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Whole Genome Data Provides Evidence of Divergent Selection And Whole genome data provides evidence of divergent selection and gene flow between two populations of red grouse Lagopus lagopus scotica with implications for conservation Grace Walsh Degree project in biology, Master of science (2 years), 2021 Examensarbete i biologi 60 hp till masterexamen, 2021 Biology Education Centre and Department of Ecology and Genetics, Uppsala University Supervisors: Jacob Höglund and Barry John McMahon External opponent: Chaz Hyseni ABSTRACT Red grouse Lagopus lagopus scotica are endangered in Ireland but are widespread in other parts of their range. Their decline in Ireland is attributed to increases in generalist predators and habitat loss due to changing land use. Once widespread in Ireland, its population is now reduced and fragmented. For the effective conservation of this species, an understanding of genomic diversity and local adaptation can be important. In this study whole-genome sequencing of contemporary and historic samples was used to assess the level of differentiation, inbreeding and population structure between two populations of red grouse as well as to identify candidate genes putatively under divergent selection. Irish and English populations are shown to be differentiated (FST=0.095). There is clear population structure between English and Irish red grouse, with evidence of admixture into the Irish population. This is evidence of gene flow from the English to the Irish population. There were signs of recent inbreeding in the contemporary Irish population more so than in the historical or English samples. The contemporary Irish population has significantly more long runs of homozygosity than the other two populations. Outlier analysis between the contemporary samples identified 661 candidate genes under putative divergent selection. These were involved in a large variety of processes including immune response, pigmentation and food intake. This study provides more evidence that Irish red grouse are locally adapted and stressed that conservation efforts should focus on conserving the Irish population as one unit. 1 TABLE OF CONTENTS 1. INTRODUCTION ........................................................................................................................................ 3 1.1 BACKGROUND ....................................................................................................................................... 3 1.2 STUDY SPECIES ...................................................................................................................................... 4 1.2.1 Red Grouse (Lagopus lagopus scotica) ........................................................................................... 4 1.2.2 Taxonomic status and overview of genetic studies .......................................................................... 6 1.2.3 Parasite mediated selection ............................................................................................................. 7 1.2.4 Pigmentation .................................................................................................................................... 8 1.3 STUDY OBJECTIVES ................................................................................................................................ 9 2. METHODS .................................................................................................................................................... 9 2.1 STUDY SAMPLES .................................................................................................................................... 9 2.2 DNA EXTRACTIONS ............................................................................................................................. 10 2.3 LIBRARY PREPARATIONS ..................................................................................................................... 10 2.4 SEQUENCING ........................................................................................................................................ 10 2.5 MAPPING AND SNP CALLING ............................................................................................................... 10 2.6 ANALYSES ........................................................................................................................................... 12 2.6.1 Genetic diversity............................................................................................................................. 12 2.6.2 Population structure and local adaptation using pcadapt ............................................................. 12 2.6.3 Analysis of Admixture .................................................................................................................... 12 2.6.4 Fst outlier analysis ......................................................................................................................... 12 2.6.5 Gene ontology (GO) enrichment analysis ...................................................................................... 13 2.6.6 Runs of Homozygosity analysis ...................................................................................................... 13 3. RESULTS .................................................................................................................................................... 13 3.1 SEQUENCES, MAPPING AND SNP CALLING .......................................................................................... 13 3.2 GENETIC DIVERSITY ............................................................................................................................ 13 3.3 PRINCIPAL COMPONENT ANALYSIS AND OUTLIER DETECTION ............................................................. 14 3.4 ANALYSIS OF ADMIXTURE ................................................................................................................... 14 3.5 WINDOW-BASED FST SCANS ................................................................................................................. 15 3.6 OUTLIER ANALYSIS ............................................................................................................................. 16 3.6.1 Immune response ............................................................................................................................ 16 3.6.2 Pigmentation .................................................................................................................................. 19 3.6.3 General genes and outlier method overlaps .................................................................................. 21 3.6.4 Gene ontology (GO) enrichment analysis ...................................................................................... 24 3.7 RUNS OF HOMOZYGOSITY ................................................................................................................... 24 3.7.1 Short/medium ROH ........................................................................................................................ 25 3.7.2 Long ROH ...................................................................................................................................... 25 4. DISCUSSION .............................................................................................................................................. 26 4.1 GENETIC DIVERSITY............................................................................................................................. 26 4.2 GENETIC DIFFERENTIATION ................................................................................................................. 27 4.3 OUTLIER ANALYSIS .............................................................................................................................. 28 4.3.1 Immune response ............................................................................................................................ 28 4.3.2 Pigmentation .................................................................................................................................. 29 4.3.3 Other relevant genes ...................................................................................................................... 30 4.3.4 Gene ontology (GO) enrichment analysis ...................................................................................... 31 4.4 RUNS OF HOMOZYGOSITY ................................................................................................................... 32 4.5 MANAGEMENT IMPLICATIONS ............................................................................................................. 33 4.6 STUDY LIMITATIONS............................................................................................................................ 34 4.7 CONCLUSIONS ...................................................................................................................................... 34 ACKNOWLEDGEMENTS ................................................................................................................................. 35 REFERENCES ..................................................................................................................................................... 36 SUPPLEMENTARY INFORMATION ............................................................................................................. 47 2 1. INTRODUCTION 1.1 Background Current global extinction rates are 100-1000 higher than what is considered to be the natural background
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