A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach

Freshwater Habitats Promote Rapid Rates of Phenotypic Evolution in Sculpin Fishes (Perciformes: Cottoidea)

AbstractInvasions of freshwater habitats by marine fishes provide exceptional cases of habitat-driven biological diversification. Freshwater habitats make up less than 1% of aquatic habitats but contain ∼50% of fish species. However, while the dominant group of freshwater fishes (Otophysi) is older than that of most marine fishes (Percomorphaceae), it is less morphologically diverse. Classically, scientists have invoked differences in the tempo and/or mode of evolution to explain such cases of unequal morphological diversification. We tested for evidence of these phenomena in the superfamily Cottoidea (sculpins), which contains substantial radiations of marine and freshwater fishes. We find that the morphology of freshwater sculpins evolves faster but under higher constraint than that of marine sculpins, causing widespread convergence in freshwater sculpins and more morphological disparity in marine sculpins. The endemic freshwater sculpins of Lake Baikal, Siberia, are exceptions that demonstrate elevated novelty akin to that of marine sculpins. Several tantalizing factors may explain these findings, such as differences in habitat stability and/or habitat connectivity between marine and freshwater systems.

Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids

The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.

No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni

Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.

Phylogenetic relationships of sleeper gobies (Eleotridae: Gobiiformes: Gobioidei), with comments on the position of the miniature genus Microphilypnus

Microphilypnus and Leptophilypnion are miniaturized genera within the family Eleotridae. The evolutionary relationships among these taxa are still poorly understood, and molecular analyses are restricted to mitochondrial genes, which have not been conclusive. We compiled both mitochondrial and nuclear genes to study the phylogenetic position of Microphilypnus and the evolutionary history and relationships of eleotrids. We propose that Microphilypnus and Leptophilypnus (a non-miniature genus) are not sister groups as suggested by previous studies, but rather separate lineages that arose in the early Eocene, with Leptophilypnus recovered as a sister group to the other analyzed eleotrids. In fact, Microphilypnus is currently associated with the Neotropical clade Guavina/Dormitator/Gobiomorus. We also identified a well-supported clade that indicated Gobiomorus and Hemieleotris as paraphyletic groups, besides a close relationship among Calumia godeffroyi, Bunaka gyrinoides, Eleotris and Erotelis species. This is the first comprehensive report about the evolutionary relationships in members of the family Eleotridae, including multiloci and multispecies approaches. Therefore, we provided new insights about the phylogenetic position of some taxa absent in previous studies, such as the miniature genus Microphilypnus and a recently described species of Eleotris from South America.

Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation

Background

The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids.

Results

We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48].

Conclusions

These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02085-8.

Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.

Polymorphism of Sex Determination Amongst Wild Populations Suggests its Rapid Turnover Within the Nile Tilapia Species

Sex-determining regions have been identified in the Nile tilapia on linkage groups (LG) 1, 20 and 23, depending on the domesticated strains used. Sex determining studies on wild populations of this species are scarce. Previous work on two wild populations, from Lake Volta (Ghana) and from Lake Koka (Ethiopia), found the sex-determining region on LG23. These populations have a Y-specific tandem duplication containing two copies of the Anti-Müllerian Hormone amh gene (named amhY and amhΔY). Here, we performed a whole-genome short-reads analysis using male and female pools on a third wild population from Lake Hora (Ethiopia). We found no association of sex with LG23, and no duplication of the amh gene. Furthermore, we found no evidence of sex linkage on LG1 or on any other LGs. Long read whole genome sequencing of a male from each population confirmed the absence of a duplicated region on LG23 in the Lake Hora male. In contrast, long reads established the structure of the Y haplotype in Koka and Kpandu males and the order of the genes in the duplicated region. Phylogenies constructed on the nuclear and mitochondrial genomes, showed a closer relationship between the two Ethiopian populations compared to the Ghanaian population, implying an absence of the LG23Y sex-determination region in Lake Hora males. Our study supports the hypothesis that the amh region is not the sex-determining region in Hora males. The absence of the Y amh duplication in the Lake Hora population reflects a rapid change in sex determination within Nile tilapia populations. The genetic basis of sex determination in the Lake Hora population remains unknown.

