Institut für Biochemie und Biologie Evolutionsbiologie/Spezielle Zoologie Inference of phylogenetic relationships in passerine birds (Aves: Passeriformes) using new molecular markers Dissertation zur Erlangung des akademischen Grades “doctor rerum naturalium” (Dr. rer. nat.) in der Wissenschaftsdisziplin “Evolutionsbiologie“ eingereicht an der Mathematisch-Naturwissenschaftlichen Fakultät der Universität Potsdam von Simone Treplin Potsdam, August 2006 Acknowledgements Acknowledgements First of all, I would like to thank Prof. Dr. Ralph Tiedemann for the exciting topic of my thesis. I’m grateful for his ongoing interest, discussions, support, and confidence in the project and me. I thank the University of Potsdam for the opportunity to perform my PhD and the financial and logistical funds. This thesis would not have been possible without many institutions and people, who provided samples: University of Kiel, Haustierkunde (Heiner Luttmann and Joachim Oesert), Zoologischer Garten Berlin (Rudolf Reinhard), Tierpark Berlin (Martin Kaiser), Transvaal Museum, South Africa (Tamar Cassidy), Vogelpark Walsrode (Bernd Marcordes), Eberhard Curio, Roger Fotso, Tomek Janiszewski, Hazell Shokellu Thompson, and Dieter Wallschläger. Additionally, I thank everybody who thought of me in the moment of finding a bird, collected and delivered it immediately. I express my gratitude to Christoph Bleidorn for his great help with the phylogenetic analyses, the fight with the cluster, the discussions, and proof-reading. Special thanks go to Susanne Hauswaldt for patiently reading my thesis and improving my English. I thank my colleagues of the whole group of evolutionary biology/systematic zoology for the friendly and positive working atmosphere, the funny lunch brakes, and the favours in the lab. I’m grateful to Romy for being my first, ‘easy-care’ diploma-student and producing many data. I’m very grateful to Katja for her patience and perpetual technical help. A very special thank goes to Philine for her friendship, encouragement, understanding, and good ideas. It would have been harder without her. Thanks to Steffi for cat-sitting on Potsdam-weekends and together with ‘the Henne’ for realistic birds. I hope you understand why I preferred Mama’s nice painting of the fieldfare for the cover. I could not have reached anything without Malte and my parents, who have supported me throughout the years and are there for me whenever I need them. Thank you for love, confidence, encouragement, and being with me. Table of contents Table of contents 1 Introduction .................................................................................................. 1 1.1 Phylogenetic relationships within Passeriformes and the need for new markers .......... 1 1.2 ZENK and CR1 as new phylogenetic molecular markers................................................ 4 1.3 Aims of this study................................................................................................................. 7 2 Summary of articles ..................................................................................... 8 2.1 Summary of article I:........................................................................................................... 8 2.2 Summary of article II: ....................................................................................................... 10 2.3 Summary of article III: ..................................................................................................... 12 3 Discussion .................................................................................................... 14 3.1 Utility of new molecular markers for Passeriformes systematics.................................. 14 3.1.1 ZENK............................................................................................................................................ 14 3.1.2 CR1 elements as apomorphic markers .......................................................................................... 15 3.1.3 Sequences of CR1 elements .......................................................................................................... 17 3.2 Phylogenetic relationships within Passeriformes inferred from new markers ............ 18 3.2.1 Suboscines..................................................................................................................................... 18 3.2.2 ‘Corvida’ ....................................................................................................................................... 19 3.2.3 Picathartidae.................................................................................................................................. 19 3.2.4 Passerida........................................................................................................................................ 20 3.3 Conclusion .......................................................................................................................... 23 4 Abstract ....................................................................................................... 25 5 Abstract (German version)........................................................................ 26 6 References ................................................................................................... 28 7 Appendix ..................................................................................................... 38 7.1 Article I:.............................................................................................................................. 38 7.2 Article II: ............................................................................................................................ 78 7.3 Article III:......................................................................................................................... 103 Introduction 1 Introduction 1.1 Phylogenetic relationships within Passeriformes and the need for new markers Among all classes of living organisms, Aves is supposed to be the best known, and some argue that presumably ‘all’ species have been discovered and named (Groth and Barrowclough, 1999). Nevertheless, their origin, phylogeny, and biogeography has been a continuous matter of debate, which has been intensified through the use of molecular data (e.g. Cracraft, 2001; Groth and Barrowclough, 1999; Sibley and Ahlquist, 1990). The difficulty in resolving these issues stems from their rapid adaptive radiation and the adaptation to flight. The anatomical characteristics correlated with the development of flight gained by the first birds are more or less conserved in recent species and thus, birds own only few taxon specific morphological synapomorphies (Feduccia, 1996). The highest diversity among living birds is found in the order Passeriformes. This by far largest avian taxon comprises roughly 59 % of all living birds (more than 5700 species, Sibley and Ahlquist, 1990). The Passeriformes form a morphologically very homogenous group and their monophyly is well established, both on morphological (Raikow, 1982) and molecular grounds (Sibley and Ahlquist, 1990). However, phylogenetic relationships within the group have been extremely puzzling, as most of the evolutionary lineages originated through rapid radiation during the early Tertiary (Feduccia, 1995). Fast diverging clades had little opportunity to acquire synapomorphies, which resulted in ill-defined groups for reconstructions of a phylogeny (Lanyon, 1988). The first extensive molecular study on avian systematics was based on DNA-DNA hybridization analyses (Sibley and Ahlquist, 1990) and corroborated the basal split of Passeriformes into the two morphologically monophyletic clades of suboscines (Tyranni) and oscines (Passeri) (e.g. Ames, 1971; Feduccia, 1975). This study, however, has been criticised by several authors concerning its reproducibility (Mindell, 1992), sparse sampling and its lack of internal consistency (Cracraft, 1992; Lanyon, 1992). Nevertheless, Sibley and Ahlquist’s (1990) phylogeny of the Passeriformes (Fig. 1) with 46 families and 46 subfamilies (classified by Sibley and Monroe (1990)) has become the basis for subsequent DNA sequence analyses. While sequence-based studies generally agree with the partition of Passeriformes into the monophyletic clades of suboscines and oscines, a third group composed of the New Zealand 1 Introduction Fig. 1 Phylogenetic relationships of passerine families and their higher-level systematic classifications based on the DNA-DNA hybridization analyses of Sibley and Ahlquist (1990). wrens (Acanthisittidae) has been established as the earliest branch within the Passeriformes and sister group to suboscines and oscines (Barker et al., 2002; Ericson et al., 2002a). The division of the oscines into the two sister taxa Corvida and Passerida, which had been hypothesised by Sibley and Ahlquist (1990), has been rejected later, as the Corvida appear to be paraphyletic (Barker et al., 2002; Ericson et al., 2002a, b). Additionally, conflicting phylogenetic hypotheses have been put forward for lower phylogenetic relationships, especially within the Passerida and their three superfamilies defined by Sibley and Ahlquist (1990): Muscicapoidea, Sylvioidea and Passeroidea (e.g. Barker et al., 2004; Beresford et al., 2 Introduction 2005; Ericson et al., 2003; Ericson and Johansson, 2003). For example, the phylogenetic position of the waxwings (Bombycillidae) at the basis of the Muscicapoidea has been questioned (e.g. Barker et al., 2002; Ericson