionary, the nucleotypic theory argues for the additional role of DNA in influencing cellular (and by extension, organismal) parameters via its bulk physico-chemical properties. The importance of the genome’s protein-coding function is not, and never has been, in dispute.





    * Or, within narrow ranges, compacting it.