Table 2.
Table summarizing the performance of the time‐slice BDSKY Model C, and the single‐pulse CoMET model (May et al. 2016) for the simulated set of phylogenies that converged in BEAST2 (see Table S1). Color code: “White” indicates the success of the model in estimating the parameter value or detecting the MEE event; “green” indicates the failure of the model; “yellow” indicates mixed results. See footnotes for an explanation (the corresponding Figure numbers illustrating these results are given under each header; posterior probability estimates and accuracy values for each parameter are given in Table S3)
| λ estimation | μ estimation | MEE detection | MEE time estimation | |||||
|---|---|---|---|---|---|---|---|---|
| Model Settings (N, ρ, μ, t) | BDSKY (5, S9) | CoMET (S14, S15) | BDSKY (5, S9) | CoMET (S14, S15) | BDSKY (2, 3) | CoMET (S10, S11) | BDSKY (4, S6) | CoMET (S11, S13) |
| (500, 0.1, 0, 2) | a | a1 | a2 | a1 | b* | b1 | c | c – λ |
| (500, 0.1, 0.1, 4) | a | a1* | a | a1* | b | b | c | c – λ |
| (500, 0.1, 0.18, 20) | a | a | a | a | b | b | c | c – λ |
| c2 – μ | ||||||||
| c2 – MEE | ||||||||
| (500, 0.5, 0, 2) | a | a | a1 | a1 | b2 | b2 | c2 | c1 – λ |
| (500, 0.5, 0.1, 4) | a | a* | a | a* | b2 | b1 | c2 | c – λ |
| (500, 0.5, 0.18, 20) | a | a | a | a | b2 | b2 | c2 | c2 |
| (500, 0.9, 0, 2) | a | a | a1 | a1 | b2 | b2 | c2 | c2 |
| (500, 0.9, 0.1, 4) | a | a | a | a* | b2 | b2 | c2 | c2 |
| (500, 0.9, 0.18, 20) | a | a | a | a* | b2 | b2 | c2 | c2 |
| (500, 1, 0, 2) | a | a | a2 | a1 | d | d | d | d |
| (500, 1, 0.1, 4) | a | a | a | a* | d | d | d | d |
| (500, 1, 0.18, 20) | a | a | a | a | d | d | d | d |
| (100, 0.1, 0, 2) | a1* | a2 | a1 | a1 | b2 | b1 | c2 | c – λ |
| (100, 0.1, 0.1, 4) | a* | a* | a2 | a* | b2 | b2 | c2 | c1‐λ |
| c2– MEE | ||||||||
| (100, 0.1, 0.18, 20) | a | a | a** | a* | b2 | b2 | c2 | c2– MEE |
| (200, 0.1, 0, 2) | a1 | a1* | a1 | a1 | b2 | b1* | c2 | c – λ |
| (200, 0.1, 0.1, 4) | a | a1 | a** | a1* | b2 | b | c2 | c – λ |
| (200, 0.1, 0.18, 20) | a | a | a** | a | b1* | b2 | c2 | c– MEE |
| (100, 1, 0, 2) | a | a1 | a1 | a1 | d | d | d | d |
| (100, 1, 0.1, 4) | a | a* | a* | a* | d | d | d | d |
| (100, 1, 0.18, 20) | a | a* | a* | a* | d | d | d | d |
| (200, 1, 0, 2) | a | a1 | a2 | a2 | d | d | d | d |
| (200, 1, 0.1, 4) | a | a | a* | a* | d | d | d | d |
| (200, 1, 0.18, 20) | a | a* | a | a* | d | d | d | d |
a: Simulated (true) value falls within 95% HPD (BDSKY) or Credible Interval (CoMET). (*) Large 95% HPD interval width (≥0.05 between lower and upper boundary). (**) Large only for post−MEE interval.
a1: Under/Overestimation of true value (falls outside the 95% HPD or Credible Interval). (*) Mean overestimated but the true value falls within 95% HPD (BDSKY); under/overestimation only observed in part of the tree length (CoMET).
a2: True value falls within 95% HPD (BDSKY) or Credible Interval (CoMET), but only in either the pre‐ or post‐MEE interval.
b: Success in detecting MEE: Mean and 95% HPD (BDSKY)/Credible Interval (CoMET) of the diversification rate estimate fall below 0 (r < 0) at MEEE (“MEE interval” in BDSKY) and goes back to simulated values after MEE (“post‐MEE interval”). (*) Only 84% of HPDn <0 for the percentage of simulated phylogenies that converged.
b1: Weak detection of MEE: Diversification rate decreases in pre‐MEE interval (BDSKY) or at MEE (CoMET), but mean and/or 95% HPD/Credible Interval of the diversification rate is not negative. (*) Only part of the HPD falls below 0.
b2: Type II error: Failure to detect the MEE through the diversification rate.
c: Good estimation. MEE time correctly bounded by rate shift times in μ (BDSKY). MEE time correctly identified by significant Bayes Factor comparisons (BF > 6) of λ shift times (c – λ) or single‐pulse MEE times (c‐MEE) (CoMET).
c1: Weak estimation (CoMET): MEE time correctly identified by non‐significant BF tests (2< BF < 6) of rate shift times in λ (c1‐λ), or in (c1‐μ), or single‐pulse MEE times (c1‐MEE).
c2: Failed estimation. MEE time incorrectly identified by rate shift times in μ (BDSKY) or by non‐significant BF tests of μ shift times (c2‐μ) or single‐pulse MEE times (c2‐MEE) (CoMET).
d: No Type I error. No MEE is detected in the control scenario (ρ = 1).
Abbreviations: λ estimation, power to estimate speciation rate; μ estimation, power to estimate extinction rate; MEE detection, power to detect the MEE through interoperating changes in the diversification rate; MEE time estimation, timing of MEE detected through successive shifts in extinction rate estimates (BDSKY) or through shifts in speciation rate (CoMET).