Characterization and phylogenetic analysis of the complete mitochondrial genome of the rainbow krib, Pelvicachromis pulcher (Perciformes: Cichlidae)

We report the complete mitochondrial genome information of the rainbow krib, Pelvicachromis pulcher (Boulenger 1901). Illumina HiSeq genome sequencing allowed the assembly of a circular mitogenome of 17,196 base pairs (bp) from P. pulcher consisting of 47% GC nucleotides, 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a putative control region in the typical teleost gene composition. The gene order of the P. pulcher mitogenome was identical to that of other cichlid species. A maximum likelihood phylogenetic tree based on mitochondrial PCGs showed a relationship of P. pulcher with a cichlid Tylochromis polylepis (Boulenger 1900), suggesting that more complete mitogenomes are needed to explore mitogenome evolution in West African tribes and riverine cichlids, as this genomic information is the first complete mitogenome in the tribe Chromidotilapiini.

The complete mitochondrial genome of Lamprologus signatus (Perciformes: Cichlidae)

In this study, the complete 16,583 bp mitochondrial genome of Lamprologus signatus (Poll, 1952) was determined from a specimen sourced from Lake Tanganyika. The mitogenome contains 37 genes [13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes] and a putative control region, which consists of 27.1% A, 27.0% T, 29.9% C, and 16.0% G, with a total G + C content of 45.9%. A maximum likelihood phylogenetic tree based on mitochondrial PCGs suggested that L. signatus is clustered with members of the tribes Haplochromini and Tropheini. As this is the first report of the entire mitogenome in the tribe Lamprologini, the complete mitochondrial sequence information of L. sigantus will be useful in determining phylogenetic relationships of Pseudocrenilabrinae tribes.

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose new challenges for inferring evolutionary histories. Most existing methods for reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as a cause of intra- or intergenomic discordance. Here, we utilize a variety of methods, including those to infer phylogenetic networks, to account for both ILS and introgression as a cause for nuclear and cytoplasmic-nuclear discordance using phylogenomic data from the recently radiated flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse genus in Western North America with known and suspected gene flow between species. We find evidence for widespread discordance among nuclear loci that can be explained by both ILS and reticulate evolution in the evolutionary history of Polemonium. Furthermore, the histories of organellar genomes show strong discordance with the inferred species tree from the nuclear genome. Discordance between the nuclear and plastid genome is not completely explained by ILS, and only one case of discordance is explained by detected introgression events. Our results suggest that multiple processes have been involved in the evolutionary history of Polemonium and that the plastid genome does not accurately reflect species relationships. We discuss several potential causes for this cytoplasmic-nuclear discordance, which emerging evidence suggests is more widespread across the Tree of Life than previously thought. [Cyto-nuclear discordance, genomic discordance, phylogenetic networks, plastid capture, Polemoniaceae, Polemonium, reticulations.].

Six new species of Cichlidogyrus Paperna, 1960 (Platyhelminthes: Monogenea) from the gills of cichlids (Teleostei: Cichliformes) from the Lomami River Basin (DRC: Middle Congo)

BACKGROUND

Monogenea van Beneden, 1858 is a group of parasitic flatworms, commonly found infecting bony fish. Several genera, such as Cichlidogyrus Paperna, 1960, are reported to include potential pathogenic species that can negatively impact aquaculture fish stocks. They can switch from introduced to native fish and vice versa. In Africa (and all over the world), fish species belonging to Cichlidae are often kept in aquaculture and represent a major source of food. Thus, research on the biodiversity and occurrence of monogenean species on these fish is of importance for aquaculture and conservation. The present study is a survey of the diversity of species of Cichlidogyrus in the south of the Democratic Republic of the Congo (DRC) on three cichlid species: Orthochromis sp. 'Lomami', Serranochromis cf. macrocephalus, and Tilapia sparrmanii Smith, 1840.

METHODS

Specimens of Cichlidogyrus were isolated from the gills and mounted on glass slides with Hoyer's medium. The genital and haptoral hard parts were measured and drawn using interference contrast.

