The strange case of East African annual fishes: aridification correlates with diversification for a savannah aquatic group?

Phenotypic plasticity in tropical butterflies is linked to climatic seasonality on a macroevolutionary scale

Phenotypic plasticity can be adaptive in fluctuating environments by providing rapid environment-phenotype matching and this applies particularly in seasonal environments. African Bicyclus butterflies have repeatedly colonized seasonal savannahs from ancestral forests around the late Miocene, and many species now exhibit seasonal polyphenism. On a macroevolutionary scale, it can be expected that savannah species will exhibit higher plasticity because of experiencing stronger environmental seasonality than forest species. We quantified seasonality using environmental niche modeling and surveyed the degree of plasticity in a key wing pattern element (eyespot size) using museum specimens. We showed that species occurring in highly seasonal environments display strong plasticity, while species in less seasonal or aseasonal environments exhibit surprisingly variable degrees of plasticity, including strong to no plasticity. Furthermore, eyespot size plasticity has a moderate phylogenetic signal and the ancestral Bicyclus likely exhibited some degree of plasticity. We propose hypotheses to explain the range of plasticity patterns seen in less seasonal environments and generate testable predictions for the evolution of plasticity in Bicyclus. Our study provides one of the most compelling cases showing links between seasonality and phenotypic plasticity on a macroevolutionary scale and the potential role of plasticity in facilitating the colonization of novel environments.

Ecological character displacement among Nothobranchius annual killifishes in Tanzania

Divergent ecological character displacement (ECD) is the competition-driven divergence in resource use-related phenotypic traits between coexisting species. It is considered one of the primary drivers of ecological diversification and adaptive radiation. We analyzed phenotypic and ecological variation in 2 African annual killifish species of the genus Nothobranchius: N. eggersi and N. melanospilus in sympatry and N. melanospilus in allopatry. Our aim was to test whether allopatric and sympatric populations of N. melanospilus differ morphologically from each other and from N. eggersi and examine whether these differences are consistent with the predictions of ECD. We find that sympatric N. melanospilus differ from allopatric N. melanospilus and differ from N. eggersi more strongly than the latter. Our data satisfy four criteria for demonstrating ECD: Differences in phenotypes between allopatric and sympatric N. melanospilus are greater than expected by chance; the divergence pattern between allopatric and sympatric N. melanospilus results from an evolutionary shift rather than from ecological sorting; morphological differences observed reflect differences in resource use; and, lastly, sites of allopatry and sympatry do not differ in food resource availability or other ecological conditions. Our results suggest that competition is the main driver of the observed divergence between two N. melanospilus populations.

Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs

Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.

Conserved satellite DNA motif and lack of interstitial telomeric sites in highly rearranged African Nothobranchius killifish karyotypes

Using African annual killifishes of the genus Nothobranchius from temporary savannah pools with rapid karyotype and sex chromosome evolution, we analysed the chromosomal distribution of telomeric (TTAGGG)n repeat and Nfu-SatC satellite DNA (satDNA; isolated from Nothobranchius furzeri) in 15 species across the Nothobranchius killifish phylogeny, and with Fundulosoma thierryi as an out-group. Our fluorescence in situ hybridization experiments revealed that all analysed taxa share the presence of Nfu-SatC repeat but with diverse organization and distribution on chromosomes. Nfu-SatC landscape was similar in conspecific populations of Nothobranchius guentheri and Nothobranchius melanospilus but slightly-to-moderately differed between populations of Nothobranchius pienaari, and between closely related Nothobranchius kuhntae and Nothobranchius orthonotus. Inter-individual variability in Nfu-SatC patterns was found in N. orthonotus and Nothobranchius krysanovi. We revealed mostly no sex-linked patterns of studied repetitive DNA distribution. Only in Nothobranchius brieni, possessing multiple sex chromosomes, Nfu-SatC repeat occupied a substantial portion of the neo-Y chromosome, similarly as formerly found in the XY sex chromosome system of turquoise killifish N. furzeri and its sister species Nothobranchius kadleci-representatives not closely related to N. brieni. All studied species further shared patterns of expected telomeric repeats at the ends of all chromosomes and no additional interstitial telomeric sites. In summary, we revealed (i) the presence of conserved satDNA class in Nothobranchius clades (a rare pattern among ray-finned fishes); (ii) independent trajectories of Nothobranchius sex chromosome differentiation, with recurrent and convergent accumulation of Nfu-SatC on the Y chromosome in some species; and (iii) genus-wide shared tendency to loss of telomeric repeats during interchromosomal rearrangements. Collectively, our findings advance our understanding of genome structure, mechanisms of karyotype reshuffling, and sex chromosome differentiation in Nothobranchius killifishes from the genus-wide perspective.

