Statistical analyses from the PhD thesis of A.G. West - University of Auckland

Bioinformatics pipelines for microbial amplicon sequence data (demultiplexed, paired-end reads) generated from gut microbial communities of Aotearoa New Zealand kākāpō and takahē.

Link to thesis (update once published).

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README.md table of contents

1.1 Bacteria_16S_pipeline_chapter_three

1.2 Fungi_ITS_pipeline_chapter_four

1.3 Bacteria_16S_pipeline_chapter_five

1.4 GWAS_microbiome_pipeline_chapter_five

1.5 Bacteria_16S_pipeline_chapter_six

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General notes

Data chapters in the thesis 'The microbiome in threatened species conservation: implications for the conservation of kākāpō and takahē':

• Chapter Three: Influence of management practice on the microbiota of a critically endangered species: A longitudinal study of kākāpō chick faeces and associated nest litter
• Chapter Four: The mycobiota of faeces from kākāpō chicks and associated nest litter
• Chapter Five: Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō
• Chapter Six: Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications

All chapters utilised amplicon sequence variants (ASVs) produced by the R package DADA2.

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Publications from this PhD thesis

Chapter Two: The microbiome in threatened species conservation

Chapter Three: Influence of management practice on the microbiota of a critically endangered species: a longitudinal study of kākāpō chick faeces and associated nest litter

Chapter Four: The mycobiota of faeces from the critically endangered kākāpō and associated nest litter

Chapter Five:Capturing species-wide diversity of the gut microbiota and its relationship with genomic variation in the critically endangered kākāpō

Chapter Six: Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications