East African Cichlid Fishes Research Articles

Sex chromosomes in the tribe Cyprichromini (Teleostei: Cichlidae) of Lake Tanganyika

Sex determining loci have been described on at least 12 of 22 chromosomes in East African cichlid fishes, indicating a high rate of sex chromosome turnover. To better understand the rates and patterns of sex chromosome replacement, we used new methods to characterize the sex chromosomes of the cichlid tribe Cyprichromini from Lake Tanganyika. Our k-mer based methods successfully identified sex-linked polymorphisms without the need for a reference genome. We confirm the three previously reported sex chromosomes in this group. We determined the polarity of the sex chromosome turnover on LG05 in Cyprichromis as ZW to XY. We identified a new ZW locus on LG04 in Paracyprichromis brieni. The LG15 XY locus in Paracyprichromis nigripinnis was not found in other Paracyprichromis species, and the sample of Paracyprichromis sp. “tembwe” is likely to be of hybrid origin. Although highly divergent sex chromosomes are thought to develop in a stepwise manner, we show two cases (LG05-ZW and LG05-XY) in which the region of differentiation encompasses most of the chromosome, but appears to have arisen in a single step. This study expands our understanding of sex chromosome evolution in the Cyprichromini, and indicates an even higher level of sex chromosome turnover than previously thought.

The repeated evolution of stripe patterns is correlated with body morphology in the adaptive radiations of East African cichlid fishes.

Color patterns are often linked to the behavioral and morphological characteristics of an animal, contributing to the effectiveness of such patterns as antipredatory strategies. Species‐rich adaptive radiations, such as the freshwater fish family Cichlidae, provide an exciting opportunity to study trait correlations at a macroevolutionary scale. Cichlids are also well known for their diversity and repeated evolution of color patterns and body morphology. To study the evolutionary dynamics between color patterns and body morphology, we used an extensive dataset of 461 species. A phylogenetic supertree of these species shows that stripe patterns evolved ~70 times independently and were lost again ~30 times. Moreover, stripe patterns show strong signs of correlated evolution with body elongation, suggesting that the stripes’ effectiveness as antipredatory strategy might differ depending on the body shape. Using pedigree‐based analyses, we show that stripes and body elongation segregate independently, indicating that the two traits are not genetically linked. Their correlation in nature is therefore likely maintained by correlational selection. Lastly, by performing a mate preference assay using a striped CRISPR‐Cas9 mutant of a nonstriped species, we show that females do not differentiate between striped CRISPR mutant males and nonstriped wild‐type males, suggesting that these patterns might be less important for species recognition and mate choice. In summary, our study suggests that the massive rates of repeated evolution of stripe patterns are shaped by correlational selection with body elongation, but not by sexual selection.

A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples

Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.

Genome sequences of Tropheus moorii and Petrochromis trewavasae, two eco-morphologically divergent cichlid fishes endemic to Lake Tanganyika

With more than 1000 species, East African cichlid fishes represent the fastest and most species-rich vertebrate radiation known, providing an ideal model to tackle molecular mechanisms underlying recurrent adaptive diversification. We add high-quality genome reconstructions for two phylogenetic key species of a lineage that diverged about ~ 3–9 million years ago (mya), representing the earliest split of the so-called modern haplochromines that seeded additional radiations such as those in Lake Malawi and Victoria. Along with the annotated genomes we analysed discriminating genomic features of the study species, each representing an extreme trophic morphology, one being an algae browser and the other an algae grazer. The genomes of Tropheus moorii (TM) and Petrochromis trewavasae (PT) comprise 911 and 918 Mbp with 40,300 and 39,600 predicted genes, respectively. Our DNA sequence data are based on 5 and 6 individuals of TM and PT, and the transcriptomic sequences of one individual per species and sex, respectively. Concerning variation, on average we observed 1 variant per 220 bp (interspecific), and 1 variant per 2540 bp (PT vs PT)/1561 bp (TM vs TM) (intraspecific). GO enrichment analysis of gene regions affected by variants revealed several candidates which may influence phenotype modifications related to facial and jaw morphology, such as genes belonging to the Hedgehog pathway (SHH, SMO, WNT9A) and the BMP and GLI families.

