Reply to Springer and Gatesy: The impact of long branches and misalignments on phylogenetic analysis is minimal

Springer and Gatesy (1) suggested that our avian species tree, constructed using NJst (2), may be inaccurate due to observed disparities with the ASTRAL tree and potential misalignments. However, akin to their critiques of our other work, their criticisms stem from subjective opinions and misconceptions of phylogenetic analysis, rendering their arguments unfounded. Springer and Gatesy argued that NJst is less accurate than ASTRAL, citing evidence from two simulation studies (3, 4). However, assessing phylogenetic methods solely through simulations cannot fully reflect real-world scenarios. Other studies have indeed suggested that NJst outperforms ASTRAL (5). Notably, NJst outcomes align closely with RAxML (SI Appendix, Figs. S1–S5 in ref. 2), indicating the robustness of NJst. In contrast, ASTRAL results differ significantly, warranting further validation.