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Genetic Characterization of the California Leaf-Nosed Bat (Macrotus Californicus) Along the Lower Colorado River, Final Report

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Genetic Characterization of the California Leaf-Nosed Bat (Macrotus Californicus) Along the Lower Colorado River, Final Report Genetic Characterization of the California Leaf-nosed Bat (Macrotus californicus) Along the Lower Colorado River Final Report February 2019 Work conducted under LCR MSCP Work Task C43 Lower Colorado River Multi-Species Conservation Program Steering Committee Members Federal Participant Group California Participant Group Bureau of Reclamation California Department of Fish and Wildlife U.S. Fish and Wildlife Service City of Needles National Park Service Coachella Valley Water District Bureau of Land Management Colorado River Board of California Bureau of Indian Affairs Bard Water District Western Area Power Administration Imperial Irrigation District Los Angeles Department of Water and Power Palo Verde Irrigation District Arizona Participant Group San Diego County Water Authority Southern California Edison Company Arizona Department of Water Resources Southern California Public Power Authority Arizona Electric Power Cooperative, Inc. The Metropolitan Water District of Southern Arizona Game and Fish Department California Arizona Power Authority Central Arizona Water Conservation District Cibola Valley Irrigation and Drainage District Nevada Participant Group City of Bullhead City City of Lake Havasu City Colorado River Commission of Nevada City of Mesa Nevada Department of Wildlife City of Somerton Southern Nevada Water Authority City of Yuma Colorado River Commission Power Users Electrical District No. 3, Pinal County, Arizona Basic Water Company Golden Shores Water Conservation District Mohave County Water Authority Mohave Valley Irrigation and Drainage District Native American Participant Group Mohave Water Conservation District North Gila Valley Irrigation and Drainage District Hualapai Tribe Town of Fredonia Colorado River Indian Tribes Town of Thatcher Chemehuevi Indian Tribe Town of Wickenburg Salt River Project Agricultural Improvement and Power District Unit “B” Irrigation and Drainage District Conservation Participant Group Wellton-Mohawk Irrigation and Drainage District Yuma County Water Users’ Association Ducks Unlimited Yuma Irrigation District Lower Colorado River RC&D Area, Inc. Yuma Mesa Irrigation and Drainage District The Nature Conservancy Other Interested Parties Participant Group QuadState Local Governments Authority Desert Wildlife Unlimited Lower Colorado River Multi-Species Conservation Program Genetic Characterization of the California Leaf-nosed Bat (Macrotus californicus) Along the Lower Colorado River Final Report Prepared by: Jeff Hill, Wildlife Group Lower Colorado River Multi-Species Conservation Program Bureau of Reclamation Lower Colorado Region Boulder City, Nevada http://www.lcrmscp.gov February 2019 Hill, J. 2019. Genetic Characterization of the California Leaf-nosed Bat (Macrotus californicus) Along the Lower Colorado River, Final Report. Lower Colorado River Multi-Species Conservation Program, Bureau of Reclamation, Boulder City, Nevada. ACRONYMS AND ABBREVIATIONS AMOVA analysis of molecular variance BIC Bayesian information criterion DAPC Discriminant Analysis of Principal Components DNA deoxyribonucleic acid Fct among-group fixation index Fsc among-population within-group fixation index Fst among-population fixation index gDNA double-stranded genomic DNA IUCN International Union for the Conservation of Nature LCR lower Colorado River LCR MSCP Lower Colorado River Multi-Species Conservation Program mm millimeter(s) mtDNA mitochondrial deoxyribonucleic acid Ne effective population size NGS Next-generation sequencing PC principal component PCR polymerase chain reaction Symbols °C degrees Celsius > greater than < less than µL microliter(s) number π pi (θ) theta CONTENTS Page Abstract .................................................................................................................. iii Introduction ............................................................................................................. 1 Life History ............................................................................................................. 3 Distribution ....................................................................................................... 3 Physical Description and Taxonomic History .................................................. 3 Habitat, Foraging, and Reproduction ................................................................ 5 Conservation Status .......................................................................................... 5 Methods................................................................................................................... 6 Sample Collection and Sequencing .................................................................. 6 Genetic Analyses .............................................................................................. 8 Results ..................................................................................................................... 9 Sequencing ........................................................................................................ 9 Genetic Analyses ............................................................................................ 12 Discussion ............................................................................................................. 27 Literature Cited ..................................................................................................... 29 Tables Table Page 1 Mitochondrial haplotype list ..................................................................... 11 2 Whole genome sequencing results for six individuals .............................. 12 3 Microsatellites and associated primer information ................................... 12 4 Summary of chi-square test of Hardy-Weinberg equilibrium .................. 13 5 Mitochondrial pooled sequence statistics ................................................. 14 6 Sequence statistics for northern range samples ........................................ 14 7 Sequence statistics for southern range samples ........................................ 14 8 Mitochondrial AMOVA results ................................................................ 15 9 Microsatellite AMOVA results ................................................................. 16 10 Tajima’s neutrality test for all sample ...................................................... 17 11 Tajima’s neutrality test for northern range samples ................................. 17 12 Tajima’s neutrality test for southern range samples ................................. 17 i Figures Figure Page 1 International Union for the Conservation of Nature distribution map (Solari 2018) for the California leaf-nosed bat. .................................... 4 2 Sample localities of the California leaf-nosed bat. ..................................... 7 3 Mitochondrial haplotype map. .................................................................. 10 4 Mitochondrial median joining network. ................................................... 15 5 Matrix of pairwise Fst values for mitochondrial data. ............................... 18 6 Matrix of pairwise differences within and between populations, and Nei’s distance for mitochondrial data. ......................................... 19 7 Mismatch distribution for all mitochondrial samples (n = 99). ................ 20 8 Mismatch distribution for mitochondrial data from the United States (n = 76). .................................................................................... 21 9 Mismatch distribution for mitochondrial data from the Baja California Sur, Mexico, and Sonora, Mexico (n = 23). ...................... 22 10 Mean natural logarithm probability of microsatellite data for K = 1 to K = 20 across 20 runs. .......................................................... 23 11 STRUCTURE results for K = 2 clusters. .................................................. 23 12 Matrix of pairwise Fst values for microsatellite data. ............................... 24 13 Matrix of pairwise differences and Nei’s distance for microsatellite data. .............................................................................. 25 14 Scatterplot showing individuals colored by clusters with inertia ellipses (based on four PCs). ............................................................... 26 15 STRUCTURE type DAPC plot: Individual bars labeled by sample site (four PCs). ........................................................................ 26 Attachments Attachment 1 Supplemental Tables ii ABSTRACT This project aims to describe the current genetic diversity and demographic history of the California leaf-nosed bat (Macrotus californicus) along the lower Colorado River (LCR) and how populations along the river relate to the genetic diversity across the species’ range. By contributing knowledge of the poorly understood demographics of the California leaf-nosed bat, we hope to assist with future conservation considerations for the species. A total of 916 base pairs of the cytochrome b mitochondrial deoxyribonucleic acid (mtDNA) gene were sequenced for 102 individuals from 17 localities along the LCR, the Southwestern United States, Baja California Sur, Mexico, and northern mainland Mexico. There were 18 haplotypes identified across the range, with 5 haplotypes present in the samples taken from the LCR, and 3 haplotypes unique to the river. Sequence statistics for microsatellite data revealed higher genetic variation in samples from the southern portion of the range. Genotypic clustering analysis of 5 microsatellite
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