Technical Comments

Comment on "A Well-Preserved Archaeopteryx Specimen with Theropod Features"

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Science  01 Sep 2006:
Vol. 313, Issue 5791, pp. 1238
DOI: 10.1126/science.1130800


On the basis of new information from the 10th specimen of Archaeopteryx, Mayr et al. (Reports, 2 December 2005, p. 1483) suggested that birds, or avian flight, originated twice. We investigate the statistical support for this phylogenetic hypothesis and show that it is no better supported by available morphological character data than the hypothesis of a single avian origin.

In a recent report, Mayr et al. (1) provided information on a new specimen of Archaeopteryx and posited a new classification of derived coelurosaurian theropods in which Aves (2) was either polyphyletic or required expansion to include deinonychosaurs, a clade previously considered to be nonavian dinosaurs. This novel phylogenetic hypothesis requires a complex pattern of parallel gains and/or secondary losses of flight and other “avian” features in the theropod-bird lineage. Given the controversial nature of a hypothesis suggesting that either birds, or avian flight, originated twice, we reexamined the evidence for their conclusions by determining support for the proposed phylogeny, carrying out statistical comparisons of the fit to the data between their hypothesis and competing alternatives, and investigating characters supporting the novel relationships suggested.

The new material (1) reveals osteological information unavailable from other Archaeopteryx specimens, permitting rescoring of eight morphological characters within an existing character matrix (3) used to resolve coelurosaur interrelationships. This principally alters the systematic relationships of Confuciusornis, which is no longer recovered as the sister taxon to Archaeopteryx within a monophyletic Aves, but placed as the sister taxon to Microraptor, within the dromaeosaurid clade.

We examined the relative support provided by the phylogenetic analysis of Mayr et al. (1) for both monophyletic and polyphyletic Aves using bootstrap proportions (4) and decay analysis (5). In general, support for the phylogeny of Mayr et al. is weak (Fig. 1), with that for the newly proposed clade Microraptor+Confuciusornis particularly low: Bootstrap proportions indicate that a monophyletic Aves (containing Archaeopteryx, Rahonavis, and Confuciusornis) is recovered in more of the bootstrap replicate data sets. To examine differences in fit to the data (1) of the competing hypotheses, we used an analysis (6) in which Aves was constrained to be monophyletic. This recovered 768 constrained trees of 600 steps, just one step longer than those from the unconstrained analysis (7). We then used the nonparametric Templeton test (8) to compare the fit of polyphyletic (unconstrained) and monophyletic (constrained) avian topologies to the data. The range of probability values obtained from pairwise comparisons (P = 0.819 to 0.853) indicates that the null hypothesis (9) cannot be rejected and that there is insufficient data to choose among the two alternative phylogenetic hypotheses (10).

Fig. 1.

Clade support on the strict consensus tree of (1). Bootstrap proportions are above the branch, decay index values below. The 50% majority rule bootstrap tree was poorly resolved, so the bipartition table was used to identify support for the relationships considered. Important results for the phylogeny presented in (1) include bootstrap proportions for Microraptor+Confuciusornis, 12.5%; for Archaeopteryx+Rahonavis, 16.9%; for a monophyletic Aves (Archaeopteryx+Rahonavis+Confuciusornis), 14.2%, which is higher than the grouping Microraptor+Confuciusornis; for Microraptor+Sinornithosaurus 16.1%, also higher than Microraptor+Confuciusornis. Decay indices are very low (1) for both Microraptor+Confuciusornis and Archaeopteryx+Rahonavis+Rahonavis. Average bootstrap proportion, 47%; average decay index, 1.93.

We carried out additional analyses using more recent versions of the Theropod Working Group's phylogenetic data matrix (11, 12), modified by the codings suggested by Mayr et al. (1). Although the modified analysis of (11) results in a polyphyletic Aves (13), use of a Templeton test to compare constrained (monophyletic Aves) and unconstrained trees (14) indicates that there is insufficient evidence to reject a monophyletic Aves (P = 0.8084 to 0.8474). Recoding (12) did not affect the topology or number of most parsimonious trees (MPTs) recovered; Confuciusornis and Archaeopteryx group together, whereas Rahonavis is recovered within Dromaeosauridae rather than Aves.

Using MacClade (15), we examined the distribution of characters (16) on the strict consensus trees of Mayr et al. (1) and Hwang et al. (3). Of the five characters (17) that unambiguously support Microraptor+Confuciusornis within Dromaeosauridae, the scoring of character 111, a separate or fused scapula and coracoid, is controversial (18). Of the two characters (19) uniting Archaeopteryx+Confuciusornis in a monophyletic Aves in (3), co-ossification of the metatarsals—character 166 (20)—is also problematic (21). After consideration of other specimens (22), we reverted to the scorings of (3) for Archaeopteryx for characters 111 and 166 but kept other rescorings as in (1). This results in avian monophyly with identical trees, tree lengths, and strict consensus topology to (3). Recoding of just two disputable characters in Archaeopteryx is sufficient to explain the hypothesis of avian polyphyly presented by Mayr et al. (1).

The new Archaeopteryx specimen provides valuable information on the morphology of basal birds and the relationships of taxa across the theropod-bird transition. However, Templeton tests and bootstrap analyses indicate that the hypothesis of a polyphyletic Aves is no better supported by available data than that of a monophyletic Aves. That alternative codings of Archaeopteryx for two controversial characters shift the resulting phylogenetic hypothesis between a monophyletic and polyphyletic Aves emphasizes the lack of robustness. We conclude that statistical support for the novel hypothesis of Mayr et al. (1) is weak and that there is little current consensus as to the relationships between Archaeopteryx, Rahonavis, and Confuciusornis within Coelurosauria (Fig. 2), complicating attempts to trace the sequence of character acquisitions during the origin of flight. In noting this, we hope to draw attention to the need for further work on coelurosaurian anatomy and phylogeny.

Fig. 2.

The relationships of the three avian taxa considered in (1) are subject to consider able uncertainty. Examining six recent phylogenies, all possible combinations of relationship are seen across either a monophyletic Aves or within Paraves (other taxa are not shown). (A) Hwang et al., 2002 (3). (B) Hwang et al., 2004 (11). (C) Chiappe, 2002 (26). (D) Forster et al., 1998 (27). (E) Makovicky et al., 2005 (12). (F) Mayr et al., 2005 (1). Four of the analyses (A, B, E, and F) are based on different iterations of the same basic data matrix. (C) and (D) are independently derived but may share characters (though the latter does not include Confuciusornis).

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