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. 2018 Jul 5;68(1):168–181. doi: 10.1093/sysbio/syy051

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© The Author(s) 2018. Published by Oxford University Press, on behalf of the Society of Systematic Biologists

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Figure 4. — Accuracy of species delimitation using the gdi with parameters estimated from data of 50 loci using (a) phrapl and (b) bpp. Species status is defined using the gdi at different cutoffs ( and ). This is calculated by simulating 10,000 gene trees under the MSC model with migration for phrapl, and analytically for bpp. Along the -axis, each group of bars gives results for different gdi cut-offs. Below the lower bound (), populations and are defined as a single species; above the upper bound (), and are defined as separate species, while between the bounds, the species status is ambiguous. The six bars within each group represent the six sets of species divergence times (s). The bar shadings are white = the inferred delimitation outcome matched the true outcome; light green/gray = ambiguity was inferred when the true delimitation is known (insufficient power); dark green/gray = delimitation was inferred (whether one or two species) when the truth was ambiguous (excessive confidence); and black = one species was inferred when there were two, or vice versa. The results for phrapl are recreated using the R code from Jackson et al. (2017, Fig. 4).

Inline graphic — Accuracy of species delimitation using the gdi with parameters estimated from data of 50 loci using (a) phrapl and (b) bpp. Species status is defined using the gdi at different cutoffs ( and ). This is calculated by simulating 10,000 gene trees under the MSC model with migration for phrapl, and analytically for bpp. Along the -axis, each group of bars gives results for different gdi cut-offs. Below the lower bound (), populations and are defined as a single species; above the upper bound (), and are defined as separate species, while between the bounds, the species status is ambiguous. The six bars within each group represent the six sets of species divergence times (s). The bar shadings are white = the inferred delimitation outcome matched the true outcome; light green/gray = ambiguity was inferred when the true delimitation is known (insufficient power); dark green/gray = delimitation was inferred (whether one or two species) when the truth was ambiguous (excessive confidence); and black = one species was inferred when there were two, or vice versa. The results for phrapl are recreated using the R code from Jackson et al. (2017, Fig. 4).