Incomplete lineage sorting and phenotypic evolution in marsupials

Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya. [Display omitted] •Whole genome data support Dromiciops as a sister lineage of all Australian marsupials•More than 50% of marsupial genomes are affected by incomplete lineage sorting (ILS)•ILS is likely to have affected complex morphological traits in extant species•Functional experiments validated representative phenotypic effects suggested by ILS The majority of marsupial genomes are affected by incomplete lineage sorting, which causes unique morphological traits in descendant species. Through in-depth phylogenetic analyses and in vivo validation, these data resolve the marsupial lineage at high resolution and suggest a strong impact of ILS on phylogenic relationships.