Data from: Community assembly in Lake Tanganyika cichlid fish: Quantifying the contributions of both niche-based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche-based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche-based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche-based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche-based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche-based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche-based or neutral-based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns. The data package contains two sets: - The zip file contains the raw STEPCAM output for each transect, 3 replicate runs (with different seeds) per transect. The zip file is organized as follows: each folder (name = fit_transectNo_repl) contains the R files used to run STEPCAM, temporary intermediate output ("particles_temp_t=XX.txt"), a text file tracking the acceptance rate ("accepted_t=XX.txt") and the final posterior distribution ( - The zip file contains the raw pictures taken along each transect. Transects are numbered following Table S1. Each folder contains all used pictures. Added are the MATLAB scripts used to calculate the relative sand cover within each quadrant. Resulting Sand cover estimates are included in the respective text files