Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation‐related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi‐complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time‐calibrated species tree based on whole‐genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre‐to‐periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination density and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chromosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between nonphysically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, differences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spectacular cichlid diversity observed today.     

Variation of anal fin egg‐spots along an environmental gradient in a haplochromine cichlid fish

Male secondary sexual traits are targets of inter‐ and/or intrasexual selection, but can vary due to a correlation with life‐history traits or as by‐product of adaptation to distinct environments. Trade‐offs contributing to this variation may comprise conspicuousness toward conspecifics versus inconspicuousness toward predators, or between allocating resources into coloration versus the immune system. Here, we examine variation in expression of a carotenoid‐based visual signal, anal‐fin egg‐spots, along a replicate environmental gradient in the haplochromine cichlid fish Astatotilapia burtoni. We quantified egg‐spot number, area, and coloration; applied visual models to estimate the trait's conspicuousness when perceived against the surrounding tissue under natural conditions; and used the lymphocyte ratio as a measure for immune activity. We find that (1) males possess larger and more conspicuous egg‐spots than females, which is likely explained by their function in sexual selection; (2) riverine fish generally feature fewer but larger and/or more intensely colored egg‐spots, which is probably to maintain signal efficiency in intraspecific interactions in long wavelength shifted riverine light conditions; and (3) egg‐spot number and relative area correlate with immune defense, suggesting a trade‐off in the allocation of carotenoids. Taken together, haplochromine egg‐spots feature the potential to adapt to the respective underwater light environment, and are traded off with investment into the immune system.     

Mouth dimorphism in scale‐eating cichlid fish from Lake Tanganyika advances individual fitness

Random asymmetry, that is the coexistence of left‐ and right‐sided (or ‐handed) individuals within a population, is a particular case of natural variation; what triggers and maintains such dimorphisms remains unknown in most cases. Here, we report a field‐based cage experiment in the scale‐eating Tanganyikan cichlid Perissodus microlepis, which occurs in two morphs in nature: left‐skewed and right‐skewed individuals with respect to mouth orientation. Using underwater cages stocked with scale‐eaters and natural prey fish, we first confirm that, under semi‐natural conditions, left‐skewed scale‐eaters preferentially attack the right flank of their prey, whereas right‐skewed individuals feed predominantly from the left side. We then demonstrate that scale‐eaters have a higher probability for successful attacks when kept in dimorphic experimental populations (left‐ and right‐skewed morphs together) as compared to monomorphic populations (left‐ or right‐skewed morphs), most likely because prey fishes fail to accustom to strikes from both sides. The significantly increased probability for attacks appears to be the selective agent responsible for the evolution and maintenance of mouth dimorphism in P. microlepis, lending further support to the hypothesis that negative frequency‐dependent selection is the stabilizing force balancing the mouth dimorphism at quasi‐equal ratios in scale‐eating cichlids.     

Evidence for divergent natural selection of a Lake Tanganyika cichlid inferred from repeated radiations in body size

Divergent natural selection is thought to play a vital role in speciation, but clear, measurable examples from nature are still few. Among the many possible sources of divergent natural selection, predation pressure may be important because predators are ubiquitous in food webs. Here, we show evidence for divergent natural selection in a Lake Tanganyika cichlid, Telmatochromis temporalis , which uses burrows under stones or empty snail shells as shelters. This species contains normal and dwarf morphs at several localities. The normal morph inhabits rocky shorelines, whereas the dwarf morph invariably inhabits shell beds, where empty snail shells densely cover the lake bottom. Genetic evidence suggested that the dwarf morph evolved independently from the normal morph at two areas, and morphological analysis and evaluation of habitat structure revealed that the body sizes of morphs closely matched the available shelter sizes in their habitats. These findings suggest that the two morphs repeatedly evolved through divergent natural selection associated with the strategy for sheltering from predators.     

Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche‐based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche‐based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche‐based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche‐based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche‐based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche‐based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche‐based or neutral‐based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.     

Neolamprologus cancellatus, a new cichlid fish from Lake Tanganyika, Africa

Neolamprologus cancellatus, a new cichlid species, is described on the basis of eight specimens from the Zambian coast of Lake Tanganyika. The new species is characterized by a subtruncate caudal fin and a body that is slender (depth 22.3–25.2% in standard length) and easily distinguishable from its congeners by having 7–8 anal fin spines, 34–37 scales in longitudinal line, 33 total vertebrae, and a gridlike body pattern on a pale brownish body color. This species is only known to inhabit the shallow (2–7 m depth), rocky bottom of Wonzye Point in the southern part of the lake.     

Developmental effects of visual environment on species‐assortative mating preferences in Lake Victoria cichlid fish

Local adaptation can be a potent force in speciation, with environmental heterogeneity leading to niche specialization and population divergence. However, local adaption often requires nonrandom mating to generate reproductive isolation. Population divergence in sensory properties can be particularly consequential in speciation, affecting both ecological adaptation and sexual communication. Pundamilia pundamila and Pundamilia nyererei are two closely related African cichlid species that differ in male coloration, blue vs. red. They co‐occur at rocky islands in southern Lake Victoria, but inhabit different depth ranges with different light environments. The species differ in colour vision properties, and females exert species‐specific preferences for blue vs. red males. Here, we investigated the mechanistic link between colour vision and preference, which could provide a rapid route to reproductive isolation. We tested the behavioural components of this link by experimentally manipulating colour perception – we raised both species and their hybrids under light conditions mimicking shallow and deep habitats – and tested female preference for blue and red males under both conditions. We found that rearing light significantly affected female preference: shallow‐reared females responded more strongly to P. pundamilia males and deep‐reared females favoured P. nyererei males – implying that visual development causally affects mate choice. These results are consistent with sensory drive predictions, suggesting that the visual environment is key to behavioural isolation of these species. However, the observed plasticity could also make the species barrier vulnerable to environmental change: species‐assortative preferences were weaker in females that were reared in the other species’ light condition.     

Description of alternative male reproductive tactics in a shell-brooding cichlid, Telmatochromis vittatus, in Lake Tanganyika

Telmatochromis vittatus (Cichlidae) is a Tanganyikan substrate brooder which spawns in the gastropod-shell nests of a cichlid, Lamprologus callipterus. We describe male reproductive tactics of T. vittatus in and around the shell nests, where males of various sizes were found. Based on utilization patterns of the shell nests, interactions among males, and spawning behaviors, males could be categorized into four types based on reproductive tactics and in order of body size: sneaker males, satellite males, territorial males and piracy males. Size range of males in tactic groups rarely overlapped. Territorial males defended shell nests harboring multiple females, but during pair-spawning they were occasionally taken over by large piracy males that visited several nests repeatedly. Small sneaker males darted to pair-spawning territorial males and might ejaculate sperm. Satellite males did not perform parasitic spawning but pair-spawned in a single shell outside the nests. Spawning of satellite males was infrequently parasitized. The largest gonado-somatic index (GSI) was found in sneaker males followed by piracy males, territorial males and satellite males, suggesting that gonadal investment of males using the four tactics may be consistent with intensity or risk of sperm competition.     

Distinct population structure in a phenotypically homogeneous rock-dwelling cichlid fish from Lake Tanganyika

