Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees - PubMed (original) (raw)

Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

Robert S Sansom et al. Sci Rep. 2013.

Abstract

Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences.

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Figures

Figure 1

Figure 1. Results of simulated fossilization analyses.

(a) Node recovery test, indicating significantly lower phylogenetic signal recovery for simulated fossilization searches (hard characters only) vs random missing characters in the same amount, but not for inverse-fossilization searches (soft characters only). Node recovery is the proportion of 2022 original strict consensus nodes recovered with systematic missing data or random missing data (the later being an average of 500 iterations with twice standard deviation error bars); (b) Taxon shift test, where soft characters are removed from individual taxa to simulate fossilization. Histograms represent shift from original position (x o), to new position (_x_†) relative to the root for all simulated fossil taxa that moved (above) and simulated fossil taxa that exhibit significant shift, given random missing data (below). In the case of the later, 61% of 491 taxa shift significantly down phylogenies, from their original position toward the root, vs 39% which shift significantly up; (c) the effect of a downward shift of a fossil taxa in a phylogeny on estimates of rates of evolution and inferences of timing of evolutionary events (pink bars represent evolutionary changes e.g. DNA base pair change or acquisition of a morphological character). Images in Figure 1a adapted from Gilbert and Duane.

Figure 2

Figure 2. Schematic protocol of analyses.

(a) Node recovery test; (b) Taxon shift test. Scripts for tests are available online (Supplementary 1–2).

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