- Email: [email protected]
Reply to Gregory’s Letter to the Editor: Genome size and its correlation with longevity in fishes
Experimental Gerontology 39 (2004) 861–862 www.elsevier.com/locate/expgero
Correspondence Reply to Gregory’s Letter to the Editor: Genome size and its correlation with longevity in fishes Different adaptive explanations for the evolution of genome size have been attempted and a very controversial one is that differences in genome size are correlated with differences in longevity in both birds and fish (Monaghan and Metcalfe, 2000, 2001; Morand and Ricklefs, 2001; Gregory, 2002; Griffith et al., 2003; Gregory, 2004). In his letter, Gregory (2004) claims that we reported direct and phylogenetically corrected positive correlations between genome size and longevity in fishes (Griffith et al., 2003) and that these correlations are meaningless because they are non-significant. A problem with his criticism is that we never reported correlations using the entire data set but only on phylogenetically corrected data (Griffith et al., 2003). Using a partial correlation analysis on our entire dataset, which is available through appendix 1 (see Griffith et al., 2003), a positive and significant correlation is found between genome size and longevity while controlling for differences in body mass (r ¼ 0:36; p , 0:01; n ¼ 113), but such correlation disappears when the more distant Chondrostei (Acipenseriformes) species are removed from the analysis. Removal of this distant group and focus on the teleosts yields a negative but non-significant correlation (r ¼ 20:12; p ¼ 0:22; n ¼ 101). Is genome size negatively correlated with longevity after removing the more distant group of Chondrostei? The most conservative answer is that we simply do not know. Using all species of fishes or only the teleosts to establish correlations between genome size and longevity is problematic because many data points are not statistically independent due to shared evolutionary history. A solution to this problem is to test correlations using phylogenetic comparative methods (see Felsenstein, 1985). In fact, a recent simulation study has shown that correlation analysis of interspecific data, as done by Gregory (2004), without considering their phylogenetic relationship leads to very poor estimates compared to results obtained taking into account their phylogeny (Martins et al., 2002). These phylogenetic comparative methods perform better than nonphylogenetic approaches even when the assumptions of the methods are somehow violated by the evolutionary history of the traits being analyzed (Martins et al., 2002). For this and no other reason, we limited our correlation analysis to orders for which phylogenies were available (Acipenseriformes, Cypriniformes and Salmoniformes) (Griffith et al., 2003). For all these orders, we detected a 0531-5565/$ - see front matter q 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.exger.2004.01.016
positive but non-significant correlation between genome size and longevity for phylogenetically independent contrasts (r ¼ 0:30; p ¼ 0:17; n ¼ 22) (Griffith et al., 2003). There is such a thing as a non-significant positive correlation. A positive correlation with a P value of 0.051 is not less positive than one with P value of 0.049. Gregory also criticizes our choice of taxa. We agree that it is problematic to perform analysis across infraclasses. This is why we used analysis of covariance to test for the effect of genome size on longevity while controlling for different orders, and why we did not report correlations using the entire dataset as Gregory does (Gregory, 2004). Our use of maximum body size can be simply explained by the well-known fact that fishes have indeterminate growth. Using mean weight values for fish would be more problematic than using maximum values. Mammals may indeed be better dealt with on the basis of mean values because they have determinate growth. So his imagined comparison based on a human value of 500 kg is irrelevant. His criticism of the fact that the significant positive correlation between mass-corrected longevity and genome size within the order Acipenseriformes could be biased due to polyploidy is relevant and deserves consideration. Using species of the Acipenseriformes order listed in Appendix 1 (Griffith et al., 2003) and controlling for both body weight and chromosome number results in a non-significant positive correlation between c-value and longevity (r ¼ 0:51; p ¼ 0:20; n ¼ 10). The problem of including non-phylogenetically independent data still remains in this dataset. The limitation due to the lack of a well-resolved phylogeny for the orders used in our original study (Griffith et al., 2003) is one that should receive closer attention in future comparative studies across species. Using sequence data from mitochondrial cytocrome b available in GenBank (http://www.ncbi.nlm.nih.gov/) for species belonging to the Acipenseriformes, Cypriniformes and Salmoniformes, a preliminary gene tree can be used to perform phylogenetically independent contrasts between differences in c-value, maximum age, body mass and chromosome numbers. A partial correlation between differences in genome size and longevity while controlling for differences in body mass and chromosome number results in a significant and positive correlation (r ¼ 0:37; p ¼ 0:034; n ¼ 35). Caution should be exercised due to the fact that a cytochrome b gene tree does not necessarily reflect the true species phylogeny. However, we found only positive partial correlations among differences in genome size and longevity when we tried different tree topologies and branch lengths.
