An evolutionary correlate of genome size change in plethodontid salamanders

Variation in the amount of nuclear DNA, the C-value, does not correlate with differences in morphological complexity. There are two classes of explanations for this observation, which is known as the ''C-value paradox''. The quantity of DNA may serve a ''nucleotypic'' function that is positively selected. Alternatively, large genomes may consist of junk DNA, which increases until it negatively affects fitness. Attempts to resolve the C-value paradox focus on the link between genome size and fitness. This link is usually sought in life history traits, particularly developmental rates. I examined the relationship among two life history traits, egg size and embryonic developmental time and genome size, in 15 species of plethodontid salamanders. Surprisingly, there is no correlation between egg size and developmental time, a relationship included in models of life history evolution. However, genome size is positively correlated with embryonic developmental time, a result that is robust with respect to many sources of variation in the data. Without information on the targets of natural selection it is not possible with these data to distinguish between nucleotypic and junk DNA explanations for the C-value paradox.     

Cytophotometric evidence of variation in genome size of desmognathine salamanders

The amount of DNA per haploid genome, the C-value, is often directly correlated with nuclear and cell volume, but inversely correlated with cell replication rate. Also, rates of cellular growth sometimes appear to be correlated with organismal developmental rates and life history patterns. Among vertebrates, salamanders exhibit the greatest variation in genome size. In the present study we have examined interspecific and intraspecific variation in blood cell DNA levels in the genus Desmognathus, which shows greater variation in life history traits than any other salamander genus. Specimens of Desmognathus quadramaculatus, D. monticola, D. ochrophaeus and D. wrighti were collected from nature at two localities in the southern Appalachian Mountains. Estimates of genome size in pg of DNA were obtained from blood smears by DNA-Feulgen cytophotometry, using erythrocyte nuclei of Xenopus laevis as an internal reference standard of 6.35 pg DNA per cell. C-values of Desmognathus are the smallest in the order Caudata. Although significant variation in DNA levels was found among the four species, the differences were small, and do not support previously proposed relationships between C-value and life-history variation.     

DEVELOPMENTAL CORRELATES OF GENOME SIZE IN PLETHODONTID SALAMANDERS AND THEIR IMPLICATIONS FOR GENOME EVOLUTION

We present an analysis of the evolutionary relationship between genome size (C-value, mass of DNA per haploid nucleus) and developmental rate using observations of limb regeneration in salamanders of the family Plethodontidae. Rates of growth and differentiation of regenerating limbs are reported for 27 plethodontid species whose C-values range from 14 to 76 picograms. A phylogenetic analysis employing Felsenstein's method of independent contrasts indicates that rate of differentiation is inversely proportional to genome size, although we have not identified any statistically significant association between genome size and the growth rate of regenerating tissue. Our results are consistent with an interpretation that genome size may place a limit on the maximum rate of regeneration attainable in plethodontid salamanders. The implications of our findings for the “junk DNA,” “nucleotypic DNA,” “selfish DNA,” and “skeletal DNA” hypotheses of genome evolution are discussed.     

The evolution of genome size: what can be learned from anuran development?

Differences in nuclear DNA content in vertebrates have been shown to be correlated with cell size, cell division rate, and embryonic developmental rate. We compare seven species of anuran amphibians with a three-fold range of genome sizes. Parameters examined include the number and density of cells in a number of embryonic structures, and the change in cell number in the CNS during development. We show that genome size is correlated with cell proliferation rate and with developmental rate at different stages of embryonic development, but that the correlation between genome size and cell size is only evident at later stages. We discuss the evolution of genome size in amphibians. Our discussion takes into account data that reportedly support two conflicting hypotheses: the "skeletal DNA" hypothesis, which claims a selective role for differences in genome size, and the "junk DNA" hypothesis, which claims that differences in genome size are a random result of the accumulation of noncoding DNA sequences. We show that these supposedly conflicting hypotheses can be integrated into a more complex and inclusive model for the evolution of genome size.     

Cytophotometric evidence of variation in genome size of desmognathine salamanders

Summary The amount of DNA per haploid genome, the C-value, is often directly correlated with nuclear and cell volume, but inversely correlated with cell replication rate. Also, rates of cellular growth sometimes appear to be correlated with organismal developmental rates and life history patterns. Among vertebrates, salamanders exhibit the greatest variation in genome size. In the present study we have examined interspecific and intraspecific variation in blood cell DNA levels in the genus Desmognathus, which shows greater variation in life history traits than any other salamander genus. Specimens of Desmognathus quadramaculatus, D. Monticola, D. ochrophaeus and D. wrighti were collected from nature at two localities in the southern Appalachian Mountains. Estimates of genome size in pg of DNA were obtained from blood smears by DNA-Feulgen cytophotometry, using erythrocyte nuclei of Xenopus laevis as an internal reference standard of 6.35 pg DNA per cell. C-values of Desmognathus are the smallest in the order Caudata. Although significant variation in DNA levels was found among the four species, the differences were small, and do not support previously proposed relationships between C-value and life-history variation.     

