Genomic evidence of reproductive isolation among the Semisulcospira snails radiated in the ancient Lake Biwa

Determining species boundaries within rapidly evolving species flocks is essential to understanding their evolutionary history but is often difficult to achieve due to the lack of clear diagnostic features. Ancient Lake Biwa harbours endemic snails in the genus Semisulcospira, a species flock with 19 described species. However, their morphological and genetic similarity cast doubt on the validity of their species status and their histories of explosive speciation. To evaluate their species boundaries, we examine patterns of gene flow among the sympatric or parapatric nominal Semisulcospira species in Lake Biwa. The principal component analysis and Bayesian structure analysis based on the genome-wide genotyping dataset demonstrated no gene flow between five pairs of the Semisulcospira species. However, we found the hybrids between the closely related species pair, Semisulcospira decipiens and S. rugosa. Despite the presence of hybrids, these nominal species still formed their own genetic clusters. There are variations in the chromosome numbers among these species, potentially providing an intrinsic barrier to panmictic gene flow. Our study showed complete or partial reproductive isolation among the sympatric or parapatric Semisulcospira species, demonstrating that the Semisulcospira snails are real species assemblages radiated in Lake Biwa. Our study provides significant implications for establishing species boundaries among rapidly evolving freshwater species in ancient lakes.

Ecology and the evolution of sex chromosomes

Sex chromosomes are common features of animal genomes, often carrying a sex determination gene responsible for initiating the development of sexually dimorphic traits. The specific chromosome that serves as the sex chromosome differs across taxa as a result of fusions between sex chromosomes and autosomes, along with sex chromosome turnover-autosomes becoming sex chromosomes and sex chromosomes 'reverting' back to autosomes. In addition, the types of genes on sex chromosomes frequently differ from the autosomes, and genes on sex chromosomes often evolve faster than autosomal genes. Sex-specific selection pressures, such as sexual antagonism and sexual selection, are hypothesized to be responsible for sex chromosome turnovers, the unique gene content of sex chromosomes and the accelerated evolutionary rates of genes on sex chromosomes. Sex-specific selection has pronounced effects on sex chromosomes because their sex-biased inheritance can tilt the balance of selection in favour of one sex. Despite the general consensus that sex-specific selection affects sex chromosome evolution, most population genetic models are agnostic as to the specific sources of these sex-specific selection pressures, and many of the details about the effects of sex-specific selection remain unresolved. Here, I review the evidence that ecological factors, including variable selection across heterogeneous environments and conflicts between sexual and natural selection, can be important determinants of sex-specific selection pressures that shape sex chromosome evolution. I also explain how studying the ecology of sex chromosome evolution can help us understand important and unresolved aspects of both sex chromosome evolution and sex-specific selection.

Female mate choice and species recognition between two closely related cichlid fish of Lake Malawi, Metriaclima estherae and M. callainos

Cichlids are one of the most diverse and colourful groups of freshwater fishes in the world. Despite much investigation, the factors that promote speciation in these fishes are still uncertain. However, previous studies suggest that sexual selection on male colour is one of the main drivers of speciation among these fishes. Metriaclima estherae is a polymorphic cichlid species from Lake Malawi, and thus provides an ideal model for the investigation of the importance of colour as a species recognition cue. M. callainos is a closely related and morphologically similar species, with male colour pattern very similar to that of M. estherae. We tested female choice by giving females of the two species a choice between conspecific and heterospecific males in the presence and absence of visual (colour) and chemical cues. The results show that females of M. callainos were able to reliably recognize conspecific males, even when colour was eliminated as a cue. However, females of M. estherae did not prefer conspecific males, although they were able to discriminate between red and blue conspecific colour morphs by using chemical cues. These results suggest that species recognition cues may differ even among closely related species of cichlid fish, and that female preferences for male coloration may be weak in certain species.

Genetic evidence for panmixia in a colony-breeding crater lake cichlid fish

Fine-scaled genetic structuring, as seen for example in many lacustrine fish, typically relates to the patterns of migration, habitat use, mating system or other ecological factors. Because the same processes can also affect the propensity of population differentiation and divergence, assessments of species from rapidly speciating clades, or with particularly interesting ecological traits, can be especially insightful. For this study, we assessed the spatial genetic relationships, including the genetic evidence for sex-biased dispersal, in a colony-breeding cichlid fish, Amphilophus astorquii, endemic to Crater Lake Apoyo in Nicaragua, using 11 polymorphic microsatellite loci (n = 123 individuals from three colonies). We found no population structure in A. astorquii either within colonies (no spatial genetic autocorrelation, r ~0), or at the lake-wide level (pairwise population differentiation FST = 0-0.013 and no clustering), and there was no sex-bias (male and female AIc values bounded 0) to this lack of genetic structure. These patterns may be driven by the colony-breeding reproductive behaviour of A. astorquii. The results suggest that strong philopatry or spatial assortative mating are unlikely to explain the rapid speciation processes associated with the history of this species in Lake Apoyo.

