Fish embryos on land: terrestrial embryo deposition lowers oxygen uptake without altering growth or survival in the amphibious fish Kryptolebias marmoratus

Genetic tools for the study of the mangrove killifish, Kryptolebias marmoratus, an emerging vertebrate model for phenotypic plasticity

Kryptolebias marmoratus (Kmar), a teleost fish of the order Cyprinodontiformes, has a suite of unique phenotypes and behaviors not observed in other fishes. Many of these phenotypes are discrete and highly plastic-varying over time within an individual, and in some cases reversible. Kmar and its interfertile sister species, K. hermaphroditus, are the only known self-fertile vertebrates. This unusual sexual mode has the potential to provide unique insights into the regulation of vertebrate sexual development, and also lends itself to genetics. Kmar is easily adapted to the lab and requires little maintenance. However, its internal fertilization and small clutch size limits its experimental use. To support Kmar as a genetic model, we compared alternative husbandry techniques to maximize recovery of early cleavage-stage embryos. We find that frequent egg collection enhances yield, and that protease treatment promotes the greatest hatching success. We completed a forward mutagenesis screen and recovered several mutant lines that serve as important tools for genetics in this model. Several will serve as useful viable recessive markers for marking crosses. Importantly, the mutant kissylips lays embryos at twice the rate of wild-type. Combining frequent egg collection with the kissylips mutant background allows for a substantial enhancement of early embryo yield. These improvements were sufficient to allow experimental analysis of early development and the successful mono- and bi-allelic targeted knockout of an endogenous tyrosinase gene with CRISPR/Cas9 nucleases. Collectively, these tools will facilitate modern developmental genetics in this fascinating fish, leading to future insights into the regulation of plasticity.

Out to sea: ocean currents and patterns of asymmetric gene flow in an intertidal fish species

Passive dispersal via wind or ocean currents can drive asymmetric gene flow, which influences patterns of genetic variation and the capacity of populations to evolve in response to environmental change. The mangrove rivulus fish (Kryptolebias marmoratus), hereafter "rivulus," is an intertidal fish species restricted to the highly fragmented New World mangrove forests of Central America, the Caribbean, the Bahamas, and Florida. Mangrove patches are biological islands with dramatic differences in both abiotic and biotic conditions compared to adjacent habitat. Over 1,000 individual rivulus across 17 populations throughout its range were genotyped at 32 highly polymorphic microsatellites. Range-wide population genetic structure was evaluated with five complementary approaches that found eight distinct population clusters. However, an analysis of molecular variance indicated significant population genetic structure among regions, populations within regions, sampling locations within populations, and individuals within sampling locations, indicating that rivulus has both broad- and fine-scale genetic differentiation. Integrating range-wide genetic data with biophysical modeling based on 10 years of ocean current data showed that ocean currents and the distance between populations over water drive gene flow patterns on broad scales. Directional migration estimates suggested some significant asymmetries in gene flow that also were mediated by ocean currents and distance. Specifically, populations in the center of the range (Florida Keys) were identified as sinks that received migrants (and alleles) from other populations but failed to export individuals. These populations thus harbor genetic variation, perhaps even from extirpated populations across the range, but ocean currents and complex arrangements of landmasses might prevent the distribution of that genetic variation elsewhere. Hence, the inherent asymmetry of ocean currents shown to impact both genetic differentiation and directional migration rates may be responsible for the complex distribution of genetic variation across the range and observed patterns of metapopulation structure.

Air exposure moderates ocean acidification effects during embryonic development of intertidally spawning fish

Ocean acidification can negatively impact the early life-stages of marine fish, due to energetic costs incurred by the maintenance of acid–base homeostasis, leaving less energy available for growth and development. The embryos of intertidally spawning fishes, such as Pacific herring, are often air exposed for hours. We hypothesized that air exposure would be beneficial to the developing embryo due to a higher oxygen availability (and thus reduced metabolic costs to secure adequate oxygen) and permitting excess CO₂ associated with ocean acidification to be off-gassed during emersion. To investigate this, we reared Pacific herring (Clupea pallasii) embryos under three tidal regimes (subtidal: fully immersed, low intertidal: 2 × 2 h air exposure, and high intertidal: 5 + 9 h air exposure) fully crossed with three aquatic CO₂ levels (400, 1500 and 3200 µatm) at a water temperature of 9.5 °C and naturally fluctuating air temperature during air exposure. We measured the effects on embryonic development and hatch, as well as carry-over effects on larval development and survival. Air exposure during embryonic development had significant positive effects on growth, condition and survival in larval Pacific herring, with some interactive effects with CO₂. Interestingly, CO₂ by itself in the fully immersed treatment had no effect, but had significant interactions with air exposure. Our research suggests that air exposure during low tide can be highly beneficial to intertidally spawning fishes and needs to be taken into account in climate change studies and modeling.

