Genome evolution in pocket gophers (genus Thomomys). II. Variation in cellular DNA content

FLOW-CYTOMETRIC ANALYSES OF NUCLEAR DNA CONTENT IN FOUR FAMILIES OF NEOTROPICAL BATS

Flow-cytometric analyses of 29 species of microchiropteran bats representing four families and 20 genera revealed that bats possess only 79% (5.43 pg) of the DNA content of a "typical" mammal (e.g., Mus musculus strain C57BL; 7 pg). Chiroptera, the second largest order of mammals, is thus an exception to the prevailing view that mammals possess a minimum nuclear DNA content of 7 pg. Limitations on cell size resulting from a high metabolic rate may have constrained evolution of DNA content and could explain why the extensive heterochromatic additions that are common in some groups of mammals are absent in bats. Chromosomes of bats have been well studied; detailed chromosomal banding data are available for nearly all the species used in this investigation. However, no significant correlations were found between DNA content and karyotypic characteristics such as 2n, fundamental number, and rate or pattern of chromosomal evolution.

The genome diversity and karyotype evolution of mammals

The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat), laboratory (mice and rat) and agricultural (cattle, pig, and horse) animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.

Diploid-Triploid Mosaicism: An Unusual Phenomenon in Side-Necked Turtles (Platemys platycephala)

Diploid and diploid-triploid mosaic individuals of Platemys platycephala were found in natural populations. In mosaic specimens, the blood, spleen, liver, and testis contained both diploid and triploid cells. The ratio of triploid to diploid cells was more variable among individuals than among somatic tissues within an individual. Only diploid cells underwent meiosis in males; haploid gametes were produced. There appears to be geographic variation for mosaicism in that only diploids were found in Bolivia, whereas diploids and diploid-triploid mosaics occured in Surinam.

Genome size in Tribolium flour-beetles: inter- and intraspecific variation

Eight species of Tribolium and the related species Alphitobius diaperinus have been microdensitometrically analysed by measuring the nuclear content (1C value) of their Feuigenstained spermatids. The range of mean genome sizes goes from 0·157 pg in T. audax to 0·388 pg in T. brevicornis, including five significantly different groups of values. Also, in ail but one species of Tribolium significant intraspecific heterogeneity of genome size was found. The resemblances in genome size are not generally correlated with genetic homologies among species, but there is a highly significant correlation between genome size and spermatid size.

Genome size variation in the North American sunfish genusLepomis(Pisces: Centrarchidae)

Genome sizes (nuclear DNA contents) were documented spectrophotometrically from individuals of each of nine species of the North American centrarchid (sunfish) genusLepomis. The distributions of DNA values within and among the nine species were essentially normal and continuous, suggesting that changes in DNA quantity inLepomisare small in amount, involve both gains and losses of DNA, and are cumulative and independent in effect. Significant differences in mean genome size were found between individuals within populations in all nine species and between species. Nested analysis of variance and comparisons of average genome size difference or distance between individuals drawn from different levels of taxonomic organization revealed that the majority of genome size divergence inLepomisoccurs above the hierarchical level of individuals within populations. TheLepomisdata when compared to similar data from North American cyprinid fishes appear to suggest that: (i) genome size evolution in these fishes at least follows a continuous rather than a discontinuous mode; (ii) the general predictions of hypothetical models relating genome size variation as a function of organismal position along adaptive continua may be oversimplified, or not applicable to complex, higher eukaryotes; and (iii) changes in genome size in these fishes may be concentrated in speciation episodes.

Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs

It has been proposed that intron and genome sizes in birds are reduced in comparison with mammals because of the metabolic demands of flight. To test this hypothesis, we examined the sizes of 14 introns in a nonflying relative of birds, the American alligator (Alligator mississippiensis), and in 19 flighted and flightless birds in 12 taxonomic orders. Our results indicate that a substantial fraction (66%) of the reduction in intron size as well as in genome size had already occurred in nonflying archosaurs. Using phylogenetically independent contrasts, we found that the proposed inverse correlation of genome size and basal metabolic rate (BMR) is significant among amniotes and archosaurs, whereas intron and genome size variation within birds showed no significant correlation with BMR. We show statistically that the distribution of genome sizes in birds and mammals is underdispersed compared with the Brownian motion model and consistent with strong stabilizing selection; that genome size differences between vertebrate clades are overdispersed and punctuational; and that evolution of BMR and avian intron size is consistent with Brownian motion. These results suggest that the contrast between genome size/BMR and intron size/BMR correlations may be a consequence of different intensities of selection for these traits and that we should not expect changes in intron size to be significantly associated with metabolically costly behaviors such as flight.

Differences in genome size between closely related species: the Drosophila melanogaster species subgroup

Genome size varies considerably among organisms due to differences in the amplification, deletion, and divergence of various kinds of repetitive sequences, including the transposable elements, which constitute a large fraction of the genome. However, while the changes in genome size observed at a wide taxonomic level have been thoroughly investigated, we still know little about the process involved in closely related species. We estimated genome sizes and the reverse transcriptase-related sequence (RTRS) content in the nine species of the Drosophila melanogaster species subgroup. We showed that the species differ with regard to their genome size and that the RTRS content is correlated with genome size for all species except Drosophila orena. The genome of D. orena, which is 1.6-fold as big as that of D. melanogaster, has in fact not undergone any major increase in its RTRS content.

Is genome size influenced by colonization of new environments in dipteran species?

Genome size differences are usually attributed to the amplification and deletion of various repeated DNA sequences, including transposable elements (TEs). Because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. We tested this hypothesis by estimating the genome size of geographically distinct populations of Drosophila ananassae, Drosophila malerkotliana, Drosophila melanogaster, Drosophila simulans, Drosophila subobscura, and Zaprionus indianus, all of which have known colonization capacities. There was no strong statistical differences between continents for most species. However, we found that populations of D. melanogaster from east Africa have smaller genomes than more recent populations. For species in which colonization is a recent event, the differences between genome sizes do not thus seem to be related to colonization history. These findings suggest either that genome size is seldom modified in a significant way during colonization or that it takes time for genome size of invading species to change significantly.

Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

BACKGROUND

Genome size is known to exhibit interspecies differences, but also to vary between populations within a given species and even between individual cells within an organism. Major differences have often been reported and attributed to differences in measurement conditions, in internal controls of genome size, and in the stains used. Flow cytometry using intercalating dyes is the most attractive method for measuring genome size.

METHODS

We estimated relative genome size of nuclei from heads of Drosophila melanogaster adult males using a FACScalibur flow cytometer and propidium iodide.

RESULTS

We have shown that the genome size estimates depended on the temperature and humidity of the rearing medium and decreased with age in adult flies. There were large differences in genome size estimates between the vials in which the flies were maintained, but only slight variations within the vials, supporting the idea that the size estimate depends on the fly rearing conditions. Changes in the temperature of the solution of head nuclei analyzed by the cytometer also influenced the genome size estimate.

CONCLUSIONS

These findings clearly show that the environmental conditions under which the flies were reared influence the genome size estimate, perhaps as a result of a change in the accessibility of the DNA to the fluorochrome. Caution is therefore called for when estimating genome size. Experimental artifact rather than adaptation may account for some of the correlations between genome size and environmental conditions reported in the literature.

Gradual and quantum genome size shifts in the hystricognath rodents

We assessed genome size variation by flow cytometry within and among 31 species of nine families of African and South American hystricognath rodents. Interspecific variation was extensive and genome size was relatively high among the South American radiation whereas only moderate variation and smaller estimates of genome size were observed in the African counterparts. The largest genome size, indicating tetraploidy was recorded in the South American octodontid, Tympanoctomys barrerae (16.8 pg DNA). This quantum shift in DNA content represents a novel mechanism of genome evolution in mammals. As expected in polyploid organisms, varying nucleotypic effects were observed in the dimensions of the sperm cells and lymphocytes of T. barrerae. The role of control mechanisms that influence cell dimensions in polyploid organisms is discussed.

Evolution of genome size in Drosophila. is the invader's genome being invaded by transposable elements?

Genome size varies considerably between species, and transposable elements (TEs) are known to play an important role in this variability. However, it is far from clear whether TEs are involved in genome size differences between populations within a given species. We show here that in Drosophila melanogaster and Drosophila simulans the size of the genome varies among populations and is correlated with the TE copy number on the chromosome arms. The TEs embedded within the heterochromatin do not seem to be involved directly in this phenomenon, although they may contribute to differences in genome size. Furthermore, genome size and TE content variations parallel the worldwide colonization of D. melanogaster species. No such relationship exists for the more recently dispersed D. simulans species, which indicates that a quantitative increase in the TEs in local populations and fly migration are sufficient to account for the increase in genome size, with no need for an adaptation hypothesis.

