Natural hybridization between divergent lineages in a selfing hermaphroditic fish

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.

Additive and non-additive epigenetic signatures of natural hybridisation between fish species with different mating systems

Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.

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.

Genetic Structure of the Mangrove Killifish Kryptolebias hermaphroditus Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations

The Kryptolebias marmoratus species group is composed of the only three vertebrate species that lack females. These species present only males and simultaneously hermaphroditic individuals; that are able to reproduce by allogamy, with males, or by autogamy, performing self-fertilization and generating clones of themselves. The proportion of males is variable among those species and even among their populations. Kryptolebias hermaphroditus has the smallest proportion of males. Indeed, no males have been recorded in most known populations. This is a mainly autogamous species, with small populations having a disjunct distribution along the eastern and northern coast of Brazil. Species presenting such adaptations would be expected to have an elevated rate of genetic population structure, reflecting any barriers that obstruct gene flow between populations. Partial sequences of the mitochondrial cytochrome c oxidase I (COI) gene from 335 individuals were sampled to perform a population analysis. Only a single haplotype of COI, widely distributed throughout all the sampled populations, was recovered for K. hermaphroditus. Here we hypothesize that the high degree of communication within populations is probably the main biological feature leading to this pattern.

Filling the gaps: phylogeography of the self-fertilizing Kryptolebias species (Cyprinodontiformes: Rivulidae) along South American mangroves

Mangrove killifishes of the genus Kryptolebias have been historically classified as rare because of their small size and cryptic nature. Major gaps in distribution knowledge across mangrove areas, particularly in South America, challenge the understanding of the taxonomic status, biogeographical patterns and genetic structuring of the lineages composing the self-fertilizing "Kryptolebias marmoratus species complex." In this study, the authors combined a literature survey, fieldwork and molecular data to fill major gaps of information about the distribution of mangrove killifishes across western Atlantic mangroves. They found that selfing mangrove killifishes are ubiquitously distributed across the Caribbean, Central and South American mangroves and report 14 new locations in South America, extending the range of both the "Central clade" and "Southern clade" lineages which overlap in the Amazon. Although substantial genetic differences were found between clades, the authors also found further genetic structuring within clades, with populations in Central America, north and northeast Brazil generally showing higher levels of genetic diversity compared to the clonal ones in southeast Brazil. The authors discuss the taxonomic status and update the geographical distribution of the Central and Southern clades, as well as potential dispersal routes and biogeographical barriers influencing the distribution of the selfing mangrove killifishes in the western Atlantic mangroves.

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.

Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin

The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.