Cytophotometric evidence of variation in genome size of desmognathine salamanders

Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders

AbstractGenome size (C-value) can affect organismal traits across levels of biological organization from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development and because genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders. If this hypothesis is correct, then genome size and body size should be correlated in this group. Using Feulgen image analysis densitometry, we estimated genome sizes for 60 species of Neotropical salamanders. We also estimated the "biological size" of species by comparing genome size and physical body sizes in a phylogenetic context. We found a significant correlation between C-value and physical body size using optimal regression with an Ornstein-Uhlenbeck model and report the smallest salamander genome found to date. Our index of biological size showed that some salamanders with large physical body size have smaller biological body size than some miniature species and that several clades demonstrate patterns of increased or decreased biological size compared with their physical size. Our results suggest a causal relationship between physical body size and genome size and show the importance of considering the impact of both on the biological size of organisms. Indeed, biological size may be a more appropriate measure than physical size when considering phenotypic consequences of genome size evolution in many groups.

Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are nonmonophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to differences in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.

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 dynamic evolutionary history of genome size in North American woodland salamanders

The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

Early development of Ensatina eschscholtzii: an amphibian with a large, yolky egg

BACKGROUND

Comparative analyses between amphibians, concentrating on the cellular mechanisms of morphogenesis, reveal a large variability in the early developmental processes that were thought to be conserved during evolution. Increased egg size is one factor that could have a strong effect on early developmental processes such as cleavage pattern and gastrulation. Salamanders of the family Plethodontidae are particularly appropriate for such comparative studies because the species have eggs of varying size, including very large yolky eggs.

RESULTS

In this paper, we describe for the first time the early development (from fertilization through neurulation) of the plethodontid salamander Ensatina eschscholtzii. This species has one of the largest eggs known for an amphibian, with a mean ± SD diameter of 6 ± 0.43 mm (range 5.3-6.9; n = 17 eggs). Cleavage is meroblastic until approximately the 16-cell stage (fourth or fifth cleavage). At the beginning of gastrulation, the blastocoel roof is one cell thick, and the dorsal lip of the blastopore forms below the equator of the embryo. The ventral lip of the blastopore forms closer to the vegetal pole, and relatively little involution occurs during gastrulation. Cell migration is visible through the transparent blastocoel roof of the gastrula. At the end of gastrulation, a small archenteron spreading dorsally from the blastopore represents the relatively small and superficial area of the egg where early embryonic axis formation occurs. The resulting pattern is similar to the embryonic disk described for one species of anuran.

CONCLUSIONS

Comparisons with the early development of other species of amphibians suggest that an evolutionary increase in egg size can result in predictable changes in the patterns and rate of early development, but mainly within an evolutionary lineage.

Cytogenetic analysis of the Asian plethodontid salamander, Karsenia koreana: evidence for karyotypic conservation, chromosome repatterning, and genome size evolution

A cytogenetic analysis, including the karyotype, C-bands, silver-stained nucleolus organizer regions and genome size, was performed on the recently discovered species, Karsenia koreana, the first plethodontid salamander from Asia. The karyotype consists of 14 pairs of bi-armed chromosomes, with no evidence of heteromorphic sex chromosomes. C-banding reveals a concentration of heterochromatin at the centromeres as well as at interstitial locations. The smallest chromosome (pair number 14) has symmetrical interstitial C-bands in each arm, resembling chromosome no. 14 of North American species of its sister group taxon, supergenus Hydromantes. Acomparative analysis of C-band heterochromatin and silver-stained nucleolus organizer regions of Karsenia and other plethodontid genera reveals that chromosomal evolution may have featured chromosome 'repatterning' within the context of conserved chromosome number and shape in this clade. Genome size is correlated with geographic distribution in plethodontids and appears to have important phenotypic correlates as well. The genome size of Karsenia is relatively large, and resembles that of the geographically closest plethodontids from western North America, especially species of the genus Hydromantes. The biological significance of these cytogenetic characteristics of plethodontid salamanders is discussed within an evolutionary context.

Effect of inhibitors of DNA replication on early zebrafish embryos: evidence for coordinate activation of multiple intrinsic cell-cycle checkpoints at the mid-blastula transition

We address the developmental activation, in the zebrafish embryo, of intrinsic cell-cycle checkpoints which monitor the DNA replication process and progression through the cell cycle. Eukaryotic DNA replication is probably carried out by a multiprotein complex containing numerous enzymes and accessory factors that act in concert to effect processive DNA synthesis (Applegren, N. et al. (1995) J. Cell. Biochem. 59, 91-107). We have exposed early zebrafish embryos to three chemical agents which are predicted to specifically inhibit the DNA polymerase alpha, topoisomerase I and topoisomerase II components of the DNA replication complex. We present four findings: (1) Before mid-blastula transition (MBT) an inhibition of DNA synthesis does not block cells from attempting to proceed through mitosis, implying the lack of functional checkpoints. (2) After MBT, the embryo displays two distinct modes of intrinsic checkpoint operation. One mode is a rapid and complete stop of cell division, and the other is an 'adaptive' response in which the cell cycle continues to operate, perhaps in a 'repair' mode, to generate daughter nuclei with few visible defects. (3) The embryo does not display a maximal capability for the 'adaptive' response until several hours after MBT, which is consistent with a slow transcriptional control mechanism for checkpoint activation. (4) The slow activation of checkpoints at MBT provides a window of time during which inhibitors of DNA synthesis will induce cytogenetic lesions without killing the embryo. This could be useful in the design of a deletion-mutagenesis strategy.

Differentiation processes in the amphibian brain with special emphasis on heterochronies

Amphibians and caecilians exhibit a great variety of adult morphologies, life histories, and developmental strategies (biphasic development, direct development, viviparity, and neoteny). While early brain development and the differentiation of neural tissues in the three amphibian orders follow a basic pattern, differences exist in the onset and offset as well as the rate of growth and differentiation processes. These differences are described within a phylogenetic framework, and special emphasis is laid on the relationship between altered ontogenies and phylogenetic diversity. We concentrate on ontogenetic differentiation processes in the motor, olfactory, and visual system. We discuss the morphological consequences of secondary simplification of the brain in the context of paedomorphosis, which has happened several times independently among amphibians and consists in the abbreviation or truncation of late developmental processes. We deal with the cellular and molecular basis of brain development and the consequences for the adult nervous system in representative species of the three amphibian orders. Our analysis reveals that differences in brain morphology are largely due to heterochrony (i.e., the desynchronization of ontogenetic processes), a phenomenon that in turn is related to changes in genome sizes and life histories.

Cell size predicts morphological complexity in the brains of frogs and salamanders

The morphological organization of the brain of frogs and salamanders varies greatly in the degree to which it is subdivided and differentiated. Members of these taxa are visually oriented predators, but the morphological complexity of the visual centers in the brain varies interspecifically. We give evidence that the morphological complexity of the amphibian tectum mesencephali, the main visual center, can be predicted from knowledge of cell size, which varies greatly among these taxa. Further, cell size is highly correlated with genome size. Frogs with small cells have more complex morphologies of the tectum than do those with large cells independent of body and brain size. In contrast, in salamanders brain-body size relationships also are correlated with morphological complexity of the brain. Small salamanders with large cells have the simplest tecta, whereas large salamanders with small cells exhibit the most complex tectal morphologies. Increases in genome, and consequently cell size, are associated with a decrease in the differentiation rate of nervous tissue, which leads to the observed differences in brain morphology. On the basis of these findings we hypothesize that important features of the structure of the brain can arise independently of functional demands, from changes at a lower level of organismal organization--in this case increase in genome size, which induces simplification of brain morphology.