RESULTS

In total, six species of Cichlidogyrus were found, all new to science: C. bulbophallus n. sp. and C. pseudozambezensis n. sp. on S. cf. macrocephalus, C. flagellum n. sp. and C. lobus n. sp. on T. sparrmanii, C. ranula n. sp. on S. cf. macrocephalus and Orthochromis sp. 'Lomami', and C. maeander n. sp. found on Orthochromis sp. 'Lomami' and T. sparrmanii. The first four species are considered to be strict specialists, C. ranula n. sp. an intermediate generalist and C. maeander n. sp. a generalist. These parasite species show morphological similarities to species found in the Lower Guinea and Zambezi ichthyofaunal provinces, which might be explained by past river capture events between river systems of the Congo Province and both these regions.

CONCLUSIONS

Serranochromis cf. macrocephalus and Orthochromis sp. 'Lomami' can harbour respectively three and two species of Cichlidogyrus, all described in this study. Tilapia sparrmanii can harbour seven species, of which three are described in the present study. These results highlight the species diversity of this parasite genus in the Congo Basin.

Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika

African cichlids are well known for their adaptive radiations, but it is now apparent that they also harbor an extraordinary diversity of sex chromosome systems. In this study, we sequenced pools of males and females from species in 3 different genera of cichlids from Lake Tanganyika. We then searched for regions that were differentiated following the patterns expected for sex chromosomes. We report 2 novel sex chromosomes systems, an XY system on LG19 in Tropheus sp. "black" and a ZW system on LG7 in Hemibates stenosoma. We also identify a ZW system on LG5 in Cyprichromis leptosoma that may be convergent with a system previously described in Lake Malawi cichlids. Our data also identify candidate single nucleotide polymorphisms for the blue/yellow tail color polymorphism observed among male C. leptosoma.

Phylogenomic Analyses Clarify True Species within the Butterfly Genus Speyeria despite Evidence of a Recent Adaptive Radiation

When confronted with an adaptive radiation, considerable evidence is needed to resolve the evolutionary relationships of these closely related lineages. The North American genus Speyeria is one especially challenging radiation of butterflies due to potential signs of incomplete lineage sorting, ongoing hybridization, and similar morphological characters between species. Previous studies have found species to be paraphyletic and have been unable to disentangle taxa, often due to a lack of data and/or incomplete sampling. As a result, Speyeria remains unresolved. To achieve phylogenetic resolution of the genus, we conducted phylogenomic and population genomic analyses of all currently recognized North American Speyeria species, as well as several subspecies, using restriction-site-associated DNA sequencing (RADseq). Together, these analyses confirm the 16 canonical species, and clarify many internal relationships. However, a few relationships within Speyeria were poorly supported depending on the evolutionary model applied. This lack of resolution among certain taxa corroborates Speyeria is experiencing an ongoing adaptive radiation, with incomplete lineage sorting and lack of postzygotic reproductive barriers contributing to hybridization and further ambiguity. Given that many Speyeria taxa are under duress from anthropogenic factors, their legal protection must be viewed cautiously and on a case by case basis in order to properly conserve the diversity being generated.

New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini

A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstätte (Tugen Hills, Kenya) in the East African Rift Valley. Parsimony analysis of morphological characters using published phylogenetic frameworks for extant cichlids combined with the application of a comprehensive best-fit approach based on morphology was employed to place the new fossil taxon in the phylogenetic context of the African cichlids. The data reveal that the fossil specimens can be assigned to the tribe Oreochromini within the haplotilapiines. †Oreochromimos kabchorensis gen. et sp. nov. shows a mosaic set of characters bearing many similarities to the almost pan-African Oreochromis and the East African lake-endemic Alcolapia. As the striking diversity of present-day African cichlids, with 1100 recognised species, has remained largely invisible in the fossil record, the material described here adds significantly to our knowledge of the Miocene diversity of the group. It effectively doubles the age of a fossil calibration point, which has hitherto been used to calibrate divergence times of the East African cichlids in molecular phylogenetic investigations. Furthermore, the comparative dataset derived from extant cichlids presented here will greatly facilitate the classification of fossil cichlids in future studies.

East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation

BACKGROUND

Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates.

RESULTS

Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43-33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89-20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88-25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23-18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40-26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93-5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: 'Orthochromis' indermauri and 'Haplochormis' vanheusdeni.

CONCLUSIONS

Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated "Melting-Pot Tanganyika" hypothesis. The radiation of the 'Lower Congo Lamprologus clade' might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi.