Fast satellite DNA evolution in Nothobranchius annual killifishes

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.

Karyotype differentiation in the Nothobranchiusugandensis species group (Teleostei, Cyprinodontiformes), seasonal fishes from the east African inland plateau, in the context of phylogeny and biogeography

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.

Multifaceted Nothobranchius

Annual killifish of the genus Nothobranchius are seeing a rapid increase in scientific interest over the years. A variety of aspects surrounding the egg-laying Cyprinodontiformes is being extensively studied, including their aging. Inhabiting drying water bodies of Africa rarely allows survival through more than one rainy season for the Nothobranchius populations. Therefore, there is no lifespan-related bias in natural selection, which has ultimately led to the decreased efficiency of DNA repair system. Aging of the Nothobranchius species is studied both under normal conditions and under the influence of potential geroprotectors, as well as genetic modifications. Most biogerontological studies are conducted using the species Nothobranchius furzeri (GRZ isolate), which has a lifespan of 3 to 7 months. However, the list of model species of Nothobranchius is considerably wider, and the range of advanced research areas with their participation extends far beyond gerontology. This review summarizes the most interesting and promising topics developing in the studies of the fish of Nothobranchius genus. Both classical studies related to lifespan control and rather new ones are discussed, including mechanisms of diapause, challenges of systematics and phylogeny, evolution of sex determination mechanisms, changes in chromosome count, occurrence of multiple repeated DNA sequences in the genome, cognitive and behavioral features and social stratification, as well as methodological difficulties in working with Nothobranchius.

The relative effects of pace of life-history and habitat characteristics on the evolution of sexual ornaments: A comparative assessment

Selection may favor greater investment into sexual ornaments when opportunities for future reproduction are limited, for example, under high adult mortality. However, predation, a key driver of mortality, typically selects against elaborate sexual ornaments. Here, we examine the evolution of sexual ornaments in killifishes, which have marked contrasts in life-history strategy among species and inhabit environments that differ in accessibility to aquatic predators. We first assessed if the size of sexual ornaments (unpaired fins) influenced swimming performance. Second, we investigated whether the evolution of larger ornamental fins is driven primarily by the pace of life-history (investment into current vs. future reproduction) or habitat type (a proxy for predation risk). We found that larger fins negatively affected swimming performance. Further, males from species inhabiting ephemeral habitats, with lower predation risk, had larger fins and greater sexual dimorphism in fin size, compared to males from more accessible permanent habitats. We show that enlarged ornamental fins, which impair locomotion, evolve more frequently in environments that are less accessible to predators, without clear associations to life-history strategy. Our results provide a rare link between the evolution of sexual ornaments, effects on locomotion performance, and natural selection on ornament size potentially through habitat differences in predation risk.

Biogeography Meets Niche Modeling: Inferring the Role of Deep Time Climate Change When Data Is Limited

Geographic range shifts are one major organism response to climate change, especially if the rate of climate change is higher than that of species adaptation. Ecological niche models (ENM) and biogeographic inferences are often used in estimating the effects of climatic oscillations on species range dynamics. ENMs can be used to track climatic suitable areas over time, but have often been limited to shallow timescales; biogeographic inference can reach greater evolutionary depth, but often lacks spatial resolution. Here, we present a simple approach that treats them as independent and complementary sources of evidence, which, when used in partnership, can be employed to reconstruct geographic range shifts over deep evolutionary timescales. For testing this, we chose two extreme African disjunctions: Camptoloma (Scrophulariaceae) and Canarina (Campanulaceae), each comprising of three species disjunctly distributed in Macaronesia and eastern/southern Africa. Using inferred ancestral ranges in tandem with preindustrial and paleoclimate ENM hindcastings, we show that the disjunct pattern was the result of fragmentation and extinction events linked to Neogene aridification cycles. Our results highlight the importance of considering temporal resolution when building ENMs for rare endemics with small population sizes and restricted climatic tolerances such as Camptoloma, for which models built on averaged monthly variables were more informative than those based on annual bioclimatic variables. Additionally, we show that biogeographic information can be used as truncation threshold criteria for building ENMs in the distant past. Our approach is suitable when there is sparse sampling on species occurrences and associated patterns of genetic variation, such as in the case of ancient endemics with widely disjunct distributions as a result of climate change.

