Transposable element and host silencing activity in gigantic genomes.

Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.

Genome size drives morphological evolution in organ-specific ways.

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases). Our results show that overall organ size is a function of body size, whereas tissue structure changes dramatically with evolutionary increases in genome size. In the heart, increased genome size is correlated with a reduction of myocardia in the ventricle, yielding proportionally less force-producing mass and greater intertrabecular space. In the liver, increased genome size is correlated with fewer and larger vascular structures, positioning hepatocytes farther from the circulatory vessels that transport key metabolites. Although these structural changes should have obvious impacts on organ function, their effects on organismal performance and fitness may be negligible because low metabolic rates in salamanders relax selective pressure on function of key metabolic organs. Overall, this study suggests large genome and cell size influence the developmental systems involved in heart and liver morphogenesis.

Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome - the caecilianIchthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

Forever young: Linking regeneration and genome size in salamanders.

BACKGROUND: Salamanders stand out among vertebrate animals in two key characteristics: their ability to regenerate body parts, and their large and variable genome sizes. RESULTS: Here we show how to unite seemingly disparate facets of salamander biology, regeneration ability, and genome size variation, into one synthetic view. Large and variable genome sizes may be the key to understanding the prodigious ability of most salamanders to regenerate damaged or lost body parts. We report a correlate of genome size variation that has been previously neglected: the impacts of genome size on the structure and function of the genes themselves. Salamanders are, in essence, paradoxically much younger, especially at the cellular level than their chronological age would suggest. CONCLUSIONS: Because of the large size and range of variation in genome size in salamanders, we hypothesize that this relationship uncouples a dynamic interaction between growth and differentiation in processes of morphogenesis, pattern formation, and regeneration in ways that are unique among vertebrates.

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.

Reflections on Bateson's rule: Solving an old riddle about why extra legs are mirror-symmetric.

William Bateson was an obsessive observer of animal oddities, and at some point in his herculean survey of museum collections leading up to his monumental 1894 monograph (Materials for the study of variation), he noticed a peculiar trend among the preserved specimens (mainly insects) that possessed extra legs: multiple legs that branched from the same socket tended to be mirror images of their adjacent neighbors. He did not know why. These symmetry relationships have come to be known as Bateson's rule, and they have defied a satisfactory explanation for 125 years. In the past few decades, tantalizing clues have emerged from various lines of investigation, and those lines have converged on a possible solution. An attempt is made here to fit all of those clues together to form a coherent picture of the etiology. Two case studies have proven to be pivotal: a fly mutant whose extra legs are caused by patches of dying cells and a frog syndrome whose extra legs are caused by a parasitic flatworm. The conclusion reached is that the extra legs of insects and vertebrates obey Bateson's rule for the same reason, but that reason has nothing to do with the specific molecules in their signaling pathways. Rather, it is an emergent property of the circuitry of the pathways and their polarized alignments along the limb axes. A parade of theoretical models have tried and failed to crack this mystery in the past, and they are reviewed here as part of the narrative.

Morphological Polymorphism Associated with Alternative Reproductive Tactics in a Plethodontid Salamander.

Understanding polymorphism is a central problem in evolution and ecology, and alternative reproductive tactics (ARTs) provide compelling examples for studying the origin and maintenance of behavioral and morphological variation. Much attention has been given to examples where "parasitic" individuals exploit the reproductive investment of "bourgeois" individuals, but some ARTs are instead maintained by environmental heterogeneity, with alternative tactics exhibiting differential fitness in discontinuous reproductive niches. We use genomic, behavioral, karyological, and field observational data to demonstrate one such example in plethodontid salamanders. These ARTs ("searching" and "guarding" males) are associated with different reproductive niches and, unlike most other examples in amphibians, demonstrate substantial morphological differences and inflexibility within a reproductive season. Evidence suggests the existence of these ARTs within three putative species in the two-lined salamander (Eurycea bislineata) species complex, with other members of this clade fixed for one of the two tactics. We highlight directions for future research in this system, including the relationship between these ARTs and parental care.

Evidence for Sex Chromosome Turnover in Proteid Salamanders.

