Incomplete lineage sorting and phenotypic evolution in marsupials

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