Phylogenetic informativeness analyses to clarify past diversification processes in Cucurbitaceae

Area of Science:

• Plant evolutionary biology
• Phylogenomics
• Bioinformatics

Background:

• Phylogenomic studies often face representation bias and lack resolution, particularly in plant families like Cucurbitaceae with controversial evolutionary histories.
• Genome skimming offers a cost-efficient approach for plant phylogenomics due to small genome sizes, but data interpretation remains challenging.

Purpose of the Study:

• To evaluate phylogenetic informativeness and tree confidence analyses for interpreting phylogenomic datasets in Cucurbitaceae.
• To resolve controversial tribal-level relationships within Cucurbitaceae and infer the evolution of floral traits.
• To guide the design of future phylogenomic studies in Cucurbitaceae and related families.

Main Methods:

• Genome skimming and Polymerase Chain Reaction (PCR) to obtain plastome, 57 single-copy nuclear genes, and nuclear ribosomal ITS data from 29 Cucurbitaceae species.
• Phylogenetic informativeness and tree confidence analyses to assess data quality and phylogenetic signal.
• Data filtering based on phylogenetic informativeness and homoplasy risk to improve phylogenetic resolution.

Main Results:

• Phylogenetic analyses revealed limited inter-locus conflict but pervasive lack of phylogenetic signal in plastid loci, indicating rapid divergence among Cucurbitaceae tribes.
• Data filtering significantly clarified tribe-level relationships within Cucurbitaceae.
• The resolved phylogeny supports two independent evolutionary events of fringed petals within the family.

Conclusions:

• Formal analysis of phylogenomic data, including phylogenetic informativeness and homoplasy risk assessment, enhances understanding of diversification processes.
• The study provides a robust framework and valuable data for future phylogenomic investigations in Cucurbitaceae.
• Resolved relationships offer insights into the convergent evolution of floral morphology within the gourd family.