Fast life-histories are associated with larger brain size in killifishes

The high energetic demands associated with the vertebrate brain are proposed to result in a trade-off between the pace of life-history and relative brain size. However, because both life-history and brain size also have a strong relationship with body size, any associations between the pace of life-history and relative brain size may be confounded by coevolution with body size. Studies on systems where contrasts in the pace of life-history occur without concordant contrasts in body size could therefore add to our understanding of the potential coevolution between relative brain size and life-history. Using one such system - 21 species of killifish - we employed a common garden design across two ontogenetic stages to investigate the association between relative brain size and the pace of life-history. Contrary to predictions, we found that relative brain size was larger in adult fast-living killifishes, compared to slow-living species. Although we found no differences in relative brain size between juvenile killifishes. Our results suggest that fast- and slow-living killifishes do not exhibit the predicted trade-off between brain size and life-history. Instead, fast and slow-living killifishes could differ in the ontogenetic timing of somatic versus neural growth or inhabit environments that differ considerably in cognitive demands.

Age-Dependent Regulation of Notch Family Members in the Neuronal Stem Cell Niches of the Short-Lived Killifish Nothobranchius furzeri

Background: The annual killifish Nothobranchius furzeri is a new experimental model organism in biology, since it represents the vertebrate species with the shortest captive life span and also shows the fastest maturation and senescence recorded in the laboratory. Here, we use this model to investigate the age-dependent decay of neurogenesis in the telencephalon (brain region sharing the same embryonic origin with the mammalian adult niches), focusing on the expression of the Notch pathway genes.

Results: We observed that the major ligands/receptors of the pathway showed a negative correlation with age, indicating age-dependent downregulation of the Notch pathway. Moreover, expression of notch1a was clearly limited to active neurogenic niches and declined during aging, without changing its regional patterning. Expression of notch3 is not visibly influenced by aging.

Conclusion: Both expression pattern and regulation differ between notch1a and notch3, with the former being limited to mitotically active regions and reduced by aging and the latter being present in all cells with a neurogenic potential, regardless of the level of their actual mitotic activity, and so is less influenced by age. This finally suggests a possible differential role of the two receptors in the regulation of the niche proliferative potential throughout the entire fish life.

Nothobranchius annual killifishes

Annual fishes of the genus Nothobranchius inhabit ephemeral habitats in Eastern and Southeastern Africa. Their life cycle is characterized by very rapid maturation, a posthatch lifespan of a few weeks to months and embryonic diapause to survive the dry season. The species N. furzeri holds the record of the fastest-maturing vertebrate and of the vertebrate with the shortest captive lifespan and is emerging as model organism in biomedical research, evolutionary biology, and developmental biology. Extensive characterization of age-related phenotypes in the laboratory and of ecology, distribution, and demography in the wild are available. Species/populations from habitats differing in precipitation intensity show parallel evolution of lifespan and age-related traits that conform to the classical theories on aging. Genome sequencing and the establishment of CRISPR/Cas9 techniques made this species particularly attractive to investigate the effects genetic and non-genetic intervention on lifespan and aging-related phenotypes. At the same time, annual fishes are a very interesting subject for comparative approaches, including genomics, transcriptomics, and proteomics. The N. furzeri community is highly diverse and rapidly expanding and organizes a biannual meeting.

Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes)

