CORRELATED EVOLUTION OF GENOME SIZE AND CELL VOLUME IN DIATOMS (BACILLARIOPHYCEAE)1

A correlation between genome size and cell volume has been observed across diverse assemblages of eukaryotes. We examined this relationship in diatoms (Bacillariophyceae), a phylum in which cell volume is of critical ecological and biogeochemical importance. In addition to testing whether there is a predictive relationship across extant species, we tested whether evolutionary divergences in genome size were correlated with evolutionary divergences in cell size (using independent contrasts). We estimated total DNA content for 16 diatom species using a flow cytometer and estimated cell volumes using critical dimensions with scaling equations. Our independent contrast analyses indicated a significant correlated evolution between genome size and cell volume. We then explored the evolutionary and ecological implications of this evolutionary relationship. Diatom cell volume is an important component of the global carbon cycle; therefore, understanding the mechanisms that drive diatom genome evolution has both evolutionary and ecological importance.     

DNA Content Variation and Its Significance in the Evolution of the Genus Micrasterias (Desmidiales,Streptophyta)

It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.     

Genome size of chrysophytes varies with cell size and nutritional mode

The cellular content of nuclear DNA varies up to 200,000-fold between eukaryotes. These differences can arise via different mechanisms. In particular, cell size and nutritional mode may influence evolution of the nuclear DNA content. Chrysophytes comprise organisms with different cell organizations and nutritional modes. Heterotrophic clades evolved independently several times from phototrophic or mixotrophic ancestors. Thus, chrysophytes are an ideal model taxon for investigating the effect of the nutritional mode on cellular DNA content. We investigated the genome size of heterotrophic, mixotrophic, and phototrophic chrysophytes. We demonstrate that cell sizes and genome sizes differ significantly between taxa with different nutritional modes. Phototrophic strains tend to have larger cell volumes and larger genomes than heterotrophic strains do. The investigated mixotrophic strains had intermediate cell volumes and small to intermediate genome sizes. Heterotrophic chrysophytes had the smallest genomes and cell volumes compared to other chrysophytes. In general, genome size increased with cell volume, but cell volume only partially explained the variation in genome size. In particular, genome sizes of mixotrophic strains were smaller than expected based on cell sizes.     

Endopolyploidy in vertebrate liver: An evolutionary perspective

Hepatocyte nuclei in several species of vertebrates were examined, to establish the frequency of polyploidy and related parameters along evolutionary lines. Nuclei were compared in terms of volume, DNA content, ploidy ranges and internal organization. Several trends emerged. When present, heterochromatin occupied 20–25% of nuclear profile areas, irrespective of nuclear volume and ploidy; the volume of heterochromatin, however, increased in direct proportion to ploidy level. Regardless of internal organization, ploidy and species, a direct correlation emerged between the volumes of nuclei and their absolute DNA content. Results are discussed in terms of structural and genic DNA.     

Chromosomal and cell size analysis of cold tolerant maize

Summary C-band number, guard cell length, and chloroplast number per guard cell were determined for eight maize populations. These populations consisted of maize selected for cold tolerance at the University of Nebraska as well as the original unselected populations. The genome size of these populations had previously been determined. C-band number fluctuated concertedly with the changes in genome size indicating that deletions and additions of constitutive heterochromatin occurred during selection, resulting in altered genome sizes. Guard cell size of all the cold tolerant populations was greater than the cell size of the respective nonselected populations. Chloroplast number per guard cell was also higher in all the cold tolerant populations than in their parental populations, but the increases were not statistically significant. The results indicate that changes in genome size that occurred during selection for cold tolerance are the result of changes in amounts of C-band heterochromatin and that the selection process results in an increase in cell size in the cold tolerant populations.     

