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Climatic Niche Estimation, Trait Evolution and Species Richness in North

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Climatic Niche Estimation, Trait Evolution and Species Richness in North Climatic niche estimation, trait evolution and species richness in North American Carex (Cyperaceae) by Jocelyn E. Pender, B.Sc. (Hons.) Thesis submitted to the Faculty of Graduate and Postdoctoral Studies University of Ottawa In partial fulfilment of the requirements for the Degree of Master of Science in the Ottawa Carleton Institute of Biology © Jocelyn E. Pender, Ottawa, Canada, 2016 Supervisor: Dr. Julian Starr Committee Members: Dr. Tyler Smith Dr. Risa Sargent (Fall 2013 - Winter 2015) Dr. Stéphane Aris-Brosou (Fall 2015 - present) ii Abstract With close to 2100 species, the flowering plant genus Carex (Cyperaceae; sedges) is an example of an evolutionary radiation. Despite its potential for use as a model taxon in evolutionary studies, the diversification of sedges remains largely unexplored. This thesis realizes the potential of Carex as an evolutionary model group by using it to ask questions about species richness patterns. More specifically, it seeks to determine the relationship, if any, between rates of trait evolution and species richness. This tests the hypothesis that organisms with increased abilities to evolve new traits, speciate more rapidly. Morphological and ecological (habitat and climatic niche) traits are modelled on a nearly complete regional (North America north of Mexico) phylogeny and rates of trait evolution are compared among non-nested sister groups. However, before trait evolution is modelled, this work evaluates the sensitivity of climatic niche estimates to underlying distribution datasets. It tests the agreement of niche estimates derived from the commonly used online repository GBIF (the Global Biodiversity Information Facility) and county-level distributions via BONAP (the Biota of North America Program). Results showed that in the context of phylogenetic comparative analyses, it is not vital to obtain highly accurate climatic niche estimates. The second study found significant positive correlations between the rates of climatic niche, habitat and reproductive morphological evolution and species richness. This result supports the role of high trait lability in generating species richness and more generally, the idea that high trait disparity through evolutionary time leads to species success. iii Statement of Contributions The studies contained in this thesis were conceived and designed by Andrew L. Hipp, Julian R. Starr and Jocelyn E. Pender. Molecular work was performed by J.E. Pender. Additional molecular data were provided by Brianna N. Chouinard, Marlene Hahn and A.L. Hipp. County distribution data were collected, assembled and provided by John T. Kartesz and Misako Nishino. Morphological, specimen-based distribution and climatic niche data were gathered by J.E. Pender. Habitat scoring was by J.R. Starr and A.L. Hipp. All data were analysed, presented and discussed by J.E. Pender. iv Acknowledgements Firstly, thank you to my supervisor Julian Starr. I thoroughly appreciate all of the guidance provided. You have revised many drafts, made many wise suggestions and provided much moral and professional support. Thank you, perhaps most importantly, for providing me with a project that has challenged me intellectually and technically (I am now a proud ‘R’tist). I am excited to see where my new skills take me. Thank you Andrew Hipp, for your enthusiasm, creativity and knowledge. You have been integral to the development of this work. Also, thank you for facilitating my visits to the Arboretum, which were invaluable research getaways. I am further grateful to Marlene Hahn, who provided data download protocols, assisted with molecular data organization, and with other tasks. Thanks to the Morton Arboretum team for providing ITS and ETS sequences. Valuable feedback and advice was provided by my committee members, Tyler Smith and Risa Sargent. Thank you for your in-depth emails and guidance. The first Chapter was achieved in collaboration with John Kartesz and Misako Nishino. They graciously supplied the Biota of North America Program (BONAP) data for all North American Carex species, undoubtedly requiring much hard work to collect and assemble. Thank you for your cooperation. Thank you Sarah Chisholm and Elyse Latreille for assistance with portions of the research. The hard work of Brianna Chouinard provided all genomic DNA and matK sequences used for the development of the phylogeny. Discussions with Étienne Léveillé-Bourret aided in the development of this work. Also, thank you Étienne for allowing me to use your sequences for outgroups in my phylogeny. v Roger Bull and Paul Sokoloff provided vital training and guidance in DNA extraction, amplification and sequencing protocols. They have been important to the development of this work, thank you. Lastly, thank you Claire Gilmour, Wayne Sawtell, Anna Ginter, Tamara Villaverde, and Warren Cardinal-McTeague for providing advice on the graduate student process. vi Table of Contents Abstract ......................................................................................................................................... iii Statement of Contributions ......................................................................................................... iv Table of Contents ........................................................................................................................ vii List of Figures ............................................................................................................................... ix List of Tables ............................................................................................................................... xii List of Appendices ...................................................................................................................... xiii Chapter 1: Introduction ............................................................................................................... 1 1.1 FIGURES .............................................................................................................................. 5 Chapter 2: How sensitive are climatic niche inferences to distribution data sampling? ....... 6 2.1 INTRODUCTION ................................................................................................................. 6 2.2 METHODS............................................................................................................................ 9 2.2.1 Study taxon ..................................................................................................................... 9 2.2.2 Occurrence data .............................................................................................................. 9 2.2.2.1 Global Biodiversity Information Facility (GBIF) dataset ........................................ 9 2.2.2.2 Biota of North America Program (BONAP) dataset ............................................. 10 2.2.3 Geographic extent ......................................................................................................... 11 2.2.4 Climate data .................................................................................................................. 11 2.2.5 Principal component analysis ....................................................................................... 12 2.2.6 Correlates of error ......................................................................................................... 12 2.2.7 Phylogeny ..................................................................................................................... 14 2.2.8 Ancestral state reconstruction ....................................................................................... 14 2.2.9 Additional analyses....................................................................................................... 15 2.3 RESULTS ............................................................................................................................ 16 2.3.1 Principal component analysis ....................................................................................... 16 2.3.2 Sampling effort influencing error ................................................................................. 17 2.3.3 Elevation influencing error ........................................................................................... 18 2.3.4 Ancestral state reconstruction ....................................................................................... 18 2.3.5 Additional analyses....................................................................................................... 19 2.4 DISCUSSION ..................................................................................................................... 20 2.4.1 Recommendations ........................................................................................................ 27 2.5 TABLES AND FIGURES .................................................................................................. 28 vii Chapter 3: Regional species richness and trait evolution in the genus Carex (Cyperaceae) 37 3.1 INTRODUCTION ............................................................................................................... 37 3.2 METHODS.......................................................................................................................... 45 3.2.1 Trait definitions ............................................................................................................ 45 3.2.2 Flora of North America region ....................................................................................
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