SPECIES FLOCK IN THE NORTH AMERICAN GREAT LAKES: MOLECULAR ECOLOGY OF LAKE NIPIGON CISCOES (TELEOSTEI: COREGONIDAE: COREGONUS)

Studies on north temperate fish species indicate that new habitat availability following the last ice sheet retreat has promoted ecological speciation in postglacial lakes. Extensive ecophenotypic polymorphisms observed among the North American Great Lakes ciscoes suggest that this fish group has radiated through trophic adaptation and reproductive isolation. This study aims at relating the ecomorphological and genetic polymorphisms expressed by the Lake Nipigon ciscoes to evaluate the likelihood of an intralacustrine divergence driven by the exploitation of alternative resources. Morphological variation and trophic and spatial niches are characterized and contrasted among 203 individuals. Genetic variation at six microsatellite loci is also analyzed to appraise the extent of genetic differentiation among these morphotypes. Ecomorphological data confirm the existence of four distinct morphotypes displaying various levels of trophic and depth niche overlap and specialization. However, ecological and morphological variations were not coupled as expected, suggesting that trophic morphology is not always predictive of ecology. Although extensive genetic variability was observed, little genetic differentiation was found among morphotypes, with only one morph being slightly but significantly differentiated. Contrasting patterns of morphological, ecological, and genetic polymorphisms did not support the hypothesis of ecological speciation: the most ecologically different forms were morphologically most similar, while the only genetically differentiated morph was the least ecologically specialized. The low levels of genetic differentiation and the congruence between θ and φ estimates altogether suggest a recent (most likely postglacial) process of divergence and/or high gene flow among morphs A, C, and D, whereas higher φ estimates for comparison involving morph B suggest that this morph may be derived from another colonizing lineage exchanging little genes with the other morphs. Patterns of ecophenotypic and genetic diversity are also compatible with a more complex evolutionary history involving hybridization and introgression.

An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid fish

Despite long-standing interest in the evolution and maintenance of discrete phenotypic polymorphisms, the molecular genetic basis of such polymorphism in the wild is largely unknown. Female sex-associated blotched colour polymorphisms found in cichlids of Lake Malawi, East Africa, represent a highly successful polymorphic phenotype, found and maintained in four genera across the geographic expanse of the lake. Previously, we identified an association with an allelic variant of the paired-box transcription factor gene pax7a and blotched colour morphs in Lake Malawi cichlid fishes. Although a diverse range of blotched phenotypes are present in Lake Malawi cichlid species, they all appeared to result from an allele of pax7a that produces increased levels of transcript. Here, we examine the developmental and genetic basis of variation among blotched morphs. First, we confirm that pax7a-associated blotch morphs result primarily from modulation of melanophore development and survival. From laboratory crosses and natural population studies, we identify at least three alleles of pax7a associated with discrete subtypes of blotched morphs, in addition to the ancestral pax7a allele. Genotypes at pax7a support initial evolution of a novel pax7a allele to produce the blotched class of morphs, followed by subsequent evolution of that pax7a blotched allele to produce additional alleles associated with discrete colour morphs. Variant alleles of pax7a produce different levels of pax7a transcript, correlating with pigmentation phenotype at the cellular level. This naturally selected allelic series should serve as a case study for understanding the molecular genetic control of pax7a expression and the evolution of sex-associated alleles.

Genetic interactions controlling sex and color establish the potential for sexual conflict in Lake Malawi cichlid fishes

Sex-determining systems may evolve rapidly and contribute to lineage diversification. In fact, recent work has suggested an integral role of sex chromosome evolution in models of speciation. We use quantitative trait loci analysis of restriction site-associated DNA -tag single nucleotide polymorphisms to identify multiple loci responsible for sex determination and reproductively adaptive color phenotypes in Lake Malawi cichlids. We detect a complex epistatic sex system consisting of a major female heterogametic ZW locus on chromosome 5, two separate male heterogametic XY loci on chromosome 7, and two additional interacting loci on chromosomes 3 and 20. Our data support the known chromosomal linkage between orange blotch color and ZW, as well as novel genetic associations between male blue nuptial color and two sex determining regions (an XY and ZW locus). These results provide further empirical evidence for a complex antagonistic sex-color system in this species flock and suggest a possible role for, and effect of, polygenic sex-determining systems in rapid evolutionary diversification.

