Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria.

Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.

High-resolution bathymetries and shorelines for the Great Lakes of the White Nile basin.

HRBS-GLWNB 2020 presents the first open-source and high-resolution bathymetry, shoreline, and water level data for Lakes Victoria, Albert, Edward, and George in East Africa. For each Lake, these data have three primary products collected for this project. The bathymetric datasets were created from approximately 18 million acoustic soundings. Over 8,200 km of shorelines are delineated across the three lakes from high-resolution satellite systems and uncrewed aerial vehicles. Finally, these data are tied together by creating lake surface elevation models collected from GPS and altimeter measures. The data repository includes additional derived products, including surface areas, water volumes, shoreline lengths, lake elevation levels, and geodetic information. These data can be used to make allocation decisions regarding the freshwater resources within Africa, manage food resources on which many tens of millions of people rely, and help preserve the region's endemic biodiversity. Finally, as these data are tied to globally consistent geodetic models, they can be used in future global and regional climate change models.