Characterization of sex chromosomes in three deeply diverged species of Pseudocrenilabrinae (Teleostei: Cichlidae)

The African cichlid radiations have created thousands of new cichlid species with a wide diversity of trophic morphologies, behaviors, sensory systems and pigment patterns. In addition, recent research has uncovered a surprising number of young sex chromosome systems within African cichlids. Here we refine methods to describe the differentiation of young sex chromosomes from whole genome comparisons. We identified a novel XY sex chromosome system on linkage group 14 in Oreochromis mossambicus, confirmed a linkage group 1 XY system in Coptodon zillii and also defined the limits of our methodology by examining a ZW system on linkage group 3 in Pelmatolapia mariae. These data further demonstrate that cichlids are an excellent model system for understanding the early stages of sex chromosome evolution.

Signatures of Microevolutionary Processes in Phylogenetic Patterns

Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.

Variations in the breeding behavior of cichlids and the evolution of the multi-functional seminal plasma protein, seminal plasma glycoprotein 120

Background

Seminal plasma proteins are associated with successful fertilization. However, their evolutionary correlation with fertilization mechanisms remains unclear. Cichlids from Lake Tanganyika show a variety-rich spawning behavior that is associated with the transfer of the sperm to the egg for fertilization. One of these behaviors, called “oral fertilization,” emerged during their speciation. In oral fertilization, females nuzzle the milt from male genitalia and pick up the released eggs in their mouths, which are then fertilized inside the oral cavity. Thus, the success of the fertilization is dependent on the retention of sperm in the oral cavity during spawning. Sperm aggregation and immobilization in viscous seminal plasma may help retain the sperm inside the oral cavity, which ultimately determines the success of the fertilization. Seminal plasma glycoprotein 120 (SPP120) is one of the major seminal plasma proteins present in cichlids. SPP120 has been implicated to immobilize sperm and increase the milt viscosity. However, the functional linkage between oral fertilization and seminal plasma proteins has not been investigated.

Results

During trials of simulated oral fertilization, it was observed that milt viscosity contributed to fertilization success by facilitating longer retention of the milt inside the mouth during spawning. Glycosylation of SPP120 was associated with high milt viscosity. Its glycosylation was specifically present in the milt of cichlid species exhibiting oral fertilization. Moreover, recombinant SPP120 from several the oral fertilization species strongly immobilized/aggregated sperm. Therefore, the functions of SPP120 (immobilization/aggregation and its glycosylation) may contribute to success of oral fertilization, and these functions of SPP120 are more prominent in oral fertilization species. In addition, comparative phylogenetic analyses showed a positive evolutionary correlation between SPP120 function and oral fertilization. Hence, these evolutions may have occurred to keep up with the transition in the mode of fertilization. In addition, rapid evolution in the molecular sequence might be associated with functional modifications of SPP120.

Conclusion

These results suggest that SPP120 might be associated with oral fertilization. In other words, reproductive traits that define the interaction between sperms and eggs could be the evolutionary selective force that cause the rapid functional modification of the fertilization-related reproductive protein, SPP120.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1292-0) contains supplementary material, which is available to authorized users.

Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa

Genetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the African cichlids. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversify and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bio-conservation of some endangered cichlids is also essential due to the threat by invasive species.

Colour pattern predicts outcome of female contest competition in a sexually monomorphic fish

Selection arising from social competition over non-mating resources, i.e. resources that do not directly and immediately affect mating success, offers a powerful alternative to sexual selection to explain the evolution of conspicuous ornaments, particularly in females. Here, we address the hypothesis that competition associated with the territoriality exhibited by both males and females in the cichlid fish Tropheus selects for the display of a conspicuous colour pattern in both sexes. The investigated pattern consists of a vertical carotenoid-coloured bar on a black body. Bar width affected the probability of winning in size-matched female-female, but not male-male, contests for territory possession. Our results support the idea that the emergence of female territoriality contributed to the evolution of sexual monomorphism from a dimorphic ancestor, in that females acquired the same conspicuous coloration as males to communicate in contest competition.