The development of the O2-sensing system in an amphibious fish: consequences of variation in environmental O2 levels

Proper development of the O₂-sensing system is essential for survival. Here, we characterized the development of the O₂-sensing system in the mangrove rivulus (Kryptolebias marmoratus), an amphibious fish that transitions between hypoxic aquatic environments and O₂-rich terrestrial environments. We found that NECs formed in the gills and skin of K. marmoratus during embryonic development and that both NEC populations are retained from the embryonic stage to adulthood. We also found that the hyperventilatory response to acute hypoxia was present in embryonic K. marmoratus, indicating that functional O₂-sensing pathways are formed during embryonic development. We then exposed embryos to aquatic normoxia, aquatic hyperoxia, aquatic hypoxia, or terrestrial conditions for the first 30 days of embryonic development and tested the hypothesis that environmental O₂ availability during embryonic development modulates the development of the O₂-sensing system in amphibious fishes. Surprisingly, we found that O₂ availability during embryonic development had little impact on the density and morphology of NECs in the gills and skin of K. marmoratus. Collectively, our results demonstrate that, unlike the only other species of fish in which NEC development has been studied to date (i.e., zebrafish), NEC development in K. marmoratus is largely unaffected by environmental O₂ levels during the embryonic stage, indicating that there is interspecies variation in O₂-induced plasticity in the O₂-sensing system of fishes.

No water, no problem: stage-specific metabolic responses to dehydration stress in annual killifish embryos

Annual killifish survive in temporary ponds by producing drought-tolerant embryos that can enter metabolic dormancy (diapause). Survival of dehydration stress is achieved through severe reduction of evaporative water loss. We assessed dehydration stress tolerance in diapausing and developing Austrofundulus limnaeus embryos. We measured oxygen consumption rates under aquatic and aerial conditions to test the hypothesis that there is a trade-off between water retention and oxygen permeability. Diapausing embryos survive dehydrating conditions for over 1.5 years, and post-diapause stages can survive for over 100 days. Diapausing embryos respond to dehydration stress by increasing oxygen consumption rates while post-diapause embryos exhibit the same or reduced rates compared with aquatic embryos. Thus, water retention does not always limit oxygen diffusion. Aerial incubation coupled with hypoxia causes some embryos to arrest development. The observed stage-specific responses are consistent with an intrinsic bet-hedging strategy in embryos that would increase developmental variation in a potentially adaptive manner.

Fluctuating environments during early development can limit adult phenotypic flexibility: insights from an amphibious fish

The interaction between developmental plasticity and the capacity for reversible acclimation (phenotypic flexibility) is poorly understood, particularly in organisms exposed to fluctuating environments. We used an amphibious killifish (Kryptolebias marmoratus) to test the hypotheses that organisms reared in fluctuating environments (i) will make no developmental changes to suit any one environment because fixing traits to suit one environment could be maladaptive for another, and (ii) will be highly phenotypically flexible as adults because their early life experiences predict high environmental variability in the future. We reared fish under constant (water) or fluctuating (water-air) environments until adulthood and assessed a suite of traits along the oxygen cascade (e.g. neuroepithelial cell density and size, cutaneous capillarity, gill morphology, ventricle size, red muscle morphometrics, terrestrial locomotor performance). To evaluate the capacity for phenotypic flexibility, a subset of adult fish from each rearing condition was then air-exposed for 14 days before the same traits were measured. In support of the developmental plasticity hypothesis, traits involved with O2 sensing and uptake were largely unaffected by water-air fluctuations during early life, but we found marked developmental changes in traits related to O2 transport, utilization and locomotor performance. In contrast, we found no evidence supporting the phenotypic flexibility hypothesis. Adult fish from both rearing conditions exhibited the same degree of phenotypic flexibility in various O2 sensing- and uptake-related traits. In other cases, water-air fluctuations attenuated adult phenotypic flexibility despite the fact that phenotypic flexibility is hypothesized to be favoured when environments fluctuate. Overall, we conclude that exposure to environmental fluctuations during development in K. marmoratus can dramatically alter the constitutive adult phenotype, as well as diminish the scope for phenotypic flexibility in later life.

