​The following tables show the taxa for which there is no consensus in the  literature that stem-group fossils exist (orange  shows vertebrates, green shows land plants):
The above tables contain a total of 100 taxa without stem-group fossils.  This number represents 51% of the 195 taxa examined for this website.  In other words, only about half of the taxa examined are known to have stem-group fossils.

There are several possible reasons for this lack of stem-group representation:
  1. The most obvious is that stem-group fossils do exist but have not yet been discovered. However, it seems unlikely that this is the case for all 100 taxa.
  2. Most of the 100 taxa have been defined using molecular data (see the table below for examples of publications that present molecule-based phylogenies for the higher taxa to which the 100 taxa belong). Stem-group fossils for any given crown group display some, but not all, of the morphological synapomorphies that define that crown group. On the other hand, crown groups defined on the basis of molecular data from extant specimens are not based exclusively on morphological synapomorphies (some phylogenetic trees are based on a combination of morphological and molecular data). In the absence of morphological synapomorphies defining the crown group, recognition of stem-group fossils will be difficult or impossible.
  3. Some of the 100 taxa might be based on phylogenetic trees that incorrectly separate crown groups from their true stem group. This is theoretically possible, given that every phylogenetic tree represents only a hypothesis of ancestor-descendant relationships (Lachance, 2016) .
​​Examples of articles describing use of molecular data in definition of taxa in phylogenetic trees
Taxon
LIterature reference
Batrachia
Zhang, P., Zhou, H., Chen, Y. Q., Liu, Y. F., & Qu, L. H. (2005). Mitogenomic perspectives on the origin and phylogeny of living amphibians. Systematic Biology, 54(3), 391-400.
Eutheria
Archibald, J. D. (2003). Timing and biogeography of the eutherian radiation: fossils and molecules compared. Molecular Phylogenetics and Evolution, 28(2), 350-359.
Actinopteri
Near, T. J., Eytan, R. I., Dornburg, A., Kuhn, K. L., Moore, J. A., Davis, M. P., ... & Smith, W. L. (2012). Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Sciences, 109(34), 13698-13703.
Marsupialia
Mitchell, K. J., Pratt, R. C., Watson, L. N., Gibb, G. C., Llamas, B., Kasper, M., ... & Cooper, A. (2014). Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular biology and evolution, 31(9), 2322-2330.
Sauria
​(Archelosauria)
Wolniewicz, A. S., Shen, Y., Li, Q., Sun, Y., Qiao, Y., Chen, Y., ... & Liu, J. (2023). An armoured marine reptile from the Early Triassic of South China and its phylogenetic and evolutionary implications. Elife, 12, e83163.
Sauria
​(Aves)
Stiller, J., Feng, S., Chowdhury, A. A., Rivas-González, I., Duchêne, D. A., Fang, Q., ... & Zhang, G. (2024). Complexity of avian evolution revealed by family-level genomes. Nature, 629(8013), 851-860.
Anthocerotophyta
Wang, Q. H., Zhang, J., Liu, Y., Jia, Y., Jiao, Y. N., Xu, B., & Chen, Z. D. (2022). Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. Journal of Experimental Botany, 73(13), 4306-4322.
Bryophyta
Liu, Y., Johnson, M. G., Cox, C. J., Medina, R., Devos, N., Vanderpoorten, A., ... & Goffinet, B. (2019). Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes. Nature Communications, 10(1), 1485.
Marchantiophyta
Dong, S., Yu, J., Zhang, L., Goffinet, B., & Liu, Y. (2022). Phylotranscriptomics of liverworts: revisiting the backbone phylogeny and ancestral gene duplications. Annals of Botany, 130(7), 951-964.
Lycophyta and Monilophyta
Pteridophyte Phylogeny Group I. (2016). A community‐derived classification for extant lycophytes and ferns. Journal of systematics and evolution, 54(6), 563-603.
Gymnosperms
Yang, Y., Yang, Z., & Ferguson, D. K. (2024). The systematics and evolution of gymnosperms with an emphasis on a few problematic taxa. Plants, 13(16), 2196.
Angiosperms
Li, H. T., Luo, Y., Gan, L., Ma, P. F., Gao, L. M., Yang, J. B., ... & Li, D. Z. (2021). Plastid phylogenomic insights into relationships of all flowering plant families. BMC biology, 19(1), 1-13.
Page last updated July 22nd, 2026.

Reference

​Lachance, M. A. (2016). Paraphyly and (yeast) classification. International Journal of Systematic and Evolutionary Microbiology, 66(12), 4924-4929.