Endopolyploidy as a potential driver of animal ecology and evolution

Endopolyploidy - the existence of higher-ploidy cells within organisms that are otherwise of a lower ploidy level (generally diploid) - was discovered decades ago, but remains poorly studied relative to other genomic phenomena, especially in animals. Our synthetic review suggests that endopolyploidy is more common in animals than often recognized and probably influences a number of fitness-related and ecologically important traits. In particular, we argue that endopolyploidy is likely to play a central role in key traits such as gene expression, body and cell size, and growth rate, and in a variety of cell types, including those responsible for tissue regeneration, nutrient storage, and inducible anti-predator defences. We also summarize evidence for intraspecific genetic variation in endopolyploid levels and make the case that the existence of this variation suggests that endopolyploid levels are likely to be heritable and thus a potential target for natural selection. We then discuss why, in light of evident benefits of endopolyploidy, animals remain primarily diploid. We conclude by highlighting key areas for future research such as comprehensive evaluation of the heritability of endopolyploidy and the adaptive scope of endopolyploid-related traits, the extent to which endopolyploid induction incurs costs, and characterization of the relationships between environmental variability and endopolyploid levels.

The skeletal function of non-genic nuclear DNA: new evidence from ancient cell chimaeras

DNA can be divided functionally into three categories: (1) genes--which code for proteins or specify non-messenger RNAs; (2) semons--short specific sequences involved in the replication, segregation, recombination or specific attachments of chromosomes, or chromosome regions (e.g. loops or domains) or selfish genetic elements; (3) secondary DNA--which does not function by means of specific sequences. Probably more than 90% of DNA in the biosphere is secondary DNA present in the nuclei of plants and phytoplankton. The amount of genic DNA is related to the complexity of the organism, whereas the amount of secondary DNA increases proportionally with cell volume, and not with complexity. This correlation is most simply explained by the skeletal DNA hypothesis, according to which nuclear DNA functions as the basic framework for the assembly of the nucleus and the total genomic DNA content functions (together with relatively invariant folding rules) in determining nuclear volumes. Balanced growth during the cell cycle requires the cytonuclear ratio to be basically constant, irrespective of cell volume; thus nuclear volumes, and therefore the overall genome size, have to be evolutionarily adjusted to changing cell volumes for optimal function. Bacteria, mitochondria, chloroplasts and viruses have no nuclear envelope; and the skeletal DNA hypothesis simply explains why secondary DNA is essentially absent from them but present in large cell nuclei. Hitherto it has been difficult to refute the alternative hypothesis that nuclear secondary DNA (whether 'junk' or selfish DNA) accumulates merely by mutation pressure, and that selection for economy is not strong enough to eliminate it, whereas accumulation in mitochondria and plastids is prevented by intracellular replicative competition between their multiple genomes. New data that discriminate clearly between these explanations for secondary DNA come from cryptomonads and chlorarachneans, two groups of algae that originated independently by secondary symbiogenesis (i.e., the merger of two radically different eukaryote cells) several hundred million years ago. In both groups the nucleus and plasma membrane of the former algal symbiont persist as the nucleomorphs and periplastid membrane, respectively. The fact that nucleomorphs have undergone a 200- to 1000-fold reduction in genome size and have virtually no secondary DNA shows that selection against non-functional nuclear DNA is strong enough to eliminate it very efficiently; therefore, the large amounts of secondary DNA in the former host nuclei of these chimaeras, and in nuclei generally, must be being maintained by positive selection. The divergent selection for secondary DNA in the nucleus and against it in nucleomorphs is readily explicable by the skeletal DNA hypothesis, given the different spectrum of gene functions that it encodes.

Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes

Genic DNA functions are commonplace: coding for proteins and specifying non-messenger RNA structure. Yet most DNA in the biosphere is non-genic, existing in nuclei as non-coding or secondary DNA. Why so much secondary DNA exists and why its amount per genome varies over orders of magnitude (correlating positively with cell volume) are central biological problems. A novel perspective on secondary DNA function comes from natural eukaryote eukaryote chimaeras (cryptomonads and chlorarachneans) where two phylogenetically distinct nuclei have coevolved within one cell for hundreds of millions of years. By comparing cryptomonad species differing 13-fold in cell volume, we show that nuclear and nucleomorph genome sizes obey fundamentally different scaling laws. Following a more than 125-fold reduction in DNA content, nucleomorph genomes exhibit little variation in size. Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA. Cryptomonad nuclear DNA content varied 12-fold: as in other eukaryotes, larger cells have extra DNA, which is almost certainly secondary DNA positively selected for a volume-related function. The skeletal DNA theory explains why nuclear genome size increases with cell volume and, using new evidence on nucleomorph gene functions, why nucleomorph genomes do not.

