[1]

Kapli P, Yang Z, Telford MJ. 2020. Phylogenetic tree building in the genomic age. Nature Reviews Genetics 21:428−444

doi: 10.1038/s41576-020-0233-0
[2]

Degnan JH, Rosenberg NA. 2006. Discordance of species trees with their most likely gene trees. PLoS Genetics 2:e68

doi: 10.1371/journal.pgen.0020068
[3]

Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24:332−340

doi: 10.1016/j.tree.2009.01.009
[4]

Hanson-Smith V, Kolaczkowski B, Thornton JW. 2010. Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Molecular Biology and Evolution 27:1988−1999

doi: 10.1093/molbev/msq081
[5]

Salichos L, Rokas A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327−331

doi: 10.1038/nature12130
[6]

Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772−780

doi: 10.1093/molbev/mst010
[7]

Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783−791

doi: 10.1111/j.1558-5646.1985.tb00420.x
[8]

Wong TKF, Ly-Trong N, Ren H, Demotte P, Baños H, et al. 2026. IQ-TREE 3: phylogenomic inference software using complex evolutionary models. Molecular Biology and Evolution 43:msag117

doi: 10.1093/molbev/msag117
[9]

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61:539−542

doi: 10.1093/sysbio/sys029
[10]

Stecher G, Suleski M, Tao Q, Tamura K, Kumar S. 2026. MEGA 12.1: cross-platform release for macOS and linux operating systems. Journal of Molecular Evolution 94:14−18

doi: 10.1007/s00239-025-10287-z
[11]

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647−1649

doi: 10.1093/bioinformatics/bts199
[12]

Community TG, Abueg LAL, Afgan E, Allart O, Awan AH, et al. 2024. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research 52:W83−W94

doi: 10.1093/nar/gkae410
[13]

Zhao D, Ye T, Gao F, Jakovlić I, La Q, et al. 2025. PhyloSuite v2: the development of an all-in-one, efficient and visualization-oriented suite for molecular dating analysis and other advanced features. iMeta 4:e70095

doi: 10.1002/imt2.70095
[14]

van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, et al. 2024. Fast and accurate protein structure search with Foldseek. Nature Biotechnology 42:243−246

doi: 10.1038/s41587-023-01773-0
[15]

Tria FDK, Landan G, Dagan T. 2017. Phylogenetic rooting using minimal ancestor deviation. Nature Ecology & Evolution 1:193

doi: 10.1038/s41559-017-0193
[16]

Smith MR. 2020. Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees. Bioinformatics 36:5007−5013

doi: 10.1093/bioinformatics/btaa614
[17]

Llabrés M, Rosselló F, Valiente G. 2021. The generalized Robinson-foulds distance for phylogenetic trees. Journal of Computational Biology 28:1181−1195

doi: 10.1089/cmb.2021.0342
[18]

Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406−425

doi: 10.1093/oxfordjournals.molbev.a040454
[19]

Yu D, Dong L, Yan F, Mu H, Tang B, et al. 2019. eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. National Science Review 6:867−869

doi: 10.1093/nsr/nwz079
[20]

Zhang S, Fang X, Chang M, Zheng M, Guo L, et al. 2024. Cross-species single-cell analysis reveals divergence and conservation of peripheral blood mononuclear cells. BMC Genomics 25:1169

doi: 10.1186/s12864-024-11030-6
[21]

Xu J, Zhang Y. 2010. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26:889−895

doi: 10.1093/bioinformatics/btq066
[22]

Zhang C, Shine M, Pyle AM, Zhang Y. 2022. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods 19:1109−1115

doi: 10.1038/s41592-022-01585-1
[23]

Illergård K, Ardell DH, Elofsson A. 2009. Structure is three to ten times more conserved than sequence—a study of structural response in protein cores. Proteins: Structure, Function, and Bioinformatics 77:499−508

doi: 10.1002/prot.22458
[24]

Chothia C, Lesk AM. 1986. The relation between the divergence of sequence and structure in proteins. The EMBO Journal 5:823−826

doi: 10.1002/j.1460-2075.1986.tb04288.x
[25]

Zhang S, Zhang T, Fu Y. 2023. Proteome-wide structural analysis quantifies structural conservation across distant species. Genome Research 33:1975−1993

doi: 10.1101/gr.277771.123
[26]

Puente-Lelievre C, Malik A, Douglas J. 2025. Protein structural phylogenetics. Genome Biology and Evolution 17:evaf139

doi: 10.1093/gbe/evaf139
[27]

Jiao A, Zhang C, Wang X, Sun L, Liu H, et al. 2024. Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species. Journal of Advanced Research 55:73−87

doi: 10.1016/j.jare.2023.02.017