From the thousands of species that have already been analyzed, it is now clear that genome size varies considerably between species. This variation is mainly because of the differing amounts of various repeated sequences, including satellite DNA, transposable elements (TEs) and ribosomal genes in different genomes. The idea of within-species variation, that is, variation between populations and between individuals, has won less general acceptance, despite various studies revealing its existence. This is sometimes because of mistrust and suspicion (Gregory and Johnston, 2008), sometimes to the concept underlying the definition of species (Murray, 2005) and sometimes to artefacts in the technique used (Greilhuber, 2005; Gregory and Johnston, 2008). For example, some of the variation observed in genome size between populations subjected to different environmental conditions over the geographical range of the species can be accounted for by the chromatin state, which can affect the accessibility of the DNA to fluorochromes (see Nardon et al., 2003 and references therein). However, we do not have to throw the baby out with the bath water as all these confounding factors can be taken into account by using appropriate protocols and statistical methods, which take different levels of sampling and replicates into account, for determining within- and between-species variation. A recent study of genome size in various Drosophila species (Bosco et al., 2007) concludes that there is a significant statistical difference in genome size between species, and some significant differences between strains in some species. Vieira et al. (1999, 2002) have also identified genome-size differences between populations of both Drosophila melanogaster and D. simulans, but no differences between replicates of batches of flies reared in the same vial. In the Bosco et al. (2007) paper, the variation in genome size was related to variation in heterochromatin composition, mostly of satellite DNA, whereas TEs were mostly involved in the Vieira et al. (1999, 2002) study. Such data give credibility to between-individual variations in the amount of heterochromatic TEs that have been estimated using dot blots and in situ hybridization in Drosophila (Charlesworth et al., 1994). These results show that both TEs and satellite DNA can influence genome size, and lead to within-species variation. Satellite DNA is indeed a major constituent of the genomes of many organisms (see Palomeque and Lorite, 2008 for a review), and it explains why the genome of the species D. orena (0.28 pg) is so much larger than that of D. melanogaster (0.18 pg) (Boulesteix et al., 2006). Marked differences in genome size between closely related lines of flax (Linum usitatissimum) have been shown to occur over a very short period, and to involve a change in rDNA amount (Cullis, 2005; Davison et al., 2007), as well as specific LIS-1 insertion events, although possible changes in the amount of other repetitive sequences were not determined. Mobilization and integration of novel copies of TEs are not always observed in genome changes, which can simply result from segmental duplication of centromeric regions, as reported in rice (Ma and Jackson, 2006).

Centromeres and the Y chromosome seem to have a major function in the change in genome size reported both within- and between-species. In most species, the heterochromatic Y chromosome consists mainly of numerous repeated sequences, mostly satellites and TEs (Palomeque and Lorite, 2008), within which only a few genes, mostly fertility genes, are embedded. For instance, it has been reported that in Anopheles gambiae the fully heterochromatic Y chromosome varies in length and banding pattern in natural populations, a finding consistent with the rapid satellite expansion mechanism in this species (Bonaccorsi et al., 1980). Hence, in addition to changes in centromere composition and whole genome structure, the Y chromosome, because of its highly degenerated heterochromatic state (Charlesworth, 2002) and the fact that it differs in size in different populations, seems to make a particular contribution to the variation in genome size, as reported in some plants (Meagher et al., 2005). This implies that the suggestion that changes in the composition of the Y chromosome could be responsible for geographical adaptive genetic differences between temperate and tropical populations of Drosophila melanogaster (Rohmer et al., 2004) warrants further investigation.

The reasons for differences in the amounts of repeated sequences present in different populations are not clearly understood. In addition to the impact of the effective population size (Lynch and Conery, 2003), at least two explanations are conceivable. A global change could have occurred as a result of the stressful environmental conditions encountered by the species when they invaded new geographical areas, or of confrontations between populations that had not encountered each other earlier (Biémont and Vieira, 2005 and references therein). TE transposition and amplification have been reported in inter-species hybrids in Drosophila and in the Australian wallaby (see references in Biémont and Vieira, 2005), but few data are available about intra-species hybridization. Only certain specific TEs, as in dysgenic crosses in Drosophila (Kidwell, 2002), or other kinds of repeated sequence, may be involved. A survey of various TEs during mating between Magnaporthe grisea isolates from Triticum and Setaria revealed new insertions of the LTR (Long Terminal Repeat) retrotransposon MAGGY in the progeny, but very rarely any movements of other TEs (Eto et al., 2001). Transposition of the LINE (Long Interspersed Nuclear Element: non-LTR retrotransposon) MGL (M. grisea LINE) was also observed in another experiment in which two M. grisea isolates from rice were crossed (Nishimura et al., 2000), and the Ds-like element, Ascot-1, has been shown to excise during mating in Ascobolus immersus b2 (Colot et al., 1998). No evidence of TE amplification was, however, found in crosses between A. nidulans strains (Li Destri Nicosia et al., 2001). These findings strongly suggest that the transposition of TEs may be enhanced during mating in fungi, but only some TE families are involved.

Although amplification, deletion and rearrangements of various repeated DNA sequences do indeed account for differences in DNA composition, the frequency of such events and their impact on natural populations are some of the main questions facing population genomics today. As repeated sequences interfere with gene regulation, for example, in human populations (Lippman et al., 2004), changes in genome composition and of whole genome structure (Parfrey et al., 2008) in terms of such sequences, may have a considerable impact on population adaptation, and also promote specific illnesses. The possible impact of such variations therefore warrants detailed investigation in human populations.