The article discusses the challenges in resolving difficult phylogenetic questions using phylogenomics, emphasizing that simply adding more sequences is not sufficient. Three recent studies on early animal diversification showed incongruent results despite using large datasets. The main issues include insufficient phylogenetic signal due to closely spaced speciation events or ancient events with long branches and homoplasy. Non-phylogenetic signal, such as long branch attraction and incorrect orthology identification, can lead to misleading results. The article highlights the need for improved bioinformatics methods and careful data selection to reduce non-phylogenetic signal. It also discusses the importance of taxon sampling, gene selection, and model of sequence evolution in phylogenetic analysis. The study concludes that while phylogenomics has the potential to resolve the Tree of Life, it requires better procedures for selecting orthologous genes and improved models of sequence evolution to overcome current limitations.The article discusses the challenges in resolving difficult phylogenetic questions using phylogenomics, emphasizing that simply adding more sequences is not sufficient. Three recent studies on early animal diversification showed incongruent results despite using large datasets. The main issues include insufficient phylogenetic signal due to closely spaced speciation events or ancient events with long branches and homoplasy. Non-phylogenetic signal, such as long branch attraction and incorrect orthology identification, can lead to misleading results. The article highlights the need for improved bioinformatics methods and careful data selection to reduce non-phylogenetic signal. It also discusses the importance of taxon sampling, gene selection, and model of sequence evolution in phylogenetic analysis. The study concludes that while phylogenomics has the potential to resolve the Tree of Life, it requires better procedures for selecting orthologous genes and improved models of sequence evolution to overcome current limitations.