Hybridization, polyploidy, and the evolution of sexual systems in Mercurialis (Euphorbiaceae)

Hybridization and polyploidy are widely believed to be important sources of evolutionary novelty in plant evolution. Both can lead to novel gene combinations and/or novel patterns of gene expression, which in turn provide the variation on which natural selection can act. Here, we use nuclear and plastid gene trees, in conjunction with morphological data and genome size measurements, to show that both processes have been important in shaping the evolution of the angiosperm genus Mercurialis, particularly a clade of annual lineages that shows exceptional variation in the sexual system. Our results indicate that hexaploid populations of M. annua, in which the rare sexual system androdioecy is common (the occurrence of males and hermaphrodites) is of allopolyploid origin involving hybridization between an autotetraploid lineage of M. annua and the related diploid species M. huetii. We discuss the possibility that androdioecy may have evolved as a result of hybridization between dioecious M. huetii and monoecious tetraploid M. annua, an event that brought together the genes for specialist males with those for hermaphrodites.     

Coincidence,coevolution, or causation? DNA content,cellsize, and the C‐value enigma

Variation in DNA content has been largely ignored as a factor in evolution, particularly following the advent of sequence-based approaches to genomic analysis. The significant genome size diversity among organisms (more than 200000-fold among eukaryotes) bears no relationship to organismal complexity and both the origins and reasons for the clearly non-random distribution of this variation remain unclear. Several theories have been proposed to explain this 'C-value enigma' (heretofore known as the 'C-value paradox'), each of which can be described as either a mutation pressure' or 'optimal DNA' theory. Mutation pressure theories consider the large portion of non-coding DNA in eukaryotic genomes as either 'junk' or 'selfish' DNA and are important primarily in considerations of the origin of secondary DNA. Optimal DNA theories differ from mutation pressure theories by emphasizing the strong link between DNA content and cell and nuclear volumes. While mutation pressure theories generally explain this association with cell size as coincidental, the nucleoskeletal theory proposes a coevolutionary interaction between nuclear and cell volume, with DNA content adjusted adaptively following shifts in cell size. Each of these approaches to the C-value enigma is problematic for a variety of reasons and the preponderance of the available evidence instead favours the nucleotypic theory which postulates a causal link between bulk DNA amount and cell volume. Under this view, variation in DNA content is under direct selection via its impacts on cellular and organismal parameters. Until now, no satisfactory mechanism has been presented to explain this nucleotypic effect. However, recent advances in the study of cell cycle regulation suggest a possible 'gene nucleus interaction model' which may account for it. The present article provides a detailed review of the debate surrounding the C-value enigma, the various theories proposed to explain it, and the evidence in favour of a causal connection between DNA content and cell size. In addition, a new model of nucleotypic influence is developed, along with suggestions for further empirical investigation. Finally, some evolutionary implications of genome size diversity are considered, and a broadening of the traditional 'biological hierarchy' is recommended.     

Nuclear DNA amounts in pacific Crustacea

Nuclear DNA amounts have been determined for 42 species of crustaceans bringing the total number of species with known nuclear DNA content to over 70. Genome size in Crustacea varies over a 25-fold range with a modal value of 2 to 3 pg haploid being common in many groups. Both average genome size and the amount of variability among species are characteristic for certain groups. A trend towards small genomes is evident in advanced and specialized crustacean groups. Somatic polyploidy is a very pronounced feature of the Crustacea. The data suggest that evolution by polyploidy may be more common in crustaceans than earlier data had indicated. These features and the presence of very characteristic satellite fractions in the nuclear DNA recommend the Crustacea for further studies in evolutionary genetics.     

Genome size, quantitative genetics and the genomic basis for flower size evolution in Silene latifolia

