Journal
CELL
Volume 185, Issue 10, Pages 1646-+Publisher
CELL PRESS
DOI: 10.1016/j.cell.2022.03.034
Keywords
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Funding
- Strategic Priority Research Program of the Chinese Academy of Sciences [XDB31020000]
- International Partnership Program of the Chinese Academy of Sciences [152453KYSB20170002]
- Carlsberg Foundation [CF16-0663]
- Villum Foundation [25900]
- National Natural Science Foundation of China [31901214, 31961143002]
- Bureau of International Cooperation, Chinese Academy of Sciences
- First-class discipline of Prataculture Science of Ningxia University [NXYLXK2017A01]
- Hainan Yazhou Bay Seed Lab [B21HJ0102]
- Guizhou Science and Technology Planning Project [2022-173]
- GDAS Special Project of Science and Technology Development [2020GDASYL-20200301003]
- NIH [OD022988]
- FONDECYT [1180917]
- Novo Nordisk Foundation [NNF18OC0031004]
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Incomplete lineage sorting (ILS) can lead to incongruences between gene trees and species trees during rapid speciation events. Through phylogenomic analyses, it has been discovered that the South American monito del monte is the sister lineage of all Australian marsupials, despite a portion of its genome being more similar to the Diprotodontia. Conflicting phylogenetic signals across the whole genome are consistent with morphological variation among extant marsupials. Furthermore, hundreds of genes have been found to encode the same amino acids in non-sister species due to stochastic fixation during ILS. Functional experiments have provided evidence of how ILS directly contributes to hemiplasy in morphological traits established during rapid marsupial speciation approximately 60 million years ago.
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.
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