Patterns of Fish Reproduction at the Interface between Air and Water

Although fishes by nature are aquatic, many species reproduce in such a way that their embryos are exposed to air either occasionally or constantly during incubation. We examine the ecological context and review specific examples of reproduction by fishes at the air-water interface, including fishes that do and do not breathe air. Four modes of reproduction at the air-water interface are described across 18 teleost orders, from fresh water, estuaries, and sea water. Mode 1, the most common type of reproduction by fishes at the air-water interface, includes 21 families of mostly marine teleosts that spawn in water onto a substrate surface, on vegetation, or into hollow objects such as shells that will later be continuously or occasionally exposed to air. Although the eggs are emerged into air, many of these species do not emerge into air as adults, and only about half of them breathe air. Mode 2 involves six families of freshwater fishes setting up and guarding a nest and guarding on the water surface, either with bubbles or in vegetation. Most of these species breathe air. In Mode 3, annual killifishes in at least two families in seasonally dry habitats bury eggs in mud in temporary pools, then die before the next generation emerges. These species neither guard nests nor breathe air. Mudskippers (Gobiidae) breathe air and use Mode 4, excavating burrows in a soft substrate and then storing air in a subterranean chamber. In a variation of Mode 4, eggs are placed on bubbles within a nesting burrow by swamp eels (Synbranchidae). No fishes from basal taxa are known to place their embryos where they will be exposed to air, although most of these species breathe air as adults. The widespread but still rare, diverse forms of fish reproduction at the air-water interface across a broad taxonomic spectrum suggest repeated independent evolutionary events and strong selection pressure for adult fishes to protect their embryos from hypoxic waters, aquatic predators, pathogens, and UV radiation. Air-breathing by adult fishes appears to be de-coupled from air exposure of developing embryos or aerial emersion of adults during spawning.

Prolonged survival out of water is linked to a slow pace of life in a selfing amphibious fish

Metabolic rate and life history traits vary widely both among and within species reflecting trade-offs in energy allocation, but the proximate and ultimate causes of variation are not well understood. We tested the hypothesis that these trade-offs are mediated by environmental heterogeneity, using isogenic strains of the amphibious fish Kryptolebias marmoratus that vary in the amount of time each can survive out of water. Consistent with pace of life theory, the strain that survived air exposure the longest generally exhibited a “slow” phenotype including the lowest metabolic rate, largest scope for metabolic depression, slowest consumption of energy stores, and least investment in reproduction under standard conditions. Growth rates were fastest in the otherwise “slow” strain, however. We then tested for fitness trade-offs between “fast” and “slow” strains using microcosms where fish were held with either constant water availability or under fluctuating conditions where water was absent for half of the experiment. Under both conditions the “slow” strain grew larger and was in better condition, and under fluctuating conditions the “slow” strain produced more embryos. However, the “fast” strain had larger adult population sizes under both conditions, indicating that fecundity is not the sole determinant of population size in this species. We conclude that genetically based differences in pace of life of amphibious fish determine survival duration out of water. Relatively “slow” fish tended to perform better under conditions of limited water availability, but there was no detectable cost under control conditions. Thus, pace of life differences may reflect a conditionally neutral instead of antagonistic trade-off.

Amphibious fishes: evolution and phenotypic plasticity

Amphibious fishes spend part of their life in terrestrial habitats. The ability to tolerate life on land has evolved independently many times, with more than 200 extant species of amphibious fishes spanning 17 orders now reported. Many adaptations for life out of water have been described in the literature, and adaptive phenotypic plasticity may play an equally important role in promoting favourable matches between the terrestrial habitat and behavioural, physiological, biochemical and morphological characteristics. Amphibious fishes living at the interface of two very different environments must respond to issues relating to buoyancy/gravity, hydration/desiccation, low/high O2 availability, low/high CO2 accumulation and high/low NH3 solubility each time they traverse the air-water interface. Here, we review the literature for examples of plastic traits associated with the response to each of these challenges. Because there is evidence that phenotypic plasticity can facilitate the evolution of fixed traits in general, we summarize the types of investigations needed to more fully determine whether plasticity in extant amphibious fishes can provide indications of the strategies used during the evolution of terrestriality in tetrapods.

The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments

The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology.