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The polychromatic and trophically polymorphic Midas cichlid fish species complex (Amphilophus cf. citrinellus) is an excellent model system for studying the mechanisms of speciation and patterns of phenotypic diversification in allopatry and in sympatry. Here, we first review research to date on the species complex and the geological history of its habitat. We analyse body shape variation from all currently described species in the complex, sampled from six crater lakes (maximally 1.2-23.9 kyr old) and both great lakes in Nicaragua. We find that Midas cichlid populations in each lake have their own characteristic body shape. In lakes with multiple sympatric species of Midas cichlid, each species has a distinct body shape. Across the species complex, most body shape change relates to body depth, head, snout and mouth shape and caudal peduncle length. There is independent parallel evolution of an elongate limnetic species in at least two crater lakes. Mitochondrial genetic diversity is higher in crater lakes with multiple species. Midas cichlid species richness increases with the size and age of the crater lakes, though no such relationship exists for the other syntopic fishes. We suggest that crater lake Midas cichlids follow the predicted pattern of an adaptive radiation, with early divergence of each crater lake colonization, followed by intralacustrine diversification and speciation by ecological adaptation and sexual selection.

An algivorous cichlid, Variabilichromis moorii (Vm), defends permanent territories in Lake Tanganyika, Africa. A zoobenthivorous cichlid, Neolamprologus mustax (Nm), spends 60% of daylight hours foraging in Vm territories, from which other zoobenthivorous fishes are chased out and consequently which are much richer in prey animals than areas outside of Vm territories. We conducted a field experiment to examine whether Nm residents and non-residents received different degrees of attacks from Vm. Nm fish were caught in their territories, released at a point distant from these territories, and followed to observe interactions with Vm fish. The frequency of attacks received by the displaced Nm fish was greater than attacks received by Nm residents, indicating that Nm residents had easier access to Vm territories than non-residents did. A possible mechanism for this is reduced aggression of Vm towards Nm residents, as a result of the 'dear enemy' effect that has been reported in territorial contests between rivals. An alternative mechanism is that tolerance towards Nm differs among Vm fish and Nm residents selectively visit more tolerant Vm fish due to previous experience while non-residents randomly approach both tolerant and hostile Vm fish. The ability of Vm to discriminate between Nm residents and non-residents is essential to the former mechanism but not to the latter. To more specifically examine which mechanism works in the Vm-Nm commensal system, we will need to follow individually identified Vm fish interacting with Nm residents and non-residents.

Eutrophication is an increasing global threat to freshwater ecosystems. East Africa's Lake Victoria has suffered from severe eutrophication in the past decades which is partly responsible for the dramatic decline in haplochromine cichlid species diversity. However, some zooplanktivorous and detritivorous haplochromine species recovered and shifted their diet towards macro invertebrates and fish. We used four formalin preserved cichlid species caught over the past 35 years to investigate whether stable isotopes of these fish are reflecting the dietary changes, habitat differences and if these isotopes can be used as indicators of eutrophication. We found that delta super(15)N signatures mainly reflected dietary shifts to larger prey in all four haplochromine species. Shifts in delta super(13)C signatures likely represented habitat differences and dietary changes. In addition, a shift to remarkably heavy delta super(13)C signatures in 2011 was found for all four species which might infer increased primary production and thus eutrophication although more research is needed to confirm this hypothesis. The observed temporal changes confirm previous findings that preserved specimens can be used to trace historical changes in fish ecology and the aquatic environment. This highlights the need for continued sampling as this information could be of essence for reconstructing and predicting the effects of environmental changes.

