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. 2021 Mar 31;70(5):961–975. doi: 10.1093/sysbio/syab024

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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 Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercialre-use, please contact journals.permissions@oup.com

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Figure 5. — Phylogenetic trees on the basis of hypotheses H1 and H2 (see Fig. 2) using sequence windows with different D-statistic values. a) ML and species trees generated from 190 sequence windows with top 0.5% D values based on the tree topology of tree1; b) ML and species trees generated from 176 windows with absolute D values 0.01 based on the tree topology of tree1; c) ML and species trees generated from 196 windows with top 0.5% D values based on the tree topology of tree2; (d) ML and species trees generated from 259 sequence windows with absolute D values 0.01 based on the tree topology of tree2. Each pair of trees in a–d shows ML trees generated by RAxML on the left, with asterisks representing 100% bootstrap support, and species trees generated by SNAPP with blue, red and green indicating majority to minority trees, respectively. All nodes of the species trees in (a), (c), and (d) are supported by posterior probability (PP) 1.00, whereas all nodes of the species trees in (b) are supported by PP 1.00 except for soror omeiensis (PP ), omeiensis whistleri/valentini (PP ), and soror whistleri/valentini (PP ).

Inline graphic — Phylogenetic trees on the basis of hypotheses H1 and H2 (see Fig. 2) using sequence windows with different D-statistic values. a) ML and species trees generated from 190 sequence windows with top 0.5% D values based on the tree topology of tree1; b) ML and species trees generated from 176 windows with absolute D values 0.01 based on the tree topology of tree1; c) ML and species trees generated from 196 windows with top 0.5% D values based on the tree topology of tree2; (d) ML and species trees generated from 259 sequence windows with absolute D values 0.01 based on the tree topology of tree2. Each pair of trees in a–d shows ML trees generated by RAxML on the left, with asterisks representing 100% bootstrap support, and species trees generated by SNAPP with blue, red and green indicating majority to minority trees, respectively. All nodes of the species trees in (a), (c), and (d) are supported by posterior probability (PP) 1.00, whereas all nodes of the species trees in (b) are supported by PP 1.00 except for soror omeiensis (PP ), omeiensis whistleri/valentini (PP ), and soror whistleri/valentini (PP ).