BACKGROUND AND AIMS: The overall goal of this paper is to construct an overview of the genetic basis for flower size evolution in Silene latifolia. It aims to examine the relationship between the molecular bases for flower size and the underlying assumption of quantitative genetics theory that quantitative variation is ultimately due to the impact of a number of structural genes. SCOPE: Previous work is reviewed on the quantitative genetics and potential for response to selection on flower size, and the relationship between flower size and nuclear DNA content in S. latifolia. These earlier findings provide a framework within which to consider more recent analyses of a joint quantitative trait loci (QTL) analysis of flower size and DNA content in this species. KEY RESULTS: Flower size is a character that fits the classical quantitative genetics model of inheritance very nicely. However, an earlier finding that flower size is correlated with nuclear DNA content suggested that quantitative aspects of genome composition rather than allelic substitution at structural loci might play a major role in the evolution of flower size. The present results reported here show that QTL for flower size are correlated with QTL for DNA content, further corroborating an earlier result and providing additional support for the conclusion that localized variations in DNA content underlie evolutionary changes in flower size. CONCLUSIONS: The search image for QTL should be broadened to include overall aspects of genome regulation. As we prepare to enter the much-heralded post-genomic era, we also need to revisit our overall models of the relationship between genotype and phenotype to encompass aspects of genome structure and composition beyond structural genes.     

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.     

Size is not everything: rates of genome size evolution,not C-value,correlate with speciation in angiosperms

Angiosperms represent one of the key examples of evolutionary success, and their diversity dwarfs other land plants; this success has been linked, in part, to genome size and phenomena such as whole genome duplication events. However, while angiosperms exhibit a remarkable breadth of genome size, evidence linking overall genome size to diversity is equivocal, at best. Here, we show that the rates of speciation and genome size evolution are tightly correlated across land plants, and angiosperms show the highest rates for both, whereas very slow rates are seen in their comparatively species-poor sister group, the gymnosperms. No evidence is found linking overall genome size and rates of speciation. Within angiosperms, both the monocots and eudicots show the highest rates of speciation and genome size evolution, and these data suggest a potential explanation for the megadiversity of angiosperms. It is difficult to associate high rates of diversification with different types of polyploidy, but it is likely that high rates of evolution correlate with a smaller genome size after genome duplications. The diversity of angiosperms may, in part, be due to an ability to increase evolvability by benefiting from whole genome duplications, transposable elements and general genome plasticity.     

Genome and chromosome structure: Twelve dynamic and evolving genomes

Chromosomes are not inert structures that haul the genome through cell division. The dynamic properties of chromosomes, during the cell cycle, the lifetime of the organism and across evolutionary time, featured prominently at the 49th Annual Drosophila Research Conference. Platform presentations, workshops and posters focused on many aspects of chromosome structure and function including chromosome interactions such as trans-silencing and pairing between homologous and non-homologous chromosomes, specialized portions of the chromosome including the centromere and telomeres, the structure, function and evolution of the large heterochromatic domains such as the Y and 4th chromosomes, centric heterochromatin and subtelomeric heterochromatin. The speed of evolutionary changes in these regions, and the consequences for speciation and hybrid-incompatibility were recurring themes. Finally, there was considerable new insight offered into the mechanics by which chromosomes are rearranged and changes in the types of alterations occurring over the lifetime of the organism, which can result in novel genes and gene flow between chromosomes. The availability of the twelve sequenced Drosophila genomes has allowed new insights into the structure, function and evolutionary transformation of chromosomes and genomes that will continue to transform our view of the chromosome as a dynamic and flexible entity that houses and regulates the genome.     

Genome and chromosome structure: Twelve dynamic and evolving genomes

Chromosomes are not inert structures that haul the genome through cell division. The dynamic properties of chromosomes, during the cell cycle, the lifetime of the organism and across evolutionary time, featured prominently at the 49(th) Annual Drosophila Research Conference. Platform presentations, workshops and posters focused on many aspects of chromosome structure and function including chromosome interactions such as trans-silencing and pairing between homologous and non-homologous chromosomes, specialized portions of the chromosome including the centromere and telomeres, the structure, function and evolution of the large heterochromatic domains such as the Y and 4(th) chromosomes, centric heterochromatin and subtelomeric heterochromatin. The speed of evolutionary changes in these regions, and the consequences for speciation and hybrid-incompatibility, were recurring themes. Finally, there was considerable new insight offered into the mechanics by which chromosomes are rearranged and changes in the types of alterations occurring over the lifetime of the organism, which can result in novel genes and gene flow between chromosomes. The availability of the twelve sequenced Drosophila genomes has allowed new insights into the structure, function and evolutionary transformation of chromosomes and genomes that will continue to transform our view of the chromosome as a dynamic and flexible entity that houses and regulates the genome.     