A major goal of genomic and reproductive biology is to understand the evolution of sex determination and sex chromosomes. Species of the 2 genera of the Salamander family Proteidae - Necturus of eastern North America, and Proteus of Southern Europe - have similar-looking karyotypes with the same chromosome number (2n = 38), which differentiates them from all other salamanders. However, Necturus possesses strongly heteromorphic X and Y sex chromosomes that Proteus lacks. Since the heteromorphic sex chromosomes of Necturus were detectable only with C-banding, we hypothesized that we could use C-banding to find sex chromosomes in Proteus. We examined mitotic material from colchicine-treated intestinal epithelium, and meiotic material from testes in specimens of Proteus, representing 3 genetically distinct populations in Slovenia. We compared these results with those from Necturus. We performed FISH to visualize telomeric sequences in meiotic bivalents. Our results provide evidence that Proteus represents an example of sex chromosome turnover in which a Necturus-like Y-chromosome has become permanently translocated to another chromosome converting heteromorphic sex chromosomes to homomorphic sex chromosomes. These results may be key to understanding some unusual aspects of demographics and reproductive biology of Proteus, and are discussed in the context of models of the evolution of sex chromosomes in amphibians.

Does the early frog catch the worm? Disentangling potential drivers of a parasite age-intensity relationship in tadpoles.

The manner in which parasite intensity and aggregation varies with host age can provide insights into parasite dynamics and help identify potential means of controlling infections in humans and wildlife. A significant challenge is to distinguish among competing mechanistic hypotheses for the relationship between age and parasite intensity or aggregation. Because different mechanisms can generate similar relationships, testing among competing hypotheses can be difficult, particularly in wildlife hosts, and often requires a combination of experimental and model fitting approaches. We used field data, experiments, and model fitting to distinguish among ten plausible drivers of a curvilinear age-intensity relationship and increasing aggregation with host age for echinostome trematode infections of green frogs. We found little support for most of these proposed drivers but did find that the parsimonious explanation for the observed age-intensity relationship was seasonal exposure to echinostomes. The parsimonious explanation for the aggregated distribution of parasites in this host population was heterogeneity in exposure. A predictive model incorporating seasonal exposure indicated that tadpoles hatching early or late in the breeding season should have lower trematode burdens at metamorphosis, particularly with simulated warmer climates. Application of this multi-pronged approach (field surveys, lab experiments, and modeling) to additional parasite-host systems could lead to discovery of general patterns in the drivers of parasite age-intensity and age-distribution relationships.

Explanations for deformed frogs: plenty of research left to do (a response to Skelly and Benard).

Our recent study (Ballengeé and Sessions, 2009. J Exp Zool (Mol Dev Evol) 312B:1-10) shows that deformed frogs with missing limbs can be explained by sublethal "selective predation" by predators that are too small, or have mouthparts that are too small, to consume whole tadpoles. Skelly and Benard do not agree with our conclusions and feel that they are not well founded. Here we respond to their critique.

Explanation for missing limbs in deformed amphibians.

We present evidence that the most commonly found deformities in wild-caught amphibians, those featuring missing limbs and missing limb segments, may be the result of selective predation. Here we report that predatory dragonfly nymphs can severely injure and even fully amputate developing hind limbs of anuran tadpoles. Developmental responses of the injured/amputated tadpole limbs range from complete regeneration to no regeneration, with intermediate conditions represented by various idiosyncratic limb deformities, depending mainly on the developmental stage of the tadpole at the time of injury/amputation. These findings were reinforced by experimental amputations of anuran tadpole hind limbs that resulted in similar deformities. Our studies suggest that selective predation by dragonfly nymphs and other aquatic predators may play a significant role in the most common kinds of limb deformities found in natural populations of amphibians.

The necessity of Darwin: this journal's tribute to the most influential scientist of all time.

Charles Darwin is considered by many to be one of the most influential scientists of all time. His theory of evolution via natural selection was astonishingly prescient in terms of what modern biology has revealed in the 150 years since the publication of The Origin of Species, especially since Darwin was unaware of even the most fundamental aspects of transmission genetics, not to mention molecular biology. Here we speculate what impact it would have had on Darwin's thinking if he had known what we now know about molecular biology and cytogenetics.

Understanding the net effects of pesticides on amphibian trematode infections.

