Species and perches
The Eastern Yellow Robin (EYR) is a small insectivorous passerine bird native to eastern Australia, their distinctive piping call is one of the first to be heard in the morning chorus, often beginning before light. They are relatively unafraid of humans, often seen perched sideways on tree trunks in a range of habitats from dry woodland to rainforest. They are mostly perch-and-pounce predators, grabbing invertebrates and some other small animals such as lizards out of leaf litter on the ground.
Eastern yellow robins have distribution spanning thousands of kilometres along north-south axis and across a large range of climates. Southern birds have an olive rump, different from the brighter yellow of northern birds. Surprisingly, there is a major genetic distinction perpendicular to this geographic colour variation. Genetically the species appears to be split approximately into ‘inland’ and ‘coastal’ forms (respectively red and blue dots on the map shown below), thought to be caused by two ecologically relevant adaptive sweeps in the mitochondrial genome (mitochondria are the powerhouses of cells which bear their own small genome) [1, 2].
Inland and coastal Eastern Yellow Robins seem not to interbreed freely where they occur side-by-side at a limited number of special locations. There is particular resistance to exchange of genomic material between the lineages in the part of the genome harbouring the greatest density of nuclear-encoded mitochondrial genes. This ‘mitonuclear cluster’ has been implicated in environmental adaptation by mitonuclear co-evolution in EYR . This genomic region was subsequently found to be sex-linked, associated with a fusion between an autosome (that is, a chromosome found in two copies in both sexes) and a sex chromosome forming a ‘neo-sex chromosome’ . The species may be on its way to becoming two species, suited to different environments and conferring different metabolisms .
Such wildlife species that have genomic variation distributed heterogeneously through environmental and geographic space are excellent models for studying evolutionary processes under natural conditions. To support ongoing scientific efforts, DNA Zoo has been working with Paul Sunnucks, Alexandra Pavlova and Gabriel Low at Monash University to obtain chromosome-length genome assemblies for one inland- and one coastal-lineage female EYRs. The coastal-lineage chromosome length was released by DNA Zoo in 2020 and today we release the inland-lineage assembly.
The inland-lineage chromosome-length assembly is based on a draft assembly published by Gan et al 2019 . This draft was scaffolded with 98,992,919 PE Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details.
This work was enabled by wildlife authorities including the Victorian Department of Environment, Land, Water and Planning, Parks Victoria, and the Australian Bird and Bat Banding Scheme. The research has been supported by the Holsworth Wildlife Endowment Fund, Australian Research Council grants DP180102359 and DP210102275, and Monash University.
The Hi-C work was supported by additional resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.
1. Morales, H., P. Sunnucks, L. Joseph, and A. Pavlova. (2017). Perpendicular axes of differentiation generated by mitochondrial introgression. Molecular Ecology 26:3241–3255.
2. Morales HE, Pavlova A, Joseph L, Sunnucks P (2015) Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Molecular Ecology 24, 2820–2837.
3. Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C (2017). Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Frontiers in Genetics 8:25. doi:10.3389/fgene.2017.00025
4. Gan HM, Falk S, Moraleś HE, Austin CM, Sunnucks P, Pavlova A. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. Gigascience. 2019;8(12):giz131. doi:10.1093/gigascience/giz131
5. Morales HE, Pavlova A, Amos JN, Major R, Kilian A, Greening C and Sunnucks P (2018) Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nature Ecology & Evolution 2, 1258–1267.