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Open Access Highly Accessed Research article

Exploring power and parameter estimation of the BiSSE method for analyzing species diversification

Matthew P Davis1*, Peter E Midford2 and Wayne Maddison3

Author Affiliations

1 The Field Museum, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA

2 NESCent: National Evolutionary Synthesis Center, 2024 W. Main Street, Suite A200, Durham, NC, 27705-4667, USA

3 University of British Columbia, 4200-6270 University Blvd, Vancouver, B.C, Canada, V6T 1Z4

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BMC Evolutionary Biology 2013, 13:38  doi:10.1186/1471-2148-13-38

Published: 11 February 2013

Additional files

Additional file 1: Table S1:

Power of asymmetrical speciation rate simulations. Remaining parameters were symmetrical for each simulation (q01= 0.01, q10= 0.01, μ0= 0.03, μ1= 0.03). Power is plotted in Figure 1A. The observed percent of terminal taxa with State 0 is indicated by the mean value from 500 simulations. Table S2. Power of simulations for character rate change. Remaining parameters were symmetrical for each simulation (μ0= 0.03, μ1= 0.03, λ 0= 0.1, λ 1= 0.1). Power is plotted in Figure 1B. The observed percent of terminal taxa with State 0 is indicated by the mean value from 500 simulations. Table S3. Power of asymmetrical extinction rate simulations. Remaining parameters were symmetrical for each simulation (q01= 0.01, q10= 0.01, λ 0= 0.1, λ 1= 0.1). Power is plotted in Figure 1C. The observed percent of terminal taxa with State 0 is indicated by the mean value from 500 simulations. Table S4. This table lists statistical power of the BiSSE model for 500 simulations containing 3:1 and 7:1 biases in terminal states for varying tree sizes for likelihood comparisons of power in four versus six parameter models. Power is plotted in Figure 2. Using the stationary frequency formula, in an iterative calculation, we obtained ratios of rates necessary to generate a low bias representative (31:10) and high bias representative (71:10) tip ratios using values symmetrically placed around base rates (λ = 0.1, μ = 0.05, and q = 0.005). For the low bias, rate ratios were 1.1425, 1.3046 and 3.0 for speciation, extinction and character change respectively, yielding simulated rates for speciation λ0=0.0936, λ1= 0.10689, for extinction, μ0=0.04378, μ1= 0.05711, and for character change q0= 0.00289, q1= 0.00866. For the high bias, rate ratios were 1.407, 1.960, and 7.000, yielding simulated rates for speciation λ0=0.0843, λ1=0.1186, for extinction μ0=0.0357, μ1= 0.07, and for character change q0=0.00189, q1= 0.01323. Simulated rates without bias were set to their base rates. (DOCX 36 kb)

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Additional file 2: Figure S1:

Parameter estimations of (a) speciation, (b) character change, and (c) extinction under different tree sizes and degrees of asymmetry in speciation rates with corresponding tip ratios. Point of intersection between red lines represents known values. (PDF 640 kb)

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