Data accompanying the manuscript "Incomplete lineage sorting and phenotypic evolution in marsupials" in Cell. In this paper, we performed comparative phylogenomic analyses in the marsupial lineage, a classic example of a successful mammalian radiation, to map and date signatures of ILS and to unravel some of the phenotypic consequences. The dataset includes - Whole genome alignment of six marsupials generated by LASTZ+MULTIZ - Monito del monte draft assembly (.fasta.gz) and gene annotation (.gff) - table including 13,320 orthologs to be present in the gray short-tailed opossum, monito del monte, at least one Diprotodontia species, and at least one Dasyuromorphia species - re-annotation of gene Wfikkn1 in Macropus eugenii: The published coding sequence of this gene in the tammar wallaby contains shifts and several very short exons. We ran Exonerate to re-annotate this gene using the pep sequence of this gene in the gray short-tailed opossum as the reference. Files, including gff, cds sequence and pep sequence, are provided. - re-annotation of gene Wfikkn1 in Antechinus stuartii: ran Exonerate to re-annotate gene Wfikkn1 in Antechinus stuartii using the pep sequence of this gene in the gray short-tailed opossum as the reference. Files, including gff, cds sequence and pep sequence, are provided. - re-annotation of gene PAPSS2 in Macropus eugenii: Due the assembly and annotation issue, the quality of the published coding sequence of this gene in wallaby is poor (e.g. containing a continuous 41bp Ns, an incomplete beginning, and a potential ~30bp annotation error). We manually corrected the sequence by mapping the published RNA-seq data and population re-sequencing data to its close species Macropus rufus genome. Files, including cds sequence and pep sequence, are provided. - species name map list - md5 for all files - Morphological image