How many species of cichlid fishes are there in African lakes?

Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

Morphometric and Genetic Description of Trophic Adaptations in Cichlid Fishes

Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection on feeding biomechanics. We investigated the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyzed morphological differences in the lateral and ventral head shape among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identified variation in a series of morphological traits—including mandible width, mandible length, and buccal length—that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we found that many genes of small effects influence these craniofacial adaptations. Intervals for some traits were enriched in genes related to potassium transport and sensory systems, the latter suggesting co-evolution of feeding structures and sensory adaptations for foraging. Despite these indications of co-evolution of structures, morphological traits did not show covariation. Furthermore, phenotypes largely mapped to distinct genetic intervals, suggesting that a common genetic basis does not generate coordinated changes in shape. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation.

Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes

A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.

New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini)

African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.

Familiarity reduces aggression but does not modify acoustic communication in pairs of Nile tilapia (Oreochromis niloticus) and black-chinned tilapia (Sarotherodon melanotheron)

Reproduction involves multiple complex behaviours, and the effects of familiarity on such social interactions are seldom described in fish. This is particularly true for sound production and communication within aggressive or non-aggressive context. This study explores the effects of a common garden rearing without parental care of two closely related cichlid species (Nile tilapia Oreochromis niloticus and black-chinned tilapia Sarotherodon melanotheron) on their sound production features and social interactions. After 9 months in common garden rearing, from embryonic stage to first maturity, sound production and associated behaviours were recorded on specimens of the two species in intraspecific and interspecific pairings. The authors found that fish were able to produce the same kind of sounds as those recorded in similar context for their parents. Drum sounds were associated to chasing, lateral attack and courtship in O. niloticus and only to fleeing or avoidance in S. melanotheron. Specific grunts were produced in chasing, after biting and in nest building by O. niloticus, and specific rolling sounds were associated to courtship in S. melanotheron. Sound production and behaviours were not correlated to sex steroid levels, but the number of sounds recorded in aggressive context was correlated to dominance in O. niloticus. The authors conclude that one generation of common garden rearing does not modify sound features, which remain specific and innate in the two cichlids. Despite the familiarity, O. niloticus remained dominant on S. melanotheron, but the aggressiveness between the two species decreased.

A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

OBJECTIVE

The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean.

RESULTS

For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.

Species Radiations in the Sea: What the Flock?

Species flocks are proliferations of closely-related species, usually after colonization of depauperate habitat. These radiations are abundant on oceanic islands and in ancient freshwater lakes, but rare in marine habitats. This contrast is well documented in the Hawaiian Archipelago, where terrestrial examples include the speciose silverswords (sunflower family Asteraceae), Drosophila fruit flies, and honeycreepers (passerine birds), all derived from one or a few ancestral lineages. The marine fauna of Hawai'i is also the product of rare colonization events, but these colonizations usually yield only one species. Dispersal ability is key to understanding this evolutionary inequity. While terrestrial fauna rarely colonize between oceanic islands, marine fauna with pelagic larvae can make this leap in every generation. An informative exception is the marine fauna that lack a pelagic larval stage. These low-dispersal species emulate a "terrestrial" mode of reproduction (brooding, viviparity, crawl-away larvae), yielding marine species flocks in scattered locations around the world. Elsewhere, aquatic species flocks are concentrated in specific geographic settings, including the ancient lakes of Baikal (Siberia) and Tanganyika (eastern Africa), and Antarctica. These locations host multiple species flocks across a broad taxonomic spectrum, indicating a unifying evolutionary phenomenon. Hence marine species flocks can be singular cases that arise due to restricted dispersal or other intrinsic features, or they can be geographically clustered, promoted by extrinsic ecological circumstances. Here, we review and contrast intrinsic cases of species flocks in individual taxa, and extrinsic cases of geological/ecological opportunity, to elucidate the processes of species radiations.

