Satellite DNA (satDNA) is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. To identify repeats associated with (peri)centromeric regions, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. Molecular cytogenetic and bioinformatic analyses revealed that two previously identified satellites, designated here as NkadSat01-77 and NfurSat01-348, are associated with (peri)centromeres only in one lineage of the Southern clade. NfurSat01-348 was, however, additionally detected outside centromeres in three members of the Coastal clade. We also identified a novel satDNA, NrubSat01-48, associated with (peri)centromeres in N. foerschi, N. guentheri, and N. rubripinnis. Our findings revealed fast turnover of satDNA associated with (peri)centromeres and different trends in their evolution in two clades of the genus Nothobranchius.

• Keywords
• Centromere drive, Constitutive heterochromatin, RepeatExplorer, Repetitive sequences, satDNA,
• MeSH
• Centromere genetics   MeSH
• Killifishes * genetics   MeSH
• Fundulidae * genetics   MeSH
• Evolution, Molecular MeSH
• DNA, Satellite MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Satellite MeSH

The karyotype differentiation of the twelve known members of the Nothobranchiusugandensis Wildekamp, 1994 species group is reviewed and the karyotype composition of seven of its species is described herein for the first time using a conventional cytogenetic protocol. Changes in the architecture of eukaryotic genomes often have a major impact on processes underlying reproductive isolation, adaptation and diversification. African annual killifishes of the genus Nothobranchius Peters, 1868 (Teleostei: Nothobranchiidae), which are adapted to an extreme environment of ephemeral wetland pools in African savannahs, feature extensive karyotype evolution in small, isolated populations and thus are suitable models for studying the interplay between karyotype change and species evolution. The present investigation reveals a highly conserved diploid chromosome number (2n = 36) but a variable number of chromosomal arms (46-64) among members of the N.ugandensis species group, implying a significant role of pericentric inversions and/or other types of centromeric shift in the karyotype evolution of the group. When superimposed onto a phylogenetic tree based on molecular analyses of two mitochondrial genes the cytogenetic characteristics did not show any correlation with the phylogenetic relationships within the lineage. While karyotypes of many other Nothobranchius spp. studied to date diversified mainly via chromosome fusions and fissions, the N.ugandensis species group maintains stable 2n and the karyotype differentiation seems to be constrained to intrachromosomal rearrangements. Possible reasons for this difference in the trajectory of karyotype differentiation are discussed. While genetic drift seems to be a major factor in the fixation of chromosome rearrangements in Nothobranchius, future studies are needed to assess the impact of predicted multiple inversions on the genome evolution and species diversification within the N.ugandensis species group.

• Keywords
• 2n uniformity, chromosome evolution, chromosome inversion, chromosomes, cytogenetics, karyotype variability,
• Publication type
• Journal Article MeSH

A vast body of studies is available that describe age-dependent gene expression in relation to aging in a number of different model species. These data were obtained from animals kept in conditions with reduced environmental challenges, abundant food, and deprivation of natural sensory stimulation. Here, we compared wild- and captive aging in the short-lived turquoise killifish (Nothobranchius furzeri). These fish inhabit temporary ponds in the African savannah. When the ponds are flooded, eggs hatch synchronously, enabling a precise timing of their individual and population age. We collected the brains of wild fish of different ages and quantified the global age-dependent regulation of transcripts using RNAseq. A major difference between captive and wild populations is that wild populations had unlimited access to food and hence grew to larger sizes and reached asymptotic size more rapidly, enabling the analysis of age-dependent gene expression without the confounding effect of adult brain growth. We found that the majority of differentially expressed genes show the same direction of regulation in wild and captive populations. However, a number of genes were regulated in opposite direction. Genes downregulated in the wild and upregulated in captivity were enriched for terms related to neuronal communication. Genes upregulated in the wild and downregulated in captive conditions were enriched in terms related to DNA replication. Finally, the rate of age-dependent gene regulation was higher in wild animals, suggesting a phenomenon of accelerated aging.

