PHYLOGENY OF NEORNITHES

Abstract This work serves as a compendium of anatomical resources upon which a companion phylogenetic analysis of Aves and related Theropoda (Avialae) was based (Livezey and Zusi 2006). Following a brief historical overview of avian anatomy and avian systematics, the rich published literature pertinent to these topics is classified chronologically and geographically. The former also was organized with respect to eras of predominant methodologies in avian systematics, with an emphasis on recent paleontological finds bearing importantly on the origins of modern birds (Neornithes). This was followed by an exposition on the theoretical and abstract underpinnings of morphological characterization for purposes of phylogenetic reconstructions (to be published separately), with aspects of analysis for phylogenetic inference (e.g., tactics for employment of currently available software, ordering, criteria for optimization of trees) considered elsewhere. The principal contribution of this exposition is a listing of characters and states manifesting what was inferred to hold promise with respect to phylogenetic or historical signal. In total, 2,954 anatomical characters were defined—2,451 osteological, 256 myological, and 247 miscellaneous—of which 981 (approximately one-third) were multiple-state (i.e., comprised three or more states), the latter including 537 characters treated as ordered. Bibliographic provenance for characters was provided, where possible, but exact equivalence of characters and states among workers was seldom feasible. In many cases, previously published characters were listed on the grounds that these pertained most closely to the structure or complex at hand in the present study, and that such listings provided at least a historical grasp of the magnitude of prior usages of a given character. We also summarized, to the extent feasible, previously published characters for which inclusion in the present work was judged to be unreliable or lacking sufficient clarity. In addition to the descriptions of characters, a limited series of figures are provided, in no small part to ameliorate the challenges posed by new terms and formal anatomical nomenclature. We are adherents to nomenclatural formalism (Livezey and Zusi 2001) in anatomical contexts sensu the ICAAN (International Committee on Avian Anatomical Nomenclature; Baumel 1993). I.e., we consider that characters and states—implicitly proposals of homology—warrant clarity with respect to surrounding text in the same sense that binomial taxa—i.e., as hypotheses of historical lineages—are subject to formal conventions. Finally, literature cited herein is listed, as a work of this kind is impossible without access to the wealth of information and insight provided by such a resource. As this literature is integrated by citation with the descriptions of characters, it is hoped that the bibliography will lessen the challenges posed by a deep, multilingual, and variably technical literature for systematists using these descriptions. The dimension of the character matrix also led us to enclose a CD of the data set in the present work to assist those seeking to improve, append, or refine our efforts. A phylogenetic (cladistic) analysis of these data will appear separately (Livezey and Zusi 2006). Soon thereafter a collaboration with an unparalleled compilation of molecular data (i.e., DNA sequences) and confirmatory paleontological data is planned to conclude with the publication of a total-evidence analysis of avian phylogeny under the auspices of the NSF “Tree of Life” program, one to encompass extant birds (Neornithes), avian relatives from the Mesozoic (outgroups), and nonavialian fossil taxa from the Mesozoic (“deep” outgroups).