This paper reports a phylogeny of the African killifishes (Genus Nothobranchius, Order Cyprinodontiformes) informed by five genetic markers (three nuclear, two mitochondrial) of 80 taxa (seven undescribed and 73 of the 92 recognized species). These short-lived annual fishes occupy seasonally wet habitats in central and eastern Africa, and their distribution coincides largely with the East African Rift System (EARS). The fossil dates of sister clades used to constrain a chronometric tree of all sampled Nothobranchius recovered the origin of the genus at ~13.27 Mya. It was followed by the radiations of six principal clades through the Neogene. An ancestral area estimation tested competing biogeographical hypotheses to constrain the ancestral origin of the genus to the Nilo-Sudan Ecoregion, which seeded a mid-Miocene dispersal event into the Coastal ecoregion, followed closely (~10 Mya) by dispersals southward across the Mozambique coastal plain into the Limpopo Ecoregion. Extending westwards across the Tanzanian plateau, a pulse of radiations through the Pliocene were associated with dispersals and fragmentation of wetlands across the Kalahari and Uganda Ecoregions. We interpret this congruence of drainage rearrangements with dispersals and cladogenic events of Nothobranchius to reflect congruent responses to recurrent uplift and rifting. The coevolution of these freshwater fishes and wetlands is attributed to ultimate control by tectonics, as the EARS extended southwards during the Neogene. Geobiological consilience of the combined evidence supports a tectonic hypothesis for the evolution of Nothobranchius.

Calcified gill filaments increase respiratory function in fishes

The morphology of fish gills is closely linked to aerobic capacity and tolerance of environmental stressors such as hypoxia. The importance of gill surface area is well studied, but little is known about how the mechanical properties of gill tissues determine function. In some fishes, the bases of the gill filaments are surrounded by a calcified 'sheath' of unknown function. We tested two non-exclusive hypotheses: (i) calcified gill filaments enhance water flow through the gill basket, improving aquatic respiratory function, and (ii) in amphibious fishes, calcification provides support for gills out of water. In a survey of more than 100 species of killifishes and related orders, we found filament calcification was widespread and thus probably arose before the evolution of amphibious lifestyles in killifishes. Calcification also did not differ between amphibious and fully aquatic species, but terrestrial acclimation caused calcium deposition on the filaments of the killifish Kryptolebias marmoratus, suggesting a possible structural role when out of water. We found strong evidence supporting a role for filament calcification in enhancing aquatic respiratory function. First, acclimation to increased respiratory demands (hypoxia, elevated temperatures) induced calcium deposition on the filaments of K. marmoratus. Next, gentle removal of filament calcification decreased branchial resistance to water flow, indicating disruption of gill basket positioning. Thus, the mechanical properties of the gill filaments appear to play an important and previously unappreciated role in determining fish respiratory function.

Genetic diversity of a widespread annual killifish from coastal Tanzania

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.

Rapid growth and large body size in annual fish populations are compromised by density-dependent regulation

We tested the effect of population density on maximum body size in three sympatric species of annual killifishes Nothobranchius spp. from African ephemeral pools. We found a clear negative effect of population density on body size, limiting their capacity for extremely fast development and rapid growth. This suggests that density-dependent population regulation and the ephemeral character of their habitat impose contrasting selective pressures on the life history of annual killifishes.

Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes

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.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1344-0) contains supplementary material, which is available to authorized users.

Limited differentiation of fundamental thermal niches within the killifish assemblage from shallow temporary waters

The coexistence of ectothermic species is enabled among other factors by the differentiation of their thermal niches. While this phenomenon is well described from deep temperate lakes, it is unclear whether the same pattern applies to temporary pools. In this study, we examined fundamental thermal niches in three coexisting annual killifish species Nothobranchius furzeri, N. orthonotus and N. pienaari from temporary pools in southern Mozambique. We hypothesized that the disparate thermal requirements of the three congeneric species are a candidate niche component that facilitates their local coexistence. We estimated species' thermal requirements as preferred body temperatures (T_pref) in a horizontal thermal gradient. Under thermal gradient conditions, sympatric killifish maintained their body temperatures within similar T_pref ranges despite some variation in mean T_pref. The daily variation in water temperature in their native habitats enables killifish to thermoregulate at least for part of the diurnal cycle. We conclude that the coexistence of African annual killifish species is possible without the differentiation of their fundamental thermal niches.

Dispersion/reaggregation in early development of annual killifishes: Phylogenetic distribution and evolutionary significance of a unique feature

