Where do fish go when stranded on land? Terrestrial orientation of the mangrove rivulus Kryptolebias marmoratus

The goal of the present study was to determine which sensory cues the mangrove rivulus Kryptolebias marmoratus, a quasi-amphibious, hermaphroditic fish, uses to orient in an unfamiliar terrestrial environment. In a laboratory setting, K. marmoratus were placed on a terrestrial test arena and were provided the opportunity to move toward reflective surfaces, water, dark colours v. light colours, and orange colouration. Compared with hermaphrodites, males moved more often toward an orange section of the test arena, suggesting that the response may be associated with camouflage or male–male competition, since only males display orange colouration. Younger individuals also moved more often toward the orange quadrant than older individuals, suggesting age-dependent orientation performance or behaviour. Sloped terrain also had a significant effect on orientation, with more movement downhill, suggesting the importance of the otolith-vestibular system in terrestrial orientation of K. marmoratus. By understanding the orientation of extant amphibious fishes, we may be able to infer how sensory biology and behaviour might have evolved to facilitate invasion of land by amphibious vertebrates millions of years ago.     

Population genetics and evolution of the mangrove rivulus Kryptolebias marmoratus,the world's only self‐fertilizing hermaphroditic vertebrate

The mangrove rivulus, Kryptolebias marmoratus (Rivulidae, Cyprinodontiformes), is phylogenetically embedded within a large clade of oviparous (egg laying) and otherwise mostly gonochoristic (separate sex) killifish species in the circumtropical suborder Aplocheiloidei. It is unique in its reproductive mode: K. marmoratus is essentially the world's only vertebrate species known to engage routinely in self‐fertilization as part of a mixed‐mating strategy of selfing plus occasional outcrossing with gonochoristic males. This unique form of procreation has profound population‐genetic and evolutionary‐genetic consequences that are the subject of this review.     

Androdioecy in Kryptolebias killifish and the evolution of self‐fertilizing hermaphroditism

Kryptolebias marmoratus is an important experimental fish, and is considered to represent the only vertebrate species comprising self‐fertilizing hermaphroditic individuals. Subsequent to the discovery of this unusual mode of reproduction, approximately 50 years ago, K. marmoratus has been the focus of a series of studies. However, little is known about the evolution of this rare reproduction mode, and data on the biology of closely related species are still unavailable. The present study aimed to histologically analyse the gonads of three K. marmoratus congeners (i.e. Kryptolebias ocellatus, Kryptolebias caudomarginatus, and Kryptolebias brasiliensis) to check the distribution of features related to hermaphroditism that are useful for forming hypotheses about the origin and evolution of the self‐fertilization mode of reproduction through the available phylogenies. The data obtained demonstrate that populations of K. caudomarginatus consist of males and hermaphrodites, which supports the hypothesis that hermaphroditism arose at the base of the clade containing K. caudomarginatus, K. marmoratus, and K. ocellatus as a first step towards a more advanced condition, uniquely shared by both K. marmoratus and K. ocellatus, in which males are rare or absent in natural populations, with the subsequent occurrence of self‐fertilization. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 344–349.     

Factors affecting terrestrial movement in the amphibious mangrove rivulus (Kryptolebias marmoratus)

We hypothesised that the exploration tendency of the amphibious mangrove rivulus Kryptolebias marmoratus would be inhibited in the terrestrial environment because of constraints on terrestrial locomotion or orientation. Using a novel object test, we showed that the fish explored objects in the aquatic but not the terrestrial environment, supporting the existence of constraints on terrestrial exploration. In further tests of the effects of extrinsic factors on terrestrial movement between aquatic refuges, shallow water depth simulating desiccation risk and the presence of a conspecific simulating intraspecific competition increased emersion outside of refuges, while high water salinity had no effect. These extrinsic factors had little effect on terrestrial movement between different aquatic refuges, except possibly for the lowest water depth tested. A significant association observed between emersion activity and movement between aquatic refuges suggested that terrestrial movement in K. marmoratus might depend on the tendency of individuals to emerse.     