A small number of genes underlie male pigmentation traits in Lake Malawi cichlid fishes

Pigmentation patterns are one of the most recognizable forms of phenotypic diversity and an important component of organismal fitness. While much progress has been made in understanding the genes controlling pigmentation in model systems, many questions remain about the genetic basis of pigment traits observed in nature. Lake Malawi cichlid fishes are known for their diversity of male pigmentation patterns, which have been shaped by sexual selection. To begin the process of identifying the genes underlying this diversity, we quantified the number of pigment cells on the body and fins of two species of the genus Metriaclima and their hybrids. We then used the Castle-Wright equation to estimate that differences in individual pigmentation traits between these species are controlled by one to four genes each. Different pigmentation traits are highly correlated in the F(2) , suggesting shared developmental pathways and genetic pleiotropy. Melanophore and xanthophore traits fall on opposite ends of the first principal component axis of the F(2) phenotypes, suggesting a tradeoff during the development of these two pigment cell types.

Concordant female mate preferences in the cichlid fish Tropheus moorii

Discriminating female mate preferences enhance the variance in reproductive success among males of a population and create a potential for sexual selection, which can account for trait evolution and diversification. Fish color patterns are among the prime targets of mate choice-driven sexual selection. Populations of the cichlid Tropheus from Lake Tanganyika display remarkable geographic color pattern variation, but the role of female choice in their rapid and rich phenotypic diversification is unclear. Males and females establish a pair bond prior to spawning monogamously, but as brood care is strictly maternal, female investment in reproduction is high and the operational sex ratio is male-biased. Therefore, variance in male reproductive success can accrue if individual males succeed repeatedly in securing a mate. To test this prediction in the red colored Tropheus moorii "Chimba", four pairs of males were presented to a series of females and female mate preferences were inferred from pairwise interactions. There was a significant difference in mating success between the males of each pair (P < 0.001 over all trials), as-with one exception-females shared preferences for the same males. Male courtship activity was strongly correlated with female choice. Our experiment suggests that female choice contributes to the variance in male reproductive success in the tested population.

The adaptive radiation of cichlid fish in lake tanganyika: a morphological perspective

Lake Tanganyika is the oldest of the Great Ancient Lakes in the East Africa. This lake harbours about 250 species of cichlid fish, which are highly diverse in terms of morphology, behaviour, and ecology. Lake Tanganyika's cichlid diversity has evolved through explosive speciation and is treated as a textbook example of adaptive radiation, the rapid differentiation of a single ancestor into an array of species that differ in traits used to exploit their environments and resources. To elucidate the processes and mechanisms underlying the rapid speciation and adaptive radiation of Lake Tanganyika's cichlid species assemblage it is important to integrate evidence from several lines of research. Great efforts have been, are, and certainly will be taken to solve the mystery of how so many cichlid species evolved in so little time. In the present review, we summarize morphological studies that relate to the adaptive radiation of Lake Tanganyika's cichlids and highlight their importance for understanding the process of adaptive radiation.

Identification and characterization of gene expression involved in the coloration of cichlid fish using microarray and qRT-PCR approaches

It has been suggested that speciation on the basis of sexual selection is an important mechanism for the generation of new species for East African cichlids, where male body coloration is one of the major discriminatory factors used by females in mate choice. To gain insight into the molecular basis of cichlid coloration, we studied the Lake Malawi cichlid Pseudotropheus saulosi, comparing transcription in the bright blue skin of males to the yellow skin of females. Our cDNA microarray experiments identified 46 clones that exhibited expression differences between the two sexes, of which five were confirmed to be differentially expressed by relative quantitative real-time PCR (qRT-PCR). This gene list includes a representative from the endosomal-to-Golgi vesicle trafficking pathway, Coatomer protein complex, subunit zeta-1 (Copz-1), which is known to be a critical determinant of pigmentation in humans and zebrafish. With the support of microscopic images of the skin of these specimens, we interpret the transcriptional differences between the blue males and yellow females. Here, we provide insight into the putative functional diversification of genes involved in the coloration of cichlids and by extension, on the evolution of coloration in teleost fish.