Annual killifishes are members of the Aplocheiloidea and live in ephemeral habitats that desiccate regularly during the dry season and refill during the rainy season. Populations of these fishes survive the dry season by producing drought-resistant diapausing eggs that are buried in the substrate. When the pool refills during the rainy season the juveniles hatch, grow rapidly and reproduce until the pool desiccates again during the next dry season. The association with such unpredictable habitats has led to the evolution to a variety of developmental adaptations such as a dispersed/reaggregation phase of the deep blastomeres, three possible diapause stages, extreme tolerance to high salinity and anoxia, an efficient DNA repair system and an extremely short life span. Here, we review the course of the dispersed/reaggregation phase, its evolution and phylogenetic distribution and diversity within the Aplocheiloidea. The phenomenon of blastomere dispersion/reaggregation in these fishes was first described in the 1960s and 70s. Blastomeres of most teleost fishes segregate into three groups that give rise to the enveloping cell layer, the yolk syncytial layer and the deep blastomeres that will form the embryo itself. When epiboly commences, the deep blastomeres form a more or less coherent cell sheet with a so called embryonic shield at it marginal zone marking the area where gastrulation takes place. In annual killifishes, the deep blastomeres segregate when epiboly starts and disperse when epiboly commences. After epiboly has been completed, the deep blastomeres are randomly distributed and migrate all over the enveloping cell layer. After several days they start to reaggregate and form the actual embryo that starts gastrulation. The evolutionary origin and mechanism behind this peculiar developmental pathway have puzzled developmental biologists for almost 50 years. However, several of these annual killifishes (Nothobranchius furzeri, Austrofundulus limnaeus, Austrolebias charrua and Austrolebias bellottii) have become model organisms in studies on developmental physiology, aging and stress tolerance. This has led to the establishment of modern genetic techniques such as transgenesis and cell fate mapping that are now used to tackle questions about the origin and mechanisms behind the dispersal/reaggregation phase.

Extensive karyotype variability of African fish genus Nothobranchius (Cyprinodontiformes)

Karyotypes of 65 species of the genus Nothobranchius Peters, 1868 were reviewed and of those 35 examined first time. The results of present study have shown that fishes of the genus Nothobranchius possessed highly diverse karyotypes. The diploid chromosome number (2n) ranged from 16 to 50. The most frequent 2n was 2n = 36 (in 35 species) while the second one 2n = 38 (in 13 species). Proportion of biarmed chromosomes varied from 0 to 95% between species. Diploid chromosome number variability apparently exists as a result of chromosomal fusions or fissions and extensive karyotypic formula alterations promoting by inversions. Multiple sex chromosomes of system X₁X₁X₂X₂/X₁X₂Y type were found only in karyotypes of 5 species. The extensive karyotype variability, unusual for teleosts, of genus Nothobranchius can be likely associated with the characteristics of its life cycle and inhabiting under unstable environment of East African savannah temporal pools.

The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso- and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation-resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso- and hypersaline habitats.

A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri

BACKGROUND

The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression.

RESULTS

Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri, as compared to other teleosts, was a duplication of the miR-29 cluster.

CONCLUSION

The completeness of the catalogue we provide is comparable to that of the zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.

Molecular phylogeny and timing of diversification in South American Cynolebiini seasonal killifishes

The rich biological diversity of South America has motivated a series of studies associating evolution of endemic taxa with the dramatic geologic and climatic changes that occurred during the Cainozoic. The organism here studied is the killifish tribe Cynolebiini, a group of seasonal fishes uniquely inhabiting temporary pools formed during the rainy seasons. The Cynolebiini are found in open vegetation areas inserted in the main tropical and subtropical South American phytogeographical regions east of the Andes. Here, we present the first molecular phylogeny sampling all the eight genera of the Cynolebiini, using fragments of two mitochondrial and four nuclear genes for 35 species of Cynolebiini plus 19 species as outgroups. The dataset, 4448bp, was analysed under Bayesian and maximum likelihood approaches, providing a relatively well solved tree, which retrieves high support values for the Cynolebiini and most included clades. The resulting tree was used to estimate the time of divergence in included lineages using two cyprinodontiform fossils to calibrate the tree. We further investigated historical biogeography through the likelihood-based DEC model. Our estimates indicate that divergence between the clades comprising New World and Old World aplocheiloids occurred during the Eocene, about 50Mya, much more recent than the Gondwanan fragmentation scenario assumed in previous studies. This estimation is nearly synchronous to estimated splits involving other South American and African vertebrate clades, which have been explained by transoceanic dispersal through an ancient Atlantic island chain during the Palaeogene. We estimate that Cynolebiini split from its sister group Cynopoecilini in the Oligocene, about 25Mya and that Cynolebiini started to diversify giving origin to the present genera during the Miocene, about 20-14Mya. The Cynolebiini had an ancestral origin in the Atlantic Forest and probably were not present in the open vegetation formations of central and northeastern South America until the Middle Miocene, when expansion of dry open vegetation was favoured by cool temperatures and strike seasonality. Initial splitting between the genera Cynolebias and Simpsonichthys during the Miocene (about 14Mya) is attributed to the uplift of the Central Brazilian Plateau.

