Genomic Data Reveals Cryptic Diversity in the Soda Lake Cichlid

The cichlid fishes of East Africa are renowned for their rapid and species‐rich adaptive radiations. However, some specialist cichlid lineages in the region have not undergone extensive diversification; it is plausible that these lineages contain cryptic allopatric diversity. The tilapiine cichlid Oreochromis amphimelas (Hilgendorf, 1905) is a distinctive species specialised for high salinity, high alkalinity and high temperature soda lakes in the East African Rift Valley. Here, we investigated variation among O. amphimelas populations using a combination of reduced‐representation genome sequences, mitochondrial DNA sequences and morphological data. Genetic data revealed two highly divergent genomic lineages, with no evidence of ongoing gene flow. Specifically, the Lake Manyara population was strongly differentiated from the four other populations studied, which show relatively low levels of genetic differentiation among them. Genetic differentiation between Lake Manyara and the other populations is seen across the genome, as characterised by elevated windowed FST. Despite the clear genomic divergence between the Lake Manyara and other soda lake populations, there were no apparent morphological differences between the two lineages, indicating they may be considered two cryptic species. It is possible that O. amphimelas lineages have diverged vicariantly following regional geomorphological change. Identification of two potential geographically separated cryptic species in the lineage has conservation implications, given that O. amphimelas is currently categorised as Endangered on the IUCN Red List of Threatened Species, due to threats from fisheries and environmental change.