The macroecology of rapid evolutionary radiation

A long-standing debate in ecology addresses whether community composition is the result of stochastic factors or assembly rules. Non-random, over-dispersed patterns of species co-occurrence have commonly been attributed to competition--a particularly important force in adaptive radiation. We thus examined the macroecology of the recently radiated cichlid rock-fish assemblage in Lake Malawi, Africa at a spectrum of increasingly fine spatial scales (entire lake to depth within rock-reef sites). Along this range of spatial scales, we observed a signal of community structure (decreased co-occurrence of species) at the largest and smallest scales, but not in between. Evidence suggests that the lakewide signature of structure is driven by extreme endemism and micro-allopatric speciation, while patterns of reduced co-occurrence with depth are indicative of species interactions. We identified a 'core' set of rock-reef species, found in combination throughout the lake, whose depth profiles exhibited replicated positive and negative correlation. Our results provide insight into how ecological communities may be structured differently at distinct spatial scales, re-emphasize the importance of local species interactions in community assembly, and further elucidate the processes shaping speciation in this model adaptive radiation.

Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes

Sex determination mechanisms differ among animal species, but it is not clear how these differences evolve. New sex determiners may arise in response to sexual conflicts, which occur when traits benefit one sex but hinder the other. We identified the genetic basis for the orange-blotch (OB) color pattern, a trait under sexually antagonistic selection in the cichlid fish of Lake Malawi, East Africa. The OB phenotype is due to a cis-regulatory mutation in the Pax7 gene. OB provides benefits of camouflage to females but disrupts the species-specific male color patterns used for mate recognition. We suggest that the resulting sexual conflict over the OB allele has been resolved by selection for a novel female sex determination locus that has invaded populations with an ancestral male sex determination system.

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.

Adaptive radiation in the Congo River: an ecological speciation scenario for African weakly electric fish (Teleostei; Mormyridae; Campylomormyrus)

The ultimate aim of this study is to better understand the diversification of African weakly electric fish in the Congo River. Based on a robust phylogenetic hypothesis we examined the radiation within the mormyrid genus Campylomormyrus. Morphological traits relevant for the divergence between the identified species were detected. Among them, the variation in the shape of the trunk-like elongated snout suggested the presence of different trophic specializations. Furthermore, the chosen model taxon, the genus Campylomormyrus, exhibits a wide diversity of electric organ discharge (EOD) waveforms. A comparison of EOD waveform types and phylogenetic relationships showed major differences in EOD between closely related species. This indicates that the EOD might function as a reproductive isolation mechanism. In conclusion, we provide a plausible scenario of an adaptive radiation triggered by sexual selection and assortative mating based on EOD characteristics, but caused by a divergent selection on the feeding apparatus. These findings point towards an adaptive radiation of at least some Campylomormyrus species occurring in the Lower Congo River.

Female mating preference functions predict sexual selection against hybrids between sibling species of cichlid fish

The evolutionary outcome of interspecific hybridization, i.e. collapse of species into a hybrid swarm, persistence or even divergence with reinforcement, depends on the balance between gene flow and selection against hybrids. If female mating preferences are open-ended but sign-inversed between species, they can theoretically be a source of such selection. Cichlid fish in African lakes have sustained high rates of speciation despite evidence for widespread hybridization, and sexual selection by female choice has been proposed as important in the origin and maintenance of species boundaries. However, it had never been tested whether hybridizing species have open-ended preference rules. Here we report the first experimental test using Pundamilia pundamilia, Pundamilia nyererei and their hybrids in three-way choice experiments. Hybrid males are phenotypically intermediate. Wild-caught females of both species have strong preferences for conspecific over heterospecific males. Their responses to F1 hybrid males are intermediate, but more similar to responses to conspecifics in one species and more similar to responses to heterospecifics in the other. We suggest that their mate choice mechanism may predispose haplochromine cichlids to maintain and perhaps undergo phenotypic diversification despite hybridization, and that species differences in female preference functions may predict the potential for adaptive trait transfer between hybridizing species.