• Keywords
• Nothobranchius furzeri, RNAseq, brain aging, gene expression, killifish,
• MeSH
• Cyprinodontiformes * genetics   MeSH
• Animals, Wild genetics   MeSH
• Fundulidae * genetics   MeSH
• Brain MeSH
• Aging genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Temporary pools are seasonal wetland habitats with specifically adapted biota, including annual Nothobranchius killifishes that survive habitat desiccation as diapausing eggs encased in dry sediment. To understand the patterns in the structure of Nothobranchius assemblages and their potential in wetland conservation, we compared biodiversity components (alpha, beta, and gamma) between regions and estimated the role and sources of nestedness and turnover on their diversity. We sampled Nothobranchius assemblages from 127 pools across seven local regions in lowland Eastern Tanzania over 2 years, using dip net and seine nets. We estimated species composition and richness for each pool, and beta and gamma diversity for each region. We decomposed beta diversity into nestedness and turnover components. We tested nestedness in three main regions (Ruvu, Rufiji, and Mbezi) using the number of decreasing fills metric and compared the roles of pool area, isolation, and altitude on nestedness. A total of 15 species formed assemblages containing 1-6 species. Most Nothobranchius species were endemic to one or two adjacent regions. Regional diversity was highest in the Ruvu, Rufiji, and Mbezi regions. Nestedness was significant in Ruvu and Rufiji, with shared core (N. melanospilus, N. eggersi, and N. janpapi) and common (N. ocellatus and N. annectens) species, and distinctive rare species. Nestedness apparently resulted from selective colonization rather than selective extinction, and local species richness was negatively associated with altitude. The Nothobranchius assemblages in the Mbezi region were not nested, and had many endemic species and the highest beta diversity driven by species turnover. Overall, we found unexpected local variation in the sources of beta diversity (nestedness and turnover) within the study area. The Mbezi region contained the highest diversity and many endemic species, apparently due to repeated colonizations of the region rather than local diversification. We suggest that annual killifish can serve as a flagship taxon for small wetland conservation.

• Keywords
• Africa, Cyprinodontiformes, dispersal, ephemeral habitats, habitat protection,
• Publication type
• Journal Article MeSH

Embryo-environment interactions are of paramount importance during the development of all organisms, and impacts during this period can echo far into later stages of ontogeny. African annual fish of the genus Nothobranchius live in temporary pools and their eggs survive the dry season in the dry bottom substrate of the pools by entering a facultative developmental arrest termed diapause. Uniquely among animals, the embryos (encased in eggs) may enter diapause at three different developmental stages. Such a system allows for the potential to employ different regulation mechanisms for each diapause. We sampled multiple Nothobranchius embryo banks across the progressing season, species, and populations. We present important baseline field data and examine the role of environmental regulation in the embryonic development of this unique system. We describe the course of embryo development in the wild and find it to be very different from the typical development under laboratory conditions. Development across the embryo banks was synchronized within and across the sampled populations with all embryos entering diapause I during the rainy season and diapause II during the dry season. Asynchrony occurred at transient phases of the habitat, during the process of habitat desiccation, and at the end of the dry season. Our findings reveal the significance of environmental conditions in the serial character of the annual fish diapauses.

• Keywords
• bet‐hedging, dormancy, egg bank, facultative, phenotypic plasticity,
• Publication type
• Journal Article MeSH

The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.

• Keywords
• aging, evolution, evolutionary biology, genetics, genomics, lifespan, nothobranchius furzeri, turquoise killifish,
• MeSH
• Mutation Accumulation * MeSH
• Biological Evolution MeSH
• Longevity genetics   MeSH
• Ecosystem MeSH
• Fundulidae MeSH
• Genome genetics   MeSH
• Population Density * MeSH
• Models, Animal MeSH
• Evolution, Molecular * MeSH
• Aging genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH

Dietary alteration is one of the most universally effective aging interventions, making its standardization a fundamental need for model organisms in aging. In this dietetic study we address the current lack of standardized formulated diet for turquoise killifish Nothobranchius furzeri - a promising model organism. We first demonstrated that N. furzeri can be fully weaned at the onset of puberty onto a commercially available pelleted diet as the sole nutrition when kept in social tanks. We then compared nine somatic and six reproductive parameters between fish fed a typical laboratory diet - frozen chironomid larvae (bloodworms) and fish weaned from bloodworms to BioMar pellets. Both dietary groups had comparable somatic and reproductive performance. There was no difference between diet groups in adult body size, specific growth rate, condition or extent of hepatocellular vacuolation. Fish fed a pelleted diet had higher juvenile body mass and more visceral fat. Pellet-fed males had lower liver mass and possessed a lipid type of hepatocellular vacuolation instead of the prevailing glycogen-like vacuolation in the bloodworm-fed group. No considerable effect was found on reproductive parameters. The negligible differences between dietary groups and good acceptance of pellets indicate their suitability as a useful starting point for the development of standardized diet for Nothobranchius furzeri.