Localized chiasmata and meiotic nodules in the tetraploid onionAllium porrum

Allium porrum L. (cultivated leek) (2n = 4x = 32) is a fertile tetraploid that forms bivalents with pericentric chiasmata at metaphase I. To investigate the basis of this unusual behavior for a tetraploid, we describe the karyotype, axial cores, synaptonemal complexes (SCs), and meiotic nodules of A. porrum. The karyotype appears to be autotetraploid. This conclusion is also supported by presynaptic alignment of axial cores in groups of four and partner trades between pairs of SCs. Numerous early nodules are distributed all along axial cores and SCs during zygonema, but they are lost by late zygonema – early pachynema. Late (recombination) nodules (RNs) are present on SCs near kinetochores throughout the remainder of pachynema. This pattern of RNs corresponds to the pattern of pericentric chiasmata. Pachytene quadrivalents usually are resolved into bivalents because partner trades between SC lateral elements rarely occur between RNs on the same segment of SC. Thus, the patterns of crossing-over and partner trades promote balanced disjunction and high fertility in autotetraploid A. porrum. Rare quadrivalents observed at metaphase I must be due to infrequent partner trades between RNs. Polycomplexes, unusual in their number and size, were observed during zygonema. Key words : synaptonemal complex, recombination nodules, localized chiasmata, polycomplex, Allium porrum.

Measurement by flow cytometry of genomic AT/GC ratio and genome size

Flow cytometry with the AT-specific fluorochrome Hoechst 33258 (HO) and the GC-specific fluorochrome olivomycin (OM) was used for measurement of base pair specific DNA content in 20 species of vertebrates. The results were found to be in good correlation with the biochemical literature on base pair frequencies (r = 0.972, P < 1 x 10(-8). This correlation allows one to determine the percent of GC/AT-pairs and genome size from flow cytometric data. The genome sizes obtained were compared with the literature data on flow cytometric genome size values determined with the use of propidium iodide (PI) that is usually believed to be non-base pair specific. The results were found to be in general agreement; however, the previously reported slight GC-preference of PI is confirmed. The optimal conditions for flow cytometry of AT/GC ratio and genome size with the use of OM and HO are discussed. The approach can be useful for research in ecology, fisheries science, species conservation, and other environmental studies as a tool for rapid survey of a vast array of specimens.

Variations in genome mass

1. Genome size varies considerably among vertebrates, ranging from less than 1 pg to more than 200 pg; the amount of DNA differing among individuals in a population can equal the amount in the entire structural gene complement. 2. Recent technological advances permit evaluation of genome size variation at several levels including sub-chromosomal, chromosomal and cellular. 3. Genome size variation may also be viewed from taxonomic levels, and across evolutionary time frames. 4. As sources of genome size variation are identified and studied, the conundrum of the C-value paradox (lack of correlations among genome size, genomic complexity and phylogenetic status of organisms) may prove to be more apparent than real. 5. For example, the limited and relatively constant genome size of avians may be related to the physiological constraints of flight.

DNA content in Eurasian sturgeon species determined by flow cytometry

The nuclear DNA content in 10 species of chondrostean fishes was measured by flow cytometry. The sterlet Acipenser ruthenus blood cells were used as an internal standard. The sterlet DNA content was calculated on the basis of comparison with the Xenopus laevis blood cells, 2C = 6.30 pg. In the tetraploid A. ruthenus and A. stellatus the DNA content comprises 3.74 pg/nucleus and is practically invariant; in Huso dauricus it is almost the same, 3.74-3.81 pg; and in A. nudiventris it is a little higher, 3.88-4.04 pg. In the oldest chondrostean, Pseudoscaphirhynchus kaufmanni, the nuclear DNA content is slightly lower, 2C = 3.46-3.48 pg, and in the American paddlefish Polyodon spathula it is lower still, 3.17 pg. In two octoploid sturgeons, A. baeri and A. gueldenstaedti, the DNA content is twice as high as that of the sterlet, 8.29-8.31 and 7.86-7.88 pg, respectively; a very similar amount, 8.24-8.42 pg, was determined in the hybrid Huso huso x A. ruthenus. In the Sakhalin sturgeon, A. medirostris (= A. mikadoi), the DNA content is two times higher than in the octoploids, 13.93-14.73 pg; therefore its ploidy may be 16n and the number of chromosomes could be 500.