Diversity in rest-activity patterns among Lake Malawi cichlid fishes suggests a novel axis of habitat partitioning

Animals display remarkable diversity in rest and activity patterns that are regulated by endogenous foraging strategies, social behaviors and predator avoidance. Alteration in the circadian timing of activity or the duration of rest–wake cycles provide a central mechanism for animals to exploit novel niches. The diversity of the >3000 cichlid species throughout the world provides a unique opportunity to examine variation in locomotor activity and rest. Lake Malawi alone is home to over 500 species of cichlids that display divergent behaviors and inhabit well-defined niches throughout the lake. These species are presumed to be diurnal, though this has never been tested systematically. Here, we measured locomotor activity across the circadian cycle in 11 Lake Malawi cichlid species. We documented surprising variability in the circadian time of locomotor activity and the duration of rest. In particular, we identified a single species, Tropheops sp. ‘red cheek’, that is nocturnal. Nocturnal behavior was maintained when fish were provided shelter, but not under constant darkness, suggesting that it results from acute response to light rather than an endogenous circadian rhythm. Finally, we showed that nocturnality is associated with increased eye size after correcting for evolutionary history, suggesting a link between visual processing and nighttime activity. Together, these findings identify diversity of locomotor behavior in Lake Malawi cichlids and provide a system for investigating the molecular and neural basis underlying variation in nocturnal activity.

Summary: Cichlids show a remarkable diversity in morphology and behavior. Cichlid species exhibit differences in strength and polarity of activity rhythms, revealing a new axis of habitat partitioning.

Biogeography of the West Indies: A complex scenario for species radiations in terrestrial and aquatic habitats

Studies of the biogeography of the West Indies are numerous but not all taxonomic groups have received the same attention. Many of the contributions to this field have historically focused on terrestrial vertebrates from a perspective closely linked to the classical theory of island biogeography. However, some recent works have questioned whether some of the assumptions of this theory are too simplistic. In this review, we compiled information about the West Indies biogeography based on an extensive and rigorous literature search. While we offer some background of the main hypotheses that explain the origin of the Caribbean biota, our main purpose here is to highlight divergent diversification patterns observed in terrestrial versus aquatic groups of the West Indian biota and also to shed light on the unbalanced number of studies covering the biogeography of these groups of organisms. We use an objective method to compile existing information in the field and produce a rigorous literature review. Our results show that most of the relevant literature in the field is related to the study of terrestrial organisms (mainly vertebrates) and only a small portion covers aquatic groups. Specifically, livebearing fishes show interesting deviations from the species-area relationship predicted by classical island biogeography theory. We found that species richness on the Greater Antilles is positively correlated with island size but also with the presence of elevations showing that not only island area but also mountainous relief may be an important factor determining the number of freshwater species in the Greater Antilles. Our findings shed light on mechanisms that may differently drive speciation in aquatic versus terrestrial environments suggesting that ecological opportunity could outweigh the importance of island size in speciation. Investigations into freshwater fishes of the West Indies offer a promising avenue for understanding origins and subsequent diversification of the Caribbean biota.

Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes

The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5' untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.

Differences among families in craniofacial shape at early life-stages of Arctic charr (Salvelinus alpinus)

BACKGROUND

Organismal fitness can be determined at early life-stages, but phenotypic variation at early life-stages is rarely considered in studies on evolutionary diversification. The trophic apparatus has been shown to contribute to sympatric resource-mediated divergence in several taxa. However, processes underlying diversification in trophic traits are poorly understood. Using phenotypically variable Icelandic Arctic charr (Salvelinus alpinus), we reared offspring from multiple families under standardized laboratory conditions and tested to what extent family (i.e. direct genetic and maternal effects) contributes to offspring morphology at hatching (H) and first feeding (FF). To understand the underlying mechanisms behind early life-stage variation in morphology, we examined how craniofacial shape varied according to family, offspring size, egg size and candidate gene expression.

RESULTS

Craniofacial shape (i.e. the Meckel's cartilage and hyoid arch) was more variable between families than within families both across and within developmental stages. Differences in craniofacial morphology between developmental stages correlated with offspring size, whilst within developmental stages only shape at FF correlated with offspring size, as well as female mean egg size. Larger offspring and offspring from females with larger eggs consistently had a wider hyoid arch and contracted Meckel's cartilage in comparison to smaller offspring.

CONCLUSIONS

This study provides evidence for family-level variation in early life-stage trophic morphology, indicating the potential for parental effects to facilitate resource polymorphism.

Context-dependent consequences of color biases in a social fish

Colorful visual signals can provide receivers with valuable information about food, danger, and the quality of social partners. However, the value of the information that color provides varies depending on the situation, and color may even act as a sensory trap where signals that evolved under one context are exploited in another. Despite some elegant early work on color as a sensory trap, few empirical studies have examined how color biases may vary depending on context and under which situations biases can be overridden. Here, using Neolamprologus pulcher, a highly social cichlid fish from Lake Tanganyika, we conducted a series of experiments to determine color biases and investigate the effects of these biases under different contexts. We found that N. pulcher interacted the most with yellow items and the least with blue items. These biases were maintained during a foraging-based associative learning assay, with fish trained using yellow stimuli performing better than those trained using blue stimuli. However, these differences in learning performance did not extend to reversal learning; fish were equally capable of forming new associations regardless of the color they were initially trained on. Finally, in a social choice assay, N. pulcher did not display a stronger preference for conspecifics whose yellow facial markings had been artificially enhanced. Together, these findings suggest that the influence of color biases varies under different contexts and supports the situational dependency of color functions.

Ecomorphological divergence and habitat lability in the context of robust patterns of modularity in the cichlid feeding apparatus

BACKGROUND

Adaptive radiations are characterized by extreme and/or iterative phenotypic divergence; however, such variation does not accumulate evenly across an organism. Instead, it is often partitioned into sub-units, or modules, which can differentially respond to selection. While it is recognized that changing the pattern of modularity or the strength of covariation (integration) can influence the range or rate of morphological evolution, the relationship between shape variation and covariation remains unclear. For example, it is possible that rapid phenotypic change requires concomitant changes to the underlying covariance structure. Alternatively, repeated shifts between phenotypic states may be facilitated by a conserved covariance structure. Distinguishing between these scenarios will contribute to a better understanding of the factors that shape biodiversity. Here, we explore these questions using a diverse Lake Malawi cichlid species complex, Tropheops, that appears to partition habitat by depth.

RESULTS

We construct a phylogeny of Tropheops populations and use 3D geometric morphometrics to assess the shape of four bones involved in feeding (mandible, pharyngeal jaw, maxilla, pre-maxilla) in populations that inhabit deep versus shallow habitats. We next test numerous modularity hypotheses to understand whether fish at different depths are characterized by conserved or divergent patterns of modularity. We further examine rates of morphological evolution and disparity between habitats and among modules. Finally, we raise a single Tropheops species in environments mimicking deep or shallow habitats to discover whether plasticity can replicate the pattern of morphology, disparity, or modularity observed in natural populations.

CONCLUSIONS

Our data support the hypothesis that conserved patterns of modularity permit the evolution of divergent morphologies and may facilitate the repeated transitions between habitats. In addition, we find the lab-reared populations replicate many trends in the natural populations, which suggests that plasticity may be an important force in initiating depth transitions, priming the feeding apparatus for evolutionary change.

A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide a time-calibrated phylogeny for this widely distributed clade. Some inferred relationships have clear precedents (e.g. the monophyly of 'core' Stromateoidei, and a clade comprising 'Gempylidae' and Trichiuridae), but others are unexpected despite strong support (e.g. Chiasmodontidae + Tetragonurus). Relaxed molecular clock analysis using node-based fossil calibrations estimates a latest Cretaceous origin for Pelagiaria, with crown-group families restricted to the Cenozoic. Estimated mean speciation rates decline from the origin of the group in the latest Cretaceous, although credible intervals for root and tip rates are broad and overlap in most cases, and there is higher-than-expected partitioning of body shape diversity (measured as fineness ratio) between clades concentrated during the Palaeocene-Eocene. By contrast, more direct measures of ecology show either no substantial deviation from a null model of diversification (diet) or patterns consistent with evolutionary constraint or high rates of recent change (depth habitat). Collectively, these results indicate a mosaic model of diversification. Pelagiarians show high morphological disparity and modest species richness compared to better-studied fish radiations in contrasting environments. However, this pattern is also apparent in other clades in open-ocean or deep-sea habitats, and suggests that comparative study of such groups might provide a more inclusive model of the evolution of diversity in fishes.

Color discrimination thresholds in a cichlid fish: Metriaclima benetos

Color vision is essential for animals as it allows them to detect, recognize and discriminate between colored objects. Studies analyzing color vision require an integrative approach, combining behavioral experiments, physiological models and quantitative analyses of photoreceptor stimulation. Here, we demonstrate, for the first time, the limits of chromatic discrimination in Metriaclima benetos, a rock-dwelling cichlid from Lake Malawi, using behavioral experiments and visual modeling. Fish were trained to discriminate between colored stimuli. Color discrimination thresholds were quantified by testing fish chromatic discrimination between the rewarded stimulus and distracter stimuli that varied in chromatic distance (ΔS). This was done under fluorescent lights alone and with additional violet lights. Our results provide two main outcomes. First, cichlid color discrimination thresholds correspond with predictions from the receptor noise limited (RNL) model but only if we assume a Weber fraction higher than the typical value of 5%. Second, cichlids may exhibit limited color constancy under certain lighting conditions as most individuals failed to discriminate colors when violet light was added. We further used the color discrimination thresholds obtained from these experiments to model color discrimination of actual fish colors and backgrounds under natural lighting for Lake Malawi. We found that, for M. benetos, blue is most chromatically contrasting against yellows and space-light, which might be important for discriminating male nuptial colorations and detecting males against the background. This study highlights the importance of lab-based behavioral experiments in understanding color vision and in parameterizing the assumptions of the RNL vision model for different species.

A population genetic assessment of taxonomic species: The case of Lake Malawi cichlid fishes

Organisms sampled for population‐level research are typically assigned to species by morphological criteria. However, if those criteria are limited to one sex or life stage, or the organisms come from a complex of closely related forms, the species assignments may misdirect analyses. The impact of such sampling can be assessed from the correspondence of genetic clusters, identified only from patterns of genetic variation, to the species identified using only phenotypic criteria. We undertook this protocol with the rock‐dwelling mbuna cichlids of Lake Malawi, for which species within genera are usually identified using adult male coloration patterns. Given high local endemism of male colour patterns, and considerable allele sharing among species, there persists considerable taxonomic uncertainty in these fishes. Over 700 individuals from a single transect were photographed, genotyped and separately assigned: (a) to morphospecies using photographs; and (b) to genetic clusters using five widely used methods. Overall, the correspondence between clustering methods was strong for larger clusters, but methods varied widely in estimated number of clusters. The correspondence between morphospecies and genetic clusters was also strong for larger clusters, as well as some smaller clusters for some methods. These analyses generally affirm (a) adult male‐limited sampling and (b) the taxonomic status of Lake Malawi mbuna, as the species in our study largely appear to be well‐demarcated genetic entities. More generally, our analyses highlight the challenges for clustering methods when the number of populations is unknown, especially in cases of highly uneven sample sizes.

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'

BACKGROUND

The molecular basis of the incipient stage of speciation is still poorly understood. Cichlid fish species in Lake Victoria are a prime example of recent speciation events and a suitable system to study the adaptation and reproductive isolation of species.

RESULTS

Here, we report the pattern of genomic differentiation between two Lake Victoria cichlid species collected in sympatry, Haplochromis pyrrhocephalus and H. sp. 'macula,' based on the pooled genome sequences of 20 individuals of each species. Despite their ecological differences, population genomics analyses demonstrate that the two species are very close to a single panmictic population due to extensive gene flow. However, we identified 21 highly differentiated short genomic regions with fixed nucleotide differences. At least 15 of these regions contained genes with predicted roles in adaptation and reproductive isolation, such as visual adaptation, circadian clock, developmental processes, adaptation to hypoxia, and sexual selection. The nonsynonymous fixed differences in one of these genes, LWS, were reported as substitutions causing shift in absorption spectra of LWS pigments. Fixed differences were found in the promoter regions of four other differentially expressed genes, indicating that these substitutions may alter gene expression levels.

CONCLUSIONS

These diverged short genomic regions may have contributed to the differentiation of two ecologically different species. Moreover, the origins of adaptive variants within the differentiated regions predate the geological formation of Lake Victoria; thus Lake Victoria cichlid species diversified via selection on standing genetic variation.

Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine Cichlid Pseudocrenilabrus philander

Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX-XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX-XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.

Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids

Background

Dissecting the genetic basis of phenotypic diversity is one of the fundamental goals in evolutionary biology. Despite growing evidence for gene expression divergence being responsible for the evolution of complex traits, knowledge about the proximate genetic causes underlying these traits is still limited. African cichlids have diverse visual systems, with different species expressing different combinations of seven cone opsin genes. Using opsin expression variation in African cichlids as a model for gene expression evolution, this study aims to investigate the genetic architecture of opsin expression divergence in this group.