An exploration of the links between parasites, trophic ecology, morphology, and immunogenetics in the Lake Tanganyika cichlid radiation

Differences in habitat and diet between species are often associated with morphological differences. Habitat and trophic adaptation have therefore been proposed as important drivers of speciation and adaptive radiation. Importantly, habitat and diet shifts likely impose changes in exposure to different parasites and infection risk. As strong selective agents influencing survival and mate choice, parasites might play an important role in host diversification. We explore this possibility for the adaptive radiation of Lake Tanganyika (LT) cichlids. We first compare metazoan macroparasites infection levels between cichlid tribes. We then describe the cichlids' genetic diversity at the major histocompatibility complex (MHC), which plays a key role in vertebrate immunity. Finally, we evaluate to what extent trophic ecology and morphology explain variation in infection levels and MHC, accounting for phylogenetic relationships. We show that different cichlid tribes in LT feature partially non-overlapping parasite communities and partially non-overlapping MHC diversity. While morphology explained 15% of the variation in mean parasite abundance, trophic ecology accounted for 16% and 22% of the MHC variation at the nucleotide and at the amino acid level, respectively. Parasitism and immunogenetic adaptation may thus add additional dimensions to the LT cichlid radiation.

Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) parasitizing the gills of Congolese cichlids from northern Lake Tanganyika

Seven new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) isolated from the gills of six cichlid host species belonging to four tribes and sampled from the Congolese coastline of Lake Tanganyika (LT) are described: Cichlidogyrus adkoningsi sp. nov. from Cyphotilapia frontosa (tribe Cyphotilapiini); C. koblmuelleri sp. nov. from Cardiopharynx schoutedeni (Ectodini); C. habluetzeli sp. nov. from C. schoutedeni and C. frontosa; C. antoineparisellei sp. nov. from Interochromis loocki (Tropheini); C. masilyai sp. nov. from Petrochromis orthognathus (Tropheini); C. salzburgeri sp. nov. from P. trewavasae, and C. sergemorandi sp. nov. from Tylochromis polylepis (Tylochromini). This study represents the first parasitological examination of cyphotilapiine cichlid hosts. Representatives of the Tanganyikan ectodine, tropheine, and tylochromine cichlids previously sampled from various localities in the lake yielded nine, twelve, and two described species of Cichlidogyrus, respectively. The study further includes a morphological characterization of the male copulatory organ of six undescribed species of Cichlidogyrus found on the gills of the tropheines I. loocki and P. orthognathus, and on those of Callochromis melanostigma and Xenotilapia flavipinnis (both Ectodini). Geographical variation in the monogenean fauna of I. loocki was observed. The most closely related cichlid species investigated in this study harboured Cichlidogyrus spp. exhibiting some similarities in their sclerotized structures. Thus, our paper provides additional evidence of the high species richness of Cichlidogyrus and the link with their hosts’s phylogenetic affinities in LT.

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.

Only true pelagics mix: comparative phylogeography of deepwater bathybatine cichlids from Lake Tanganyika

In the absence of dispersal barriers, species with great dispersal ability are expected to show little, if at all, phylogeographic structure. The East African Great Lakes and their diverse fish faunas provide opportunities to test this hypothesis in pelagic fishes, which are presumed to be highly mobile and unrestricted in their movement by physical barriers. Here, we address the link between panmixis and pelagic habitat use by comparing the phylogeographic structure among four deepwater cichlid species of the tribe Bathybatini from Lake Tanganyika. We show that the mitochondrial genealogies (based on the most variable part or the control region) of the four species are very shallow (0.8-4% intraspecific divergence across entire distribution ranges) and that all species experienced recent population growth. A lack of phylogeographic structure in the two eupelagic species, Bathybates fasciatus and B. leo, was consistent with expectations and with findings in other pelagic cichlid species. Contrary to expectations, a clear phylogeographic structure was detected in the two benthopelagic species, B. graueri and Hemibates stenosoma. Differences in genetic diversity between eupelagic and benthopelagic species may be due to differences in their dispersal propensity, mediated by their respective predatory niches, rather than precipitated by external barriers to dispersal.

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.

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.