Evolution of a cichlid fish in a Lake Malawi satellite lake

Allopatric divergence in peripheral habitats may lead to rapid evolution of populations with novel phenotypes. In this study we provide the first evidence that isolation in peripheral habitats may have played a critical role in generation of Lake Malawi's cichlid fish diversity. We show that Lake Chilingali, a satellite lake 11.5 km from the shore of Lake Malawi, contains a breeding population of Rhamphochromis, a predatory genus previously thought to be restricted to Lake Malawi and permanently connected water bodies. The Lake Chilingali population is the smallest known Rhamphochromis, has a unique male nuptial colour pattern and has significant differentiation in mitochondrial DNA from Lake Malawi species. In laboratory mate choice trials with a candidate sister population from Lake Malawi, females showed a strong tendency to mate assortatively indicating that they are incipient biological species. These data support the hypothesis that isolation and reconnection of peripheral habitats due to lake level changes have contributed to the generation of cichlid diversity within African lakes. Such cycles of habitat isolation and reconnection may also have been important in evolutionary diversification of numerous other abundant and wide-ranging aquatic organisms, such as marine fishes and invertebrates.

Size-dependent use of territorial space by a rock-dwelling cichlid fish

Territoriality fundamentally influences animal mating systems and patterns of population structure. Although territory ownership is already known to contribute importantly to male reproductive success and the ecological coexistence of African rock-dwelling cichlids, the significance of variation in territory features has received little attention in these fishes. In Lake Malawi, males of Pseudotropheus tropheops "orange chest" defend territories on either of two substrate classes at Harbour Island: flat rock slabs lacking crevices and caves, or structurally complex boulder fields containing cave shelters. Focal watches of this species demonstrated that both territory size and occupancy on either substrate type depend on the size of male residents. Males larger than a threshold size exclusively held the largest and most structurally complex territories. After removal of conspecific residents, more vacant territorial areas on cave-containing substrate were reoccupied by "orange chest" males in full breeding coloration compared to vacant areas on flat substrate. These findings suggest competition among "orange chest" males for complex rocky substrate. Defense of caves was associated with enhanced male courtship rates: the number of caves within a male's territory was a better predictor of courtship activity than was male size or territory area. In addition to territories being crucial for male reproductive success and therefore likely playing a role in sexual selection, male-male competition for caves in rock-dwelling cichlids may be promoted by the ecological advantage of enemy-free space. Smaller "orange chest" males lacking caves tended to move into adjacent boulder fields in the presence of predators, particularly at night. In contrast, males defending caves were more likely to remain on their territories when nocturnal predators were present. The territorial behaviors of P. tropheops "orange chest" that we observed in situ provide an instructive natural framework for testing the roles of substrate and ecology in the mating systems of rock-dwelling cichlid fishes.

The genetic architecture of male colour differences between a sympatric Lake Malawi cichlid species pair

The genetic basis of traits involved in reproductive isolation is a key parameter in models of sympatric speciation by sexual selection, a potential mechanism driving the explosive radiation of East African cichlids. Analysis of hybrid crosses between two sympatric Lake Malawi cichlid species, representing the extremes of the extant colour distribution, generated Castle-Wright estimates of four to seven loci controlling colour differences. Segregation patterns deviated from a purely additive model with a significant contribution from dominance, and possibly also epistasis. Evidence was found for a strong influence of autosomal loci. As departures from simple additive variation could effect the operation of models of sympatric speciation, dominance and epistasis should not be neglected.

The relative role of male vs. female mate choice in maintaining assortative pairing among discrete colour morphs

Mate choice has important evolutionary consequences because it influences assortative mating and the level of genetic variation maintained within populations. In species with genetically determined polymorphisms, nonrandom mate choice may affect the evolutionary stability and maintenance (or loss) of alternative phenotypes. We examined the mating pattern in the colour polymorphic Gouldian finch (Erythrura gouldiae), and the role of mate choice, both female and male, in maintaining the three discrete head colours (black, red and yellow). In both large captive and wild populations, Gouldian finches paired assortatively with respect to head colour. In mate choice trials, females showed a strong preference for mates with the most elaborate sexually dimorphic traits (i.e. more chromatic UV/blue plumage and longer pin-tail feathers), but did not discriminate assortatively. Unexpectedly, however, males were particularly choosy, associating and pairing only with females of their own morph-type. Although female mate choice is generally invoked as the major selective force maintaining conspicuous male colouration in sexually dichromatic species, and is typically thought to drive nonrandom mating, these findings suggest that mutual mate choice and male mate choice in particular, are an important yet neglected component of selection.