Results

Results from a genome-wide linkage mapping on the F₂ progeny of an intergeneric cross, between two species with differential opsin expression show that opsins in Lake Malawi cichlids are controlled by multiple quantitative trait loci (QTLs). Most of these QTLs are located in trans to the opsins except for one cis-QTL for SWS1 on LG17. A closer look at this major QTL revealed the presence of a 691 bp deletion in the promoter of the SWS1 opsin (located 751 bp upstream of the start site) that is associated with a decrease in its expression. Phylogenetic footprinting indicates that the region spanning the deletion harbors a microRNA miR-729 and a conserved non-coding element (CNE) that also occurs in zebrafish and other teleosts. This suggests that the deletion might contain ancestrally preserved regulators that have been tuned for SWS1 gene expression in Lake Malawi. While this deletion is not common, it does occur in several other species within the lake.

Conclusions

Differential expression of cichlid opsins is associated with multiple overlapping QTL, with all but one in trans to the opsins they regulate. The one cis-acting factor is a deletion in the promoter of the SWS1 opsin, suggesting that ancestral polymorphic deletions may contribute to cichlid’s visual diversity. In addition to expanding our understanding of the molecular landscape of opsin expression in African cichlids, this study sheds light on the molecular mechanisms underlying phenotypic variation in natural populations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5328-z) contains supplementary material, which is available to authorized users.

Unusual Diversity of Sex Chromosomes in African Cichlid Fishes

African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.

Early developmental and allometric patterns in the electric yellow cichlid Labidochromis caeruleus

The electric yellow cichlid Labidochromis caeruleus is a mouth-brooding haplochromine cichlid from Lake Malawi and one of the most popular cichlids in the ornamental fish industry. To investigate the early development of L. caeruleus from hatching until the juvenile stage, we studied its morphological development and allometric growth patterns. In newly-hatched larvae, most organs and body parts were not yet differentiated and continued to develop until 15 days post hatching (dph). The yolk sac was depleted at 13 dph. There was allometric growth, primarily in the anterior and posterior regions of the body, and inflection points when trajectories of allometric growth changed. Head and tail growth was prioritized, suggesting that body parts linked to feeding and swimming behaviour mature earlier than the rest of the body. Additionally, growth patterns revealed that development of organs related to vital functions such as branchial respiration, sensation, exogenous feeding and swimming was prioritized. Comparisons with other African and Neotropical cichlids revealed differences in ontogenetic processes and allometric growth along the anterior-posterior axis as well as variation in developmental timing. These results indicate how early morphological development and ontogenic processes might respond to the distinctive parental care observed in mouth-brooding cichlids.

The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni

Astatotilapia burtoni is a member of the "modern haplochromines," the most species-rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d-loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction-associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP-based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake-level fluctuations leading to past contact zones between otherwise isolated populations and large-scale migration events.

Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata

B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.

Visual adaptation in Lake Victoria cichlid fishes: depth-related variation of color and scotopic opsins in species from sand/mud bottoms

Background

For Lake Victoria cichlid species inhabiting rocky substrates with differing light regimes, it has been proposed that adaptation of the long-wavelength-sensitive (LWS) opsin gene triggered speciation by sensory drive through color signal divergence. The extensive and continuous sand/mud substrates are also species-rich, and a correlation between male nuptial coloration and the absorption of LWS pigments has been reported. However, the factors driving genetic and functional diversity of LWS pigments in sand/mud habitats are still unresolved.

Results

To address this issue, nucleotide sequences of eight opsin genes were compared in ten Lake Victoria cichlid species collected from sand/mud bottoms. Among eight opsins, the LWS and rod-opsin (RH1) alleles were diversified and one particular allele was dominant or fixed in each species. Natural selection has acted on and fixed LWS alleles in each species. The functions of LWS and RH1 alleles were measured by absorption of reconstituted A1- and A2-derived visual pigments. The absorption of pigments from RH1 alleles most common in deep water were largely shifted toward red, whereas those of LWS alleles were largely shifted toward blue in both A1 and A2 pigments. In both RH1 and LWS pigments, A2-derived pigments were closer to the dominant light in deep water, suggesting the possibility of the adaptation of A2-derived pigments to depth-dependent light regimes.