Phenotypically plastic responses to predation threat in the mangrove rivulus fish (<Emphasis Type="Italic">Kryptolebias marmoratus</Emphasis>): behavior and morphology

Early life environments have important effects on phenotype development, but it can be difficult to disentangle the relative influences of genotype and environment on phenotypic variation within and among populations. Mangrove rivulus fish (Kryptolebias marmoratus) reproduce by self-fertilization and can generate isogenic lineages, which provides opportunities to resolve how the environment shapes the phenotype independent of genetic variation. Rivulus’ ecology is not well understood, but mangrove water snakes (Nerodia clarkii compressicauda) are thought to be a major predator. To test developmental responses to predator-related cues, four rivulus lineages (two that naturally co-exist with snakes; two that do not) were exposed to one of three treatments for 30 days post-hatching: cues from snakes that were fasted, fed rivulus, or fed heterospecifics. One week after exposure, fear and boldness responses were quantified. Individuals were photographed at 2 and 6 months of age for body size, growth, and body shape analysis. Animals that have historically encountered snakes were more risk averse and had wider heads than animals that historically have not encountered snakes. Rivulus exposed to cues from snakes fed conspecifics or heterospecifics grew faster than those exposed to fasted snake cues. Body shape was more streamlined in animals exposed to cues from snakes fed conspecifics, which may facilitate increased jumping performance as a way to escape aquatic predators. Our results suggest that rivulus exhibit phenotypic plasticity in response to cues associated with predator threat and that historical effects from selection or other evolutionary processes also are important determinants of behavioral and morphological variation.     

Environmental enrichment induces intergenerational behavioural and epigenetic effects on fish

Parental effects influence offspring phenotypes through pre‐ and post‐natal routes but little is known about their molecular basis, and therefore their adaptive significance. Epigenetic modifications, which control gene expression without changes in the DNA sequence and are influenced by the environment, may contribute to parental effects. We investigated the effects of environmental enrichment on the behaviour, metabolic rate and brain DNA methylation patterns of parents and offspring of the highly inbreed mangrove killifish (Kryptolebias marmoratus). Parental fish reared in enriched environments had lower cortisol levels, lower metabolic rates and were more active and neophobic than those reared in barren environments. They also differed in 1,854 methylated cytosines (DMCs). Offspring activity and neophobia were determined by the parental environment. Among the DMCs of the parents, 98 followed the same methylation patterns in the offspring, three of which were significantly influenced by parental environments irrespective of their own rearing environment. Our results suggest that parental environment influences the behaviour and, to some extent, the brain DNA methylation patterns of the offspring.     

Seeing in the swamp: hydrogen sulfide inhibits eye metabolism and visual acuity in a sulfide-tolerant fish

In fish, vision may be impaired when eye tissue is in direct contact with environmental conditions that limit aerobic ATP production. We hypothesized that the visual acuity of fishes exposed to hydrogen sulfide (H₂S)-rich water would be altered owing to changes in cytochrome c oxidase (COX) activity. Using the H₂S-tolerant mangrove rivulus (Kryptolebias marmoratus), we showed that a 10 min exposure to greater than or equal to 200 µM of H₂S impaired visual acuity and COX activity in the eye. Visual acuity and COX activity were restored in fish allowed to recover in H₂S-free water for up to 1 h. Since K. marmoratus are found in mangrove pools with H₂S concentrations exceeding 1000 µM, visual impairment may impact predator avoidance, navigation and foraging behaviour in the wild.     

Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers

In mammalian development, epigenetic modifications, including DNA methylation patterns, play a crucial role in defining cell fate but also represent epigenetic barriers that restrict developmental potential. At two points in the life cycle, DNA methylation marks are reprogrammed on a global scale, concomitant with restoration of developmental potency. DNA methylation patterns are subsequently re-established with the commitment towards a distinct cell fate. This reprogramming of DNA methylation takes place firstly on fertilization in the zygote, and secondly in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. In each reprogramming window, a unique set of mechanisms regulates DNA methylation erasure and re-establishment. Recent advances have uncovered roles for the TET3 hydroxylase and passive demethylation, together with base excision repair (BER) and the elongator complex, in methylation erasure from the zygote. Deamination by AID, BER and passive demethylation have been implicated in reprogramming in PGCs, but the process in its entirety is still poorly understood. In this review, we discuss the dynamics of DNA methylation reprogramming in PGCs and the zygote, the mechanisms involved and the biological significance of these events. Advances in our understanding of such natural epigenetic reprogramming are beginning to aid enhancement of experimental reprogramming in which the role of potential mechanisms can be investigated in vitro. Conversely, insights into in vitro reprogramming techniques may aid our understanding of epigenetic reprogramming in the germline and supply important clues in reprogramming for therapies in regenerative medicine.     

Genome‐wide DNA methylation alterations of Alternanthera philoxeroides in natural and manipulated habitats: implications for epigenetic regulation of rapid responses to environmental fluctuation and phenotypic variation

Alternanthera philoxeroides (alligator weed) is an invasive weed that can colonize both aquatic and terrestrial habitats. Individuals growing in different habitats exhibit extensive phenotypic variation but little genetic differentiation in its introduced range. The mechanisms underpinning the wide range of phenotypic variation and rapid adaptation to novel and changing environments remain uncharacterized. In this study, we examined the epigenetic variation and its correlation with phenotypic variation in plants exposed to natural and manipulated environmental variability. Genome‐wide methylation profiling using methylation‐sensitive amplified fragment length polymorphism (MSAP) revealed considerable DNA methylation polymorphisms within and between natural populations. Plants of different source populations not only underwent significant morphological changes in common garden environments, but also underwent a genome‐wide epigenetic reprogramming in response to different treatments. Methylation alterations associated with response to different water availability were detected in 78.2% (169/216) of common garden induced polymorphic sites, demonstrating the environmental sensitivity and flexibility of the epigenetic regulatory system. These data provide evidence of the correlation between epigenetic reprogramming and the reversible phenotypic response of alligator weed to particular environmental factors.     

Extensive hybridization and past introgression between divergent lineages in a quasi‐clonal hermaphroditic fish: Ramifications for species concepts and taxonomy

Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self‐fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a ‘Central clade’ closely related to K. hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K. marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self‐fertilization for 1–3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K. marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.     

A longitudinal study of epigenetic variation in twins

DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twin-pairs and 45 DZ twin-pairs (total n=182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research.     

TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells

TET1 is a 5-methylcytosine dioxygenase and its DNA demethylating activity has been implicated in pluripotency and reprogramming. However, the precise role of TET1 in DNA methylation regulation outside of developmental reprogramming is still unclear. Here, we show that overexpression of the TET1 catalytic domain but not full length TET1 (TET1-FL) induces massive global DNA demethylation in differentiated cells. Genome-wide mapping reveals that 5-hydroxymethylcytosine production by TET1-FL is inhibited as DNA methylation increases, which can be explained by the preferential binding of TET1-FL to unmethylated CpG islands (CGIs) through its CXXC domain. TET1-FL specifically accumulates 5-hydroxymethylcytosine at the edges of hypomethylated CGIs, while knockdown of endogenous TET1 induces methylation spreading from methylated edges into hypomethylated CGIs. We also found that gene expression changes after TET1-FL overexpression are relatively small and independent of its dioxygenase function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically prevents aberrant methylation spreading into CGIs in differentiated cells.     

