Factors affecting egg production in the selfing mangrove rivulus (Kryptolebias marmoratus)

Detection of relatedness in chemical alarm cues by a selfing vertebrate depends on population and the life stage producing the alarm cue

Aquatic prey have impressive abilities to extract information from a variety of chemical cues. For example, they can use the alarm cues released by wounded individuals during a predator attack to learn about predation risk, and they can also distinguish kin from non-kin individuals during interactions. However, it remains unclear whether animals can combine this information on predation risk with kin recognition of the particular individuals under threat. To examine how the relatedness of the individuals in alarm cue affects behaviour we used the self-fertilizing hermaphroditic mangrove rivulus (Kryptolebias marmoratus), in which lineages produce genetically identical offspring through selfing. We explored this in two populations that differ in their level of outcrossing. We measured activity before and after exposure to alarm cue made from individuals (either adults or embryos) from their own lineage or an unrelated lineage from the same population. Fish responded weakly to embryo alarm cues, but tended to reduce their activity more when the alarm cues were from an unrelated lineage compared to alarm cues from their own lineage, particularly in fish from the outcrossing population. In contrast, there was no effect of cue relatedness on the response to adult alarm cues but there was a strong population effect. Specifically, individuals from the outcrossing population tended to react more strongly to alarm cues compared to individuals from the predominantly selfing population. We discuss the potential roles of the major histocompatibility complex in cue detection, differences between adult vs embryo alarm cues in terms of concentration and information, and underlying differences among populations and genetic lineages in their production and detection of chemical cues. Whether this kin recognition offers adaptive benefits or is simply a consequence of being able to detect relatedness in living individuals would be an exciting area for future research.

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.

Age-dependent genetic variation in aggression

Understanding the extent to which behavioural variance is underlain by genotypic, environmental and genotype-by-environment effects is important for predicting how behavioural traits might respond to selection and evolve. How behaviour varies both within and among individuals can change across ontogeny, leading to differences in the relative contribution of genetic and environmental effects to phenotypic variation across ages. We investigated among-individual and among-genotype variation in aggression across ontogeny by measuring, twice as juveniles and twice as adults, both approaches and attacks against a three-dimensional-printed model opponent in eight individuals from each of eight genotypes (N = 64). Aggression was only significantly repeatable and heritabile in juveniles. Additionally, how aggression changed between juvenile and adult life-history stages varied significantly among individuals and genotypes. These results suggest that juvenile aggression is likely to evolve more rapidly via natural selection than adult aggression and that the trajectory of behavioural change across the lifespan has the potential to evolve. Determining when genetic variation explains (or does not explain) behavioural variation can further our understanding of key life-history stages during which selection might drive the strongest or swiftest evolutionary response.

Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias

Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on the evolutionary relationships within the killifish genus Kryptolebias. In addition, we tested for evidence of past introgression in the genus given the multiple reports of undergoing hybridization between its members. Our mtDNA phylogeny generally agreed with the relationships previously proposed for the genus. However, our reconstruction based on nuclear DNA revealed an unknown lineage - Kryptolebias sp. 'ESP' - as the sister group of the self-fertilizing mangrove killifishes, K. marmoratus and K. hermaphroditus. All individuals sequenced of Kryptolebias sp. 'ESP' had the same mtDNA haplotype commonly observed in K. hermaphroditus, demonstrating a clear case of mito-nuclear discordance. Our analysis further confirmed extensive history of introgression between Kryptolebias sp. 'ESP' and K. hermaphroditus. Population genomics analyses indicate no current gene flow between the two lineages, despite their current sympatry and history of introgression. We also confirmed introgression between other species pairs in the genus that have been recently reported to form hybrid zones. Overall, our study provides a phylogenomic reconstruction covering most of the Kryptolebias species, reveals a new lineage hidden in a case of mito-nuclear discordance, and provides evidence of multiple events of ancestral introgression in the genus. These findings underscore the importance of investigating different genomic information in a phylogenetic framework, particularly in taxa where introgression is common as in the sexually diverse mangrove killifishes.

Against the Odds: Hybrid Zones between Mangrove Killifish Species with Different Mating Systems

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization between two mangrove killifish species with different mating systems, Kryptolebias ocellatus (obligately outcrossing) and K. hermaphroditus (predominantly self-fertilizing) in two hybrid zones in southeast Brazil. Hybridization rates were relatively high (~20%), representing the first example of natural hybridization between species with different mating systems in vertebrates. All F1 individuals were sired by the selfing species. Backcrossing was small, but mostly asymmetrical with the SI parental species, suggesting pattern commonly observed in plant hybrid zones with different mating systems. Our findings shed light on how contrasting mating systems may affect the direction and extent of gene flow between sympatric species, ultimately affecting the evolution and maintenance of hybrid zones.

Choice consequences: salinity preferences and hatchling survival in the mangrove rivulus (Kryptolebias marmoratus)

In heterogeneous environments, mobile species should occupy habitats in which their fitness is maximized. Mangrove rivulus fish inhabit mangrove ecosystems where salinities range from 0 to 65 ppt, but are most often collected from areas with salinities of ∼25 ppt. We examined the salinity preference of mangrove rivulus in a lateral salinity gradient, in the absence of predators and competitors. Fish could swim freely for 8 h throughout the gradient with chambers containing salinities ranging from 5 to 45 ppt (or 25 ppt throughout in the control). We defined preference as the salinity in which the fish spent most of their time, and also measured preference strength, latency to begin exploring the arena, and number of transitions between chambers. To determine whether these traits were repeatable, each fish experienced three trials. Mangrove rivulus spent a greater proportion of time in salinities lower (5-15 ppt) than they occupy in the wild. Significant among-individual variation in the (multivariate) behavioral phenotype emerged when animals experienced the gradient, indicating strong potential for selection to drive behavioral evolution in areas with diverse salinity microhabitats. We also showed that mangrove rivulus had a significantly greater probability of laying eggs in low salinities compared with control or high salinities. Eggs laid in lower salinities also had higher hatching success compared with those laid in higher salinities. Thus, although mangrove rivulus can tolerate a wide range of salinities, they prefer low salinities. These results raise questions about factors that prevent mangrove rivulus from occupying lower salinities in the wild, whether higher salinities impose energetic costs, and whether fitness changes as a function of salinity.

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate

The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.

Ontogeny of the morphology-performance axis in an amphibious fish (Kryptolebias marmoratus)

Establishing links between morphology and performance is important for understanding the functional, ecological, and evolutionary implications of morphological diversity. Relationships between morphology and performance are expected to be age dependent if, at different points during ontogeny, animals must perform in different capacities to achieve high fitness returns. Few studies have examined how the relationship between form and function changes across ontogeny. Here, we assess this relationship in the amphibious mangrove rivulus (Kryptolebias marmoratus) fish, a species that is both capable of and reliant on "tail-flip jumping" for terrestrial locomotion. Tail-flip jumping entails an individual transferring its weight to the caudal region of the body, launching itself from the substrate to navigate to new aquatic or semi-aquatic habitats. By combining repeated trials of jumping performance in 237 individuals from distinct age classes with a clearing and staining procedure to visualize bones in the caudal region, we test the hypotheses that as age increases (i) average jumping performance (body lengths jumped) will increase, (ii) the amount of variation for each trait will change, and (iii) the patterns of covariation/correlation among traits, which tell us about the integration of form with function, will also change. We find a significant increase in size-adjusted jumping performance with age, and modification to the correlation structure among traits across ontogeny. However, we also find that significant links between form and function evident in young animals disappear at later ontogenetic stages. Our study suggests that different functional mechanisms may be associated with high performance at different stages of development.