Conclusions

The RH1 and LWS sequences may be diversified for adaptation of A2-derived pigments to different light environments in sand/mud substrates. Diversification of the LWS alleles may have originally taken place in riverine environments, with a new mutation occurring subsequently in Lake Victoria.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1040-x) contains supplementary material, which is available to authorized users.

Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish, Bagrus docmak, in East Africa

The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (-3.769 and -5.049; p < .05). Heterozygosity deficiencies and restricted effective population size (NeLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (ɸST = 0.62 for mtDNA; p < .001) and contemporary (microsatellite FST = 0.460; p < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro- and micro-evolutionary forces in the formation of the East African teleost fauna.

Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa

Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.

Behavioral color vision in a cichlid fish: Metriaclima benetos

Color vision is the capacity to discriminate color regardless of brightness. It is essential for many fish species as they rely on color discrimination for numerous ecological tasks. The study of color vision is important because it can unveil the mechanisms that shape coloration patterns, visual system sensitivities and, hence, visual signals. In order to better understand the mechanisms underlying color vision, an integrative approach is necessary. This usually requires combining behavioral, physiological and genetic experiments with quantitative modeling, resulting in a distinctive characterization of the visual system. Here, we provide new data on the color vision of a rock-dwelling cichlid from Lake Malawi: Metriaclima benetos. For this study we used a behavioral approach to demonstrate color vision through classical conditioning, complemented with modeling of color vision to estimate color contrast. For our experiments we took into account opsin coexpression and considered whether cichlids exhibit a dichromatic or a trichromatic visual system. Behavioral experiments confirmed color vision in M. benetos; most fish were significantly more likely to choose the trained over the distracter stimuli, irrespective of brightness. Our results are supported by visual modeling that suggests that cichlids are trichromats and achieve color vision through color opponency mechanisms, which are a result of three different photoreceptor channels. Our analyses also suggest that opsin coexpression can negatively affect perceived color contrast. This study is particularly relevant for research on the cichlid lineage because cichlid visual capabilities and coloration patterns are implicated in their adaptive radiation.

How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations

There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.

Weak link between dispersal and parasite community differentiation or immunogenetic divergence in two sympatric cichlid fishes

Geographical isolation, habitat variation and trophic specialization have contributed to a large extent to the astonishing diversity of cichlid fishes in the Great East African lakes. Because parasite communities often vary across space and environments, parasites can accompany and potentially enhance cichlid species diversification. However, host dispersal may reduce opportunities for parasite-driven evolution by homogenizing parasite communities and allele frequencies of immunity genes. To test for the relationships between parasite community variation, host dispersal and parasite-induced host evolution, we studied two sympatric cichlid species with contrasting dispersal capacities along the shores of southern Lake Tanganyika. Whereas the philopatric Tropheus moorii evolved into several genetically differentiated colour morphs, Simochromis diagramma is phenotypically rather uniform across its distribution range and shows only weak population structure. Populations of both species were infected with divergent parasite communities and harbour differentiated variant pools of an important set of immune genes, the major histocompatibility complex (MHC). The overall extent of geographical variation of parasites and MHC genes was similar between host species. This indicates that immunogenetic divergence among populations of Lake Tanganyika cichlids can occur even in species that are strongly dispersing. However, because this also includes species that are phenotypically uniform, parasite-induced evolution may not represent a key factor underlying species diversification in this system.

Cichlids: A Host of Opportunities for Evolutionary Parasitology

Thanks to high species diversity and a broad range of speciation mechanisms, cichlid fishes represent a textbook model in evolutionary biology. They are also of substantial economic value. Despite this importance, cichlid parasites remain understudied, although some are more diverse than their hosts. They may offer important insights into cichlid evolution and the evolution of host-parasite interactions. We review five major lines of research conducted on cichlid parasites so far: the study of parasite diversity and speciation; the role of parasites in cichlid diversification; the evolutionary ecology of host specificity; historical biogeography; and biological invasions. We call for more research in these areas and suggest approaches to valorise the potential that cichlid parasites hold for the study of evolutionary parasitology.

