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Overall branching pattern
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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)
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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)
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Branching pattern is oriented vertically (tree grows from bottom to top)
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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
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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
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Branching pattern is oriented horizontally
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Deemphasizes preconceived association of uppermost species with superiority (Alters and Nelson 2002); orientation may suggest the passage of time (Tversky 2001)
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Superiority and inferiority may be inferred from horizontal arrangement of taxa
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Branches have different lengths
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Emphasizes the distinctiveness of major phyla; in phylograms, branch length indicates relative divergence from common ancestors (Gregory 2008)
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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)
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Tree trunk depicted as a single thick stem
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Emphasizes the unitary origin of life and the relatedness of all organisms (Torrens and Barahona 2012)
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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)
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Placement of taxonomic names on branch tips
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Enables viewers to trace the evolutionary relationships between clades
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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)
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Placement of taxonomic names at nodes
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Downplays idea of “missing links” between ancestral and descendent clades (Catley and Novick 2008)
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Suggests known ancestor-descendant relationships when these may only be inferred (Catley and Novick 2008)
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Placement of multiple taxonomic names along a branch
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Situates fossil evidence along hypothesized evolutionary pathway
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Overemphasizes anagenesis; suggests known ancestor-descendant relationships (Catley and Novick 2008)
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Lack of explicit link between time and the vertical dimension (for vertically-oriented trees)
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(None for this feature)
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Sense of time passing becomes blurred (Catley and Novick 2009)
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