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Of Eyes and Gut Microbiomes in Nicaraguan Cichlid Fishes – Convergent Diversification at Different Levels of Biological Organization

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Of Eyes and Gut Microbiomes in Nicaraguan Cichlid Fishes – Convergent Diversification at Different Levels of Biological Organization Of eyes and gut microbiomes in Nicaraguan cichlid fishes – convergent diversification at different levels of biological organization Dissertation submitted for the degree of Doctor of Natural Sciences Presented by Andreas Härer at the Faculty of Sciences Department of Biology Date of the oral examination: 24.09.2018 First supervisor: Prof. Dr. Axel Meyer Second supervisor: Prof. Dr. Cameron Ghalambor Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-2-72sv5vlomhtp5 i Sit down before fact as a little child, be prepared to give up every conceived notion, follow humbly wherever and whatever abysses nature leads, or you will learn nothing. Thomas Henry Huxley ii Table of contents Table of contents ..................................................................................................................................... iii List of Figures ........................................................................................................................................... vi List of Tables ............................................................................................................................................ vi Summary ................................................................................................................................................ vii Zusammenfassung .................................................................................................................................... x General Introduction ............................................................................................................................... 1 Chapter I .................................................................................................................................................. 6 Abstract ............................................................................................................................................... 6 Introduction ......................................................................................................................................... 7 Methods ............................................................................................................................................ 10 Rearing conditions ......................................................................................................................... 10 Opsin expression analysis .............................................................................................................. 12 Predicted sensitivities of single and double cones ........................................................................ 13 Thyroid hormone signaling ............................................................................................................ 14 Results ............................................................................................................................................... 14 Ontogenetic changes in cone opsin expression ............................................................................ 14 dio2 and dio3 expression as a proxy for Thyroid hormone signaling............................................ 16 Effects of light environment on cone opsin expression ................................................................ 17 Discussion .......................................................................................................................................... 18 Chapter II ............................................................................................................................................... 23 Abstract ............................................................................................................................................. 23 Impact Summary ............................................................................................................................... 24 Introduction ....................................................................................................................................... 25 Methods ............................................................................................................................................ 28 Sample collection .......................................................................................................................... 28 Library preparation & Illumina Sequencing................................................................................... 29 Quality control, transcript assembly and mapping ....................................................................... 29 Sequence analyses......................................................................................................................... 29 Gene expression analyses ............................................................................................................. 30 Results ............................................................................................................................................... 31 Discussion .......................................................................................................................................... 36 Conclusion ......................................................................................................................................... 39 Chapter III .............................................................................................................................................. 41 Abstract ............................................................................................................................................. 41 Introduction ....................................................................................................................................... 42 iii Methods ............................................................................................................................................ 44 Sample collection .......................................................................................................................... 44 Trophic analysis ............................................................................................................................. 44 Library preparation & Illumina Sequencing................................................................................... 44 Sequence processing ..................................................................................................................... 45 Gut microbiota analysis ................................................................................................................. 45 Results ............................................................................................................................................... 46 Diet differentiation among Midas cichlids .................................................................................... 46 Gut microbiome differentiation across habitats ........................................................................... 47 Gut microbiome differentiation within crater lakes ..................................................................... 50 Genetic bases of gut microbiome differentiation ......................................................................... 51 Discussion .......................................................................................................................................... 52 Gut microbiome differentiation across habitats ........................................................................... 52 Gut microbiome differentiation within crater lakes ..................................................................... 54 Genetic bases of gut microbiome differentiation ......................................................................... 55 Chapter IV .............................................................................................................................................. 57 Abstract ............................................................................................................................................. 57 Introduction ....................................................................................................................................... 58 Methods ............................................................................................................................................ 60 Study area and sample collection ................................................................................................. 60 DNA analysis .................................................................................................................................. 61 Results ............................................................................................................................................... 61 Geographic distribution ................................................................................................................. 61 Genetic diversity ............................................................................................................................ 62 Discussion .......................................................................................................................................... 64 Habitat alteration and destruction ................................................................................................ 65 Invasion by non-native species.....................................................................................................
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