DNA methylation and hydroxymethylation in stem cells

In mammals, DNA methylation and hydroxymethylation are specific epigenetic mechanisms that can contribute to the regulation of gene expression and cellular functions. DNA methylation is important for the function of embryonic stem cells and adult stem cells (such as haematopoietic stem cells, neural stem cells and germline stem cells), and changes in DNA methylation patterns are essential for successful nuclear reprogramming. In the past several years, the rediscovery of hydroxymethylation and the TET enzymes expanded our insights tremendously and uncovered more dynamic aspects of cytosine methylation regulation. Here, we review the current knowledge and highlight the most recent advances in DNA methylation and hydroxymethylation in embryonic stem cells, induced pluripotent stem cells and several well‐studied adult stems cells. Our current understanding of stem cell epigenetics and new advances in the field will undoubtedly stimulate further clinical applications of regenerative medicine in the future. Copyright © 2015 John Wiley & Sons, Ltd.     

Variable histone modifications at the Avy metastable epiallele

The ability of environmental factors to shape health and disease involves epigenetic mechanisms that mediate gene-environment interactions. Metastable epiallele genes are variably expressed in genetically identical individuals due to epigenetic modifications established during early development. DNA methylation within metastable epialleles is stochastic due to probabilistic reprogramming of epigenetic marks during embryogenesis. Maternal nutrition and environment have been shown to affect metastable epiallele methylation patterns and subsequent adult phenotype. Little is known, however, about the role of histone modifications in influencing metastable epiallele expression and phenotypic variation. Utilizing chromatin immunoprecipitation followed by qPCR, we observe variable histone patterns in the 5’ long terminal repeat (LTR) of the murine viable yellow agouti (A^vy) metastable epiallele. This region contains 6 CpG sites, which are variably methylated in isogenic A^vy/a offspring. Yellow mice, which are hypomethylated at the Avy LTR and exhibit constitutive ectopic expression of agouti (a), also display enrichment of H3 and H4 di-acetylation (p=0.08 and 0.09, respectively). Pseudoagouti mice, in which A^vy hypermethylation is thought to silence ectopic expression, exhibit enrichment of H4K20 tri-methylation (p=0.01). No differences are observed for H3K4 tri-methylation (p=0.7), a modification often enriched in the promoter of active genes. These results show for the first time the presence of variable histone modifications at a metastable epiallele, indicating that DNA methylation acts in concert with histone modifications to affect inter-individual variation of metastable epiallele expression. Therefore, the potential for environmental factors to influence histone modifications, in addition to DNA methylation, should be addressed in environmental epigenomic studies.     

Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates

Self-fertilization (selfing) favours reproductive success when mate availability is low, but renders populations more vulnerable to environmental change by reducing genetic variability. A mixed-breeding strategy (alternating selfing and outcrossing) may allow species to balance these needs, but requires a system for regulating sexual identity. We explored the role of DNA methylation as a regulatory system for sex-ratio modulation in the mixed-mating fish Kryptolebias marmoratus. We found a significant interaction between sexual identity (male or hermaphrodite), temperature and methylation patterns when two selfing lines were exposed to different temperatures during development. We also identified several genes differentially methylated in males and hermaphrodites that represent candidates for the temperature-mediated sex regulation in K. marmoratus. We conclude that an epigenetic mechanism regulated by temperature modulates sexual identity in this selfing species, providing a potentially widespread mechanism by which environmental change may influence selfing rates. We also suggest that K. marmoratus, with naturally inbred populations, represents a good vertebrate model for epigenetic studies.     

A longitudinal study of epigenetic variation in twins

DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twinpairs and 45 DZ twin-pairs (total n = 182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research.Key words: epigenetics, DNA methylation, twin, heritability, dynamic, environment     

Fighting experience alters brain androgen receptor expression dependent on testosterone status

Contest decisions are influenced by the outcomes of recent fights (winner–loser effects). Steroid hormones and serotonin are closely associated with aggression and therefore probably also play important roles in mediating winner–loser effects. In mangrove rivulus fish, Kryptolebias marmoratus, individuals with higher testosterone (T), 11-ketotestosterone and cortisol levels are more capable of winning, but titres of these hormones do not directly mediate winner–loser effects. In this study, we investigated the effects of winning/losing experiences on brain expression levels of the receptor genes for androgen (AR), oestrogen α/β (ER_α/β), glucocorticoid (GR) and serotonin (5-HT_1AR). The effect of contest experience on AR gene expression depended on T levels: repeated losses decreased, whereas repeated wins increased AR gene expression in individuals with low T but not in individuals with medium or high T levels. These results lend strong support for AR being involved in mediating winner–loser effects, which, in previous studies, were more detectable in individuals with lower T. Furthermore, the expression levels of ER_α/β, 5-HT_1AR and GR genes were higher in individuals that initiated contests against larger opponents than in those that did not. Overall, contest experience, underlying endocrine state and hormone and serotonin receptor expression patterns interacted to modulate contest decisions jointly.     

Variable histone modifications at the Avy metastable epiallele

The ability of environmental factors to shape health and disease involves epigenetic mechanisms that mediate gene-environment interactions. Metastable epiallele genes are variably expressed in genetically identical individuals due to epigenetic modifications established during early development. DNA methylation within metastable epialleles is stochastic due to probabilistic reprogramming of epigenetic marks during embryogenesis. Maternal nutrition and environment have been shown to affect metastable epiallele methylation patterns and subsequent adult phenotype. Little is known, however, about the role of histone modifications in influencing metastable epiallele expression and phenotypic variation. Utilizing chromatin immunoprecipitation followed by qPCR, we observe variable histone patterns in the 5′ long terminal repeat (LTR) of the murine viable yellow agouti (A^vy) metastable epiallele. This region contains 6 CpG sites, which are variably methylated in isogenic A^vy/a offspring. Yellow mice, which are hypomethylated at the A^vy LTR and exhibit constitutive ectopic expression of Agouti (a), also display enrichment of H3 and H4 di-acetylation (p = 0.08 and 0.09, respectively). Pseudoagouti mice, in which A^vy hypermethylation is thought to silence ectopic expression, exhibit enrichment of H4K20 tri-methylation (p = 0.01). No differences are observed for H3K4 tri-methylation (p = 0.7), a modification often enriched in the promoter of active genes. These results show for the first time the presence of variable histone modifications at a metastable epiallele, indicating that DNA methylation acts in concert with histone modifications to affect inter-individual variation of metastable epiallele expression. Therefore, the potential for environmental factors to influence histone modifications, in addition to DNA methylation, should be addressed in environmental epigenomic studies.Key words: epigenetics, metastable epiallele, viable yellow agouti, histone, environmental epigenomics     

Predicting the in-between: Present and future habitat suitability of an intertidal euryhaline fish

New World mangrove trees are foundation species, and their range is predicted to expand northward with climate change. Foundation species are commonly prioritized for conservation, with the goal of preserving the entire community that depends on them. However, no studies have explicitly investigated whether mangrove-dependent species' ranges will track the northward expansion of New World mangrove forests. We use the mangrove rivulus fish, Kryptolebias marmoratus, to investigate shifts in habitat suitability in response to various climate change scenarios (Representative Concentration Pathways 2.6, 4.5, 6.0, and 8.5). Niche models for coastal species focus on traditional climatic variables (e.g., precipitation, temperature) even though coastal habitats also are directly influenced by marine variables (e.g., sea surface salinity). We employ a novel data integration method that combines marine and climatic variables, and that accounts for model selection uncertainty using model averaging to provide robust estimates of habitat suitability. Contrary to expectation, suitability of rivulus habitat is predicted to increase in the south and decrease or remain unchanged in the north across all climate change scenarios. Thus, rivulus might experience range contraction, not expansion. Habitat became more suitable with increased salinity of the saltiest month and precipitation of the driest quarter. In laboratory settings, rivulus have higher survival, reproductive success, and growth rates in low salinities. This discrepancy suggests that some combination of the responses of rivulus and its competitors to environmental change will restrict rivulus to habitats that laboratory experiments consider suboptimal. Our models suggest that focusing conservation decisions on foundation species could overestimate habitat availability and resilience of affiliated communities while simultaneously underestimating species declines and extinction risks.