Radical change: temporal patterns of oxidative stress during social ascent in a dominance hierarchy

Dominant individuals have priority access to mates and resources. However, high rank can be costly too, especially when it is maintained by intense agonistic behavior. Oxidative stress has been proposed as a potential cost of social dominance. However, social dominance hierarchies can be dynamic, and few studies have examined the cost of social dominance when males are changing status. We studied temporal changes in markers of oxidative stress during social ascent in the East African cichlid fish Astatotilapia burtoni. After removing the dominant male, males ascended from subordinate to dominant status. On the first day of social ascent, immediately after the dominant male removal, the newly dominant male showed lower levels of plasma total antioxidant capacity (TAC). However, we found that liver TAC and liver superoxide dismutase (SOD), an enzymatic antioxidant, were significantly upregulated on day 1 and 2 of social ascent, respectively. No temporal variation in nicotinamide adenine dinucleotide phosphate-oxidase (NADPH-oxidase) activity, blood DNA damage, and liver DNA damage was observed. By day 14, all markers of oxidative stress were similar to those observed in stable dominant males, which had higher levels of reactive oxygen metabolites (ROM) compared to subordinate males. We conclude that markers of oxidative stress vary dramatically during social ascent in a time- and tissue-dependent manner. Our study provides a more nuanced look at the oxidative cost of social dominance and highlights the importance of considering temporal changes in markers of oxidative stress during important life-history events. High social status gives priority access to resources but also entails costs. Since dominant individuals tend to have higher metabolic rates, oxidative stress could be a potential cost of high social status. Oxidative stress can occur when reactive oxygen species, produced during metabolic activities, cannot be effectively neutralized by antioxidants, leading to oxidative cellular damage. Social hierarchies can be dynamic, yet how the cost of rank varies when males are changing social status is unknown. We allowed subordinate males to ascend to dominant status in the cichlid fish Astatotilapia burtoni. At the beginning of social ascent when males suddenly increase aggressive behavior, the total antioxidant defense was lower in blood plasma, as expected, when males suddenly increase their metabolism during aggressive interactions. However, antioxidant defense was increased in the liver suggesting that males can compensate for the potential cost of becoming dominant. Circulating reactive oxygen metabolites gradually increased over time reaching levels similar to stable dominant males, possibly due to males upregulating their reproductive axis. Our results highlight that markers of oxidative stress can vary dramatically over time during important events in life.

Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii

East African cichlid fishes represent a model to tackle adaptive changes and their connection to rapid speciation and ecological distinction. In comparison to bony craniofacial tissues, adaptive morphogenesis of soft tissues has been rarely addressed, particularly at the molecular level. The nuchal hump in cichlids fishes is one such soft-tissue and exaggerated trait that is hypothesized to play an innovative role in the adaptive radiation of cichlids fishes. It has also evolved in parallel across lakes in East Africa and Central America. Using gene expression profiling, we identified and validated a set of genes involved in nuchal hump formation in the Lake Malawi dolphin cichlid, Cyrtocara moorii. In particular, we found genes differentially expressed in the nuchal hump, which are involved in controlling cell proliferation (btg3, fosl1a and pdgfrb), cell growth (dlk1), craniofacial morphogenesis (dlx5a, mycn and tcf12), as well as regulators of growth-related signals (dpt, pappa and socs2). This is the first study to identify the set of genes associated with nuchal hump formation in cichlids. Given that the hump is a trait that evolved repeatedly in several African and American cichlid lineages, it would be interesting to see if the molecular pathways and genes triggering hump formation follow a common genetic track or if the trait evolved in parallel, with distinct mechanisms, in other cichlid adaptive radiations and even in other teleost fishes.

Immigrant and extrinsic hybrid inviability contribute to reproductive isolation between lake and river cichlid ecotypes.

