Evolutionary BiologybioRxiv
Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index
K. Wicke, M. R. Haque, L. Kubatko
The paper examines how gene tree heterogeneity affects phylogenetic diversity indices, showing that species rankings vary significantly depending on whether gene trees or species trees are used.
DOI 10.1371/journal.pone.0300900