Contrasting geographic structure in evolutionarily divergent Lake Tanganyika catfishes

Geographic isolation is suggested to be among the most important processes in the generation of cichlid fish diversity in East Africa's Great Lakes, both through isolation by distance and fluctuating connectivity caused by changing lake levels. However, even broad scale phylogeographic patterns are currently unknown in many non-cichlid littoral taxa from these systems. To begin to address this, we generated restriction-site-associated DNA sequence (RADseq) data to investigate phylogeographic structure throughout Lake Tanganyika (LT) in two broadly sympatric rocky shore catfish species from independent evolutionary radiations with differing behaviors: the mouthbrooding claroteine, Lophiobagrus cyclurus, and the brood-parasite mochokid, Synodontis multipunctatus. Our results indicated contrasting patterns between these species, with strong lake-wide phylogeographic signal in L. cyclurus including a deep divergence between the northern and southern lake basins. Further structuring of these populations was observed across a heterogeneous habitat over much smaller distances. Strong population growth was observed in L. cyclurus sampled from shallow shorelines, suggesting population growth associated with the colonization of new habitats following lake-level rises. Conversely, S. multipunctatus, which occupies a broader depth range, showed little phylogeographic structure and lower rates of population growth. Our findings suggest that isolation by distance and/or habitat barriers may play a role in the divergence of non-cichlid fishes in LT, but this effect varies by species.

Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes

Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.

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.

Underexplored diversity of gill monogeneans in cichlids from Lake Tanganyika: eight new species of Cichlidogyrus Paperna, 1960 (Monogenea: Dactylogyridae) from the northern basin of the lake, with remarks on the vagina and the heel of the male copulatory organ

Background

Lake Tanganyika harbours the most diverse cichlid assemblage of the Great African Lakes. Considering its cichlid flocks consist of approximately 250 endemic species, we can hypothesize a high species-richness in their often quite host-specific monogenean ectoparasites belonging to Cichlidogyrus Paperna, 1960. Yet, only 24 species were described from Tanganyikan hosts and some host tribes have never been investigated for monogeneans. This study presents the first parasitological examination of species of the tribes Cyprichromini (Cyprichromis microlepidotus (Poll, 1956)), Eretmodini (Eretmodus marksmithi Burgess, 2012 and Tanganicodus irsacae Poll, 1950) and Ectodini (Aulonocranus dewindti (Boulenger, 1899)). Specimens of the ectodine Ophthalmotilapia nasuta (Poll & Matthes, 1962) from which four Cichlidogyrus spp. have been previously described from more southern localities were also studied. Further, we discuss the haptor configuration in Tanganyikan Cichlidogyrus spp. and highlight the morphological diversity of the vagina, and that of the heel, a sclerotized part of the male copulatory organ, absent in some species of Cichlidogyrus.

Methods

Cichlidogyrus spp. were isolated from gills and fixed using GAP. Haptoral and genital hard parts were measured and drawn by means of a phase contrast microscopic examination.

Results

We describe eight new species: Cichlidogyrus milangelnari n. sp. on C. microlepidotus; C. jeanloujustinei n. sp. on E. marksmithi; C. evikae n. sp. on T. irsacae; C. aspiralis n. sp., C. glacicremoratus n. sp. and C. rectangulus n. sp. on O. nasuta; and C. pseudoaspiralis n. sp. and C. discophonum n. sp. on A. dewindti. Three haptoral morphotypes were recognized among the new species. Species of Cichlidogyrus from closely related hosts exhibited the same morphotypes. Geographical variation in Cichlidogyrus spp. fauna as observed in O. nasuta and three morphotypes were distinguished. Finally, we listed 111 Cichlidogyrus species, of which 27 and three Tanganyikan species lack sclerotized vagina and heel, respectively, just like 19 and seven species outside of the lake.

Conclusions

Haptoral and genital features in the Tanganyikan Cichlidogyrus fauna reflect the phylogenetic relationships of their cichlid hosts. It seems that several lineages of Cichlidogyrus spp. exist in Lake Tanganyika but further studies are necessary to confirm this hypothesis and answer questions related to Lake Tanganyika and its cichlids.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2460-6) contains supplementary material, which is available to authorized users.

Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock

The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co-occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co-ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species-specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.

