Genomic insights into the critically endangered King Island scrubtit

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopula..., 2.1 Sample collection
To obtain indicative genetic diversity metrics across mainland Tasmania, we sampled between five and eleven scrubtits from seven a-priori subpopulations on mainland Tasmania (including Bruny Island) during the non-breeding season (January – March 2021). Due to small population sizes and licensing restrictions on King Island, we sampled five individuals from each of the three locations during the same non-breeding season (Table 1, Figure 1). We trapped scrubtits using a single 6m mist net and one minute of scrubtit song broadcast using portable speakers (ANU animal ethics permit # A2021/33). We sampled blood (< 20 μl per individual) using the standard brachial venepuncture technique with a 0.7mm needle into 70% ethanol. For two individuals from whom we were unable to safely obtain blood, we collected feathers shed during handling. One male Tasmanian scrubtit was collected under licence (see acknowledgements) for genome sequencing, from which organ tissue samples ..., , # Genomic insights into the critically endangered King Island scrubtit

[https://doi.org/10.5061/dryad.12jm63z66](https://doi.org/10.5061/dryad.12jm63z66)

The dataset comprises:

1\) the raw .vcf file \"CAGRF220911987_GA.vcf\"

2\) a csv of the final filtered dataset used for genomic analysis within the manuscript:  \"scrubtit_genos_140623.csv\". Rows contain samples and columns contain SNPs

3\) a csv of sample metadata: \"Sampinfo_ross_check.csv\". Rows contain samples and columns contain metadata

4\) an annotated R- script for repeat analysis 

## Description of the data and file structure

2\) a csv of the final filtered dataset used for genomic analysis within the manuscript:  \"scrubtit_genos_140623.csv\". Rows contain samples and columns contain SNPs

column 1: sample ID (as per 'sample1') in sample medtadata (column 1). 

columns 2-5239: SNP ids

Missing data code: NA

3\) a csv of sample metadata: \"Sampinfo_ross_check.csv\". Rows contain samples and columns contain metadate

column 1-...