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MIAMI UNIVERSITY the Graduate School MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Mohammed Abdullah Al-Saffar Candidate for the Degree DOCTOR OF PHILOSOPHY ______________________________________ David J. Berg, Director ______________________________________ Bruce J. Cochrane, Reader ______________________________________ John C. Morse, Reader ______________________________________ Michael J. Vanni, Reader ______________________________________ Thomas O. Crist, Reader ______________________________________ Mary C. Henry, Graduate School Representative ABSTRACT CONSERVATION BIOLOGY IN POORLY STUDIED FRESHWATER ECOSYSTEMS: FROM ACCELERATED IDENTIFICATION OF WATER QUALITY BIOINDICATORS TO CONSERVATION PLANNING by Mohammed A. Al-Saffar The Tigris and Euphrates Rivers and their tributaries form the arteries of life in the central part of the Middle East, where climate change and anthropogenic disturbance have been evident in recent decades. While the Tigris River has a long history of human use, the conservation status for the majority of its basin is poorly known. In addition, planning for conservation, given limited time, funds, and prior information, has remained a challenge. In my dissertation research, I sampled 53 randomly selected sites in the Kurdistan Region (the KR) of northern Iraq, a poorly studied region of the Upper Tigris and Euphrates freshwater ecoregion, for water quality bioindicators, mayflies (Insecta, Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera) (a.k.a. EPT). I identified the mayflies to the finest possible taxonomic level and created the first Iraqi checklist and larval key to nine families, nine subfamilies, 19 genera, and 13 subgenera, and supported it with 117 state-of-the-art scientific illustrations using fresh specimens collected during my study (Chapter 1). I performed an initial species morphological identification for mayflies and stoneflies, then identified them genetically after sequencing the full-length of the mitochondrial cytochrome oxidase subunit 1 (COI) gene (658 base pairs). I introduced Genetic Similarity Blocks (GSBs), a genetic-based analysis which was used along with morphology and other genetic-based analyses to overcome the taxonomic impediment and accelerate species identification. I delineated Operational Taxonomic Units (OTUs) using genetic-based analyses, then matched OTUs to delineate Species-Like Units (SpLUs). I compared and contrasted SpLUs morphologically and found five stonefly and more than 55 mayfly taxa, the majority of them being new records for Iraq, and many of them potentially new to science (Chapter 2). I identified 76 planning units within aquatic ecosystems in the KR and prioritized a subset of them for EPT conservation using my mayfly and stonefly data as well as caddisfly data from other studies. I identified samples of healthy aquatic habitats from this subset and used them along with various predictor variables to predict the distribution of healthy aquatic habitats across the entire KR. I identified one natural lake and 23 stream segments as habitats of conservation priority in the KR (Chapter 3). In my dissertation, I showed that in developing countries where knowledge about aquatic ecosystems and most extant species is unavailable, conservation priorities can still be identified after rapid assessment for water quality bioindicators. CONSERVATION BIOLOGY IN POORLY STUDIED FRESHWATER ECOSYSTEMS: FROM ACCELERATED IDENTIFICATION OF WATER QUALITY BIOINDICATORS TO CONSERVATION PLANNING A DISSERTATION Presented to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Ecology, Evolution, & Environmental Biology by Mohammed A. Al-Saffar The Graduate School Miami University Oxford, Ohio 2016 Dissertation Director: David J. Berg © Mohammed Abdullah Al-Saffar 2016 TABLE OF CONTENTS GENERAL INTRODUCTION ........................................................................................... 1 REFERENCES ................................................................................................................ 5 TABLES AND FIGURES ............................................................................................ 10 Chapter 1: Identification Key to the Families, Subfamilies, Genera, and Subgenera of Mayfly Larvae (Insecta: Ephemeroptera) from the Kurdistan Region, Northern Iraq ..... 14 ABSTRACT .................................................................................................................. 14 INTRODUCTION ......................................................................................................... 14 METHODS.................................................................................................................... 16 Study Area.................................................................................................................. 16 Sampling and Preservation ....................................................................................... 16 Morphological Identification and Construction of the Dichotomous Key ................ 17 RESULTS...................................................................................................................... 18 List of Mayfly Larvae from the Kurdistan Region, Northern Iraq ............................ 18 Identification Key to Mayfly Larvae from the Kurdistan Region, Northern Iraq ...... 20 REFERENCES .............................................................................................................. 61 Chapter 2: Genetics-Based Analyses Facilitate Delineating Unknown Faunas: A Case Study on Ephemeroptera and Plecoptera in the Headwaters of the Tigris River, Iraq ..... 69 ABSTRACT .................................................................................................................. 69 INTRODUCTION ......................................................................................................... 70 METHODS.................................................................................................................... 72 Study Area.................................................................................................................. 72 Sampling and Initial Morphological Identifications ................................................. 73 DNA Sequencing ........................................................................................................ 74 Genetic Similarity Blocks (GSBs) Analysis ............................................................... 74 Refined Single Linkage (RESL) Analysis and Barcode Index Numbers (BINs) ........ 75 Automatic Barcode Gap Discovery (ABGD) ............................................................. 76 Phylogenetic Analyses ............................................................................................... 76 Guided Discovery of Species-Like Units (SpLUs) ..................................................... 78 RESULTS...................................................................................................................... 79 Genetic-Based Analyses ............................................................................................ 79 Species Discovery ...................................................................................................... 81 DISCUSSION ............................................................................................................... 82 iii Unknown Diversity of Mayflies and Stoneflies from Northern Iraq .......................... 82 Findings of this Study Compared to Previous Findings from Northern Iraq ............ 83 Findings of this Study Compared to the Known Fauna of Turkey ............................ 84 Performance of Genetic-Based Analyses .................................................................. 86 Genetic-Morphological Cross-Validation Facilitated Species Discovery ................ 87 Morphological Examination after Genetic-Based Analyses Is Critical .................... 88 Emphasizing Morphology Key Points and Discovering Others ................................ 89 Flagging Species versus Subspecies Taxonomy ........................................................ 90 Facilitating Cryptic and Controversial Species Delineation .................................... 91 CONCLUSION ............................................................................................................. 92 REFERENCES .............................................................................................................. 93 TABLES AND FIGURES .......................................................................................... 106 Chapter 3: Rapid Solution Given Limited Information is a Challenge in Conservation Biology: A Strategy to Identify and Prioritize Aquatic Hotspots of Conservation Concern in a Poorly Studied Region ............................................................................................. 133 ABSTRACT ................................................................................................................ 133 INTRODUCTION ....................................................................................................... 134 METHODS.................................................................................................................. 137 Study Area................................................................................................................ 137 Identifying Planning Units......................................................................................
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