The complete mitochondrial genome of the Cyathochromis obliquidens

The Cyathochromis obliquidens, the only member of Cyathochromis genus, is widely spread in Africa. In this study, we firstly reported the complete mitochondrial genome of C. obliquidens. The whole mitochondrial genome is 16,581 bp in length, including 2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-coding genes. Its GC content is 45.94%, similar to the other species from the same family, like Alticorpus geoffreyi (45.82%). We also analyzed the complete mitochondrial genome of C. obliquidens and its phylogenic relationship with other 14 related species, which would help our better understanding of the evolution of Cichlidae mitochondrial genome.

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes

Ecoevolutionary dynamics of the gut microbiota at the macroscale level, that is, in across-species comparisons, are largely driven by ecological variables and host genotype. The repeated explosive radiations of African cichlid fishes in distinct lakes, following a dietary diversification in a context of reduced genetic diversity, provide a natural setup to explore convergence, divergence and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny and environment. Here we characterized by 16S rRNA amplicon sequencing the gut microbiota of 29 cichlid species from two distinct lakes/radiations (Tanganyika and Barombi Mbo) and across a broad dietary and phylogenetic range. Within each lake, a significant deviation between a carnivorous and herbivorous lifestyle was found. Herbivore species were characterized by an increased bacterial taxonomic and functional diversity and converged in key compositional and functional community aspects. Despite a significant lake effect on the microbiota structure, this process has occurred with remarkable parallels in the two lakes. A metabolic signature most likely explains this trend, as indicated by a significant enrichment in herbivores/omnivores of bacterial taxa and functions associated with fiber degradation and detoxification of plant chemical compounds. Overall, compositional and functional aspects of the gut microbiota individually and altogether validate and predict main cichlid dietary habits, suggesting a fundamental role of gut bacteria in cichlid niche expansion and adaptation.

Reduced host-specificity in a parasite infecting non-littoral Lake Tanganyika cichlids evidenced by intraspecific morphological and genetic diversity

Lake Tanganyika is well-known for its high species-richness and rapid radiation processes. Its assemblage of cichlid fishes recently gained momentum as a framework to study parasite ecology and evolution. It offers a rare chance to investigate the influence of a deepwater lifestyle in a freshwater fish-parasite system. Our study represents the first investigation of parasite intraspecific genetic structure related to host specificity in the lake. It focused on the monogenean flatworm Cichlidogyrus casuarinus infecting deepwater cichlids belonging to Bathybates and Hemibates. Morphological examination of C. casuarinus had previously suggested a broad host range, while the lake's other Cichlidogyrus species are usually host specific. However, ongoing speciation or cryptic diversity could not be excluded. To distinguish between these hypotheses, we analysed intraspecific diversity of C. casuarinus. Monogeneans from nearly all representatives of the host genera were examined using morphometrics, geomorphometrics and genetics. We confirmed the low host-specificity of C. casuarinus based on morphology and nuclear DNA. Yet, intraspecific variation of sclerotized structures was observed. Nevertheless, the highly variable mitochondrial DNA indicated recent population expansion, but no ongoing parasite speciation, confirming, for the first time in freshwater, reduced parasite host specificity in the deepwater realm, probably an adaptation to low host availability.

Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

Decoupling of the upper jaw bones--jaw kinesis--is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity--African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Lake Tanganyika and Lake Malawi cichlid radiations. We filmed a diverse array of over 50 cichlid species capturing live prey and quantified the extent of jaw kinesis in the premaxillary and maxillary bones. Our combination of phylogenomic and kinematic data reveals a strong association between biting modes of feeding and reduced jaw kinesis, suggesting that the contrasting demands of biting and suction feeding have strongly influenced cranial evolution in both cichlid radiations.

Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes

Background

Understanding the genetic basis of novel traits is a central topic in evolutionary biology. Two novel pigmentation phenotypes, egg-spots and blotches, emerged during the rapid diversification of East African cichlid fishes. Egg-spots are circular pigmentation markings on the anal fins of hundreds of derived haplochromine cichlids species, whereas blotches are patches of conspicuous anal fin pigmentation with ill-defined boundaries that occur in few species that belong to basal cichlid lineages. Both traits play an important role in the breeding behavior of this group of fishes. Knowledge about the origin, homology and underlying genetics of these pigmentation traits is sparse.

