Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals
θmit = 0.025. υmit = 0.01. The population size parameter for nuclear genes was 2.5 times smaller. Nuclear markers were simulated with two different average substitution rates: υnuc = 0.001 (A) and υnuc = 0.0005 (B). n = 5. The line with circles shows the average percent error across replicates. Solid lines indicate the lowest and the highest estimate still within the range IQ±1.5 IQR. MB, substitution rates estimated by the Multilocus Bayesian (MB) software. ML, substitution rates estimated from Maximum Likelihood (ML) individual gene trees.