Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably less than 20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation-by-distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow. 

Fish were collected on a research transect in the Mwanza Gulf of Lake Victoria. We measured 15 morphological traits that have proven powerful for quantifying intraspecific and interspecific morphological variation in haplochromine cichlids of Lake Victoria: standard length (SL), head length (HL), head width (HW), body depth (BD), lower jaw length (LJL), lower jaw width (LJW), snout length (SnL), snout width (SnW), cheek depth (ChD), preorbital depth (POD), preorbital width (POW), interorbital width (IOW), eye length (EyL) and depth (EyD), and premaxillary pedicel length (PPL). We measured 661 individuals using digital calipers.

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