2.1 Empirical SNP datasets
DNA samples from two species of common eastern Australian passerine birds were genotyped commercially with Diversity Arrays Technology Pty. Ltd. (Canberra, Australia; Kilian et al. 2012). Briefly, DArTseq starts with DNA digestion, adapter ligation, and amplification of adaptor-ligated fragments. Amplification products are pooled and sequenced (single-read) on the Illumina HiSeq 2500 in batches of 94 samples per sequence lane, with 25% random technical replicates to enable assessment of loci scoring repeatability. Sequencing reads are processed using DArT proprietary analytical pipelines (for details see Harrisson et al. 2019). The end product is a spreadsheet with locus information and individual genotypes for each locus scored as ‘0’ (homozygous reference), ‘1’ (heterozygous), and ‘2’ (homozygous alternate; Gruber et al. 2019). Both species are sexually monomorphic, with most individuals sexed using PCR-based methods (Pavlova et al. 2013).
Eastern yellow robin (EYR). The eastern yellow robin (Eopsaltria australis ) is an avian model system for climate adaptation through mitonuclear interactions, with two diverged mitochondrial lineages occurring roughly east and west of the Great Dividing Range, and corresponding differentiation on neo-sex chromosomes enriched with mitonuclear genes (Morales et al. 2019, Gan et al 2021, Pavlova et al. 2013). In this study, we used data for 782 individuals sampled between 2016 and 2021 in four locations in Central Victoria (Crusoe, Muckleford, Timor and Wombat), in the zone of contact between the mitochondrial lineages (Austin et al. unpublished manuscript ). Blood samples were collected under DELWP permit 10007910 under the Wildlife Act 1975 and the National Parks Act 1975, and NW11047F under section 52 of the Forest Act 1958, Australian Bird and Bat Banding Scheme permit, and approval 24225 of Monash University animal ethics committee. DArTseq yielded 53,324 binary SNPs for 238 Crusoe, 421 Muckleford, 52 Timor and 71 Wombat individuals.
Yellow-tufted honeyeater (YTH). The yellow-tufted honeyeater (Lichenostomus melanops ) is a bird comprising four subspecies (‘cassidix’, ‘gippslandicus’, ‘melanops’ and ‘meltoni’ , Pavlova et al. 2014). Of these, cassidix (helmeted honeyeater) is Critically Endangered (Environment Protection and Biodiversity Conservation Act 1999, Advisory List of Threatened Vertebrate Fauna in Victoria 2013), restricted to a single small population, and supplemented by a captive breeding program (Harrisson et al. 2016). We used existing DArT SNP data of 641 YTH individuals used in a previous study (Harrisson et al. 2019). Of these, 540 werecassidix , 48 gippslandicus , 12 melanops , 33meltoni , 4 cassidix × gippslandicus crosses (hereafter ‘hybrids’), 2 presumed hybrids, 1 presumedgippslandicus and 1 presumed gippslandicus ×melanops F1 individual. The initial DArTseq dataset consisted of 118,732 binary SNPs for 641 individuals.