Table 1 Potential affordances and constraints introduced by various features of tree diagrams

Overall branching pattern

Emphasizes the shared descent of all organisms from a single ancestor; emphasizes the importance of cladogenesis (branching events) in the origin of new clades (Catley and Novick 2008; Archibald 2009)

Overemphasizes hierarchical (parent to offspring) gene transfer in groups where polyploidy, hybridization, and horizontal gene transfer are important (Stevens 1984; Doolittle and Bapteste 2007); emphasis of historical pattern omits causal mechanisms (O’Hara 1988); angled branches may overemphasize anagenesis (evolution within a lineage) rather than cladogenesis (Catley and Novick 2008); topology may facilitate confusion between ancestral and sibling clades (Gregory 2008)

Branching pattern is oriented vertically (tree grows from bottom to top)

Enables viewers to attach a loose sense of time to the diagram (Catley and Novick 2009); emphasizes the increase in phylogenetic diversity over evolutionary time

Implies progress, improvement, directional evolution, and superiority of uppermost species (Alters and Nelson 2002); overemphasizes anagenesis rather than cladogenesis (Catley and Novick 2008); suggests a drive toward diversity that is linked to superiority

Branching pattern is oriented horizontally

Deemphasizes preconceived association of uppermost species with superiority (Alters and Nelson 2002); orientation may suggest the passage of time (Tversky 2001)

Superiority and inferiority may be inferred from horizontal arrangement of taxa

Branches have different lengths

Emphasizes the distinctiveness of major phyla; in phylograms, branch length indicates relative divergence from common ancestors (Gregory 2008)

Evolutionary branching events occurred long ago and no longer happen today (Archibald 2009); suggests a “main line” of evolutionary progress with other phyla being “side tracks,” long branches imply primitiveness (Gregory 2008)

Tree trunk depicted as a single thick stem

Emphasizes the unitary origin of life and the relatedness of all organisms (Torrens and Barahona 2012)

Suggests a “main line” of evolutionary progress (O’Hara 1992); hides complex historical pattern (Costa 2009); hides diversity of fossil groups and may overemphasize historical drive toward diversity (Gould 1995; Maderspacher 2006)

Placement of taxonomic names on branch tips

Enables viewers to trace the evolutionary relationships between clades

Implies that evolutionary units are clearly defined entities with fixed characteristics, rather than populations whose characteristics change over time (O’Hara 1988); relationships may be “read” along branch tips, rather than by nodes (Gregory 2008)

Placement of taxonomic names at nodes

Downplays idea of “missing links” between ancestral and descendent clades (Catley and Novick 2008)

Suggests known ancestor-descendant relationships when these may only be inferred (Catley and Novick 2008)

Placement of multiple taxonomic names along a branch

Situates fossil evidence along hypothesized evolutionary pathway

Overemphasizes anagenesis; suggests known ancestor-descendant relationships (Catley and Novick 2008)

Lack of explicit link between time and the vertical dimension (for vertically-oriented trees)

(None for this feature)

Sense of time passing becomes blurred (Catley and Novick 2009)