Figure 1.
Phylogeny of LT cichlids reconstructed by Bayesian Inference and dated using a relaxed molecular clock (Yule speciation prior).
Timescales for the two alternative calibrations are shown. The gray bars on each node indicate 95% credible intervals for the node ages. Black circle indicates the node used to date the tree. P = Principle lineage, C = C-lineage, L = L-lineage. Gray branches indicate non-endemic taxa. LM = Lake Malawi species.
Figure 2.
Average net diversification rates of LT cichlid clades (with missing species added) and the minimum rate estimate for LM and LV cichlid species flocks.
Lines show the 95% confidence intervals incorporating both variation across sampled trees and the inherent stochasticity of the branching process.
Figure 3.
Lineage-through-time (LTT) plots, including missing species, based on 1000 sampled Bayesian trees: a) LT radiation (black); b) L-lineage (black) and C-lineage (gray); c) tribes: Lamprologini (purple), Ectodini (green), Tropheini (plum), Limnochromini (fawn), Cyprichromini (aqua), Bathybatini (yellow).
A single LLT plot is highlighted for all tribes, but is only displayed for the latter three tribes for clarity. Timescales for the two alternative calibrations are shown.
Figure 4.
Net diversification rate through time fitted by General Additive Models (GAMs) for a) the entire flock and b) the L- (black) and C- (gray) lineages.
Scale bars (x-axis) represent both 28 Myr and 12 Myr calibrations and the y-axis is the per lineage diversification rate in species per million years. Dashed lines show standard errors combining those across Bayesian samples and those due to uncertainty in the model in a), but only those across Bayesian samples in b). In the latter case, standard errors due to uncertainty in the model are extremely large.
Table 1.
Lake Tanganyika cichlid clades, including life history traits and age estimates (mean and 95% confidence intervals), based on 12 and 28 Myr calibrations [27] using a Bayesian relaxed-clock model enforcing the Yule prior [31].