862
Correspondence / Experimental Gerontology 39 (2004) 861–862
In summary, the use of our entire dataset (see Appendix 1, Griffith et al., 2003) shows only a positive correlation between genome size and longevity for phylogenetically independent comparisons after controlling for differences in body mass and chromosome number. Gregory’s finding of a significant negative correlation within the teleosts and using only Acipenseriformes is flawed by the problem of comparing non-phylogenetically independent data points which will produce less accurate results than correlation analysis in the context of phylogenetic corrections (Martins et al., 2002). Add to this his discomfort with the use of maximum lifespan data; and one wonders why Gregory is willing to use this data set to suggest his potential negative relationship between genome size and longevity in fishes. Correlation studies will constantly face the brick wall of being unable to make a connection between an interesting observation and its causal explanation. Many studies on the evolution of genome size that use correlation approaches are particularly vulnerable to this problem as experimental genome size manipulations are not feasible. In the meantime, studies about the evolution of genome size will certainly benefit from more accurate measures of genome size, than the currently used literature collection of picogram per diploid cell (Gregory, 2001), coming out of genome sequencing projects and the analysis of interspecies data in the context of well-resolved species phylogenies.
References Felsenstein, J., 1985. Phylogenies and the comparative method. Am. Nat. 125, 1–15.
Gregory, T.R., 2001. Animal Genome Size Database, http://www. genomesize.com/. Gregory, T.R., 2002. Genome size and developmental parameters in the homeothermic vertebrates. Genome 45, 833 –838. Gregory, T.R., 2004. Genome size is not correlated positively with longevity in fishes (or homeotherms). Exp. Gerontol. This issue. Griffith, O.L., Moodie, G.E.E., Civetta, A., 2003. Genome size and longevity in fish. Exp. Gerontol. 38, 333–337. Martins, E.P., Diniz-Filho, J.A.F., Housworth, E.A., 2002. Adaptive constraints and the phylogenetic comparative method: a computer simulation test. Evolution 56, 1–13. Monaghan, P., Metcalfe, N.B., 2000. Genome size and longevity. Trends Genet. 16, 331–332. Monaghan, P., Metcalfe, N.B., 2001. Genome size, longevity and development in birds. Trends Genet. 17, 568. Morand, S., Ricklefs, R.E., 2001. Genome size, longevity and development in birds. Trends Genet. 17, 567– 568.
A. Civettap G.E.E. Moodie a Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, Man., Canada R3B 2E9 E-mail address: [email protected] O.L. Griffith Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
b
Accepted 29 January 2004
* Corresponding author. Tel.: þ1-204-786-9436; fax: þ 1-204-774-4134.
Correspondence Reply to Gregory’s Letter to the Editor: Genome size and its correlation with longevity in fishes Different adaptive explanations for the evolution of genome size have been attempted and a very controversial one is that differences in genome size are correlated with differences in longevity in both birds and fish (Monaghan and Metcalfe, 2000, 2001; Morand and Ricklefs, 2001; Gregory, 2002; Griffith et al., 2003; Gregory, 2004). In his letter, Gregory (2004) claims that we reported direct and phylogenetically corrected positive correlations between genome size and longevity in fishes (Griffith et al., 2003) and that these correlations are meaningless because they are non-significant. A problem with his criticism is that we never reported correlations using the entire data set but only on phylogenetically corrected data (Griffith et al., 2003). Using a partial correlation analysis on our entire dataset, which is available through appendix 1 (see Griffith et al., 2003), a positive and significant correlation is found between genome size and longevity while controlling for differences in body mass (r ¼ 0:36; p , 0:01; n ¼ 113), but such correlation disappears when the more distant Chondrostei (Acipenseriformes) species are removed from the analysis. Removal of this distant group and focus on the teleosts yields a negative but non-significant correlation (r ¼ 20:12; p ¼ 0:22; n ¼ 101). Is genome size negatively correlated with longevity after removing the more distant group of Chondrostei? The most conservative answer is that we simply do not know. Using all species of fishes or only the teleosts to establish correlations between genome size and longevity is problematic because many data points are not statistically independent due to shared evolutionary history. A solution to this problem is to test correlations using phylogenetic comparative methods (see Felsenstein, 1985). In fact, a recent simulation study has shown that correlation analysis of interspecific data, as done by Gregory (2004), without considering their phylogenetic relationship leads to very poor estimates compared to results obtained taking into account their phylogeny (Martins et al., 2002). These phylogenetic comparative methods perform better than nonphylogenetic approaches even when the assumptions of the methods are somehow violated by the evolutionary history of the traits being analyzed (Martins et al., 2002). For this and no other reason, we limited our correlation analysis to orders for which phylogenies were available (Acipenseriformes, Cypriniformes and Salmoniformes) (Griffith et al., 2003). For all these orders, we detected a 0531-5565/$ - see front matter q 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.exger.2004.01.016
