The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the Universityof of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University The phylogenetics and evolution of Africa's Larks (Alaudidae) Keith Neville Barnes Thesis presented for the degree of DOCTOR OF l'llJLOSOI'HY Town I'~rcy Filzl'atrick Jns(i(ule of AITican Ornithology. [)cpanmcnt of Zoology U>JIVERS\TY OF CAPE TOViN Cape of Supervisor: Assoc.iate Professor P~ter G, Ryan. I'ercy FitzPatrick Institute of African Ornithology, UnivcrsityofCapc Town Co-supervisor: Associate Prol"ssor l'aul~U~ BI(~)lTI<er, M()l~eular Ecology and Evolution Programme,University [)epartment of Genetics. University of Pretoria April 2007 The phylogenetics and evolution of Africa's Larks (Alaudidae) Keith Neville Barnes Thesis presented for the degree of DOCTOR OF PHILOSOPHY Town Percy FitzPatrick Institute of African Ornithology, Department of Zoology UNIVERSITY OF CAPE TOWN Cape of Supervisor: Associate Professor Peter G. Ryan, Percy FitzPatrick Institute of African . Ornithology, University of Cape Town Co-supervisor: Associate Professor Paulette Bloomer, Molecular Ecology and Evolution Programme,University Department of Genetics, University of Pretoria ... April 2007 To my parents, without whom this would have never begun, to Yi­ fang without whom this would have never been completed, to Joshua without whom this might have been completed sooner .... Town Cape of University Declaration I declare that the work presented in this thesis is my own, unaided work, both in concept and execution. Apart from the normal guidance of my supervisors, any assistance acquired is duly acknowledged. The thesis is presented for examination by me for the degree of PhD, at the University of Cape Town. It has not been previously submitted for any degree or examination at this or any other university. ~----------?~ Keith N. Barnes Town Cape of University Larks have been both confused ..... .. "It is doubtful whether the matter (of lark systematics) will ever be satisfactorily resolved" - Gordon L. Maclean (1969) In A review of the Alaudidae, perhaps the most flawed taxonomic treatise on the family ever produced, the author stated "I make no apology for my methods, for 1 believe that they correctly interpret the facts and that posterity will concur. My view on the validity of geographical races is not orthodox. Having been a sinner myself 1 can expiate my indiscretions without exultation and in repentance" - Richard Meinertzhagen (1951) Town Cape of Maclean ventured a cautious and pessimistic view of lark systematics in strong contrast to Meinertzhagen's self-assured and somewhat misguided statements. The truth of the matter probably lies somewhere between the two great lark men's perspectives. While the advent of molecular techniques has hopefully improved the situation somewhat, I imagine that many statements made in this work will, like the larks themselves, change and evolve. University · ...and celebrated To hear the lark begin his flight, And singing startle the dull Night, From his watch-tower in the skies, Till the dappled dawn doth rise. John Milton, L 'Allegro The bird that soars on highest wing, Builds on the ground her lowly nest; And she that doth most sweetly sing, Sings in the shade when all things rest: In lark and nightingale we see What honor hath humility. Town James Montgomery, Humility Better than all measures of delightful sound, Cape Better than all treasures that in books are fOlmd, Thy skilled poet were, thou scorner of theof ground! Percy Bysshe Shelly, To a Skylark Leave to the nightingale her shady wood; A privacy of glorious light is thine: When thou dost pour upon the world a flood Of harmony, with instinct more divine: Type of the wise who soar, but never roam: True to the kindredUniversity points of Heaven and Home! William Wordsworth, To a Skylark Acknowledgements Many people and institutions contributed to this work. First and foremost, my supervisors, Peter Ryan and Paulette Bloomer provided financial assistance and supervision. Fellow students at the Molecular Ecology and Evolution Programme (MEEP) laboratory in Pretoria were superb sources of technical expertise and in this regard I cannot thank Wayne Delport, Lisel Solms and lsa-rita Russo enough. Wayne helped sequence the Saudi Arabian larks and Lisel showed me the sequencing ropes and assisted hugely by extracting some samples. F.K. Barker from the Bell Museum of Natural History, University of Minnesota, sequenced the samples and performed phylogenetic analyses for RAG-I (Chapter 3). Many of the species in this study were collected by me during extensive periods in