Date of Graduation

5-2019

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Biology (PhD)

Degree Level

Graduate

Department

Biological Sciences

Advisor/Mentor

Douglas, Marlis R.

Committee Member

Alverson, Andrew J.

Second Committee Member

Edds, David R.

Third Committee Member

Douglas, Michael E.

Keywords

Anatomical landmark; Convergence evolution; ddRAD dna sequence; Lake Rara endemism; Machine learning; Speciation

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.

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