Understanding angiosperm diversification using small and large phylogenetic trees.

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Plant Science

Background:

• Understanding diversification rate shifts is crucial for evolutionary biology.
• Inferring large-scale phylogenies is an emerging area with potential impacts.
• Previous studies often used smaller datasets, potentially limiting insights into major clades.

Purpose of the Study:

• To investigate how ultra-large phylogenies influence the identification of diversification rate shifts.
• To compare diversification patterns using backbone trees versus a mega-phylogeny approach for angiosperm clades.

Main Methods:

• Contrasted two methods: backbone trees with inferred species counts vs. a mega-phylogeny of 55,473 seed plant species from GenBank.
• Assessed species sample proportionality in GenBank to actual diversity for major angiosperm lineages.
• Analyzed diversification rate shifts across several large angiosperm clades (e.g., Angiospermae, Orchidaceae, Fabaceae).

Main Results:

• Diversification rate shifts were generally not associated with major named angiosperm clades.
• Fabaceae was the sole exception, showing a diversification shift in the GenBank mega-phylogeny.
• Mega-phylogeny indicated diversification shifts are evenly distributed across angiosperms, suggesting nested clades or increased extinction in early lineages.

Conclusions:

• Major diversification shifts in angiosperms may occur within nested clades, not necessarily at the level of major named groups.
• Ultra-large phylogenies (mega-phylogenies) are promising for revealing diversification patterns.
• Future research requires careful specification of null expectations for mega-phylogenetic diversification studies.