DOI: 10.5061/dryad.53686
title: Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling

description: We estimated the effective population sizes (Ne) and tested for short-term
 temporal demographic stability of populations of two Lake Malawi cichlids:
 Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread
 species found across the lake. We sampled a total of 351 individuals,
 genotyped them at 13 microsatellite loci and sequenced their mitochondrial
 D-loop to estimate genetic diversity, population structure, demographic
 history and effective population sizes. At the microsatellite loci,
 genetic diversity was high in all populations. Yet, genetic diversity was
 relatively low for the sequence data. Microsatellites yielded mean Ne
 estimates of 481 individuals (±99 SD) for M. benetos and between 597
 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M.
 zebra. The microsatellite data indicated no deviations from mutation–drift
 equilibrium. Maylandia zebra was further found to be in migration–drift
 equilibrium. Temporal fluctuations in allele frequencies were limited
 across the sampling period for both species. Bayesian Skyline analyses
 suggested a recent expansion of M. zebra populations in line with
 lake-level fluctuations, whereas the demographic history of M. benetos
 could only be estimated for the very recent past. Divergence time
 estimates placed the origin of M. benetos within the last 100 ka after the
 refilling of the lake and suggested that it split off the sympatric M.
 zebra population. Overall, our data indicate that micro-endemics and
 populations in less favourable habitats have smaller Ne, indicating that
 drift may play an important role driving their divergence. Yet, despite
 small population sizes, high genetic variation can be maintained.
description: Maylandia_13usats_GENEPOP_Mol_EcolGenepop file containing data from 13 microsatellites for three temporal samples (1996, 2010, 2012) of three populations of Maylandia zebra (Mazinzi Reef, Harbor Island, Illala Gap) and Maylandia benetos (Mazinzi Reef)Maylandia_DLoop_alignment_Mol_EcolAlignment (Geneious) of 695 bp of the mitochondrial DLoop for 317 individuals sampled at three points in time (1996, 2010, 2012) from three populations of Maylandia zebra (Mazinzi Reef, Harbour Island, Illala Gap) and Maylandia benetos (Mazinzi Reef).Maylandia_DLoop_dated_tree_Mol_EcolDated phylogenetic tree for 317 individuals of Maylandia zebra and Maylandia benetos generated with BEAST v.1.7.4. We used the HKY + I model and a substitution rate of 0.0324. The simplest coalescent model (constant size) was used. The best clock model was estimated by running all four available clock models and using Tracer to determine the best model for our data set. All analyses were run for 100 million generations sampling every 10,000 generations for a total of 10,000 samples. Convergence of the run was confirmed with Tracer by checking the highest effective sample size (ESS). The exponential relaxed clock had the best likelihood scores (-1371.613, second best: lognormal relaxed clock -1381.808) and was therefore chosen as best clock model. The tree was summarized with TreeAnnotator v.1.7.4.