Understanding how reproductive barriers evolve and which barriers contribute to speciation requires the examination of organismal lineages that are still in the process of diversification and the study of the full range of reproductive barriers acting at different life stages. Lake and river ecotypes of the East African cichlid fish Astatotilapia burtoni show habitat-specific adaptations, despite different levels of genetic differentiation, and thus represent an ideal model to study the evolution of reproductive barriers. To evaluate the degree of reproductive isolation between genetically divergent lake and river populations, we performed a mesocosm mating experiment in a semi-natural setting at Lake Tanganyika. We assessed reproductive isolation in the presence of male-male competition by analyzing survival and growth rates of introduced adults and their reproductive success from genetic parentage of surviving offspring. The genetically divergent river population showed reduced fitness in terms of survival, growth rate, and mating success in a lake-like environment. Hybrid offspring between different populations showed intermediate survival consistent with extrinsic postzygotic reproductive barriers. Our results suggest that both prezygotic (immigrant inviability) and postzygotic reproductive barriers contribute to divergence, and highlight the value of assessing multiple reproductive barriers acting at different stages and in natural contexts to understand speciation mechanisms.

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes

Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species’ dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.

Adaptive phenotypic plasticity contributes to divergence between lake and river populations of an East African cichlid fish.

Adaptive phenotypic plasticity and fixed genotypic differences have long been considered opposing strategies in adaptation. More recently, these mechanisms have been proposed to act complementarily and under certain conditions jointly facilitate evolution, speciation, and even adaptive radiations. Here, we investigate the relative contributions of adaptive phenotypic plasticity vs. local adaptation to fitness, using an emerging model system to study early phases of adaptive divergence, the generalist cichlid fish species Astatotilapia burtoni. We tested direct fitness consequences of morphological divergence between lake and river populations in nature by performing two transplant experiments in Lake Tanganyika. In the first experiment, we used wild‐caught juvenile lake and river individuals, while in the second experiment, we used F1 crosses between lake and river fish bred in a common garden setup. By tracking the survival and growth of translocated individuals in enclosures in the lake over several weeks, we revealed local adaptation evidenced by faster growth of the wild‐caught resident population in the first experiment. On the other hand, we did not find difference in growth between different types of F1 crosses in the second experiment, suggesting a substantial contribution of adaptive phenotypic plasticity to increased immigrant fitness. Our findings highlight the value of formally comparing fitness of wild‐caught and common garden‐reared individuals and emphasize the necessity of considering adaptive phenotypic plasticity in the study of adaptive divergence.

Molecular investigation of genetic assimilation during the rapid adaptive radiations of East African cichlid fishes.

Adaptive radiations are characterized by adaptive diversification intertwined with rapid speciation within a lineage resulting in many ecologically specialized, phenotypically diverse species. It has been proposed that adaptive radiations can originate from ancestral lineages with pronounced phenotypic plasticity in adaptive traits, facilitating ecologically driven phenotypic diversification that is ultimately fixed through genetic assimilation of gene regulatory regions. This study aimed to investigate how phenotypic plasticity is reflected in gene expression patterns in the trophic apparatus of several lineages of East African cichlid fishes, and whether the observed patterns support genetic assimilation. This investigation used a split brood experimental design to compare adaptive plasticity in species from within and outside of adaptive radiations. The plastic response was induced in the crushing pharyngeal jaws through feeding individuals either a hard or soft diet. We find that nonradiating, basal lineages show higher levels of adaptive morphological plasticity than the derived, radiated lineages, suggesting that these differences have become partially genetically fixed during the formation of the adaptive radiations. Two candidate genes that may have undergone genetic assimilation, gif and alas1, were identified, in addition to alterations in the wiring of LPJ patterning networks. Taken together, our results suggest that genetic assimilation may have dampened the inducibility of plasticity related genes during the adaptive radiations of East African cichlids, flattening the reaction norms and canalizing their feeding phenotypes, driving adaptation to progressively more narrow ecological niches.

Demography and genome divergence of lake and stream populations of an East African cichlid fish.

Disentangling the processes and mechanisms underlying adaptive diversification is facilitated by the comparative study of replicate population pairs that have diverged along a similar environmental gradient. Such a setting is realized in a cichlid fish from southern Lake Tanganyika, Astatotilapia burtoni, which occurs within the lake proper as well as in various affluent rivers. Previously, we demonstrated that independent lake and stream populations show similar adaptations to the two habitat regimes. However, little is known about the evolutionary and demographic history of the A.burtoni populations in question and the patterns of genome divergence among them. Here, we apply restriction site-associated DNA sequencing (RADseq) to examine the evolutionary history, the population structure and genomic differentiation of lake and stream populations in A.burtoni. A phylogenetic reconstruction based on genome-wide molecular data largely resolved the evolutionary relationships among populations, allowing us to re-evaluate the independence of replicate lake-stream population clusters. Further, we detected a strong pattern of isolation by distance, with baseline genomic divergence increasing with geographic distance and decreasing with the level of gene flow between lake and stream populations. Genome divergence patterns were heterogeneous and inconsistent among lake-stream population clusters, which is explained by differences in divergence times, levels of gene flow and local selection regimes. In line with the latter, we only detected consistent outlier loci when the most divergent lake-stream population pair was excluded. Several of the thus identified candidate genes have inferred functions in immune and neuronal systems and show differences in gene expression between lake and stream populations.

Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes.

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.

Gene duplications and the evolution of c-type lysozyme during adaptive radiation of East African cichlid fish

The adaptive radiation of African cichlids is a prime model system for studying vertebrate speciation. Cichlid species are distributed in lakes and rivers with various water conditions such as various pH values. The innate immune system in fish is particularly important because water contains a wide range of pathogenic microorganisms. To investigate the evolution of the host defense system in cichlids, we isolated the c-type lysozyme gene, which functions in the innate immune system of fish. Southern blot and sequence analyses showed that the lysozyme gene underwent several gene duplication events and evolved with amino acid replacements during the adaptive radiation of cichlids. The inferred 3D structure revealed that the amino acid substitutions were localized on the lysozyme surface. Moreover, more than half of the surface substitutions changed the charge of amino acid residues, suggesting changes in the optimum pH for enzymatic activity. In African cichlids, the lysozyme genes may have played and still play an important role in defense against pathogens.

Inhibition of Aromatase Induces Partial Sex Change in a Cichlid Fish: Distinct Functions for Sex Steroids in Brains and Gonads

Sex steroids are major drivers of sexual development and also responsible for the maintenance of the established gender. Especially fishes exhibit great plasticity and less conservation in sex determination and sexual development compared to other vertebrate groups. In addition, fishes have a constant sex steroid production throughout their entire lifespan, which makes them particularly susceptible to interferences with the endogenous sex steroid system. This susceptibility has recently been used to show that inhibition of the key enzyme of estrogen synthesis, aromatase Cyp19a1, can induce functional sex reversal even in adult fish. Here, we investigated the impact of the aromatase inhibitor (AI) fadrozole in adult females of the East African cichlid fish Astatotilapia burtoni. Using gene expression, phenotypic measurements, behavioral experiments, and hormone measurements, we assessed if females treated with fadrozole develop a male-like phenotype. We found that AI treatment has a different effect on gene expression in the gonad compared to the brain, the 2 tissues mostly implicated in sexual development. In contrast to observations in other gonochoristic species, A. burtoni ovaries cannot be transformed into functional testis by AI. However, rapid changes towards a male-like phenotype can be induced with AI in coloration, hormone levels, and behavior.

Constraint and diversification of developmental trajectories in cichlid facial morphologies.

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

Parallel evolution in Ugandan crater lakes: repeated evolution of limnetic body shapes in haplochromine cichlid fish

BackgroundThe enormous diversity found in East African cichlid fishes in terms of morphology, coloration, and behavior have made them a model for the study of speciation and adaptive evolution. In particular, haplochromine cichlids, by far the most species-rich lineage of cichlids, are a well-known textbook example for parallel evolution. Southwestern Uganda is an area of high tectonic activity, and is home to numerous crater lakes. Many Ugandan crater lakes were colonized, apparently independently, by a single lineage of haplochromine cichlids. Thereby, this system could be considered a natural experiment in which one can study the interaction between geographical isolation and natural selection promoting phenotypic diversification.ResultsWe sampled 13 crater lakes and six potentially-ancestral older lakes and, using both mitochondrial and microsatellite markers, discovered strong genetic and morphological differentiation whereby (a) geographically close lakes tend to be genetically more similar and (b) three different geographic areas seem to have been colonized by three independent waves of colonization from the same source population. Using a geometric morphometric approach, we found that body shape elongation (i.e. a limnetic morphology) evolved repeatedly from the ancestral deeper-bodied benthic morphology in the clear and deep crater lake habitats.ConclusionsA pattern of strong genetic and morphological differentiation was observed in the Ugandan crater lakes. Our data suggest that body shape changes have repeatedly evolved into a more limnetic-like form in several Ugandan crater lakes after independent waves of colonization from the same source population. The observed morphological changes in crater lake cichlids are likely to result from a common selective regime.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0287-3) contains supplementary material, which is available to authorized users.