Genome size variation and its phenotypic consequences in Phyllotis rodents

Constitutive heterochromatin and genome size were studied in Phyllotis darwini, three Phyllotis xanthopygus subspecies, and their interspecific laboratory hybrids. P. darwini, with no or only small C-bands, had the smallest genome size; P. xanthopygus rupestris and P. x. vaccarum, with large C-bands in all the chromosomes, had the largest; and P. x. xanthopygus, with heterochromatin only in a few chromosomes, showed intermediate genome size. To examine some phenotypic consequences of nuclear DNA content, we measured nuclear and cellular surfaces and volumes. Linear regression analyses showed that all these cellular characters had a highly significant direct relationship with genome size. Hybrids had always the expected intermediate parental characteristics. Previous results indicate that P. x. vaccarum should have longer mitotic cycles and lower reproductive capacity than P. darwini. Our findings suggest that the "nucleotypic DNA" hypothesis, which considers genome size as an adaptive feature in higher plants and lower vertebrates, could be extended to these mammals. The analysis of heterochromatin and nuclear DNA amounts of other phyllotine and akodontine rodents supports the idea that small C-bands and genomes are ancestral conditions, from which independent and parallel events occurred until large genomes were produced.

Genetic stock assessment of spawning arctic cisco (Coregonus autumnalis) populations by flow cytometric determination of DNA content

Intraspecific variation in cellular DNA content was measured in five Coregonus autumnalis spawning populations from the Mackenzie River drainage, Canada, using flow cytometry. The rivers assayed were the Peel, Arctic Red, Mountain, Carcajou, and Liard rivers. DNA content was determined from whole blood preparations of fish from all rivers except the Carcajou, for which kidney tissue was used. DNA content measurements of kidney and blood preparations of the same fish from the Mountain River revealed statistically indistinguishable results. Mosaicism was found in blood preparations from the Peel, Arctic Red, Mountain, and Liard rivers, but was not observed in kidney tissue preparations from the Mountain or Carcajou rivers. The Liard River sample had significantly elevated mean DNA content relative to the other four samples; all other samples were statistically indistinguishable. Significant differences in mean DNA content among spawning stocks of a single species reinforces the need for adequate sample sizes of both individuals and populations when reporting "C" values for a particular species.

Intraspecific variation in nuclear DNA content among world populations of a mosquito, Aedes albopictus (Skuse)

Aedes albopictus is commonly distributed in most parts of the Oriental region and on many islands in the Indian and the Pacific Oceans. The species was recently introduced into the United States and Brazil. Feulgen cytophotometric quantitation of haploid nuclear DNA content was carried out for 37 populations of Ae. albopictus to determine the extent of intraspecific variation in nuclear DNA content and whether the range expansion of the species has coincided with an increase in DNA content. The haploid nuclear DNA content varied nearly three-fold. The minimum DNA content was 0.62 pg in Koh Samui from Thailand, and the maximum DNA content was 1.66 pg in Houston-61 from the United States. Statistical comparisons of populations revealed significant differences in DNA contents. No geographic clustering of populations was noted with respect to DNA content. In general, populations from the United States and Brazil had higher DNA contents, but there was no indication that the range expansion had occurred hand in hand with an increase in DNA content. Each population had a specific amount of DNA that is probably imposed by the microenvironment.

Reference standards for flow cytometry and application in comparative studies of nuclear DNA content

Nuclear DNA mass in cells from a reference species can be used to obtain high-resolution estimates of DNA mass from a target species. In our study of DNA mass in cells from 45 selected species, representing each of the major vertebrate classes, we have obtained values of from 1.5 to 110.0 pg of DNA. Because values in or near this range would be expected in the study of nuclear DNA mass in vertebrates and other organisms, the species in this report can provide a useful catalogue of references for comparative studies of DNA.

Estimation of nuclear DNA content by flow cytometry in fishes of the genus Xiphophorus

1. By use of flow cytometry we measured nuclear DNA content in cells from 16 stocks representing 9 species of the genus Xiphophorus. 2. Significant differences were detected between certain stocks and species with respect to DNA content. 3. Male-female differences were apparent in 5 of 7 stocks in which males and females were studied. 4. Estimation of nuclear DNA content is of potential significance in connection with the genetics of sex determination and the study of taxonomic relationships.

Genome Size in Conodonts (Chordata): Inferred Variations During 270 Million Years

DNA is too unstable to be preserved during fossilization, but it still seems possible to infer the genome content of fossils because in every group of organisms investigated cell size is proportional to quantity of DNA. Accordingly, information on macroevolutionary trends in genome size through millions of years is potentially available. This survey of inferred variation in genome content in fossils is based on measurements of epithelial cells in extinct conodonts over a period of 270 million years. Why genome size varies so widely amongst living organisms is a subject of continuing debate. Paleontology offers a distinct temporal perspective, but lack of data on conodont paleoecology make the proposed adaptive explanations for genome variation difficult to test.