A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves

For half a century, variation in genome size (C-value) has been an unresolved puzzle in evolutionary biology. While the initial "C-value paradox" was solved with the discovery of noncoding DNA, a much more complex "C-value enigma" remains. The present study focuses on one aspect of this puzzle, namely the small genome sizes of birds. Significant negative correlations are reported between resting metabolic rate and both C-value and erythrocyte size. Cell size is positively correlated with both nucleus size and C-value in birds, as in other vertebrates. These findings shed light on the constraints acting on genome size in birds and illustrate the importance of interactions among various levels of the biological hierarchy, ranging from the subchromosomal to the ecological. Following from a discussion of the mechanistic bases of the correlations reported and the processes by which birds achieved and/or maintain small genomes, a pluralistic approach to the C-value enigma is recommended.     

Nucleotypic effects without nuclei: genome size and erythrocyte size in mammals.

Previously reported haploid genome sizes (C-values) and erythrocyte sizes (measured as mean dry diameters) were compared for 67 species of mammals representing 31 families and 16 orders. Measurements on erythrocytes of four species of bats were also included in the study. Erythrocyte size was significantly positively correlated with genome size at each of the specific, generic, familial, and ordinal levels, with the relationship becoming much stronger following the exclusion of the order Artiodactyla, a group unique among mammals in terms of red blood cell morphology. Physiologically, these results are relevant in light of the known relationship between C-value and mass-corrected metabolic rate in homeotherms. In evolutionary terms, they provide insights into the constraints on genome expansion among mammals and are therefore of interest in attempts to solve the long-standing C-value enigma (also known as the C-value paradox).     

Variation across amphibian species in the size of the nuclear genome supports a pluralistic, hierarchical approach to the C-value enigma

Amphibians have featured prominently in discussions of the C-value enigma, the still-unresolved puzzle regarding the evolution of genome size. Their wide range in nuclear DNA contents and diverse ecological and developmental lifestyles make them excellent subjects for addressing the key elements of the C-value enigma. However, in some cases the importance of work on amphibians appears to be overstated. This is especially true of claims that patterns of variation in salamanders support a particular theory of genome size evolution to the exclusion of others. This study provides a critical re-examination of some of these claims, as well as an investigation of the relationships between genome size, cell and nuclear size, and metabolism in amphibians. The results of these analyses, combined with an overview of previous amphibian genome size literature, strongly indicate the need for a pluralistic approach to the C-value enigma. In particular, it must be recognized that evolutionary forces operating and interacting at several levels of biological organization (of which the genome itself is one) are responsible for the observed patterns in amphibian genome size distributions.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 329–339.     

Mutational equilibrium model of genome size evolution

The paper describes a mutational equilibrium model of genome size evolution. This model is different from both adaptive and junk DNA models of genome size evolution in that it does not assume that genome size is maintained either by positive or stabilizing selection for the optimum genome size (as in adaptive theories) or by purifying selection against too much junk DNA (as in junk DNA theories). Instead the genome size is suggested to evolve until the loss of DNA through more frequent small deletions is equal to the rate of DNA gain through more frequent long insertions. The empirical basis for this theory is the finding of a strong correlation and of a clear power-function relationship between the rate of mutational DNA loss (per bp) through small deletions and genome size in animals. Genome size scales as a negative 1.3 power function of the deletion rate per nucleotide. Such a relationship is not predicted by either adaptive or junk DNA theories. However, if genome size is maintained at equilibrium by the balance of mutational forces, this empirilical relationship can be readily accommodated. Within this framework, this finding would imply that the rate of DNA gain through large insertions scales up a quarter-power function of genome size. On this view, as genome size grows, the rate of growth through large insertions is increasing as a quarter power function of genome size and the rate of DNA loss through small deletions increases linearly, until eventually, at the stable equilibrium genome size value, rates of growth and loss equal each other. The current data also suggest that the long-term variation is genome size in animals is brought about to a significant extent by changes in the intrinsic rates of DNA loss through small deletions. Both the origin of mutational biases and the adaptive consequences of such a mode of evolution of genome size are discussed.     