Species of Gyrodactylus von Nordmann, 1832 (Platyhelminthes: Monogenea) from cichlids from Zambezi and Limpopo river basins in Zimbabwe and South Africa: evidence for unexplored species richness

New findings on Gyrodactylus spp. parasitising African cichlids in southern Africa are presented, comprising data from Zimbabwe and South Africa. Morphometry of opisthaptoral hard parts in combination with nuclear ribosomal DNA sequences confirmed the presence of six species of Gyrodactylus von Nordmann, 1832. Three new species are described from fishes in Zimbabwe: Gyrodactylus chitandiri n. sp. from the gill arches of Coptodon rendalli (Boulenger) and Pseudocrenilabrus philander (Weber); Gyrodactylus occupatus n. sp. from the fins of Oreochromis niloticus (L.), Pharyngochromis acuticeps (Steindachner) and P. philander; and Gyrodactylus parisellei n. sp. from the fins of O. niloticus, P. philander and Tilapia sp. Gyrodactylus nyanzae Paperna, 1973 was also identified from the gills of O. niloticus and C. rendalli collected from two localities in Zimbabwe; these findings represent new host and locality records for this parasite. Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 was identified from P. philander collected in South Africa and Zimbabwe thereby providing new host and locality records for this parasite. Finally, Gyrodactylus yacatli García-Vásquez, Hansen, Christison, Bron & Shinn, 2011 was collected from the fins of O. niloticus and P. philander studied in Zimbabwe; this represents the first record of this species from the continent of Africa. Notably, this study improves upon the knowledge of Gyrodactylus spp. parasitising cichlids from these southern African regions. All species studied were recorded from at least two different cichlid host species indicating trend for a wide range of Gyrodactylus hosts in Africa. Accordingly, this supports the idea of intensive host switching in the course of their evolution.

Cichlid fishes as a model to understand normal and clinical craniofacial variation

We have made great strides towards understanding the etiology of craniofacial disorders, especially for 'simple' Mendelian traits. However, the facial skeleton is a complex trait, and the full spectrum of genetic, developmental, and environmental factors that contribute to its final geometry remain unresolved. Forward genetic screens are constrained with respect to complex traits due to the types of genes and alleles commonly identified, developmental pleiotropy, and limited information about the impact of environmental interactions. Here, we discuss how studies in an evolutionary model - African cichlid fishes - can complement traditional approaches to understand the genetic and developmental origins of complex shape. Cichlids exhibit an unparalleled range of natural craniofacial morphologies that model normal human variation, and in certain instances mimic human facial dysmorphologies. Moreover, the evolutionary history and genomic architecture of cichlids make them an ideal system to identify the genetic basis of these phenotypes via quantitative trait loci (QTL) mapping and population genomics. Given the molecular conservation of developmental genes and pathways, insights from cichlids are applicable to human facial variation and disease. We review recent work in this system, which has identified lbh as a novel regulator of neural crest cell migration, determined the Wnt and Hedgehog pathways mediate species-specific bone morphologies, and examined how plastic responses to diet modulate adult facial shapes. These studies have not only revealed new roles for existing pathways in craniofacial development, but have identified new genes and mechanisms involved in shaping the craniofacial skeleton. In all, we suggest that combining work in traditional laboratory and evolutionary models offers significant potential to provide a more complete and comprehensive picture of the myriad factors that are involved in the development of complex traits.

Genetic evidence for prevalence of alloparental care in a socially monogamous biparental cichlid fish, Perissodus microlepis, from Lake Tanganyika supports the "selfish shepherd effect" hypothesis

Alloparental care – care for unrelated young – is rare in animals, and its ecological or evolutionary advantages or, alternative maladaptive nature, remain unclear. We investigate alloparental care in the socially monogamous cichlid fish Perissodus microlepis from Lake Tanganyika that exhibits bi‐parental care. In a genetic parentage analysis, we discovered a surprisingly high percentage of alloparental care represented by brood mixing, extra‐pair paternity and extra‐pair maternity in all broods that we investigated. The percentage of nondescendant juveniles of other parents, i.e., brood mixing, ranged from 5% to 57% (mean = 28%). The distribution of genetic parentage also suggests that this socially monogamous species has, in fact, polygamous mating system. The prevalence of genetically mixed broods can be best explained by two, not mutually exclusive hypotheses on farming‐out and fostering behaviors. In the majority of broods, the sizes of the parents’ own (descendant) offspring were significantly larger than those of the adopted (nondescendant) juveniles, supporting the ‘selfish shepherd effect’ hypothesis, i.e., that foster parents preferentially accept unrelated “smaller or not larger” young since this would tend to lower the predation risks for their own larger offspring. There was also a tendency for larger parents particularly mothers, more so than smaller parents, to care predominantly for their own offspring. Larger parents might be better at defending against cuckoldry and having foreign young dumped into their broods through farming‐out behavior. This result might argue for maladaptive effects of allopatric care for the foster parents that only larger and possibly more experienced pairs can guard against. It needs to be determined why, apparently, the ability to recognize one's own young has not evolved in this species.