Several lineages of cichlid fishes in the East African Great Lakes display stunning levels of morphological diversification. The rapid evolution of rock-dwelling polygynous mouthbrooders in Lake Malawi, for example, was in part ascribed to their allopatric distribution on disjunct stretches of rocky coast, where even short habitat discontinuities reduce gene flow effectively. However, as seen in other cichlids, ecological barriers do not always prevent gene flow, whereas genetic structure can develop along continuous habitat, and morphological diversification does not necessarily accompany genetic differentiation. The present study investigates the population structure of Variabilichromis moorii, a monogamous substrate-brooding lamprologine of rocky coasts in Lake Tanganyika, which occurs over about 1000 km of shoreline almost without phenotypic variation. Phylogeographic analyses of mitochondrial DNA sequences indicated that dispersal is infrequent and generally occurs between adjacent locations only. Exceptions to this pattern are closely related haplotypes from certain locations on opposite lakeshores, a phenomenon which has been observed in other species and is thought to reflect lake crossing along an underwater ridge in times of low water level. Genetic population differentiation, estimated from mitochondrial DNA and microsatellite data in six adjacent populations, was equally high across localities separated by sandy shores and along uninterrupted stretches of rocky shore. Our results suggest that ecological barriers are not required to induce philopatric behavior in Variabilichromis, and that morphological stasis persists in the face of high levels of neutral genetic differentiation.     

Polygynandry inPseudotropheus zebra, a cichlid fish from Lake Malawi

Synopsis Parental care in the Malawian cichlid fishPseudotropheus zebra BB is extensive and exclusively maternal; males contribute only genetic material. The costs of searching for multiple mates (in this case risk of predation on orally incubated eggs) suggested that females should be monandrous; microsatellite genetypes of seven brooding females and their young, however, reveal extensive multiple paternity in this species, with a mean of 3.8 paternal individuals per brood. Polygynandry inP. zebra is probably not maintained by selection for genetically diverse offspring; potential explanations include avoidance of inbreeding, and bet-hedging on other male characteristics that females are unable to evaluate when selecting a mate. The observed degree of multiple paternity strongly suggests that females are free to choose mates as they will, a prerequisite of many theories positing sexual selection as a key element in Malawi chichlid evolution. It should also result in elevation of effective population sizes, and thus be antagonistic to runaway evolution of male secondary sexual characteristics, but not necessarily to other modes of sexual selection.     

Geometric morphometrics applied to viscerocranial bones in three populations of the Lake Tanganyika cichlid fish Tropheus moorii

Lake Tanganyika comprises the oldest and most diverse species flock of cichlid fishes. Many species are subdivided into numerous populations, often classified as geographical races, colour morphs or sister species. Unlike younger species flocks, in which speciation is accompanied by eco-morphological diversification that of Lake Tanganyika is at a mature stage with little further morphological change, most probably caused by stabilizing selection. This study addresses body shape differences among three genetically distinct but morphologically similar populations of Tropheus  moorii , by focusing on bony structures of the cichlid head. We test by means of geometric morphological methods whether shape changes in the cichlid head are based on particular osteological differences. Specimens were disarticulated enzymatically, and standardized digital images of the disarticulated bony elements were taken. A landmark system was established for the dentary, articular, premaxilla, quadrate and the preopercle. Only the dentary shows significant differentiation among the three populations. Since all three populations live in similar cobble habitats and occupy the same trophic niche, the observed difference in the shape of the dentary can either be explained by different directional selection due to subtle habitat differences, or by neutral drift constrained by borders enforced through stabilizing selection. Lack of difference might indicate stabilizing selection on bone shape.     

Function of nuchal humps of a cichlid fish from Lake Tanganyika: inferences from morphological data