Evolution of genome size: a phylogenetic test of the DNA loss hypothesis

It has been recently suggested that the C-value paradox, the lack of an obvious association between organismal complexity and genome size, can result simply from biases in insertion and deletion rates--the DNA loss hypothesis. This hypothesis has been heavily criticized, particularly because its evidence, a negative relationship between genome size and DNA loss rate, is based on a highly selective use of the available data. In this study it is show that even the even the most favorable interpretation of the data favoring the DNA loss hypothesis is largely an artifact of phylogenetic nonindependence, supporting the assertion made by other authors that the mechanisms underlying genome size evolution might be more complex than envisioned by the DNA loss hypothesis.     

Correlations of geographic distribution and temperature of embryonic development with the nuclear DNA content in the Salamandridae (Urodela, Amphibia).

We used flow cytometry to measure the nuclear DNA content in erythrocytes of 27 salamandrid species. Across these species, diploid genome size varied more than 2 fold (51.3-104.4 pg). According to genome size and geographic distribution, 3 groups of newt species were recognized: West Palearctics with smaller amounts of nuclear DNA; Nearctic, with intermediate values; and East Asiatic, with higher genome sizes. Viviparous West Palearctic salamanders differed from most of the oviparous West Palearctic newts in possessing larger genome sizes. The nuclear DNA content strongly correlates with species range limits. At the same temperature, embryos of salamandrid species with larger genome sizes have a markedly longer developmental time than those with smaller genomes. We present an analysis of the relationships between the amount of nuclear DNA and water temperature at the breeding sites.     

论DNA C-值与植物入侵性的关系

外来植物的入侵已引起世界普遍关注,强调并迅速提高对外来植物的预警能力是目前首当其冲的任务,由此,如何预测植物的入侵能力,也就成为入侵生态学的一个核心问题。20世纪90年代以来,关于植物入侵争论的焦点集中于入侵植物本身的生物学特点或入侵生境特点,然而,争议多于结论,至今未能找出有效预测外来植物入侵性的答案。着重从DNAC-值与植物入侵性关系这一角度进行论述。自20世纪30年代以来,染色体数目、大小、倍性在细胞水平的变化被认为可能与植物入侵性相关,因为染色体数目、大小变化是物种在细胞水平上的一种表型变异形式,而细胞水平累积的效应有可能决定着植物整体水平上对环境的适应能力,从而决定植物的分布范围,最终与入侵性相关。但是,这些领域的研究也没有得到一致的结论。近年来,人们将注意力转移至被子植物DNAC-值变化在植物环境适应中的生物学意义。现有资料表明,DNAC-值与细胞大小、体积、重量、发育速率等细胞水平上的表型特征存在正相关关系,这些与核型相关的DNAC-值的影响效应,可扩展到多细胞植物有机体的发育速率,在植物生活史的各个阶段起作用,其中就影响到两个受时间因子限制同时又与植物分布相关联的特征——最短世代时间及生活周期类型,而许多入侵成功植物即表现为世代时间短等特点,对于入侵性植物,其不可避免会受生长时间及分布环境的限制,如能保证其在这两方面占有优势便能入侵成功。已有研究结果表明,某些外来入侵种比同属其它种类具有较低的核DNA含量,由此,提出通过研究植物DNAC值,就有可能预测植物入侵能力的强弱,低DNAC-值的植物具有更强的适应环境的能力,即与入侵性大小呈负相关,这为发现新的植物入侵性预测指标提供了思路。     

Evolution of genome size: A phylogenetic test of the DNA loss hypothesis

It has been recently suggested that the C-value paradox, the lack of an obvious association between organismal complexity and genome size, can result simply from biases in insertion and deletion rates—the DNA loss hypothesis. This hypothesis has been heavily criticized, particularly because its evidence, a negative relationship between genome size and DNA loss rate, is based on a highly selective use of the available data. In this study it is shown that the even the most favorable interpretation of the data favoring the DNA loss hypothesis is largely an artifact of phylogenetic nonindependence, supporting the assertion made by other authors that the mechanisms underlying genome size evolution might be more complex than envisioned by the DNA loss hypothesis. The text was submitted by the author in English.     

C-value estimates for 31 species of ladybird beetles (Coleoptera: Coccinellidae)

This study provides C-value (haploid nuclear DNA content) estimates for 31 species of ladybird beetles (representing 6 subfamilies and 8 tribes), the first such data for the family Coccinellidae. Despite their unparalleled diversity, the Coleoptera have been very poorly studied in terms of genome size variation, such that even this relatively modest sample of species makes the Coccinellidae the third best studied family of beetles, behind the Tenebrionidae and Chrysomelidae. The present study provides a comparison of patterns of genome size variation with these two relatively well-studied families. No correlation was found between genome size and body size in the ladybirds, in contrast to some other invertebrate groups but in keeping with findings for other beetle families. However, there is some indication that developmental time and/or feeding ecology is related to genome size in this group. Some phylogenetic patterns and possible associations with subgenomic features are also discussed.     