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

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.

Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

Chemical communication in cichlids: A mini-review

The family Cichlidae is well-known for pair-formation, parental care, territoriality, elaborate courtship and social organization. Do cichlids use chemical communication to mediate any of these behaviours? Early studies suggest that parent cichlids can discriminate between conspecific and heterospecific wrigglers (but not eggs) using olfactory cues. Some species are able to discriminate between their own brood and other conspecific broods based on olfaction. The young recognise conspecific adults (although not necessarily their parents) through the odorants they release. In both scenarios, protection of the young from predation is the likely selective force. Some male cichlids use urinary pheromones during courtship and spawning to attract females and induce ovulation. Females--in their turn--may base their mate-choice in part on assessment of those self-same pheromones. The same pheromonal system may be involved in establishing and maintaining the social hierarchies in lek-breeding cichlids. Individual recognition is also mediated by chemical communication. Finally, there is ample behavioural evidence that cichlids--like ostariophysan fish--release alarm cues that alert conspecifics to predation danger. Although the effects of these cues may be similar (e.g., increased shelter use, tighter schooling), they are different substances which remain to be identified. Cichlids, then, use chemical communication associated with many different behaviours. However, given the diversity of cichlids, little is known about the mechanisms of chemical communication or the chemical identity of the cues involved. The aim of this mini-review is to persuade those working with cichlids to consider the involvement of chemical communication, and those working in chemical communication to consider using cichlids.

Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichtys minckleyi

Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The 'desert cichlid' Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.

Constraint and diversification of developmental trajectories in cichlid facial morphologies

Background

A major goal of evolutionary biology is to understand the origins of phenotypic diversity. Changes in development, for instance heterochrony, can be a potent source of phenotypic variation. On the other hand, development can also constrain the spectrum of phenotypes that can be produced. In order to understand these dual roles of development in evolution, we examined the developmental trajectory of a trait central to the extensive adaptive radiation of East African cichlid fishes: craniofacial adaptations that allow optimal exploitation of ecological niches. Specifically, we use geometric morphometric analysis to compare morphological ontogenies among six species of Lake Malawi cichlids (n > 500 individuals) that span a major ecomorphological axis. We further evaluate how modulation of Wnt signaling impacts the long-term developmental trajectory of facial development.

Results

We find that, despite drastic differences in adult craniofacial morphologies, there are general similarities in the path of craniofacial ontogeny among species, suggesting that natural selection is working within a conserved developmental program. However, we also detect species-specific differences in the timing, direction, and/or duration of particular developmental trajectories, including evidence of heterochrony. Previous work in cichlids and other systems suggests that species-specific differences in adult morphology are due to changes in molecular signaling pathways that regulate early craniofacial development. In support of this, we demonstrate that modulation of Wnt signaling at early stages can shift a developmental trajectory into morphospace normally occupied by another species. However, without sustained modulation, craniofacial shape can recover by juvenile stages. This underscores the idea that craniofacial development is robust and that adult head shapes are the product of many molecular changes acting over extended periods of development.

Conclusions

Our results are consistent with the hypothesis that development acts to both constrain and promote morphological diversity. They also illustrate the modular nature of the craniofacial skeleton and hence the ability of selection to act upon distinct anatomical features in an independent manner. We propose that trophic diversity among cichlids has been achieved via shifts in both specific (e.g., stage-specific changes in gene expression) and global (e.g., heterochrony) ontogenetic processes acting within a conserved developmental program.

Electronic supplementary material

The online version of this article (doi:10.1186/s13227-015-0020-8) contains supplementary material, which is available to authorized users.