Results

Here, we present a comparative transcriptomic and differential gene expression analysis of egg-spots and blotches. We first conducted an RNA sequencing experiment where we compared egg-spot tissue with the remaining portion of egg-spot-free fin tissue using six individuals of Astatotilapia burtoni. We identified 1229 differentially expressed genes between the two tissue types. We then showed that rates of evolution of these genes are higher than average estimated on whole transcriptome data. Using quantitative real-time PCR, we found that 29 out of a subset of 46 differentially expressed genes showed an analogous expression pattern in another haplochromine species’ egg-spots, Cynotilapia pulpican, strongly suggesting that these genes are involved in the egg-spot phenotype. Among these are the previously identified egg-spot gene fhl2a, two known patterning genes (hoxC12a and bmp3) as well as other pigmentation related genes such as asip. Finally, we analyzed the expression patterns of the same gene subset in two species that feature blotches instead of egg-spots, one haplochromine species (Pseudocrenilabrus philander) and one ectodine species (Callochromis macrops), revealing that the expression patterns in blotches and egg-spots are rather distinct.

Conclusions

We identified several candidate genes that will serve as an important and useful resource for future research on the emergence and diversification of cichlid fishes’ egg-spots. Only a limited degree of conservation of gene expression patterns was detected between the egg-spots of the derived haplochromines and blotches from ancestral haplochromines, as well as between the two types of blotches, suggesting an independent origin of these traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3046-y) contains supplementary material, which is available to authorized users.

discomark: nuclear marker discovery from orthologous sequences using draft genome data

High-throughput sequencing has laid the foundation for fast and cost-effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole-genome (or whole-transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well-supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome-scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.

Widespread adaptive evolution during repeated evolutionary radiations in New World lupins

The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification.

Species radiations can be driven by both adaptive and non-adaptive processes, but the relative importance of these drivers is unknown. Here, Nevado et al. show that multiple radiations in the New World lupins were associated with genome-wide accelerations in both coding and regulatory evolution, suggesting a strong influence of adaptive processes.

Deep-water parasite diversity in Lake Tanganyika: description of two new monogenean species from benthopelagic cichlid fishes

Background

Lake Tanganyika is the world’s second deepest lake. Its diverse cichlid assemblage offers a unique opportunity for studying a deep-water host-parasite model in freshwater. Low host specificity and a broad host range including representatives of the Bathybatini tribe in the only monogenean parasite described from this habitat, Cichlidogyrus casuarinus Pariselle, Muterezi Bukinga & Vanhove, 2015 suggest a link between lower specificity and lower host density. Conversely, high host specificity and species richness are reported for monogeneans of the lake’s littoral cichlids. We further investigated whether the deep-water environment in Lake Tanganyika is really monogenean species-depauperate by investigating the monogenean fauna of Trematocara unimaculatum (a representative of the tribe Trematocarini, the sister lineage of the Bathybatini) and Benthochromis horii, a member of the tribe Benthochromini, found in the same deep-water habitat as the already known hosts of C. casuarinus.

Methods

Sclerotised structures of the collected monogenean individuals were characterised morphologically using light microscopy and morphometrics.

Results

Both examined cichlid species are infected by a single monogenean species each, which are new to science. They are described as Cichlidogyrus brunnensis n. sp., infecting T. unimaculatum, and Cichlidogyrus attenboroughi n. sp., parasitising on B. horii. Diagnostic characteristics include the distal bifurcation of the accessory piece in C. brunnensis n. sp. and the combination of long auricles and no heel in C. attenboroughi n. sp. In addition C. brunnensis n. sp. does not resemble C. casuarinus, the only species of Cichlidogyrus thus far reported from the Bathybatini. Also Cichlidogyrus attenboroughi n. sp. does not resemble any of the monogenean species documented from the pelagic zone of the lake and is among the few described species of Cichlidogyrus without heel.

Conclusions

As two new and non-resembling Cichlidogyrus species are described from T. unimaculatum and B. horii, colonisation of the deep-water habitat by more than one morphotype of Cichlidogyrus is evident. Based on morphological comparisons with previously described monogenean species, parasite transfers with the littoral zone are possible. Therefore, parasites of pelagic cichlids in the lake do not seem to only mirror host phylogeny and the evolutionary history of this host-parasite system merits further attention.

A robust phylogeny among major lineages of the East African cichlids

The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.