positive but non-significant correlation between genome size and longevity for phylogenetically independent contrasts (r ¼ 0:30; p ¼ 0:17; n ¼ 22) (Griffith et al., 2003). There is such a thing as a non-significant positive correlation. A positive correlation with a P value of 0.051 is not less positive than one with P value of 0.049. Gregory also criticizes our choice of taxa. We agree that it is problematic to perform analysis across infraclasses. This is why we used analysis of covariance to test for the effect of genome size on longevity while controlling for different orders, and why we did not report correlations using the entire dataset as Gregory does (Gregory, 2004). Our use of maximum body size can be simply explained by the well-known fact that fishes have indeterminate growth. Using mean weight values for fish would be more problematic than using maximum values. Mammals may indeed be better dealt with on the basis of mean values because they have determinate growth. So his imagined comparison based on a human value of 500 kg is irrelevant. His criticism of the fact that the significant positive correlation between mass-corrected longevity and genome size within the order Acipenseriformes could be biased due to polyploidy is relevant and deserves consideration. Using species of the Acipenseriformes order listed in Appendix 1 (Griffith et al., 2003) and controlling for both body weight and chromosome number results in a non-significant positive correlation between c-value and longevity (r ¼ 0:51; p ¼ 0:20; n ¼ 10). The problem of including non-phylogenetically independent data still remains in this dataset. The limitation due to the lack of a well-resolved phylogeny for the orders used in our original study (Griffith et al., 2003) is one that should receive closer attention in future comparative studies across species. Using sequence data from mitochondrial cytocrome b available in GenBank (http://www.ncbi.nlm.nih.gov/) for species belonging to the Acipenseriformes, Cypriniformes and Salmoniformes, a preliminary gene tree can be used to perform phylogenetically independent contrasts between differences in c-value, maximum age, body mass and chromosome numbers. A partial correlation between differences in genome size and longevity while controlling for differences in body mass and chromosome number results in a significant and positive correlation (r ¼ 0:37; p ¼ 0:034; n ¼ 35). Caution should be exercised due to the fact that a cytochrome b gene tree does not necessarily reflect the true species phylogeny. However, we found only positive partial correlations among differences in genome size and longevity when we tried different tree topologies and branch lengths.
862
Correspondence / Experimental Gerontology 39 (2004) 861–862
In summary, the use of our entire dataset (see Appendix 1, Griffith et al., 2003) shows only a positive correlation between genome size and longevity for phylogenetically independent comparisons after controlling for differences in body mass and chromosome number. Gregory’s finding of a significant negative correlation within the teleosts and using only Acipenseriformes is flawed by the problem of comparing non-phylogenetically independent data points which will produce less accurate results than correlation analysis in the context of phylogenetic corrections (Martins et al., 2002). Add to this his discomfort with the use of maximum lifespan data; and one wonders why Gregory is willing to use this data set to suggest his potential negative relationship between genome size and longevity in fishes. Correlation studies will constantly face the brick wall of being unable to make a connection between an interesting observation and its causal explanation. Many studies on the evolution of genome size that use correlation approaches are particularly vulnerable to this problem as experimental genome size manipulations are not feasible. In the meantime, studies about the evolution of genome size will certainly benefit from more accurate measures of genome size, than the currently used literature collection of picogram per diploid cell (Gregory, 2001), coming out of genome sequencing projects and the analysis of interspecies data in the context of well-resolved species phylogenies.
References Felsenstein, J., 1985. Phylogenies and the comparative method. Am. Nat. 125, 1–15.
Gregory, T.R., 2001. Animal Genome Size Database, http://www. genomesize.com/. Gregory, T.R., 2002. Genome size and developmental parameters in the homeothermic vertebrates. Genome 45, 833 –838. Gregory, T.R., 2004. Genome size is not correlated positively with longevity in fishes (or homeotherms). Exp. Gerontol. This issue. Griffith, O.L., Moodie, G.E.E., Civetta, A., 2003. Genome size and longevity in fish. Exp. Gerontol. 38, 333–337. Martins, E.P., Diniz-Filho, J.A.F., Housworth, E.A., 2002. Adaptive constraints and the phylogenetic comparative method: a computer simulation test. Evolution 56, 1–13. Monaghan, P., Metcalfe, N.B., 2000. Genome size and longevity. Trends Genet. 16, 331–332. Monaghan, P., Metcalfe, N.B., 2001. Genome size, longevity and development in birds. Trends Genet. 17, 568. Morand, S., Ricklefs, R.E., 2001. Genome size, longevity and development in birds. Trends Genet. 17, 567– 568.
A. Civettap G.E.E. Moodie a Department of Biology, University of Winnipeg, 515 Portage Ave., Winnipeg, Man., Canada R3B 2E9 E-mail address: [email protected] O.L. Griffith Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
b
Accepted 29 January 2004
* Corresponding author. Tel.: þ1-204-786-9436; fax: þ 1-204-774-4134.