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COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species

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COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species by Rebecca Elbourne A thesis submitted in conformity with the requirements for the degree of Master of Science Ecology and Evolutionary Biology University of Toronto © Copyright by Rebecca Elbourne 2011 COI Barcoding of the Shorebirds: Rates of Evolution and the Identification of Species Rebecca Elbourne Master of Science Ecology and Evolutionary Biology University of Toronto 2011 Abstract This study assembles COI barcodes from 1814 specimens from the shorebird order, Charadriiformes and examines variation relative to time, rate of evolution and taxonomic level. In the suborder Scolopaci, 95% of sampled species were identified correctly. COI barcode variation within monotypic species was low (0-1% maximum distance) but showed a wide range within polytypic species (0-5%). Preliminary Charadrii results suggest similar trends but success is reduced in the third suborder, Lari. Rates of COI evolution are found to be lowest in the Lari and this leads to reduced species identification in recently radiated families: just 49% of the Laridae and 57% of the Stercoraridae are identified but 100% of the older Alcidae. In the faster Scolopaci, subspecies are at the limit of resolution with some well differentiated subspecies not distinguished by barcodes. The interplay of evolutionary rates, divergence dates and gene flow appears to determine COI barcode differentiation between taxa. ii Acknowledgments I must first thank my supervisor Allan Baker for bringing me into the fascinating world of the Royal Ontario Museum and allowing me to explore the amazing collection of the Department of Ornithology. His passion for his work has been inspiring and his patience as I learned the ropes has been deeply appreciated. I have had the good fortune to have been helped along by many excellent people while completing my degree. Fellow bird barcoder, Erika Sendra Tavares, was always innovative, cheerful and generous. Oliver Haddrath taught me everything I know about lab work and tirelessly guided all of us students over endless hurdles while somehow managing to carry on with his own innovative research. Mark Peck, a fine naturalist who collected and preserved many of the specimens used in this study, was always keen to solve mysteries and help me see the birds behind the barcodes. Sergio Pereira got me hooked on evolutionary rates and answered many late-night emails about crazy software and weird ideas. My lab mates Alison Cloutier, Nichola Chong, Yvonne Verkeuil, Maryann Burbridge, Rosemary Gibson and Pasan Samarisin were always interesting, fun, helpful and a pleasure to work with. Kristen Choffe kept her great sense of humour even while juggling all of our ABI needs. Cathy Dutton and Sue Chopra always knew how to get things done (and organised fine Christmas parties!). Professors Sue Varmuza and Peter Andolfatto opened my eyes to just how exciting biology can be. Doug Currie told me to “Go for it” at a critical time and has been consistently helpful and supportive. The biggest thanks must go to my family: Simon and Alex who make things easy by being decent, caring individuals and my husband Brian who has supported me throughout. Brian, it was your belief in me that pulled me through. Thank-you. Many thanks to Jan Bolding Christensen of the Zoological Museum of the University of Copenhagen, Sharon Birks of the Burke Museum, Janet Hinshaw of the Museum of Zoology of the University of Michigan, and Robb Brumfield of the Louisiana State University Museum of Zoology for tissue loans. Thanks also to Mark Peck and Erica Sendra Tavares for generously allowing the use of unpublished sequences. Funding for this work was provided by OGS and the Canadian Barcode of Life Network from Genome Canada through the Ontario Genomics Institute, NSERC and other sponsors listed at www.BOLNET.ca. iii Table of Contents Acknowledgments .......................................................................................................................... iii Table of Contents ........................................................................................................................... iv List of Tables ................................................................................................................................. vi List of Figures ............................................................................................................................... vii List of Appendices ....................................................................................................................... viii CHAPTER ONE Introduction: Barcoding the Birds of the World ............................................................................. 1 CHAPTER TWO Barcoding the Scolopaci and Charadrii: Species, Subspecies and Patterns of Variation ............. 12 2.1 Introduction ............................................................................................................................. 13 2.2 Methods ................................................................................................................................... 16 Taxon sampling ......................................................................................................................... 16 DNA amplification and sequencing .......................................................................................... 17 Analysis ..................................................................................................................................... 18 2.3 Results ..................................................................................................................................... 20 Species Identification ................................................................................................................ 20 Subspecies identification and putative new species .................................................................. 30 Preliminary results from the suborder Charadrii ...................................................................... 37 2.4 Discussion ............................................................................................................................... 44 Scolopaci barcodes support current research findings .............................................................. 44 Deep splits within polytypic species point to new research directions ..................................... 46 Distances within and between species and subspecies form a continuous spectrum ............... 47 Phenotypes may differentiate faster than COI barcodes ........................................................... 47 Conclusion ................................................................................................................................ 51 CHAPTER THREE Barcoding the Lari: Rates of Evolution and the Identification of Species ................................... 53 3.1 Introduction ............................................................................................................................. 53 3.2 Methods ................................................................................................................................... 57 Taxon sampling ......................................................................................................................... 57 DNA amplification and sequencing .......................................................................................... 58 iv Analysis ..................................................................................................................................... 59 Substitution rates ....................................................................................................................... 60 3.3 Results ..................................................................................................................................... 62 Species identification in Gulls and skuas .................................................................................. 62 Species Indentification in Auks and Terns ............................................................................... 76 Poor resolution in Lari matched by low rates of COI substitution ........................................... 78 3.4 Discussion ............................................................................................................................... 81 Reduced rate of COI substitution may slow barcode differentiation ........................................ 81 Gene flow may slow barcode differentiation ............................................................................ 82 Skuas and Masked Gulls: further evidence ............................................................................... 84 Alcids: slow substitution rate is overcome by species age ....................................................... 85 Conclusion: interplay of dates, rates and flow determines barcoding success ......................... 86 CHAPTER FOUR Conclusion .................................................................................................................................... 87 REFERENCES ............................................................................................................................. 91 Appendix 1: Charadriiformes specimens used in this study ....................................................... 103 v List of Tables CHAPTER TWO Table 2.1: Barcoding statistics for Scolopaci species. ................................................................
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