Trophic specialization plays a major role in ecological speciation. Multiple adaptive radiations among cyprinid fish of the genus Labeobarbus were recently discovered in riverine environments of the Ethiopian Highlands, East Africa. These radiations contain parallel diversifications of trophic morphology, including thick-lipped or ‘rubberlip’ phenotype, whose trophic function remains largely unexplored. To test the adaptive value of thickened lips, to identify the ecological niche of the thick-lipped ecomorphs, and to test of these ecomorphs are the products of speciation we studied six sympatric pairs of ecomorphs with hypertrophied lips and the normal lip structure from different riverine basins. Trophic morphology, diet, stable isotope (15N and 13C) signatures as well as mtDNA markers and genome-wide SNP variation were analyzed. Our results show that thick-lipped ecomorphs partition trophic resources with generalized ecomorphs in only one half of the examined sympatric pairs despite the pronounced divergence in lip structure. In these thick-lipped ecomorphs that were trophically diverged, the data on their diet along with the elevated 15N values suggest an insectivorous specialization different from the basal omnivorous-detritivouros feeding mode of generalized ecomorphs. Genetic data confirmed an independent and parallel origin of all six lipped ecomorphs. Yet, only one of those six thick-lipped ecomorphs had a notable genetic divergence with sympatric non-lipped ecomorphs based on nuclear SNPs data (FST = 0.21). Sympatric pairs can be sorted by combinations of phenotypic, ecological, and genetic divergence within the speciation continuum from an ecologically non-functional mouth polymorphism via ecologically functional polymorphism to completed speciation via divergent evolution.

High-throughput DNA sequencing technologies make it possible now to sequence entire genomes relatively easily. Complete genomic information obtained by whole genome resequencing (WGS) can aid in identifying and delineating species even if they are extremely young, cryptic or morphologically difficult to discern and closely related. Yet for taxonomic or conservation biology purposes WGS can remain cost-prohibitive, too time-consuming, and often constitute a “data overkill”. Rapid and reliable identification of species (and populations) that is also cost-effective is possible based on species-specific markers that can be discovered by WGS. Based on WGS data we designed a PCR restriction fragment length polymorphism (PCR-RFLP) assay for 19 Neotropical Midas cichlid populations (Amphilophus cf. citrinellus), that includes all 13 described species of this species complex. Our work illustrates that identification of species and populations (i.e., fish from different lakes) can be greatly improved by designing genetic markers using available “high resolution” genomic information. Yet, our work also shows that even in the best-case scenario, when whole-genome resequencing information is available, unequivocal assignments remain challenging when species or populations diverged very recently, or gene flow persists. In summary, we provide a comprehensive workflow on how to design RFPL markers based on genome re-sequencing data, how to test and evaluate their reliability, and discuss the benefits and pitfalls of our approach.

Adaptive radiation of fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that also riverine and stream environments provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeastern Asia to Western Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have been found among these new species in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra (‘thick-lipped’ and ‘predatory’) that were not described before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intra-basin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide SNP data, mtDNA was unable to identify any genetic structure suggesting a recent and rapid speciation event. Furthermore, we found evidence for a hybrid origin of the novel ‘thick-lipped’ phenotype, as being the result of the hybridization of two other sympatrically occurring species. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly adaptively radiated in a riverine environment, and that this radiation was promoted by the evolution of novel feeding strategies.