Incomplete lineage sorting and phenotypic evolution in marsupials.

Area of Science:

• Evolutionary Biology
• Genomics
• Phylogenetics

Background:

• Incomplete lineage sorting (ILS) causes gene tree and species tree incongruences, complicating evolutionary studies, especially in rapidly speciating lineages like hominids.
• Empirical evidence linking ILS to incongruent phenotypic variation has been lacking, hindering a full understanding of its evolutionary impact.

Purpose of the Study:

• To investigate the role of incomplete lineage sorting (ILS) in generating incongruent phylogenetic signals and phenotypic variation within marsupials.
• To provide empirical evidence for ILS directly contributing to morphological trait evolution during rapid marsupial speciation.

Main Methods:

• Performed phylogenomic analyses on marsupial genomes to reconstruct evolutionary relationships and identify patterns of ILS.
• Analyzed genomic data to detect conflicting phylogenetic signals and genes with stochastic fixation across the genome.
• Conducted functional experiments to assess the impact of ILS on morphological trait development.

Main Results:

• Established the monito del monte as the sister lineage to all Australian marsupials, with over 31% of its genome showing closer affinity to Diprotodontia due to ILS.
• Identified pervasive conflicting phylogenetic signals across the genome, correlating with observed morphological variation in extant marsupials.
• Detected hundreds of genes with stochastic fixation during ILS, resulting in identical amino acid sequences in non-sister species.

Conclusions:

• Incomplete lineage sorting significantly impacts marsupial phylogenomics, explaining genomic discordance and the evolutionary history of Australian marsupials.
• ILS directly contributed to hemiplasy in morphological traits, demonstrating its role in shaping phenotypic diversity during rapid marsupial speciation approximately 60 million years ago.