Sequence analysis of the mitochondrial genome of Sarcophyton glaucum: conserved gene order among octocorals

The nucleotide sequence for an 11,715-bp segment of the mitochondrial genome of the octocoral Sarcophyton glaucum is presented, completing the analysis of the entire genome for this anthozoan member of the phylum Cnidaria. The genome contained the same 13 protein-coding and 2 ribosomal RNA genes as in other animals. However, it also included an unusual mismatch repair gene homologue reported previously and codes for only a single tRNA gene. Intermediate in length compared to two other cnidarians (17,443 and 18,911 bp), this organellar genome contained the smallest amount of noncoding DNA (428, compared to 1283 and 781 nt, respectively), making it the most compact one found for the phylum to date. The mitochondrial genes of S. glaucum exhibited an identical arrangement to that found in another octocoral, Renilla kolikeri, with five protein-coding genes in the same order as has been found in insect and vertebrate mitochondrial genomes. Although gene order appears to be highly conserved among octocorals, compared to the hexacoral, Metridium senile, few similarities were found. Like other metazoan mitochondrial genomes, the A + T composition was elevated and a general bias against codons ending in G or C was observed. However, an exception to this was the infrequent use of TGA compared to TGG to code for tryptophan. This divergent codon bias is unusual but appears to be a conserved feature among two rather distantly related anthozoans.

Patterns of DNA synthesis and mitotic activity during the intermoult of Daphnia

Among insects, the epidermal cell cycle pattern is related to the type of ontogenetic development. In taxa undergoing complete metamorphosis, cells are commonly maintained in the G2 stage of interphase between bouts of cell division. In crustaceans, as in insects exhibiting incomplete metamorphosis, it is believed that cells ordinarily remain in G1 for much of the intermoult, with DNA replication occurring late in the moult cycle followed closely by cell division. The present study reveals a differing pattern of epidermal cell division in two distantly related members of the cladoceran crustacean genus Daphnia. Cell cycle kinetics were examined in the last juvenile instar of each species using DNA content determinations and estimates of mitotic frequency. These analyses confirm that each epidermal cell possessed the diploid DNA amount, completed a single cell cycle, and remained in G1 for the majority of the instar. However, DNA replication occurred shortly after moulting and was followed by intense mitotic activity so that cell proliferation was restricted to a short period soon after ecdysis. Cell densities during the instar increased by approximately 60 and 100% for D. pulex and D. magna, respectively.

Breeding system and genome size of the rhabdocoel turbellarian Mesostoma ehrenbergii

Rhabdocoel turbellarians, such as Mesostoma ehrenbergii, are hermaphrodites which produce both subitaneous and resting eggs. Both genotypic frequencies in natural populations as well as parent–offspring genotypes at a polymorphic allozyme locus confirm that, under natural conditions, M. ehrenbergii produces subitaneous eggs via self-fertilization and resting eggs probably by outcrossing. Chromosome counts show, contrary to an earlier report, that North American populations of the species possess the same chromosome number as European populations. However, other karyotypic differences do exist between Old World and New World populations. DNA quantification studies revealed that M. ehrenbergii possesses one of the largest haploid genome sizes (14.8 pg) yet reported for an invertebrate. Among organisms showing similar genome size, this species appears to be unique for its rapid developmental rate.Key words: Turbellaria, allozyme, breeding system, genome size, cytogenetics, selfing.

Miniature genomes and endopolyploidy in cladoceran crustaceans

The haploid genome sizes (0.37 and 0.47 pg) of two members of the cladoceran crustacean genus Daphnia rank among the smallest known for Crustacea. An examination of cladoceran somatic tissues by scanning microdensitometry revealed abundant endopolyploidy in both species. Although cells in the labrum possessed the highest DNA content (1024C), endopolyploid cells (4–512C) were widely distributed throughout the body. Daphnia pulex and D. magna exhibited similar ploidy levels in most tissues, but differences between the two species were noted in the epidermis and labrum. The prevalence of polyploid nuclei suggests that endopolyploidy is an important process in organisms whose genomes have been miniaturized by nucleotypic selection.Key words: somatic polyploidy, genome size, Daphnia, ploidy shifts, macroevolution.