Nuchal humps occur in various fish groups, but their functions are rarely studied. Both sexes of Cyphotilapia gibberosa, a cichlid fish endemic to Lake Tanganyika, possess nuchal humps. This study morphologically analysed the humps of this species to assess the primary factors responsible for hump development. Semi-landmarks showed that the size of male humps positively correlated with body condition, and thicknesses of hypodermises implied that the humps were larger in males than in females. These facts suggest that sexual selection on male humps is intense. Semi-landmarks showed that the humps were less prominent in females than in males, and that the transformation of nuchal humps with growth (becoming more prominent) ceased at medium body size in females. These facts suggest that sex recognition likely plays a role in the evolution of the uniform humps of large females, because, according to this hypothesis, a morphologically moderate hump may be favoured. If male humps also function as a sex recognition trait, the transformation of nuchal humps is expected to cease at a certain body size, as did female humps. However, the male humps became continuously more prominent from the smallest to the largest individuals examined. The body size at which hump transformation stops or at which extreme hump shape interferes with sex recognition may be outside of the size range of the present samples. A prominent nuchal hump may also function as a species recognition trait, because sympatric cichlid species do not develop nuchal humps as prominent as this species. In short, the present morphological analyses do not contradict the hypotheses that C. gibberosa individuals recognise conspecifics and their sex from the shapes of the nuchal humps, and that females prefer males with larger humps.     

Microdontochromis rotundiventralis, a new cichlid fish (perciformes: Cichlidae) from Lake Tanganyika

Microdontochromis rotundiventralis, a new species of cichlid fish, is described on the basis of 13 specimens from Nkumbula Island, Lake Tanganyika (Zambia). It is distinct from its only congener,M. tenuidentatus, in having two (rarely one) rows of teeth on both jaws, a rounded distal margin on the pelvic fin, the outermost pelvic fin soft ray length 1.23–1.43 times the innermost ray, a deeper body (depth 26.8–29.1% standard length) and the anal fin with 9 (rarely 8 or 10) soft rays.     

Global population structure and adaptive evolution of aflatoxin‐producing fungi

Aflatoxins produced by several species in Aspergillus section Flavi are a significant problem in agriculture and a continuous threat to human health. To provide insights into the biology and global population structure of species in section Flavi, a total of 1,304 isolates were sampled across six species (A. flavus, A. parasiticus, A. nomius, A. caelatus, A. tamarii, and A. alliaceus) from single fields in major peanut‐growing regions in Georgia (USA), Australia, Argentina, India, and Benin (Africa). We inferred maximum‐likelihood phylogenies for six loci, both combined and separately, including two aflatoxin cluster regions (aflM/alfN and aflW/aflX) and four noncluster regions (amdS, trpC, mfs and MAT), to examine population structure and history. We also employed principal component and STRUCTURE analysis to identify genetic clusters and their associations with six different categories (geography, species, precipitation, temperature, aflatoxin chemotype profile, and mating type). Overall, seven distinct genetic clusters were inferred, some of which were more strongly structured by G chemotype diversity than geography. Populations of A. flavus S in Benin were genetically distinct from all other section Flavi species for the loci examined, which suggests genetic isolation. Evidence of trans‐speciation within two noncluster regions, whereby A. flavus S_BG strains from Australia share haplotypes with either A. flavus or A. parasiticus, was observed. Finally, while clay soil and precipitation may influence species richness in Aspergillus section Flavi, other region‐specific environmental and genetic parameters must also be considered.     

Colour-assortative mating among populations of Tropheus moorii, a cichlid fish from Lake Tanganyika, East Africa

The species flocks of cichlid fishes in the East African Lakes Tanganyika, Malawi and Victoria are prime examples of adaptive radiation and explosive speciation. Several hundreds of endemic species have evolved in each of the lakes over the past several thousands to a few millions years. Sexual selection via colour-assortative mating has often been proposed as a probable causal factor for initiating and maintaining reproductive isolation. Here, we report the consequences of human-mediated admixis among differentially coloured populations of the endemic cichlid fish Tropheus moorii from several localities that have accidentally been put in sympatry in a small harbour bay in the very south of Lake Tanganyika. We analysed the phenotypes (coloration) and genotypes (mitochondrial control region and five microsatellite loci) of almost 500 individuals, sampled over 3 consecutive years. Maximum-likelihood-based parenthood analyses and Bayesian inference of population structure revealed that significantly more juveniles are the product of within-colour-morph matings than could be expected under the assumption of random mating. Our results clearly indicate a marked degree of assortative mating with respect to the different colour morphs. Therefore, we postulate that sexual selection based on social interactions and female mate choice has played an important role in the formation and maintenance of the different colour morphs in Tropheus, and is probably common in other maternally mouthbrooding cichlids as well.     