Microanatomical diversification of the zona pellucida in aplochelioid killifishes

This study investigates zona pellucida (ZP) ultrastructure in fertilized eggs of annual killifishes (suborder Aplocheiloidei), a group of highly specialized fishes that are able to survive desiccation for several weeks to months before they hatch. Little is known about ZP or chorionic ultrastructure sustaining these life-history modes, so scanning electron microscopy (SEM) was used to describe this trait in a large number of aplocheiloids with a focus on the family Rivulidae and the genus Hypsolebias. New images of ZP ultrastructure for 52 aplocheiloid species are provided, more than doubling the number characterized thus far. The evolution of chorionic structure within this group is studied using these new data. Characters were coded into a morphological matrix and optimized onto a consensus phylogeny to assess phylogenetic signal and reconstruct ancestral character states. Although ZP characters seem highly homoplastic and exhibit a large amount of structural convergence among lineages, aplocheiloid killifishes have evolved a number of unique structures associated with the chorion. Some annual species seem to have lost long filaments because eggs are deposited in the soil instead of being adhered to aquatic plants.

A global community effort to decipher the unique biology of annual killifish

Over the past 50 years, annual killifishes arose as alternative model organisms for studies of vertebrate biology. The annual fish offers exceptional advantages for studies of genetics, genomics, developmental biology, population dynamics, ecology, biogeography, and evolution. They inhabit extremely variable freshwater environments in Africa and South America, have a short lifespan and a set of unique and fascinating developmental characteristics. Embryos survive within the dry substrate during the dry season, whereas the adult population dies. Thus, the survival of the populations is entirely dependent on the buried embryos that hatch the next rainy season. Although Old and New World species share similarities in their life cycle, they also have different adaptive responses associated with climate-related selective pressures. Therefore, contrasting different species from these areas is essential to understand unique adaptations to heterogeneous environment. A network of laboratories (United States, Czech Republic, Italy, Brazil, Chile, and Uruguay) is working and collaborating on many aspects of the biology of annual fishes. Participating researchers share projects and cross-training undergraduate and graduate students. These efforts resulted in two International Symposia (2010 and 2015) that took place in Montevideo and an international book. Herein, we summarize the progress made by this global community of scientists. Developmental Dynamics 246:807-811, 2017. © 2017 Wiley Periodicals, Inc.

Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes

The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single‐gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short‐lived) and nonannual (i.e., longer‐lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long‐lived mammals such as bats and mole‐rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.

Community assembly in Nothobranchius annual fishes: Nested patterns, environmental niche and biogeographic history

The assembly of local communities from regional species pools is shaped by historical aspects of distribution, environmental conditions, and biotic interactions. We studied local community assembly patterns in African annual killifishes of the genus Nothobranchius (Cyprinodontiformes), investigating data from 168 communities across the entire range of regionally co-existing species. Nothobranchius are small fishes associated with annually desiccating pools. We detected a nested pattern of local communities in one region (Southern Mozambique, with Nothobranchius furzeri as the core and dominant species), but no nestedness was found in the second region (Central Mozambique, with Nothobranchius orthonotus being the dominant species). A checkerboard pattern of local Nothobranchius community assembly was demonstrated in both regions. Multivariate environmental niche modeling revealed moderate differences in environmental niche occupancy between three monophyletic clades that largely co-occurred geographically and greater differences between strictly allopatric species within the clades. Most variation among species was observed along an altitudinal gradient; N. furzeri and Nothobranchius kadleci were absent from coastal plains, Nothobranchius pienaari, Nothobranchius rachovii, and Nothobranchius krysanovi were associated with lower altitude and N. orthonotus was intermediate and geographically most widespread species. We discuss implications for ecological and evolutionary research in this taxon.