Reproductive isolation among deep-water cichlid fishes of Lake Malawi differing in monochromatic male breeding dress

Male nuptial colour hues are important for the maintenance of reproductive isolation among cichlid fish species, and environmental changes that lead to narrower light spectra can lead to hybridization. However, cichlid species can naturally co-occur in narrow light spectrum habitats, such as turbid shallow lakes and the deep benthic zones of African rift lakes. Closely related species from narrow light spectrum habitats tend to differ little in the palette of male nuptial colours, thus for these taxa differences in colour patterns may be more important than differences in colour hue for species recognition. To investigate this hypothesis we examined morphometric and genetic differentiation among males of four sympatric putative species within the deep-water genus Diplotaxodon. These taxa live in a narrow-light spectrum environment where only blue light is present, and males differ primarily in 'monochromatic' black, white and silver patterning of the body and fins. Significant genetic differentiation was present among taxa in both microsatellite DNA and mitochondrial DNA, including one pair with no significant morphometric differentiation. Thus, these taxa represent reproductively isolated biological species, a result consistent with male nuptial patterning being important for species recognition and assortative mating. As such, we suggest that narrow-light spectra need not always represent barriers to effective visually mediated mate recognition.

Microsatellite analysis of Japanese sea cucumber, Stichopus (Apostichopus) japonicus, supports reproductive isolation in color variants

The genetic relationship among the three color variants (Red, Green, and Black) of the Japanese sea cucumber, S. japonicus, was investigated using 11 microsatellite markers. Genetic differentiation testing among the three sympatric color types showed the strong heterogeneity of Red (p<0.001), while no significant difference was observed between Green and Black (p=0.301 to 0.961). UPGMA trees constructed from 10 sample lots from 5 localities showed two distinct clusters, one from the Red types and the other from the Green and Black types. In addition, the sympatric Green and Black formed one subcluster with strong bootstrap support at each locality. These results indicate the separate species status of Red and the other color types, and also support the population identity of sympatric Green and Black.

Monogamy in the maternally mouthbrooding Lake Tanganyika cichlid fish Tropheus moorii

Supported by evidence for assortative mating and polygynandry, sexual selection through mate choice was suggested as the main force driving the evolution of colour diversity of haplochromine cichlids in Lakes Malawi and Victoria. The phylogenetically closely related tribe Tropheini of Lake Tanganyika includes the genus Tropheus, which comprises over 100 colour variants currently classified into six morphologically similar, polyphyletic species. To assess the potential for sexual selection in this sexually monochromatic maternal mouthbrooder, we used microsatellite-based paternity inference to investigate the mating system of Tropheus moorii. In contrast to haplochromines in Lake Malawi, multiple paternity is rare or even absent in broods of T. moorii. Eighteen of the 19 analysed families were consistent with genetic monogamy, while either a mutation or more than one sire explained the genotype of one offspring in another brood. We discuss the differences in breeding behaviour between T. moorii and the Lake Malawi haplochromines, and evaluate additional factors or alternatives to sexual selection as promoters of colour diversification. A preliminary survey of other Tropheini species suggested that multiple paternity is infrequent in the entire tribe.

Electrophysiological and molecular genetic evidence for sympatrically occuring cryptic species in African weakly electric fishes (Teleostei: Mormyridae: Campylomormyrus)

For two sympatric species of African weakly electric fish, Campylomormyrus tamandua and Campylomormyrus numenius, we monitored ontogenetic differentiation in electric organ discharge (EOD) and established a molecular phylogeny, based on 2222bp from cytochrome b, the S7 ribosomal protein gene, and four flanking regions of unlinked microsatellite loci. In C. tamandua, there is one common EOD type, regardless of age and sex, whereas in C. numenius we were able to identify three different male adult EOD waveform types, which emerged from a single common EOD observed in juveniles. Two of these EOD types formed well supported clades in our phylogenetic analysis. In an independent line of evidence, we were able to affirm the classification into three groups by microsatellite data. The correct assignment and the high pairwise F(ST) values support our hypothesis that these groups are reproductively isolated. We propose that in C. numenius there are cryptic species, hidden behind similar and, at least as juveniles, identical morphs.

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.

Sympatric speciation in Nicaraguan crater lake cichlid fish

Sympatric speciation, the formation of species in the absence of geographical barriers, remains one of the most contentious concepts in evolutionary biology. Although speciation under sympatric conditions seems theoretically possible, empirical studies are scarce and only a few credible examples of sympatric speciation exist. Here we present a convincing case of sympatric speciation in the Midas cichlid species complex (Amphilophus sp.) in a young and small volcanic crater lake in Nicaragua. Our study includes phylogeographic, population-genetic (based on mitochondrial DNA, microsatellites and amplified fragment length polymorphisms), morphometric and ecological analyses. We find, first, that crater Lake Apoyo was seeded only once by the ancestral high-bodied benthic species Amphilophus citrinellus, the most common cichlid species in the area; second, that a new elongated limnetic species (Amphilophus zaliosus) evolved in Lake Apoyo from the ancestral species (A. citrinellus) within less than approximately 10,000 yr; third, that the two species in Lake Apoyo are reproductively isolated; and fourth, that the two species are eco-morphologically distinct.

Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei

The haplochromine cichlids of Lake Victoria constitute a classical example of explosive speciation. Extensive intra- and interspecific variation in male nuptial coloration and female mating preferences, in the absence of postzygotic isolation between species, has inspired the hypothesis that sexual selection has been a driving force in the origin of this species flock. This hypothesis rests on the premise that the phenotypic traits that underlie behavioural reproductive isolation between sister species diverged under sexual selection within a species. We test this premise in a Lake Victoria cichlid, by using laboratory experiments and field observations. We report that a male colour trait, which has previously been shown to be important for behavioural reproductive isolation between this species and a close relative, is under directional sexual selection by female mate choice within this species. This is consistent with the hypothesis that female choice has driven the divergence in male coloration between the two species. We also find that male territoriality is vital for male reproductive success and that multiple mating by females is common.

Laboratory mating trials indicate incipient speciation by sexual selection among populations of the cichlid fish Pseudotropheus zebra from Lake Malawi

It has been suggested that sexual selection may have played a major role in the rapid evolution of hundreds of species of cichlid fishes in Lake Malawi. We report the results of a laboratory test of assortative mating among Lake Malawi cichlid fishes from five closely related geographical populations differing in male courtship colour. Paternity of clutches was tested using microsatellite DNA typing of offspring. Out of 1955 offspring typed, 1296 (66.3%) were sired by the male from the same population as the female, which is more than three times the rate expected if females do not differentiate among males of the different populations (20%). This result indicates that mate preferences of geographical races are strongly differentiated, consistent with the races representing incipient geographical species diverging under sexual selection exerted by female preferences for different male courtship colours.

Genetic mosaic in a marine species flock

We used molecular approaches to study the status of speciation in coral reef fishes known as hamlets (Serranidae: Hypoplectrus). Several hamlet morphospecies coexist on Caribbean reefs, and mate assortatively with respect to their strikingly distinct colour patterns. We provide evidence that, genetically, the hamlets display characteristics common in species flocks on land and in freshwaters. Substitutions within two mitochondrial DNA (mtDNA) protein-coding genes place hamlets within a monophyletic group relative to members of two related genera (Serranus and Diplectrum), and establish that the hamlet radiation must have been very recent. mtDNA distances separating hamlet morphospecies were slight (0.6 +/- 0.04%), yielding a coalescent estimate for the age of the hamlet flock of approximately 430 000 years. Morphospecies did not sort into distinct mtDNA haplotype phylogroups, and alleles at five hypervariable microsatellite loci were shared broadly across species boundaries. None the less, molecular variation was not distributed at random. Analyses of mtDNA haplotype frequencies and nested clades in haplotype networks revealed significant genetic differences between geographical regions and among colour morphospecies. We also observed significant microsatellite differentiation between geographical regions and in Puerto Rico, among colour morphospecies; the latter providing evidence for reproductive isolation between colour morphospecies at this locale. In our Panama collection, however, colour morphospecies were mostly genetically indistinguishable. This mosaic pattern of DNA differentiation implies a complex interaction between population history, mating behaviour and geography and suggests that porous boundaries separate species in this flock of brilliantly coloured coral reef fishes.

Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration

Repeated evolution of the same phenotypic difference during independent episodes of speciation is strong evidence for selection during speciation. More than 1,000 species of cichlids, >10% of the world's freshwater fish species, have arisen within the past million years in Lakes Malawi and Victoria in eastern Africa. Many pairs of closely related sympatric species differ in their nuptial coloration in very similar ways. Nuptial coloration is important in their mate choice, and speciation by sexual selection on genetically or ecologically constrained variation in nuptial coloration had been proposed, which would repeatedly produce similar nuptial types in different populations, a prediction that was difficult to test in the absence of population-level phylogenies. We measured genetic similarity between individuals within and between populations, species, and lake regions by typing 59 individuals at >2,000 polymorphic genetic loci. From these data, we reconstructed, to our knowledge, the first larger species level phylogeny for the most diverse group of Lake Malawi cichlids. We used the genetic and phylogenetic data to test the divergent selection scenario against colonization, character displacement, and hybridization scenarios that could also explain diverse communities. Diversity has arisen by replicated radiations into the same color types, resulting in phenotypically very different, yet closely related, species within and phenotypically highly similar yet unrelated sets of species between regions, which is consistent with divergent selection during speciation and is inconsistent with colonization and character displacement models.

Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity

The importance of species recognition to taxonomic diversity among Lake Malawi cichlids has been frequently discussed. Hybridization - the apparent breakdown of species recognition - has been observed sporadically among cichlids and has been viewed as both a constructive and a destructive force with respect to species diversity. Here we provide genetic evidence of a natural hybrid cichlid population with a unique colour phenotype and elevated levels of genetic variation. We discuss the potential evolutionary consequences of interspecific hybridization in Lake Malawi cichlids and propose that the role of hybridization in generating both genetic variability and species diversity of Lake Malawi cichlids warrants further consideration.

No evidence for parallel sympatric speciation in cichlid species of the genus Pseudotropheus from north-western Lake Malawi

To test the hypothesis of parallel speciation by sexual selection, we examined length variation at six microsatellite loci of samples from four sites of four to six putative species belonging to two subgenera of rocky shore mbuna cichlids from Lake Malawi. Almost all fixation indices were significantly different from zero, suggesting that there is presently little or no gene flow among allopatric populations or sympatric species. Analysis of variance indicated that genetic distances among allopatric populations of putative conspecifics were significantly lower than among sympatric populations of heterospecifics. The topology of trees based on distance matrices was also largely consistent with the hypothesis that the putative species are monophyletic and have thus not evolved in parallel in their present locations. If parallel speciation does occur in Malawi cichlids, it may be on a larger spatial scale than investigated in our study.

Extreme microallopatric divergence in a cichlid species from Lake Malawi

We demonstrate significant population structuring on an extremely small spatial scale between adjacent demes of a Lake Malawi haplochromine cichlid species of the mbuna group, Pseudotropheus callainos, separated by only 35 m of habitat discontinuity. This substantiates further the notion that intralacustrine allopatric divergence may help to explain the high level of species richness of the mbuna in comparison to other Malawian cichlids, as well as of the Malawian haplochromines as a whole.

Discovery and phylogenetic analysis of a riverine species flock of African electric fishes (Mormyridae: Teleostei)

The evolution of species-specific mate recognition signals is of particular interest within speciose monophyletic groups with restricted distributions (known as "species flocks"). However, the explosive nature of speciation in these clades makes difficult the reconstruction of their phylogenetic history. Here we describe a species flock of riverine mormyrid fishes from west-central Africa in which electric signals may play a role in the reproductive isolation of sympatric species. In our recent field collections, totaling more than 1400 specimens from many localities, we recognize 38 forms that are distinct in their morphologies and electric organ discharge (EOD) characteristics. Of these 38, only four clearly correspond to described species. Here we treat these forms as operational taxonomic units (OTUs) in a phylogenetic analysis of cytochrome b sequence data from a sample of 86 specimens. We examined support in the molecular data for the monophyly of these 38 OTUs considered together, the monophyly of each phenotypically delimited OTU considered individually, and for relationships among OTUs congruent with those inferred from the distribution of morphological and EOD character states. Trees obtained by both maximum-parsimony and maximum-likelihood analyses, rooted with sequence data from outgroup taxa, provide evidence for the monophyly of these 38 OTUs with respect to other mormyrid fishes. The small genetic distances between many distinct forms suggest their recent divergence. However, in many instances the cytochrome b tree topology fails to support the monophyly of individual OTUs and close relationships between OTUs that are similar in morphology and EOD characteristics. In other cases, individuals from distinct OTUs share identical or nearly identical haplotypes. Close examination of these cases suggests that unnatural OTU definition is not the sole cause of this pattern, and we infer an incongruence between the mitochondrial gene tree and the organismal phylogeny caused by incomplete mitochondrial lineage sorting and/ or introgression across forms. The apparently rapid diversification in this clade of riverine electric fishes and the problems associated with recovering a meaningful species-level phylogeny from mitochondrial data parallel findings in other species flocks. Selection on EOD waveforms as mate recognition signals may be involved in the radiation of these fishes. This is the first description of a freshwater fish species flock from a riverine, as opposed to a lacustrine, environment.