Ecological speciation is well-known from adaptive radiations in cichlid fishes inhabiting lentic ecosystems throughout the African rift valley and Central America. Here, we investigate the ecological and morphological diversification of a recently discovered lotic predatory Neotropical cichlid species flock in subtropical South America. We document morphological and functional diversification using geometric morphometrics, stable C and N isotopes, stomach contents and character evolution. This species flock displays species-specific diets and skull and pharyngeal jaw morphology. Moreover, this lineage appears to have independently evolved away from piscivory multiple times and derived forms are highly specialized morphologically and functionally relative to ancestral states. Ecological speciation played a fundamental role in this radiation and our data reveal novel conditions of ecological speciation including a species flock that evolved: 1) in a piscivorous lineage, 2) under lotic conditions and 3) with pronounced morphological novelties, including hypertrophied lips that appear to have evolved rapidly.

The polytypic Nicaraguan Midas cichlids (Amphilophus cf. citrinellus) have been established as a model system for studying the mechanisms of speciation and patterns of diversification in allopatry and sympatry. The species assemblage in Crater Lake Apoyo has been accepted as a textbook example for sympatric speciation. Here, we present a first comprehensive data set of population genetic (mtDNA & AFLPs) proxies of species level differentiation for a representative set of individuals of all six endemic Amphilophus species occurring in Crater Lake Apoyo. AFLP genetic differentiation was partitioned into a neutral and non-neutral component based on outlier-loci detection approaches, and patterns of species divergence were explored with Bayesian clustering methods. Substantial levels of admixture between species were detected, indicating different levels of reproductive isolation between the six species. Analysis of neutral genetic variation revealed several A. zaliosus as being introgressed by an unknown contributor, hereby rendering the sympatrically evolving L. Apoyo flock polyphyletic. This is contrasted by the mtDNA analysis delivering a clear monophyly signal with Crater Lake Apoyo private haplotypes characterising all six described species, but also demonstrating different demographic histories as inferred from pairwise mismatch distributions.

For many animals, the ability to distinguish cues indicative of predation risk from cues unrelated to predation risk is not entirely innate, but rather is learned and improved with experience. Two pathways to such learning are possible. First, an animal could initially express antipredator behaviour toward a wide range of cues and subsequently learn which of those cues are non-threatening. Alternatively, it could initially express no antipredator behaviour toward a wide range of cues and subsequently learn which of them are threatening. While the learned recognition of threatening cues may occur either through personal interaction with a cue (asocial learning) or through observation of the behaviour of social companions toward a cue (social learning), the learned recognition of non-threatening cues seems to occur exclusively through habituation, a form of asocial learning. Here, we tested whether convict cichlid fish (Amatitlania siquia) can socially learn to recognize visual cues in their environment as either threatening or non-threatening. We exposed juvenile convict cichlids simultaneously to a novel visual cue and one of three (visual) social cues: a social cue indicative of non-risk (the sight of conspecifics that had previously been habituated to the novel cue), a social cue indicative of predation risk (the sight of conspecifics trained to fear the novel cue), or a control treatment with no social cue. The subsequent response of focal fish, when presented with the novel cue alone, was not influenced by the social cue that they had previously witnessed. We therefore did not find evidence that convict cichlids in our study could use social learning to recognize novel visual cues as either threatening or non-threatening. We consider alternative explanations for our findings.

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic \"islands\" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.

The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and 'non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia ( Oreochromis niloticus ), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification. Signs of adaptive radiation in the cichlid genome The 2,000 or so species of cichlid fish, to be found in the lakes and rivers of Africa's Rift Valley, provide the classic example of adaptive radiations. This large-scale international collaboration has sequenced and analysed the genomes and transcriptomes of five distinct lineages of African cichlids. The data reveal an excess of gene duplications in comparison to other fish species. There is an abundance of non-coding element divergence; accelerated coding sequence evolution; expression divergence associated with transposable element insertions in orthologous gene pairs; and regulation by novel miRNAs. Sequencing data from sixty individuals from six closely related Lake Victoria species point to rapid cichlid speciation associated with genome-wide diversifying selection on coding and regulatory variants, and imply that ancient periods of relaxed purifying selection enabled the accumulation of standing variation, which may have been important in facilitating diversification.

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.