Aquatic insects in a multistress environment: cross-tolerance to salinity and desiccation

Exposing organims to a particular stressor may enhance tolerance to a subsequent stress, when protective mechanisms against both stressors are shared. Such cross-tolerance is a common adaptive response in dynamic multivariate environments and often indicates potential co-evolution of stress traits. Many aquatic insects in inland saline waters from Mediterranean-climate regions are sequentially challenged with salinity and desiccation stress. Thus, cross-tolerance to these physiologically similar stressors could have been positively selected in insects of these regions. We used adults of the saline water beetles Enochrus jesusarribasi (Hydrophilidae) and Nebrioporus baeticus (Dytiscidae) to test cross-tolerance responses to desiccation and salinity. In independent laboratory experiments, we evaluated the effects of i) salinity stress on the subsequent resistance to desiccation and ii) desiccation stress (rapid and slow dehydration) on the subsequent tolerance to salinity. Survival, water loss and haemolymph osmolality were measured. Exposure to stressful salinity improved water control under subsequent desiccation stress in both species, with a clear cross-tolerance (enhanced performance) in N. baeticus. In contrast, general negative effects on performance were found under the inverse stress sequence. The rapid and slow dehydration produced different water loss and haemolymph osmolality dynamics that were reflected in different survival patterns. Our finding of cross-tolerance to salinity and desiccation in ecologically similar species from distant lineages, together with parallel responses between salinity and thermal stress previously found in several aquatic taxa, highlights the central role of adaption to salinity and co-occurring stressors in arid inland waters, having important implications for the species' persistence under climate change.

Divergent karyotypes of the annual killifish genus Nothobranchius (Cyprinodontiformes, Nothobranchiidae)

Karyotypes of two species of the African annual killifish genus Nothobranchius Peters, 1868, Nothobranchius brieni Poll, 1938 and Nothobranchius sp. from Kasenga (D.R. Congo) are described. Both species displayed diploid chromosome number 2n = 49/50 for males and females respectively with multiple-sex chromosome system type X₁X₂Y/X₁X₁X₂X₂. The karyotypes of studied species are considerably different from those previously reported for the genus Nothobranchius and similar to the Actinopterygii conservative karyotype.

Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish

The killifish Nothobranchius furzeri is the shortest-lived vertebrate that can be bred in the laboratory. Its rapid growth, early sexual maturation, fast aging, and arrested embryonic development (diapause) make it an attractive model organism in biomedical research. Here, we report a draft sequence of its genome that allowed us to uncover an intra-species Y chromosome polymorphism representing-in real time-different stages of sex chromosome formation that display features of early mammalian XY evolution "in action." Our data suggest that gdf6Y, encoding a TGF-β family growth factor, is the master sex-determining gene in N. furzeri. Moreover, we observed genomic clustering of aging-related genes, identified genes under positive selection, and revealed significant similarities of gene expression profiles between diapause and aging, particularly for genes controlling cell cycle and translation. The annotated genome sequence is provided as an online resource (http://www.nothobranchius.info/NFINgb).

Otoliths of five extant species of the annual killifish Nothobranchius from the East African savannah

This study presents, for the first time, a comprehensive dataset that documents the range of inter- and intraspecific otolith variation in aplocheiloid killifish, based on a total of 86 individuals representing five extant species of Nothobranchius PETERS, 1868, from East Africa: the sympatric pairs N. rubripinnis SEEGERS, 1986 and N. ruudwildekampi COSTA, 2009 (Eastern Tanzania), and N. orthonotus (PETERS, 1844) and N. furzeri JUBB, 1971 (Southern Mozambique), and two isolated populations of N. korthausae MEINKEN, 1973 (Eastern Tanzania). Otolith characters were analysed based on SEM images, and otolith morphometry was conducted using uni- and multivariate statistics. Two ancient clades of probably Early to Middle Miocene age in eastern Tanzania and southern Mozambique can be recognized based on otolith morphologies, which is consistent with previous work based on molecular data. The distinctive sulcus morphologies in the otoliths of sympatric species may be linked to species-specific hearing capabilities, perhaps constituting a case of character displacement in an area of secondary sympatry. The otoliths of the studied species of Nothobranchius are diagnostic at the species level, even in the case of closely related species diagnosable otherwise only by minor differences in coloration. The two populations of N. korthausae also displayed some differences in their otolith characters. The new data may facilitate future recognition of fossil species of Nothobranchius. As no fossil remains of extant aplocheiloid killifishes have yet been described, the discovery of fossil otoliths of Nothobranchius would significantly advance understanding of the evolutionary history of this interesting group of fishes.