Incongruent evolution of chromosomal size in rice

To investigate genome size evolution, it is usually informative to compare closely related species that vary dramatically in genome size. A whole genome duplication (polyploidy) that occurred in rice (Oryza sativa) about 70 million years ago has been well documented based on current genome sequencing. The presence of three distinct duplicate blocks from the polyploidy, of which one duplicated segment in a block is intact (no sequencing gap) and less than half the length of its syntenic duplicate segment, provided an excellent opportunity for elucidating the causes of their size variation during the post-polyploid time. The results indicated that incongruent patterns (shrunken, balanced and inflated) of chromosomal size evolution occurred in the three duplicate blocks, spanning over 30 Mb among chromosomes 2, 3, 6, 7, and 10, with an average of 20.3% for each. DNA sequences of chromosomes 2 and 3 appeared to had become as short as about half of their initial sequence lengths, chromosomes 6 and 7 had remained basically balanced, and chromosome 10 had become dramatically enlarged (approximately 70%). The size difference between duplicate segments of rice was mainly caused by variations in non-repetitive DNA loss. Amplification of long terminal repeat retrotransposons also played an important role. Moreover, a relationship seems to exist between the chromosomal size differences and the nonhomologous combination in corresponding regions in the rice genome. These findings help shed light on the evolutionary mechanism of genomic sequence variation after polyploidy and genome size evolution.     

Gene duplication: past, present and future

Gene duplication is of central interest to evolutionary developmental biology, having been implicated in evolutionary increases in complexity. These ideas stem principally from the Lewis model for the evolution of the BX-C and Ohno's proposal for genome duplications during chordate evolution. Here I revisit these models and show how recent data have confirmed their essential features, but forced some important revisions. These include revised dates for homeotic gene duplications and for widespread gene duplication in vertebrate evolution. I also outline the major unresolved questions in the study of gene duplication, and its relevance to evolution and development.     

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

Polyploidy, the condition of possessing more than two complete genomes in a cell, has intrigued biologists for almost a century. Polyploidy is found in many plants and some animal species and today we know that polyploidy has had a role in the evolution of all angiosperms. Despite its widespread occurrence, the direct effect of polyploidy on evolutionary success of a species is still largely unknown. Over the years many attractive hypotheses have been proposed in an attempt to assign functionality to the increased content of a duplicated genome. Among these hypotheses are the proposal that genome doubling confers distinct advantages to a polyploid and that these advantages allow polyploids to thrive in environments that pose challenges to the polyploid''s diploid progenitors. This article revisits these long-standing questions and explores how the integration of recent genomic developments with ecological, physiological and evolutionary perspectives has contributed to addressing unresolved problems about the role of polyploidy. Although unsatisfactory, the current conclusion has to be that despite significant progress, there still isn''t enough information to unequivocally answer many unresolved questions about cause and effect of polyploidy on evolutionary success of a species. There is, however, reason to believe that the increasingly integrative approaches discussed here should allow us in the future to make more direct connections between the effects of polyploidy on the genome and the responses this condition elicits from the organism living in its natural environment.     

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.     

Evolvability of cell specification mechanisms

The architecture of gene action during development is relevant to phenotypic evolution as it links genotype to morphological phenotype. Analysis of development at the level of cell fate specification mechanisms illuminates some of the properties of developmental evolution. In this article, we first review examples of evolutionary change in mechanisms of cell fate specification, with an emphasis on evolution in the dependence on inductive signaling and on evolution of the mechanisms that result in spatial asymmetries. We then focus on properties of development that bias possible phenotypic change and present how the distribution of phenotypes that are available by mutational change of the starting genotype can be experimentally tested by systematic mutagenesis. We finally discuss ways in which selection pressures on phenotypes can be inferred from a comparison of the phenotypic spectrum found on mutation with that found in the wild.