Author contributions
I.S. and G.F. initiated and coordinated the project. C.P., K.M, and A.B.M. collected Antechinus flavipes samples. L.K.C. dissectedAntechius flavipes . A.M.B. provided voucher specimens ofAntechinus arktos and Antechinus argentus . P.B.T., L.K.C. provided frozen tissue samples for whole-genome, Hi-C, and transcriptome sequencing. C.S. led the sequencing and assembly efforts with G.F. R.T., K.H., and C.S. contributed to genome assembly and annotation. R.T., K.H., C.S., and I.S. performed comparative genomics analyses. The de novo and reference-based assemblies of A. arktos , A. argentus , and M. melanurus were generated by I.S. I.S. performed population history analysis. K.H. performed diversity analysis. I.S. assembled transcriptomes and performed gene expression analysis. R.T. performed molecular evolution analyses. L.K.C., D.O.F., N.O.L., and A.M.B. provided direction on marsupial ecology and physiology. R.T., L.K.C., D.O.F., A.M.B., and I.S. wrote the paper with input from all authors.