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Molecular Phylogeny and Phylogeography of Reed Warblers and Allies (Aves: Acrocephalidae)

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Molecular Phylogeny and Phylogeography of Reed Warblers and Allies (Aves: Acrocephalidae) Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Tayebeh Arbabi Born in Mashhad, Iran Oral examination: 26 June 2014 Molecular Phylogeny and Phylogeography of Reed Warblers and Allies (Aves: Acrocephalidae) Referees: Prof. Dr. Michael Wink Prof. Dr. Marcus Koch i Table of contents Zusammenfassung..................................................................................................................... v Summary .................................................................................................................................. vi Abbreviations ......................................................................................................................... vii Publications ........................................................................................................................... viii 1 Introduction ............................................................................................................................ 1 1.1 General introduction ......................................................................................................... 1 1.1.1 Avian taxonomy ......................................................................................................... 1 1.1.2 Phylogeny and phylogeography ................................................................................. 2 1.1.3 Molecular markers ..................................................................................................... 4 1.1.4 Phylogenetic tree ........................................................................................................ 8 1.1.5 Molecular clocks ........................................................................................................ 9 1.2 Introduction to the reed warblers .................................................................................... 10 1.2.1 History of the systematic classification of the Acrocephalidae ............................... 10 1.2.2 Characterization of the family‘s genera and subgenera ........................................... 15 1.2.2.1 Large reed warblers......................................................................................... 15 1.2.2.2 Small reed warblers......................................................................................... 16 1.2.2.3 Hippolais species ............................................................................................ 17 1.2.2.4 Iduna species ................................................................................................... 17 1.2.2.5 Calamonastides gracilirostris ......................................................................... 18 1.2.2.6 Nesillas ............................................................................................................ 19 1.3 Objectives of the thesis ................................................................................................... 20 2 Material and Methods ......................................................................................................... 21 2.1 Sample material .............................................................................................................. 21 2.2 Equipment ....................................................................................................................... 21 2.3 Solutions and chemicals .................................................................................................. 22 ii 2.4 DNA extraction, amplification and sequencing .............................................................. 23 2.5 Data preparation .............................................................................................................. 24 2.6 Data analysis ................................................................................................................... 26 2.6.1 Population genetics .................................................................................................. 26 2.6.2 Reconstruction of phylogenetic trees ....................................................................... 26 2.6.3 Historical demography ............................................................................................. 27 2.6.4 Molecular dating ...................................................................................................... 27 2.7 Genomic fingerprinting by Inter-Simple Sequence Repeats (ISSR) .............................. 28 3 Results ................................................................................................................................... 29 3.1 A re-evaluation of phylogenetic relationships within reed warblers (Aves: Acrocephalidae) based on eight molecular loci and ISSR profiles ....................................... 29 3.1.1 Abstract .................................................................................................................... 29 3.1.2 Introduction .............................................................................................................. 29 3.1.3 Methods.................................................................................................................... 30 3.1.4 Results ...................................................................................................................... 35 3.1.5 Discussion ................................................................................................................ 41 3.1.6 Conclusions .............................................................................................................. 42 3.2 Mitochondrial phylogeography of the Eurasian reed warbler (Acrocephalus scirpaceus) and a first report of A. s. fuscus in Central Europe ............................................................... 47 3.2.1 Abstract .................................................................................................................... 47 3.2.2 Introduction .............................................................................................................. 47 3.2.3 Methods.................................................................................................................... 49 3.2.4 Results ...................................................................................................................... 56 3.2.5 Discussion ................................................................................................................ 58 3.3 Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the marsh warbler Acrocephalus palustris (Aves: Acrocephalidae) ................................ 69 3.3.1 Abstract .................................................................................................................... 69 3.3.2 Introduction .............................................................................................................. 69 iii 3.3.3 Methods.................................................................................................................... 71 3.3.4 Results ...................................................................................................................... 73 3.3.5 Discussion ................................................................................................................ 80 4 Conclusions ........................................................................................................................... 83 5 Acknowledgements .............................................................................................................. 87 6 References ............................................................................................................................. 88 iv Zusammenfassung Rohrsänger und Artverwandte (Familie Acrocephalidae ) blicken auf eine lange Geschichte der Klassifikation und kontinuierlichen Revision zurü ck . Aufgrund einer beachtlichen Ä hnlichkeit in der Morphologie und schnelle Radiation konnten frü here Studien nicht alle phyloge netischen Beziehungen zwischen und innerhalb der Gattungen lö sen . In dieser Studie wurden DNA-Sequenzen von acht mtDNA und Kerngenen (insgesamt, 6.280 nt) sowie die Analysen des genomischen ISSR- Fingerprintings verwendet, um die Verwandtschaftsverhältnisse unter den 35 Arten von Rohrsä ngern zu rekonstruieren . Die Ergebnisse sind kongruent mit frü heren molekular genetischen Analysen (Leisler et al, 1997; Helbig und Seibold, 1999; Fregin et al, 2009), sie stellen jedoch einige der Schwesterbeziehungen deutlicher heraus als zuvor. Basierend auf den Analysen der Hauptklade von Acrocephalus, Iduna (außer I. aedon) wurden Hippolais, Nesillas und Calamonastides bestätigt. Die gegenwärtige Situation der Taxonomie von Calamonastides gracilirostris als eine monotypische Gattung wurde durch Phylogenierekosntruktion aufgezeigt. Obwohl die Integration von Chloropeta natalensis und Chloropeta similis in die Gattung Iduna nicht vollstä ndig bewiesen werden konnte , kann eine enge Beziehung dennoch nicht ausgeschlossen werden. Es konnte im Gegensatz zur Vermutung von Fregin et al. (2009) kein Beleg fü r die Aufnahme von aedon in die Gattung Iduna gefunden werden; aus diesem Grund wird die Wiedereinfü hrung der Gattung Phragamaticola für diese Spezies vorgeschlagen. Eine molekulare Uhr Analyse bestä tigt die Hypothese von der schnellen Radiation der Familie im mittleren
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