Likelihood reinstates Archaeopteryx as a primitive bird

Abstract

The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs. However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1. These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx-deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx-bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.

Figure 1.

Archaeopteryx robustly reinstated as the most basal bird by maximum likelihood (RaxML tree, log L −7608.41). Birds (including Archaeopteryx) is supported by likelihood bootstrap of 73%.

Figure 2.

(a) Archaeopteryx united with other birds (posterior probability 1.0) in Bayesian analysis. Relevant part of MrBayes majority-rule consensus shown; remainder of tree was also very similar to the likelihood tree in figure 1. Harmonic mean log L of sampled trees −5689.40. (b) Frequencies of splits found in Bayesian run 1, plotted against frequencies found in the other three runs, using AWTY [14]; all splits occurred at similar frequencies across all runs.