Repeated evolution of local adaptation in swimming performance: population‐level trade‐offs between burst and endurance swimming in Brachyrhaphis freshwater fish

Specialization is fundamentally important in biology because specialized traits allow species to expand into new environments, in turn promoting population differentiation and speciation. Specialization often results in trade‐offs between traits that maximize fitness in one environment but not others. Despite the ubiquity of trade‐offs, we know relatively little about how consistently trade‐offs evolve between populations when multiple sets of populations experience similarly divergent selective regimes. In the present study, we report a case study on Brachyrhaphis fishes from different predation environments. We evaluate apparent within/between population trade‐offs in burst‐speed and endurance at two levels of evolutionary diversification: high‐ and low‐predation populations of Brachyrhaphis rhabdophora, and sister species Brachyrhaphis roseni and Brachyrhaphis terrabensis, which occur in high‐ and low‐predation environments, respectively. Populations of Brachyrhaphis experiencing different predation regimes consistently evolved swimming specializations indicative of a trade‐off between two swimming forms that are likely highly adaptive in the environment in which they occur. We show that populations have become similarly locally adapted at both levels of diversification, suggesting that swimming specialization has evolved rather rapidly and persisted post‐speciation. Our findings provide valuable insight into how local adaptation evolves at different stages of evolutionary divergence.     

Repeated parallel evolution of parental care strategies within Xenotilapia, a genus of cichlid fishes from Lake Tanganyika

The factors promoting the evolution of parental care strategies have been extensively studied in experiment and theory. However, most attempts to examine parental care in an evolutionary context have evaluated broad taxonomic categories. The explosive and recent diversifications of East African cichlid fishes offer exceptional opportunities to study the evolution of various life history traits based on species-level phylogenies. The Xenotilapia lineage within the endemic Lake Tanganyika cichlid tribe Ectodini comprises species that display either biparental or maternal only brood care and hence offers a unique opportunity to study the evolution of distinct parental care strategies in a phylogenetic framework. In order to reconstruct the evolutionary relationships among 16 species of this lineage we scored 2,478 Amplified Fragment Length Polymorphisms (AFLPs) across the genome. We find that the Ectodini genus Enantiopus is embedded within the genus Xenotilapia and that during 2.5 to 3 million years of evolution within the Xenotilapia clade there have been 3-5 transitions from maternal only to biparental care. While most previous models suggest that uniparental care (maternal or paternal) arose from biparental care, we conclude from our species-level analysis that the evolution of parental care strategies is not only remarkably fast, but much more labile than previously expected.     

Patterns of molecular evolution in dioecious and non‐dioecious Silene

Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from a high probability of extinction in dioecious species because of less efficient dispersal and the costs of sexual selection, which are expected to harm dioecious species' survival on the long term. These handicaps should decrease the effective population size () of dioecious species, which in turn should reduce the efficacy of selection. Moreover, sexual selection in dioecious species is expected to specifically affect some genes, which will evolve under positive selection. The relative contribution of these effects is currently unknown and we tried to disentangle them by comparing sequence evolution between dioecious and non‐dioecious species in the Silene genus (Caryophyllaceae), where dioecy has evolved at least twice. For the dioecious species in the section Melandrium, where dioecy is the oldest, we found a global reduction of purifying selection, while on some, male‐biased genes, positive selection was found. For section Otites, where dioecy evolved more recently, we found no significant differences between dioecious and non‐dioecious species. Our results are consistent with the view that dioecy is an evolutionary dead end in flowering plants, although other scenarios for explaining reduced cannot be ruled out. Our results also show that contrasting forces act on the genomes of dioecious plants, and suggest that some time is required before the genome of such plants bears the footprints of dioecy.