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

. 2021 Dec 28;71(5):1255–1270. doi: 10.1093/sysbio/syab100

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

© 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.

PMC Copyright notice

Figure 1. — Different distances can impose tree spaces with different characteristics. First two dimensions of PCoA mappings of tree spaces, with minimum spanning tree of 350 points (solid lines). Higher dimensions depicted in Supplementary Information available on Dryad (Smith 2021). a, b) 2500 Bayesian (dots) and 100 parsimony (rings) trees from analysis of Yates (2003), colored by stratigraphic congruence (MIG, millions of years); (a) RF tree space does not exhibit clear structure; MST indicates that the two apparent clusters do not correspond to clusters in the original tree space, and that the mapping is highly distorted (MST extension factor ); (b) path distance tree space (MST extension factor ), showing stratigraphic structure and clear separation of parsimony and Bayesian trees; (c) cumulative correlation of stratigraphic fit (MIG) with first tree space axes; (d–f) 2500 Bayesian and 54 parsimony trees from analysis of Carpenter (2001); points colored by tree balance (TCI; dark balanced): (d) strong clustering in RF mapping (silhouette coefficient ) has no underlying basis (silhouette coefficient ), as suggested by tortuous minimum spanning tree (extension factor ); (e) vertical axis in KC mapping (MST extension factor ) shows clear correspondence with tree balance; (f) quartet mapping (MST extension factor ) faithfully represents the absence of clustering and tree balance correlation present in the original space; (g–i) trees from analysis of Fischer et al. (2016), showing (lack of) correspondence between original clusters (point color, corresponding to Bayesian vs. parsimony trees) and clusters identified from mappings (using hierarchical clustering; dashed lines convex hulls); (j–l) trees from analysis of Schoch and Milner (2008), colored by stratigraphic fit; different metrics result in spaces with different (non-clustering) structures, whose validity is supported by inspection of MST and of higher dimensions. CID clustering information distance tree space; KC Kendall–Colijn tree space; MIG Minimum implied gap; Q’tet Quartet tree space; RF Robinson–Foulds tree space; SV split size vector tree space; TCI total cophenetic index.

Inline graphic — Different distances can impose tree spaces with different characteristics. First two dimensions of PCoA mappings of tree spaces, with minimum spanning tree of 350 points (solid lines). Higher dimensions depicted in Supplementary Information available on Dryad (Smith 2021). a, b) 2500 Bayesian (dots) and 100 parsimony (rings) trees from analysis of Yates (2003), colored by stratigraphic congruence (MIG, millions of years); (a) RF tree space does not exhibit clear structure; MST indicates that the two apparent clusters do not correspond to clusters in the original tree space, and that the mapping is highly distorted (MST extension factor ); (b) path distance tree space (MST extension factor ), showing stratigraphic structure and clear separation of parsimony and Bayesian trees; (c) cumulative correlation of stratigraphic fit (MIG) with first tree space axes; (d–f) 2500 Bayesian and 54 parsimony trees from analysis of Carpenter (2001); points colored by tree balance (TCI; dark balanced): (d) strong clustering in RF mapping (silhouette coefficient ) has no underlying basis (silhouette coefficient ), as suggested by tortuous minimum spanning tree (extension factor ); (e) vertical axis in KC mapping (MST extension factor ) shows clear correspondence with tree balance; (f) quartet mapping (MST extension factor ) faithfully represents the absence of clustering and tree balance correlation present in the original space; (g–i) trees from analysis of Fischer et al. (2016), showing (lack of) correspondence between original clusters (point color, corresponding to Bayesian vs. parsimony trees) and clusters identified from mappings (using hierarchical clustering; dashed lines convex hulls); (j–l) trees from analysis of Schoch and Milner (2008), colored by stratigraphic fit; different metrics result in spaces with different (non-clustering) structures, whose validity is supported by inspection of MST and of higher dimensions. CID clustering information distance tree space; KC Kendall–Colijn tree space; MIG Minimum implied gap; Q’tet Quartet tree space; RF Robinson–Foulds tree space; SV split size vector tree space; TCI total cophenetic index.