the field in 1999 in Morocco and East Africa and in South Africa in 2001. Fieldwork in Morocco was facilitated and funded by the International FoundationTown for the Development and Conservation of Wildlife (IFCOW); sampling was permitted at their facility near Er­ rachedia, and help was provided by Dr Lubomir Pesce, Dr Robert Dawson and Abdul Wahid. Miles Coverdale, Callan Cohen, Peter HeuthCape and Malcolm Wilson provided critical support during collecting in Kenya and Uganda. Razo Lark samples were kindly provided by Dr. Cornelius Hazevoet and ofwere collected during the Cape Verde Petrel survey, funded by the Royal Society for the Protection of Birds. Madagascar Lark and Homed Lark samples were supplied by Dr. John M. Bates of the Chicago Field Museum of Natural History. Peter Ryan provided samples for larks in southern and central Africa and D. Moyer provided Flappet Lark samples from Tanzania. Samples of Palearctic lark taxa were provided by I. Tieleman and J. Williams of the Department of Evolution, Ecology, and OrganismalUniversity Biology, Ohio State University. Foot scraping samples that provided DNA material were taken from the_ British Museum of Natural History (Tring) and the National Museum of Kenya (Nairobi). Or Robert Prys-Jones and Mark Adams (BMNH), Dr Leon Bennun and George Amutete (KNM) are thanked for their assistance in providing access to the respective collections. The study to investigate Beesley's Lark was conceived and graciously supported by Neil and Liz Baker in Tanzania. The Bakers provided a vehicle, accommodation and assistance wherever they could and Njano Mhilinyi was a fantastic field assistant and companion. Marc Herremans and Michele Louette assisted with some crucial infonnation about a Spike-heeled Lark specimen in the Tervuren Museum. Other institutions that issued collecting pennits, access to collections, provided samples or assisted elsewhere include the American Museum of Natural History, Field Museum of Natural History, Kenya Wildlife Services, Northern Flagship Institution, South African Museum and Western Cape Nature Conservation Board. Vi-fang Bames and David Nkosi assisted loading morphometric data into spreadsheets. Penn Lloyd helped with some statistical analyses. The National Research Foundation provided financial support, as did Tropical Birding. To members of the Fitz, Richard Dean, Phil Hockey and Penn Lloyd, many thanks for commenting on various drafts of chapters. Other comments by Christopher Matthews and Rauri Bowie were also very helpful. Finishing this thesis while running a thriving business and having a 16 month old son at home is undoubtedly the biggest personal challenge I have ever faced. Vi-fang provided critical personal support when I was close to meltdown.Town I am extremely grateful to my colleagues at Tropical Birding for affording me the time to finish this work, when they really did not have to. Cape of University ABSTRACT Barnes, K.N. 2007. The phylogenetics and evolution ofAfrica's Larks (Alaudidae). PhD thesis, Percy FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, 7701, South Africa. The larks are a group of dull coloured birds that are conservative in plumage coloration and pattern due to the requirements for camouflage in open habitats. Because many species inhabit structurally similar habitats the group is also characterised by a great deal of morphological convergence. Variation in plumage and morphology is frequently as great within species as it is between species, leading to many inconsistent and controversial taxonomic treatments and classifications at an intra- and inter-generic level, and when defining specific and sub-specific boundaries. The advent of genetic techniques and success at applying these to species complexes in southern Africa suggested that a molecular phylogeny of the family would elucidate relationshipsTown that could not be determined via traditional taxonomic practices. In this study 2009 nucleotides of two mitochondrial DNA genes, cytochrome b and 16S rRNA (Chapter 2), and 2872 nucleotides ofCape the nuclear exon RAG-l (Chapter 3) were used to generate a robust phylogeny of the family Alaudidae. The former analysis included 55 species and the latter 25. Theseof data were also combined to construct a combined evidence phylogeny (Chapter 7). Within the family, several genera recognised by more traditional taxonomies are polyphyletic, including Ammomanes, Eremalauda .and Certhilauda. Two other genera, Calandrella and Mirafra, are best treated as multiple genera (Chapter 2). The sampled Alaudidae can be divided into three main radiations, the ammomanid larks,University