Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Apr 23;68(6):937–955. doi: 10.1093/sysbio/syz019

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2019. 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 (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 7. — Support for observed topological heterogeneity in estimated gene trees. (a–c) Distributions for the average bootstrap support for all clades recovered in majority rule extended consensus gene trees (“MRE consensus topology”, drawn as solid bars), and the average support when bootstrap replicates for each gene are constrained to the inferred species tree topology (open bars) are shown for CNEEs (a), introns (b), and UCEs (c). Values above each panel indicate the decrease in the grand mean of average support across genes when bootstrap replicates are constrained to the species tree topology. (d) Support that observed gene tree topologies differs from the inferred species tree. Dark gray bars indicate the difference in AIC from values calculated using the MRE consensus topology for each gene, relative to that obtained when the sequence alignment is constrained to the species tree topology. The baseline at 0 corresponds to AIC = -2, thus values beneath this line indicate loci where likelihood values support the gene tree topology substantially better than that of the species tree. Results of AU tests are indicated with medium gray bars showing the proportion of loci that reject (below baseline) and fail to reject (above baseline) the species tree topology at a -value cutoff of 0.05, and light gray bars showing the proportion of loci where the species tree topology occurs among the top 5% of candidate topologies (above baseline), or is within the bottom 95% of tested topologies (below baseline) for AU -values ranked in ascending order. AU tests for the 105 and 1575 candidate tree sets produced similar results and are shown for the 105 candidate set only.

Inline graphic — Support for observed topological heterogeneity in estimated gene trees. (a–c) Distributions for the average bootstrap support for all clades recovered in majority rule extended consensus gene trees (“MRE consensus topology”, drawn as solid bars), and the average support when bootstrap replicates for each gene are constrained to the inferred species tree topology (open bars) are shown for CNEEs (a), introns (b), and UCEs (c). Values above each panel indicate the decrease in the grand mean of average support across genes when bootstrap replicates are constrained to the species tree topology. (d) Support that observed gene tree topologies differs from the inferred species tree. Dark gray bars indicate the difference in AIC from values calculated using the MRE consensus topology for each gene, relative to that obtained when the sequence alignment is constrained to the species tree topology. The baseline at 0 corresponds to AIC = -2, thus values beneath this line indicate loci where likelihood values support the gene tree topology substantially better than that of the species tree. Results of AU tests are indicated with medium gray bars showing the proportion of loci that reject (below baseline) and fail to reject (above baseline) the species tree topology at a -value cutoff of 0.05, and light gray bars showing the proportion of loci where the species tree topology occurs among the top 5% of candidate topologies (above baseline), or is within the bottom 95% of tested topologies (below baseline) for AU -values ranked in ascending order. AU tests for the 105 and 1575 candidate tree sets produced similar results and are shown for the 105 candidate set only.