The current fairy tern species complex is comprised of three subspecies, the Australian fairy tern (Sterna nereis nereis), New Zealand fairy tern | tara iti (S. n. davisae), and the New Caledonian fairy tern (S. n. exsul). Population monitoring for each of the three taxa indicate that populations are declining (Australia and New Caledonia), or are chronically small (n <=30 tara iti adults).
There remain questions around the relative population diversity and differentiation among the three taxa. Here, we examine samples collected from the largest (Western Australia) and smallest (tara iti) recorded fairy tern populations as a 'first-look' into fairy tern genomic diversity. We also examine genomic diversity for a subset of individuals from Galla et al. (2020) using an improved genome asembly for kakī (Himantopus novaezelandiae).
Each of the markdown files included in this repository are described below, including the software and their versions used for data manipulation and analyses.
- 00 Tara iti genome assembly
- 01 Genome Repeat Annotation
- 02 Illumina read QC and alignment
- 03 SNP-based population genomics with ANGSD
- 04 Structural variant discovery, genotyping and population genomics
- 05 Visualisation of results