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. 2021 Jul 10;71(2):367–381. doi: 10.1093/sysbio/syab056

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© The Author(s) 2021. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Characteristics of the simulated data under different settings of the duplication/loss rates and tree topologies. The duplication/loss rates are denoted by the rate multiplier (0, 1, 2, 5 and 10), where 1 is the rate found in nature for the clade represented by each species tree topology (see Methods section). a,b) Distribution of the total number of gene copies in individual gene families in the 16-taxon and 12-taxon data sets, respectively. Note that the two tree topologies also have different simulated effective population sizes in these figures (see Supplementary Fig. S1a,b available on Dryad for more conditions). c,d) Scatter plots of XL (Species tree, Locus tree), the number of extra lineages when reconciling the true locus trees with the true species tree, for the 16-taxon and 12-taxon data sets, respectively. These plots therefore represent the effects of GDL alone. e,f) Scatter plots of XL (Locus tree, Gene tree), the number of extra lineages when reconciling the true gene trees with the true locus tree, for the 16-taxon and 12-taxon data sets, respectively. These plots therefore represent the effects of ILS alone, though note that higher rates of GDL allow there to be more gene tree branches on which ILS can act.

Inline graphic — Characteristics of the simulated data under different settings of the duplication/loss rates and tree topologies. The duplication/loss rates are denoted by the rate multiplier (0, 1, 2, 5 and 10), where 1 is the rate found in nature for the clade represented by each species tree topology (see Methods section). a,b) Distribution of the total number of gene copies in individual gene families in the 16-taxon and 12-taxon data sets, respectively. Note that the two tree topologies also have different simulated effective population sizes in these figures (see Supplementary Fig. S1a,b available on Dryad for more conditions). c,d) Scatter plots of XL (Species tree, Locus tree), the number of extra lineages when reconciling the true locus trees with the true species tree, for the 16-taxon and 12-taxon data sets, respectively. These plots therefore represent the effects of GDL alone. e,f) Scatter plots of XL (Locus tree, Gene tree), the number of extra lineages when reconciling the true gene trees with the true locus tree, for the 16-taxon and 12-taxon data sets, respectively. These plots therefore represent the effects of ILS alone, though note that higher rates of GDL allow there to be more gene tree branches on which ILS can act.