Hi all, I'm a little bit confused about gene expression phylogenies and the structure of hierarchical clustering. I got two different structures from hierarchical clustering (Pearson correlation coefficient, "complete" hclust method from pheatmap package) and gene expression phylogeny(Neighbour-joining trees based on pairwise distance matrices(1-r, r is Spearman's correlation coefficient)) using the same expression data, and the details are in the attachment. And the topology from hierarchical clustering seemed more consistent with species tree. What does anybody think about that? Why does the different topologies happen to this? Which one is better to explain phylogeny relatedness?
hierarchical clustering: https://ibb.co/kmxDik
gene expression phylogeny: https://ibb.co/cmZn9Q
Any help will be highly appreciated.