Anthropogenic factors can have simultaneous positive and negative effects on parasite transmission, and thus it is important to quantify their net effects on disease risk. Net effects will be a product of changes in the survival and traits (e.g., susceptibility, infectivity) of both hosts and parasites. In separate laboratory experiments, we exposed cercariae of the trematode Echinostoma trivolvis, and its first and second intermediate hosts, snails (Planorbella trivolvis) and green frog tadpoles (Rana clamitans), respectively, to one of four common pesticides (atrazine, glyphosate, carbaryl, and malathion) at standardized, ecologically relevant concentrations (201.0, 3700.0, 33.5, and 9.6 microg/L, respectively). We measured effects of pesticide exposure on six mechanisms important to this host-parasite interaction: (1) survival of E. trivolvis cercariae over 26 hours, (2) tadpole survival over two weeks, (3) snail survival over four weeks, (4) snail growth and fecundity, (5) cercarial infectivity, and (6) tadpole susceptibility to a fixed number of cercariae. Pesticides, in general, caused significantly greater mortality of E. trivolvis cercariae than did control treatments, but atrazine was the lone chemical to significantly reduce cercarial survival (LC50 value = 267 mg/L) and then only at concentrations greater than commonly found in aquatic ecosystems (> or =200 microg/L). None of the pesticides significantly enhanced E. trivolvis virulence, decreased tadpole survival, or reduced snail survival, growth, or fecundity. Sublethal exposure of the cercariae to the pesticides (4 h) did not significantly affect trematode encystment in R. clamitans. In contrast, sublethal exposure of R. clamitans to each of the four pesticides increased their susceptibility as measured by the percentage of cercariae that encysted. The reduction in exposure to trematodes due to pesticide-induced cercarial mortality (a density-mediated effect) was smaller than the pesticide-induced increase in amphibian susceptibility (a trait-mediated effect), suggesting that the net effect of exposure to environmentally realistic levels of pesticides will be to elevate amphibian trematode infections. These findings highlight the importance of elucidating the lethal and sublethal effects of anthropogenic factors on both hosts and parasites to understand the mechanisms underlying changes in parasite transmission and virulence, an approach that is especially needed for amphibians, a taxon experiencing global disease-related declines.

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.

Evolutionary cytogenetics in salamanders.

Salamanders (Amphibia: Caudata/Urodela) have been the subject of numerous cytogenetic studies, and data on karyotypes and genome sizes are available for most groups. Salamanders show a more-or-less distinct dichotomy between families with large chromosome numbers and interspecific variation in chromosome number, relative size, and shape (i.e. position of the centromere), and those that exhibit very little variation in these karyological features. This dichotomy is the basis of a major model of karyotype evolution in salamanders involving a kind of 'karyotypic orthoselection'. Salamanders are also characterized by extremely large genomes (in terms of absolute mass of nuclear DNA) and extensive variation in genome size (and overall size of the chromosomes), which transcends variation in chromosome number and shape. The biological significance and evolution of chromosome number and shape within the karyotype is not yet understood, but genome size variation has been found to have strong phenotypic, biogeographic, and phylogenetic correlates that reveal information about the biological significance of this cytogenetic variable. Urodeles also present the advantage of only 10 families and less than 600 species, which facilitates the analysis of patterns within the entire order. The purpose of this review is to present a summary of what is currently known about overall patterns of variation in karyology and genome size in salamanders. These patterns are discussed within an evolutionary context.

Functional evaluation of isolated zebrafish hearts.

Traditional working heart preparations, based on the original Langendorff setup, are widely used experimental models that have tremendously advanced the cardiovascular field. However, these systems can be deceivingly complex, requiring the maintenance of pH with CO(2), the delivery of oxygenated perfusate, and the need for extensive laboratory equipment. We have examined the feasibility of using isolated zebrafish (Danio rerio) hearts as an experimental model system, in which experimental procedures can be performed in the absence of the traditional requirements and sophisticated setup equipment. Isolated zebrafish hearts exhibited spontaneous contractile activity, could be electrically paced, and were responsive to pharmacologic stimulation with isoproterenol for 1.5 h after in vivo removal. Isolated zebrafish hearts offer a time- and cost-effective alternative to traditional Langendorff/working heart preparation models, and could be used to investigate cardiac function and repair.

How trematodes cause limb deformities in amphibians.

We used trematode cyst infestation to induce limb deformities in two species of frogs of the genus Rana and compared them to deformities induced by surgical limb bud rotations. The specific deformities produced by both treatments closely resemble those of wild-caught deformed amphibians and are consistent with a known developmental response to disruption of the spatial organization of cells in developing limb buds. Histological analysis showed that trematode cysts cause massive disruption and abnormal cellular growth involving the limb buds of infected individuals. Our results indicate that trematode cyst infestation causes deformities in frogs by perturbation of the positional relationships of cells in developing limb buds. The crippling effects of cyst-infection on frogs may reflect complex co-evolutionary interactions among trematodes, frogs, and other hosts in the trematode's life cycle.

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.