Some conclusions on the role of redundant DNA and the mechanisms of eukaryotic genome evolution inferred from studies of chromatin diminution in Cyclopoida

The absence of progress in understanding the problem of redundant eukaryotic DNA is stated. This is caused primarily by the attempts to solve this problem either in terms of the traditional approaches (the general phenotypic parameters such as developmental rate, body size, etc. depend on the genome size) or by introducing such vague terms as egoistic, parasitic, or junk DNA. Studying chromatin diminution (CD) in copepods yielded two important conclusions. First, part of the genome of a certain size (94% in Cyclops kolensis first described by the authors) is not needed for somatic functions as it is eliminated during the early (third to seventh) cleavage divisions from the presumptive somatic cells. Second, this DNA is not redundant, let alone selfish or junk, relative to the germline cells. In this sense, it can be regarded as invariant (monomorphic) trait that characterizes the species. Analysis of cloned and sequenced DNA regions eliminated from the somatic cell genome by CD (i.e., confined to the germline), which was first carried out for C. kolensis, showed that the molecular structure of this DNA has at least two features of regular organization: a mosaic structure of repetitive sequences and high (sometimes up to 100%) homology between different repeats and subrepeats. We have suggested that the germline-restricted DNA forms a unique molecular portrait of the species genome, thus acting as a significant factor of genetic isolation. Yet, the phenomenon of CD proper as it occurs in Cyclopoida without disintegration of the chromosome structure) may be regarded as a model of reductional genome evolution, which has repeatedly occurred in the history of eukaryotes.     

长三角及邻近地区138种草本植物DNA C-值测定及其生物学意义

为了评估DNA C-值和基因组大小(genome size)在植物入侵性评估中的价值,应用流式细胞仪测定了长三角及邻近地区138种草本植物的核DNA含量,其中111种为首次报道。在此基础上比较了不同植物类群这两个值的差异,特别是入侵性与非入侵性植物这两个值的差异。结果表明:(1)138种草本植物平均DNA C-值为1.55 pg,最大者是最小者的37.17倍。127个类群平均基因组大小为1.08 pg,最大者是最小者的34.11倍;(2)统计了菊科(Asteraceae)、禾本科(Poaceae)、石竹科(Caryophyllaceae)、十字花科(Brassicaceae)、玄参科(Scrophulariaceae)、蓼科(Polygonaceae)、唇形科(Labiatae)和伞形科(Umbelliferae)的DNA C-值和基因组大小,发现禾本科植物的这两个值显著地大于其他7个科(P0.01)。单子叶的DNA C-值和基因组极显著地大于双子叶植物(P0.01);(3)杂草比非杂草具有更低的DNA C-值(P0.01)和基因组大小(P0.001);与DNA C-值相比,基因组大小在这两个类群之间的差异更为明显(P0.001),这种现象也体现在菊科植物中。随着基因组(X1)和DNA C-值(X2)由大变小,植物的杂草性(入侵性,Y)由弱变强,两者关系分别符合:Y=2.2334-1.2847 ln(X1)(r=0.4612,P0.01)和Y=2.4421-0.7234 ln(X2)(r=0.2522,P0.01),DNA C-值和基因组大小可以作为植物入侵性评估的一个指标;(4)多倍体杂草的基因组极明显地小于二倍体杂草(P0.01),前者为后者的0.63倍。在非杂草中,多倍体基因组比二倍体的略小,前者仅为后者的0.84倍,差异不显著(P0.5)。菊科植物中多倍体杂草的基因组也显著地小于二倍体杂草(P0.1)。基因组变小和多倍体化相结合,进一步增强了植物的入侵性。在多倍体植物入侵性评估中,基因组大小比DNA C-值更有价值。     

