Extant and extinct bilby genomes combined with indigenous knowledge improve conservation of a unique Australian marsupial

The Ninu (Greater bilby, Macrotis lagotis) is a desert-dwelling, culturally and ecologically important marsupial. In collaboration with Indigenous rangers and conservation managers, we generated the first Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (Lesser bilby, Macrotis leucura). We developed and tested a scat SNP panel, based on our genomic datasets, to inform current and future conservation actions, to undertake future ecological assessments, and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of targeted conservation actions, like translocations, in the contemporary metapopulation (N=363 Ninu). Resequenced genomes (temperate Ninu=6; semi-arid Ninu=6; Yallara=4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathway adaptations to aridity. Despite their 45-..., There are two datasets included in the Excel workbook:

A set of SNPs (n=9906) generated using DArTseq, a form of reduced representation sequencing and used in the population genetic analyses of the Ninu (n=363 samples). See Supplementary Note 2.4 for details of SNP calling and filtering. Briefly, reads were cleaned and aligned to the Ninu reference genome generated in this study (v1.9). Variants were called with Stacks and filtered to retain SNPs with a minor allele frequency of ≥0.01, minimum average allelic depth of 2.5 x per allele, allelic coverage difference ≤80%, call rate ≥70%, locus heterozygosity ≤90%, and reproducibility between technical replicates ≥90%, and remove putatively sex-linked SNPs.
A set of SNPs (n=35) generated using DArTseq, a form of reduced representation sequencing and selected for use in the MassARRAY Ninu scat genotyping assay. The DArTseq reads were mapped to an earlier version of the Ninu reference genome generated in this study (v1.4.3). See Supplementar..., , # Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial

[https://doi.org/10.5061/dryad.gtht76htz](https://doi.org/10.5061/dryad.gtht76htz)

This accession contains both code used to generate the MassARRAY SNPs and DArTseq genotype data associated with the Ninu (Greater bilby, *Macrotis lagotis*) 1) scat genotyping MassARRAY design and 2) population genetic analysis described in Hogg et al.

## Description of the data and file structure

The text file \"Bilby_03_Supplementary_Text_File-code-final\" contains R code in RMarkdown format used in the design of the SNP panel used in the custom MassARRAY scat genotyping assay. The code is annotated throughout and includes the following steps:

* Extracting allele depth and genotype depth
* Filtering on genotyping quality
* Removing replicate samples and lower quality samples
* SNP selection as detailed in the annotated code. SNP selection included selecting only one SNP ...