Quantitative Genetic Analyses of Male Color Pattern and Female Mate Choice in a Pair of Cichlid Fishes of Lake Malawi, East Africa.

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1–2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.

Genetics and timing of sex determination in the East African cichlid fish Astatotilapia burtoni.

BackgroundThe factors determining sex are diverse in vertebrates and especially so in teleost fishes. Only a handful of master sex-determining genes have been identified, however great efforts have been undertaken to characterize the subsequent genetic network of sex differentiation in various organisms. East African cichlids offer an ideal model system to study the complexity of sexual development, since many different sex-determining mechanisms occur in closely related species of this fish family. Here, we investigated the sex-determining system and gene expression profiles during male development of Astatotilapia burtoni, a member of the rapidly radiating and exceptionally species-rich haplochromine lineage.ResultsCrossing experiments with hormonally sex-reversed fish provided evidence for an XX-XY sex determination system in A. burtoni. Resultant all-male broods were used to assess gene expression patterns throughout development of a set of candidate genes, previously characterized in adult cichlids only.ConclusionsWe could identify the onset of gonad sexual differentiation at 11–12 dpf. The expression profiles identified wnt4B and wt1A as the earliest gonad markers in A. burtoni. Furthermore we identified late testis genes (cyp19a1A, gsdf, dmrt1 and gata4), and brain markers (ctnnb1A, ctnnb1B, dax1A, foxl2, foxl3, nanos1A, nanos1B, rspo1, sf-1, sox9A and sox9B).Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0140-5) contains supplementary material, which is available to authorized users.

Adaptive divergence between lake and stream populations of an East African cichlid fish.

Divergent natural selection acting in different habitats may build up barriers to gene flow and initiate speciation. This speciation continuum can range from weak or no divergence to strong genetic differentiation between populations. Here, we focus on the early phases of adaptive divergence in the East African cichlid fish Astatotilapia burtoni, which occurs in both Lake Tanganyika (LT) and inflowing rivers. We first assessed the population structure and morphological differences in A.burtoni from southern LT. We then focused on four lake-stream systems and quantified body shape, ecologically relevant traits (gill raker and lower pharyngeal jaw) as well as stomach contents. Our study revealed the presence of several divergent lake-stream populations that rest at different stages of the speciation continuum, but show the same morphological and ecological trajectories along the lake-stream gradient. Lake fish have higher bodies, a more superior mouth position, longer gill rakers and more slender pharyngeal jaws, and they show a plant/algae and zooplankton-biased diet, whereas stream fish feed more on snails, insects and plant seeds. A test for reproductive isolation between closely related lake and stream populations did not detect population-assortative mating. Analyses of F1 offspring reared under common garden conditions indicate that the detected differences in body shape and gill raker length do not constitute pure plastic responses to different environmental conditions, but also have a genetic basis. Taken together, the A.burtoni lake-stream system constitutes a new model to study the factors that enhance and constrain progress towards speciation in cichlid fishes.

Immune-related functions of the Hivep gene family in East African cichlid fishes.

Immune-related genes are often characterized by adaptive protein evolution. Selection on immune genes can be particularly strong when hosts encounter novel parasites, for instance, after the colonization of a new habitat or upon the exploitation of vacant ecological niches in an adaptive radiation. We examined a set of new candidate immune genes in East African cichlid fishes. More specifically, we studied the signatures of selection in five paralogs of the human immunodeficiency virus type I enhancer-binding protein (Hivep) gene family, tested their involvement in the immune defense, and related our results to explosive speciation and adaptive radiation events in cichlids. We found signatures of long-term positive selection in four Hivep paralogs and lineage-specific positive selection in Hivep3b in two radiating cichlid lineages. Exposure of the cichlid Astatotilapia burtoni to a vaccination with Vibrio anguillarum bacteria resulted in a positive correlation between immune response parameters and expression levels of three Hivep loci. This work provides the first evidence for a role of Hivep paralogs in teleost immune defense and links the signatures of positive selection to host–pathogen interactions within an adaptive radiation.