• MeSH
• Animal Husbandry standards   MeSH
• Diet standards   veterinary   MeSH
• Fundulidae physiology   MeSH
• Animal Feed standards   MeSH
• Models, Animal * MeSH
• Body Composition MeSH
• Aging * MeSH
• Animals MeSH
• Check Tag
• Male MeSH
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND: African annual killifishes (Nothobranchius spp.) are adapted to seasonally desiccating habitats (ephemeral pools), surviving dry periods as dormant eggs. Given their peculiar life history, geographic aspects of their diversity uniquely combine patterns typical for freshwater taxa (river basin structure and elevation gradient) and terrestrial animals (rivers acting as major dispersal barriers). However, our current knowledge on fine-scale inter-specific and intra-specific genetic diversity of African annual fish is limited to a single, particularly dry region of their distribution (subtropical Mozambique). Using a widespread annual killifish from coastal Tanzania and Kenya, we tested whether the same pattern of genetic divergence pertains to a wet equatorial region in the centre of Nothobranchius distribution. RESULTS: In populations of Nothobranchius melanospilus species group across its range, we genotyped a part of mitochondrial cytochrome oxidase subunit 1 (COI) gene (83 individuals from 22 populations) and 10 nuclear microsatellite markers (251 individuals from 16 populations). We found five lineages with a clear phylogeographic structure but frequent secondary contact. Mitochondrial lineages were largely congruent with main population genetic clusters identified on microsatellite markers. In the upper Wami basin, populations are isolated as a putative Nothobranchius prognathus, but include also a population from a periphery of the middle Ruvu basin. Other four lineages (including putative Nothobranchius kwalensis) coexisted in secondary contact zones, but possessed clear spatial pattern. Main river channels did not form apparent barriers to dispersal. The most widespread lineage had strong signal of recent population expansion. CONCLUSIONS: We conclude that dispersal of a Nothobranchius species from a wet part of the genus distribution (tropical lowland) is not constrained by main river channels and closely related lineages frequently coexist in secondary contact zones. We also demonstrate contemporary connection between the Ruvu and Rufiji river basins. Our data do not provide genetic support for existence of recently described cryptic species from N. melanospilus complex, but cannot resolve this issue.

• Keywords
• Dispersal, Eastern Africa, Historical demography, River morphology, Temporary pool, mtDNA,
• MeSH
• Killifishes genetics   MeSH
• Ecosystem * MeSH
• Phylogeny MeSH
• Phylogeography MeSH
• Genetic Variation * MeSH
• Genetic Drift MeSH
• Microsatellite Repeats MeSH
• DNA, Mitochondrial genetics   MeSH
• Genetics, Population MeSH
• Rivers MeSH
• Electron Transport Complex IV genetics   MeSH
• Fresh Water MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Tanzania MeSH
• Names of Substances
• DNA, Mitochondrial MeSH
• Electron Transport Complex IV MeSH

The turquoise killifish, Nothobranchius furzeri, is a promising vertebrate model in ageing research and an emerging model organism in genomics, regenerative medicine, developmental biology and ecotoxicology. Its lifestyle is adapted to the ephemeral nature of shallow pools on the African savannah. Its rapid and short active life commences when rains fill the pool: fish hatch, grow rapidly and mature in as few as two weeks, and then reproduce daily until the pool dries out. Its embryos then become inactive, encased in the dry sediment and protected from the harsh environment until the rains return. This invertebrate-like life cycle (short active phase and long developmental arrest) combined with a vertebrate body plan provide the ideal attributes for a laboratory animal.

• Keywords
• Ageing, Natural History, Nothobranchius furzeri, Senescence, The Natural History of Model Organisms, Turquoise killifish, ecology, evolutionary biology,
• MeSH
• Cyprinodontiformes genetics   growth & development   physiology   MeSH
• Diet MeSH
• Ecosystem * MeSH
• Embryo, Nonmammalian physiology   MeSH
• Models, Animal MeSH
• Pigmentation MeSH
• Sexual Behavior, Animal MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

BACKGROUND: Adaptive radiations are triggered by ecological opportunity - the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when 'spatial opportunity' (i.e. areas with suitable 'ancestral' ecological conditions) is available. Traditionally, most research has focused on adaptive radiations, while empirical studies on non-adaptive radiations remain lagging behind. A prolific clade of African fish with extremely short lifespan (Nothobranchius killifish), show the key evolutionary features of a candidate non-adaptive radiation - primarily allopatric species with minimal niche and phenotypic divergence. Here, we test the hypothesis that Nothobranchius killifish have non-adaptively diversified. We employ phylogenetic modelling to investigate the tempo and mode of macroevolutionary diversification of these organisms. RESULTS: Nothobranchius diversification has proceeded with minor niche differentiation and minimal morphological disparity among allopatric species. Additionally, we failed to identify evidence for a role of body size or biogeography in influencing diversification rates. Diversification has been homogeneous within this genus, with the only hotspot of species-richness not resulting from rapid diversification. However, species in sympatry show higher disparity, which may have been caused by character displacement among coexisting species. CONCLUSIONS: Nothobranchius killifish have proliferated following the tempo and mode of a non-adaptive radiation. Our study confirms that this exceptionally short-lived group have diversified with minimal divergent niche adaptation, while one group of coexisting species seems to have facilitated spatial overlap among these taxa via the evolution of ecological character displacement.

• Keywords
• Diversification, Macroevolution, Non-adaptive radiation, Nothobranchius, Spatial opportunity, Speciation,
• MeSH
• Biodiversity * MeSH
• Biological Evolution * MeSH
• Species Specificity MeSH
• Fundulidae physiology   MeSH
• Phylogeny MeSH
• Phylogeography MeSH
• Adaptation, Physiological * MeSH
• Likelihood Functions MeSH
• Body Size MeSH
• Genetic Speciation MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH