River Reorganization Affects Populations of Dwarf Cichlid Species (Apistogramma Genus) in the Lower Negro River, Brazil

Alterations, such as drainage network reorganization, in the landscape in the Amazon basin influence the distribution range and connectivity of aquatic biota and, therefore, their evolution. River capture is a geomorphic mechanism of network reorganization by which a basin captures large portions of the network of a neighboring basin, thus creating a barrier against species dispersal. In this study, the influence of river capture on the genetic differentiation and structuring of two dwarf cichlids species (Apistogramma pertensis and Apistogramma gephyra) is investigated in two tributaries of the lower Negro River. The analysis of 11 loci microsatellite and three mitochondrial DNA genes (Cytochrome b, Citochrome c Oxidase subunit I and 16S ribosomal RNA) confirmed the populational isolation of two dwarf cichlids species, suggesting that they represent evolutionary significant units (ESU) that have been isolated—probably due to the river capture event. The paleovalley that resulted from the river capture is therefore an important physical barrier that separates the populations of the Cuieiras and Tarumã-Mirim Rivers. The findings herein provide evidence of a mechanistic link between the isolation and differentiation of fish populations and the drainage evolution of the Amazon basin, and indicate that the dynamic geological history of the region has promoted species diversification. The process described here partially explains the high diversity in the genus Apistogramma and the information obtained is beneficial to conservation programs.

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes

Copy number variation is an important source of genetic variation, yet data are often lacking due to technical limitations for detection given the current genome assemblies. Our goal is to demonstrate the extent to which an array-based platform (aCGH) can identify genomic loci that are collapsed in genome assemblies that were built with short-read technology. Taking advantage of two cichlid species for which genome assemblies based on Illumina and PacBio are available, we show that inter-species aCGH log2 hybridization ratios correlate more strongly with inferred copy number differences based on PacBio-built genome assemblies than based on Illumina-built genome assemblies. With regard to inter-species copy number differences of specific genes identified by each platform, the set identified by aCGH intersects to a greater extent with the set identified by PacBio than with the set identified by Illumina. Gene function, according to Gene Ontology analysis, did not substantially differ among platforms, and platforms converged on functions associated with adaptive phenotypes. The results of the current study further demonstrate that aCGH is an effective platform for identifying copy number variable sequences, particularly those collapsed in short read genome assemblies.

Expression variations in Ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in Haplochromine cichlids

BackgroundElasmoid scales are one of the most common dermal appendages and can be found in almost all species of bony fish differing greatly in their shape. Whilst the genetic underpinnings behind elasmoid scale development have been investigated, not much is known about the mechanisms involved in the shaping of scales. To investigate the links between gene expression differences and morphological divergence, we inferred shape variation of scales from two different areas of the body (anterior and posterior) stemming from ten haplochromine cichlid species from different origins (Lake Tanganyika, Lake Malawi, Lake Victoria and riverine). Additionally, we investigated transcriptional differences of a set of genes known to be involved in scale development and morphogenesis in fish.ResultsWe found that scales from the anterior and posterior part of the body strongly differ in their overall shape, and a separate look on scales from each body part revealed similar trajectories of shape differences considering the lake origin of single investigated species. Above all, nine as well as 11 out of 16 target genes showed expression differences between the lakes for the anterior and posterior dataset, respectively. Whereas in posterior scales four genes (dlx5, eda, rankl and shh) revealed significant correlations between expression and morphological differentiation, in anterior scales only one gene (eda) showed such a correlation. Furthermore, eda displayed the most significant expression difference between species of Lake Tanganyika and species of the other two younger lakes. Finally, we found genetic differences in downstream regions of eda gene (e.g. in the eda-tnfsf13b inter-genic region) that are associated with observed expression differences. This is reminiscent of a genetic difference in the eda-tnfsf13b inter-genic region which leads to gain or loss of armour plates in stickleback.ConclusionThese findings provide evidence for cross-species transcriptional differences of an important morphogenetic factor, eda, which is involved in formation of ectodermal appendages. These expression differences appeared to be associated with morphological differences observed in the scales of haplochromine cichlids indicating potential role of eda mediated signal in divergent scale morphogenesis in fish.

Molecular Identification of an Invasive Sarotherodon Species from the Atchakpa Freshwater Reservoir (Ouémé River Basin, Benin) and Comparison within S. melanotheron Using COI Markers

The Atchakpa freshwater reservoir (Ouémé Basin, Benin) was found to harbour an unexpected population of a cichlid species that was presumed to be Sarotherodon melanotheron. This species became dominant in the reservoir and became the main fisheries target species. We applied DNA barcoding to identify this population. Besides specimens from the reservoir, we also sequenced S. melanotheron from its native range in Benin at the lower Ouémé and Sô Rivers, and from Lake Nokoué, and Porto-Novo Lagoon. High sequence similarity indicated that all specimens were conspecific. Hence, we cannot exclude that a natural range extension led to the presence of the species in the reservoir. A comparison with sequences from NCBI GenBank confirmed that all samples belonged to the subspecies S. m. melanotheron, which is native to Benin. This comparison also showed that this subspecies was previously introduced in the Philippines. We call for further studies to investigate the socioeconomic, ecological and environmental impacts of the species in the Atchakpa reservoir.

Molecular Systematic Investigations of Three Fin Fish Cichlid Species of Oreochromis niloticus (Nile Tilapia), Genetically Improved Farmed Tilapia (GIFT) and Astronotus ocellatus (Oscar Cichlid)

Fisheries in India contribute significantly to the total GDP of agriculture and earn significant foreign exchange. Aquaculture is playing an important role in India and is bestowed with a huge biodiversity of aquatic organisms. India ranks second in total fish production in the world. Nile tilapia has become the world’s second most popular farmed fish, after carps. Oscars is a popular aquarium fish around the world. In the present study, efforts were made to analyze the extent of divergence or similarity among three cichlid finfishes (Nile Tilapia, GIFT Tilapia, and Oscar Cichlid) using molecular biology techniques such as Random Amplification of Polymorphic DNA (RAPD) and Restriction Fragment Length Polymorphism (RFLP). The Phylogenetic tree was constructed using PhyElph software to study the evolutionary relationship between the three cichlid finfish species. The Phylogenetic or evolutionary relationship was established for the three fishes, Nile tilapia, GIFT, and Oscar cichlid, with the Phylogenetic tree. It was found that Nile tilapia and GIFT share a recent common ancestor, while Oscar cichlid does not share any evolutionary relationship with Nile tilapia and GIFT.

Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

Background The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks. Results We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus. Conclusion This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Multiproxy paleolimnological reconstruction of Lake Victoria’s environmental history, East Africa

<p>Lake Victoria (LV), Africa’s largest lake is situated in the African Great Rift Valley. Due to its shallowness (max.68 m; mean 40 m) and limited river inflow, LV is very sensitive to variations in climate and lake level fluctuations. As a result, LV has undergone repeated low stand periods, or even complete desiccation during the Late Pleistocene with profound effects on the aquatic ecosystem. One example is the emergence of a unique biodiversity of endemic cichlid species following the lake’s last desiccation event during the last glacial and subsequent refilling commencing ~15,000 years ago.</p><p>In an interdisciplinary project we aim at reconstructing linkages between paleoenvironmental variability, disturbances and adaptive species radiation by combining approaches from paleogenomics, paleoecology and paleolimnology. For this purpose, four sediment cores along a depth-transect (near-shore to offshore), covering ca. the past 14,000 years, are analyzed.</p><p>We present first paleolimnological results of long-term changes of using (isotope-)geochemical indicators including: Sedimentary pigments and biogenic silica to infer aquatic productivity supported by micro X-ray Fluorescence (XRF) derived element geochemistry, <sup>13</sup>C and <sup>15</sup>N, and sedimentary phosphorus fraction analyses providing information on changes in sediment composition.</p><p>The results suggest that the infilling of the LV basin was a long-term step-wise process. This is shown by elevated and variable indicators for lithogenic input (e.g Ti, Zr and K) and interpreted as mobilization of substrate from the shorelines by a dynamic lake level prior to its stabilization in the Early and Mid-Holocene.  This process is mainly reflected in the core taken at the greatest water depth (65 m). Simultaneously, the aquatic productivity (BSi and chloropigments) increased rapidly after the refilling of the lake basin in the Late-Glacial. A gradual drying of the climate and a following shift to a more oxygenated water column is observed in the Mid-to Late Holocene indicated by a decline in chemically weathered material (e.g Rb/K & K/Al ratios) and abundance of Mn.</p>