Inter and intraspecific variation in nuclear DNA content in Aedes mosquitoes

Haploid nuclear DNA of 23 species of Aedes, as determined by Feulgen cytophotometry, was found to vary 3-fold. This was accompanied by a 2-fold variation in total chromosomal length. There was a significant correlation (r = 0.765, P less than 0.001) between these two parameters. Genome size varied from 0.87 pg to 1.3 pg among 10 strains of Aedes albopictus, from wide geographic regions. Large scale differences in chromosomal DNA amounts have accompanied speciation and evolution in aedine mosquitoes.

Genome evolution in pocket gophers (genus Thomomys). III. Fluorochrome-revealed heterochromatin heterogeneity

Heterochromatin is a dominant component of the genome in the bottae group of the pocket gopher genus Thomomys, having had a major role in the karyotypic evolution of member species. Heterochromatin characteristics of two subspecies of T. bottae and one of T. umbrinus were examined with fluorochrome dyes identifying presumptive GC- and AT-rich regions. In two karyotype forms of T. b. fulvus and in T. umbrinus, chromatin that fluoresces brightly with chromomycin A3 is also C-band positive, although not all heterochromatin fluoresces. However, in T. b. bottae, only euchromatic regions fluoresce brightly with chromomycin. Fluorescence patterns produced with DAPI are the reverse of the chromomycin banding in all karyotypic forms. Heterochromatin in these taxa is thus highly differentiated, exhibiting heterogeneity in staining characteristics, and presumably in underlying DNA sequences, both across the genome within a given chromosomal complement as well as among the different karyotypic races and species of the bottae group of pocket gophers.

Genome size variation among north american minnows (Cyprinidae). I. Distribution of the variation in five species

Genome sizes (nuclear DNA contents) were examined spectrophotometrically from ten individuals of each of five species of North American cyprinid fishes (minnows). The distributions of DNA values both within and between the five species were essentially continuous and normal. Differences between individuals within populations were significant and contributed to approximately 16 per cent of the total variation. Variation between individuals within species ranged from 4.7-13.5 per cent and averaged ca. 7.4 per cent. Variation between species ranged from 0-9.5 per cent and the average difference between any species pair was ca. 4.6 per cent. Statistical analyses showed that the methodology used was sufficient to detect significant differences in genome size as small as 2-3 per cent. Consideration of these data lead to the following tentative conclusions: (i) changes in genome size in cyprinids appear small in amount, frequent in occurrence, to involve both gains and losses of DNA, and to be cumulative and independent in effect; (ii) differences within and between cyprinid taxa are likely the result of accumulations of small changes in DNA quantity; and (iii) the primary focus of quantitative DNA variation in cyprinids is between individuals within populations. The extent of DNA quantity variation which occurs within species would appear to preclude any direct relationship between genome size variation and many of the organismal parameters (including speciation) which differentiate the five species. In short, the data suggest that a significant fraction of the cyprinid genome, perhaps more than 10 per cent, is free to vary quantitatively without phenotypic constraint or biological consequence. This fraction is considerably larger than that theoretically needed for the structural gene component.

Genome evolution in pocket gophers (genus Thomomys). I. Heterochromatin variation and speciation potential

A basic dichotomy exists in the amount and chromosomal position of constitutive heterochromatin (C-bands) in species of pocket gophers, genus Thomomys. Members of the "talpoides-group" of species (e.g., T. talpoides and T. monticola) have C-bands restricted to the centromeric regions. These taxa are characterized by Robertsonian patterns of karyotypic evolution. In contrast, species within the "bottae-group" are characterized by extensive amounts of heterochromatin, placed as whole-arm and apparent whole-chromosome (T. bottae) or as large interstitial blocks (T. umbrinus). These species are characterized by extensive non-Robertsonian variation in karyotype, variation which may be expressed from local population polymorphism to between population or species polytypy. Within T. bottae, the number of whole-arm heterochromatic autosomes is inversely proportional to the number of uniarmed chromosomes in the complement, which ranges from 0 to 36 across the species populations. In all-biarmed karyotypic populations, upward to 60 percent of the linear length of the genome is composed of heterochromatin. Populations with extensive heterochromatin variation and those with similar amounts meet and hybridize freely in nature. The implications of these date for current ideas on the function of heterochromatin, particularly as related to speciation models, are discussed.