Ascovirus and its Evolution

Ascoviruses, iridoviruses, asfarviruses and poxviruses are all cytoplasmic DNA viruses. The evolutionary origins of cytoplasmic DNA viruses have never been fully addressed. Morphological, genetic and molecular data were used to test if all four cytoplasmic virus families (Ascoviridae, Iridoviridae, Asfarviridae, and Poxvirirdae) evolved from nuclear replicating baculoviruses and how the four virus groups are related. Molecular phylogenetic analyses using DNA polymerase predicted that cytoplasmic DNA viruses might have evolved from nuclear replicating baculoviruses, and that poxviruses and asfarviruses share a common ancestor with iridoviruses. These three cytoplasmic viruses again shared a common ancestor with ascoviruses. Morphological and genetic data predicted the same evolutionary trend as molecular data predicted. A genome sequence comparison showed that ascoviruses have more baculovirus protein homologues than do iridoviruses, which suggested that ascoviruses have evolved from baculoviruses and iridoviruses evolved from ascoviruses. Poxviruses showed genetic and morphological similarity to other cytoplamic viruses, such as ascoviruses, suggesting it has undergone reticulate evolution via hybridization, recombination and lateral gene transfer with other viruses. Within the ascovirus family, we tested if molecular phylogenetic analyses agree with biological inference; that is, ascovirus had an evolutionary trend of increasing genome size, expanding host range and widening tissue tropism for these viruses. Both molecular and biological data predicted this evolutionary trend. The phylogenetic relationship among the four species of ascovirus was predicted to be that TnAV-2 and HvAV-3 shared a common ancestor with SfAV-1 and the three virus species again shared a common ancestor with DpAV-4.     

The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints

BACKGROUND AND AIMS: Nuclear DNA content (C-value) varies approximately 1000-fold across the angiosperms, and this variation has been reported to have an effect on the quality of AFLP fingerprints. Various methods have been proposed for circumventing the problems associated with small and large genomes. Here we investigate the range of nuclear DNA contents across which the standard AFLP protocol can be used. METHODS: AFLP fingerprinting was conducted on an automated platform using the standard protocol (with 3 + 3 selective bases) in which DNA fragments are visualized as bands. Species with nuclear DNA contents ranging from 1C = 0.2 to 32.35 pg were included, and the total number of bands and the number of polymorphic bands were counted. For the species with the smallest C-value (Bixa orellana) and for one of the species with a large C-value (Damasonium alisma), alternative protocols using 2 + 3 and 3 + 4 selective bases, respectively, were also used. KEY RESULTS: Acceptable AFLP traces were obtained using the standard protocol with 1C-values of 0.30-8.43 pg. Below this range, the quality was improved by using 2 + 3 selective bases. Above this range, the traces were generally characterized by a few strongly amplifying bands and noisy baselines. Damasonium alisma, however, gave more even traces, probably due to it being a tetraploid. CONCLUSIONS: We propose that for known polyploids, genome size is a more useful indicator than the 1C-value in deciding which AFLP protocol to use. Thus, knowledge of ploidy (allowing estimation of genome size) and C-value are both important. For small genomes, the number of interpretable bands can be increased by decreasing the number of selective bases. For larger genomes, increasing the number of bases does not necessarily decrease the number of bands as predicted. The presence of a small number of strongly amplifying bands is likely to be linked to the presence of repetitive DNA sequences in high copy number in taxa with large genomes.     

Ascovirus and its evolution

Ascoviruses, iridoviruses, asfarviruses and poxviruses are all cytoplasmic DNA viruses. The evolutionary origins of cytoplasmic DNA viruses have never been fully addressed. Morphological, genetic and molecular data were used to test if all four cytoplasmic virus families (Ascoviridae, Iridoviridae, Asfarviridae, and Poxvirirdae) evolved from nuclear replicating baculoviruses and how the four virus groups are related. Molecular phylogenetic analyses using DNA polymerase predicted that cytoplasmic DNA viruses might have evolved from nuclear replicating baculoviruses, and that poxviruses and asfarviruses share a common ancestor with iridoviruses. These three cytoplasmic viruses again shared a common ancestor with ascoviruses. Morphological and genetic data predicted the same evolutionary trend as molecular data predicted. A genome sequence comparison showed that ascoviruses have more baculovirus protein homologues than do iridoviruses, which suggested that ascoviruses have evolved from baculoviruses and iridoviruses evolved from ascoviruses. Poxviruses showed genetic and morphological similarity to other cytoplamic viruses, such as ascoviruses, suggesting it has undergone reticulate evolution via hybridization, recombination and lateral gene transfer with other viruses. Within the ascovirus family, we tested if molecular phylogenetic analyses agree with biological inference; that is, ascovirus had an evolutionary trend of increasing genome size, expanding host range and widening tissue tropism for these viruses. Both molecular and biological data predicted this evolutionary trend. The phylogenetic relationship among the four species of ascovirus was predicted to be that TnAV-2 and HvAV-3 shared a common ancestor with SfAV-1 and the three virus species again shared a common ancestor with DpAV-4.