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, 149 (1), 1-95

Higher-order Phylogeny of Modern Birds (Theropoda, Aves: Neornithes) Based on Comparative Anatomy. II. Analysis and Discussion

Higher-order Phylogeny of Modern Birds (Theropoda, Aves: Neornithes) Based on Comparative Anatomy. II. Analysis and Discussion

Bradley C Livezey et al. Zool J Linn Soc.

Abstract

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

Figures

Figure 4
Figure 4
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IV. A, Sibley & Ahlquist (1990: figs 354–356), simplified to orders, wherein parenthetical ‘para’ indicates paraphyly of sampled members, and ‘aug’ indicates unconventional content; B, Mindell et al. (1997).
Figure 1
Figure 1
Morphological phylogenetic trees proposed in previous studies, I. A, Cracraft (1988); B, Mayr et al. (2003). Some trees were subjected to topologically neutral modifications of taxa to facilitate comparisons (also Figs 2–9). See corresponding papers for analytical methods and topological statistics.
Figure 2
Figure 2
Morphological phylogenetic trees proposed in previous studies (see Fig. 1 for details), II. A, Mayr & Clarke (2003); B, Bourdon et al. (2005).
Figure 5
Figure 5
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), V. A, Espinosa de los Monteros (2000); B, Johansson et al. (2001).
Figure 9
Figure 9
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), IX. A, Pereira & Baker (2006a); B, Slack et al. (2006a).
Figure 10
Figure 10
Ordinal-level strict consensus tree for orders of Neornithes based on 2954 morphological characters, indicating delimitations of segments detailed in Figures 12–18.
Figure 12
Figure 12
Detailed segments of strict consensus tree of all MPTs recovered in present study. Part A. Outgroup (non-neornithine) taxa. Nodes are labelled by percentages of bootstrapped replicates in which node was retained (numerator), and below by Bremer support indices (denominator).
Figure 18
Figure 18
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part G. Neornithes: Piciformes, and Passeriformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 11
Figure 11
Simplified summary tree for uppermost, supraordinal ranks of avian classification. Dashed internodes correspond to marginally supported clades. For complete classification, see Appendix 1.
Figure 7
Figure 7
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VII. A, Paton et al. (2002); B, Sorenson et al. (2003).
Figure 8
Figure 8
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VIII. A, Chubb (2004a); B, Harrison et al. (2004).
Figure 13
Figure 13
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part B. Neornithes: Palaeognathae and Galloanserae. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 3
Figure 3
Morphological phylogenetic trees proposed in previous studies (see Fig. 1 for details), III. A, Mayr (2005b); B, Mayr (2005f: fig. 9), excluding fossils Prefica and Paraprefica.
Figure 14
Figure 14
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part C. Neornithes: nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 6
Figure 6
Molecular phylogenetic trees proposed in previous studies (see Fig. 1 for details), VI. A, Van Tuinen et al. (2000); B, Van Tuinen et al. (2001).
Figure 15
Figure 15
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part D. Neornithes: Gruiformes and Charadriiformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 16
Figure 16
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part E. Neornithes: Falconiformes, Strigiformes, Cuculiformes and Psittaciformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).
Figure 17
Figure 17
Detailed segment of strict consensus tree of all MPTs recovered in present study. Part F. Neornithes: Columbiformes, Caprimulgiformes, Apodiformes, Coliiformes, Trogoniformes and Coraciiformes. Nodes are labelled above by percentages of bootstrapped replicates in which node was retained (italics), and below by Bremer support indices (bold type).

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