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(Teleostei: Schizothorax) in the Central Himalayas Binod Regmi University of Arkansas, Fayetteville

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(Teleostei: Schizothorax) in the Central Himalayas Binod Regmi University of Arkansas, Fayetteville University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2019 Phylogenomics and Geometric Morphometrics Define pS ecies Flocks of Snowtrout (Teleostei: Schizothorax) in the Central Himalayas Binod Regmi University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Developmental Biology Commons, Evolution Commons, and the Terrestrial and Aquatic Ecology Commons Recommended Citation Regmi, Binod, "Phylogenomics and Geometric Morphometrics Define peS cies Flocks of Snowtrout (Teleostei: Schizothorax) in the Central Himalayas" (2019). Theses and Dissertations. 3170. https://scholarworks.uark.edu/etd/3170 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. Phylogenomics and Geometric Morphometrics Define Species Flocks of Snowtrout (Teleostei: Schizothorax) in the Central Himalayas A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Sciences by Binod Regmi Tribhuvan University, Institute of Forestry, Nepal Bachelor of Science in Forestry, 2001 Wildlife Institute of India Post Graduate Diploma (Honors) in Wildlife Management, 2007 University of Louisiana Master of Science in Biology, 2012 University of Arkansas Master of Science in Statistics and Analytics, 2018 May 2019 University of Arkansas The dissertation is approved for recommendation to the Graduate Council. ____________________________________ Marlis R. Douglas, Ph.D. Dissertation Director _______________________________ ____________________________________ Michael E. Douglas, Ph.D. Andrew J. Alverson, Ph.D. Committee Member Committee Member ____________________________ David R. Edds, Ph.D. Committee Member Abstract Schizothorax (Snowtrout) is a genus of medium-sized minnows (Cypriniformes) inhabiting glacier-fed streams, rivers, and lakes in the Himalayas. There are more than 30 species of Schizothorax across the region. The speciation and diversity of the Snowtrout in the vast hinterlands of the Himalayan Region has not been fully explored. Three species in Lake Rara, Western Nepal are considered a species flock, comprising endemic ecotypes that are morphologically differentiated and reproductively isolated. My dissertation research examined the diversity of Schizothorax in the Central Himalayan region and evolutionary relationships among species distributed in the Tibet, Central and Southeast Asia. Chapter I describes the historical biogeography and distribution of Schizothorax species in the Himalayas and Tibetan Region. In Chapter II, morphological and genetic variation was examined among Schizothorax collected from three major drainage systems in Nepal using 18 anatomical landmarks (number of images, N=565) and mitochondrial gene (cytochrome b) sequence analysis (n=115). In Chapter III, machine learning algorithms were evaluated to discriminate morphological species based on head and body shape using Procrustes aligned data generated in Chapter 2. In Chapter IV, a phylogenetic tree of Schizothorax was constructed comprising Central (Nepal, haplotypes=14) and Eastern (Bhutan, haplotypes=18) Himalayan species to explore their evolutionary relationships within in a global species phylogeny based on GenBank data (n=51, outgroups=5). Chapter V employed a phylogenomic approach to examine fine-scale relationships amongst Schizothorax in Nepal and assess uniqueness of endemic forms in Lake Rara. Double digest restriction associated DNA (ddRAD)sequences were generated to extract 20,000 single nucleotide polymorphism (SNPs) loci. These data were used to trace the selection driven phenotypic convergence among species isolated largely due to the geographical and ecological barriers. Both species and basins were significant predictors of the shape. Classifiers, such as Linear Discriminant Analysis (LDA) and Support Vector Machine (SVM), assigned individuals to morphological species with high accuracy. However, a strong geographic structure was reflected in the mitochondrial (cytochrome b) gene sequence data. Conversely, phylogenomic analysis of SNPs uncovered basin-specific upstream and downstream clades, as well as Lake Rara endemic species as a monophyletic group that mitochondrial gene analyses failed to resolve in previous studies. Table of Content Chapter I Introduction……………………………………………………………………..1 References ................................................................................................................ 10 Appendix .................................................................................................................. 13 Chapter II Morphological and genetic variability in a species-complex of Central Himalayan fish (Cyprinidae:Schizothorax) inhabiting Lake Rara in Nepal Abstract .................................................................................................................... 15 Introduction .............................................................................................................. 17 Methods .................................................................................................................... 20 Results ...................................................................................................................... 25 Discussion ................................................................................................................. 29 Conclusion ................................................................................................................ 31 Acknowledgements .................................................................................................... 32 References ................................................................................................................ 33 Appendix .................................................................................................................. 37 Chapter III Can machine learning accurately delimit morphological species: Central Himalayan Snowtrout (Schizothorax) as a test case Abstract .................................................................................................................... 53 Background ............................................................................................................... 54 Methods .................................................................................................................... 58 Results ...................................................................................................................... 63 Discussion ................................................................................................................. 66 Conclusion ................................................................................................................ 69 Abbreviations ............................................................................................................ 70 Acknowledgements .................................................................................................... 71 Funding ..................................................................................................................... 71 References ................................................................................................................ 72 Appendix .................................................................................................................. 76 Chapter IV Paleodrainages and the biogeography of Snowtrout (Cyprinidae: Schizothorax) in South and Central Asia Abstract .................................................................................................................... 87 Introduction .............................................................................................................. 89 Methods .................................................................................................................... 91 Results ...................................................................................................................... 96 Discussion ................................................................................................................. 98 Conclusion .............................................................................................................. 103 Acknowledgement ................................................................................................... 103 References .............................................................................................................. 105 Appendix ................................................................................................................ 113 Chapter V Species flocks of Snowtrout (Schizothorax) in the Central Himalayas: convergent evolution along elevation gradient Abstract .................................................................................................................. 122 Introduction ............................................................................................................ 123 Methods .................................................................................................................. 125 Results .................................................................................................................... 127 Discussion ..............................................................................................................
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