Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64119 (1983).

Article PubMed CAS Google Scholar

Martindale, M. Q. & Henry, J. Q. Intracellular fate mapping in a basal metazoan, the ctenophore Mnemiopsis leidyi, reveals the origins of mesoderm and the existence of indeterminate cell lineages. Dev. Biol. 214, 243257 (1999).

Article PubMed CAS Google Scholar

Spencer Chapman, M. et al. Lineage tracing of human development through somatic mutations. Nature 595, 8590 (2021).

Article PubMed CAS Google Scholar

Tanay, A. & Seb-Pedrs, A. Evolutionary cell type mapping with single-cell genomics. Trends Genet. 37, 919932 (2021).

Article PubMed CAS Google Scholar

Shekhar, K. et al. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166, 13081323 (2016).

Gilbert, E. et al. Molecular and cellular architecture of the larval sensory organ in the cnidarian Nematostella vectensis. Development 149, dev200833 (2022).

Article PubMed PubMed Central CAS Google Scholar

Kin, K., Nnamani, M. C., Lynch, V. J., Michaelides, E. & Wagner, G. P. Cell-type phylogenetics and the origin of endometrial stromal cells. Cell Rep. 10, 13981409 (2015).

Article PubMed CAS Google Scholar

Liang, C., Forrest, A. R. R. & Wagner, G. P. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nat. Commun. 6, 6066 (2015).

Article PubMed CAS Google Scholar

Musser, J. M. et al. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 374, 717723 (2021).

Article PubMed PubMed Central CAS Google Scholar

Hughes, A. L. & Friedman, R. A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes. Evol. Dev. 11, 382390 (2009).

Article PubMed PubMed Central CAS Google Scholar

Wagner, G. P. Homology, Genes, and Evolutionary Innovation (Princeton Univ. Press, 2014).

Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744757 (2016).

Article PubMed CAS Google Scholar

Arendt, D. The evolution of cell types in animals: emerging principles from molecular studies. Nat. Rev. Genet. 9, 868882 (2008).

Article PubMed CAS Google Scholar

Arendt, D. Evolution of eyes and photoreceptor cell types. Int. J. Dev. Biol. 47, 563571 (2003).

PubMed Google Scholar

Arendt, D., Bertucci, P. Y., Achim, K. & Musser, J. M. Evolution of neuronal types and families. Curr. Opin. Neurobiol. 56, 144152 (2019).

Article PubMed PubMed Central CAS Google Scholar

Serb, J. M. & Oakley, T. H. Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology. Bioessays 27, 11581166 (2005).

Article PubMed CAS Google Scholar

Packer, J. S. et al. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science 365, eaax1971 (2019).

Article PubMed PubMed Central CAS Google Scholar

Wagner, D. E. & Klein, A. M. Lineage tracing meets single-cell omics: opportunities and challenges. Nat. Rev. Genet. 21, 410427 (2020).

Article PubMed PubMed Central CAS Google Scholar

Whitman, C. O. The embryology of Clepsine. J. Cell Sci. s2-18, 215315 (1878).

Article Google Scholar

Raj, B. et al. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat. Biotechnol. 36, 442450 (2018).

Article PubMed PubMed Central CAS Google Scholar

Nowell, P. C. The clonal evolution of tumor cell populations. Science 194, 2328 (1976).

Article PubMed CAS Google Scholar

Navin, N. et al. Tumour evolution inferred by single-cell sequencing. Nature 472, 9094 (2011).

Article PubMed PubMed Central CAS Google Scholar

Yang, D. et al. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell 185, 19051923 (2022).

Levy, S. et al. A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity. Cell 184, 29732987 (2021).

Seidel, S. & Stadler, T. TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data. Proc. R. Soc. B 289, 20221844 (2022).

Article PubMed PubMed Central Google Scholar

Zhao, Z.-M. et al. Early and multiple origins of metastatic lineages within primary tumors. Proc. Natl Acad. Sci. USA 113, 21402145 (2016).

Article PubMed PubMed Central CAS Google Scholar

Moravec, J. C., Lanfear, R., Spector, D. L., Diermeier, S. D. & Gavryushkin, A. Testing for phylogenetic signal in single-cell RNA-seq data. J. Comput. Biol. 30, 518537 (2023).

Article PubMed PubMed Central CAS Google Scholar

Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406425 (1987).

PubMed CAS Google Scholar

Paganos, P., Voronov, D., Musser, J. M., Arendt, D. & Arnone, M. I. Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. Elife 10, e70416 (2021).

Article PubMed PubMed Central CAS Google Scholar

Wang, Y. et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512, 155160 (2014).

Article PubMed PubMed Central CAS Google Scholar

Frumkin, D., Wasserstrom, A., Kaplan, S., Feige, U. & Shapiro, E. Genomic variability within an organism exposes its cell lineage tree. PLoS Comput. Biol. 1, e50 (2005).

Article PubMed PubMed Central Google Scholar

Tarashansky, A. J. et al. Mapping single-cell atlases throughout Metazoa unravels cell type evolution. Elife 10, e66747 (2021).

Article PubMed PubMed Central CAS Google Scholar

van Zyl, T. et al. Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis. Proc. Natl Acad. Sci. USA 117, 1033910349 (2020).

Article PubMed PubMed Central Google Scholar

Seb-Pedrs, A. et al. Early metazoan cell type diversity and the evolution of multicellular gene regulation. Nat. Ecol. Evol. 2, 11761188 (2018).

Article PubMed PubMed Central Google Scholar

Wang, R. et al. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res. 51, 501516 (2023).

Article PubMed CAS Google Scholar

Chen, D. et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat. Commun. 12, 7083 (2021).

Article PubMed PubMed Central CAS Google Scholar

Dunn, C. W., Zapata, F., Munro, C., Siebert, S. & Hejnol, A. Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc. Natl Acad. Sci. USA 115, E409E417 (2018).

Article PubMed PubMed Central CAS Google Scholar

Felsenstein, J. Phylogenies and the comparative method. Am. Nat. 125, 115 (1985).

Article Google Scholar

Grafen, A. The phylogenetic regression. Phil. Trans. R. Soc. Lond. B 326, 119157 (1997).

Google Scholar

Seb-Pedrs, A., Degnan, B. M. & Ruiz-Trillo, I. The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. 18, 498512 (2017).

Article PubMed Google Scholar

Mah, J. L., Christensen-Dalsgaard, K. K. & Leys, S. P. Choanoflagellate and choanocyte collar-flagellar systems and the assumption of homology. Evol. Dev. 16, 2537 (2014).

Article PubMed CAS Google Scholar

Laundon, D., Larson, B. T., McDonald, K., King, N. & Burkhardt, P. The architecture of cell differentiation in choanoflagellates and sponge choanocytes. PLoS Biol. 17, e3000226 (2019).

Article PubMed PubMed Central Google Scholar

Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

Article PubMed PubMed Central CAS Google Scholar

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 35733587 (2021).

Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 18881902 (2019).

McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at http://arxiv.org/abs/1802.03426 (2020).

Felsenstein, J. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25, 471492 (1973).

PubMed PubMed Central CAS Google Scholar

Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783791 (1985).

Article PubMed Google Scholar

Lemoine, F. et al. Renewing Felsensteins phylogenetic bootstrap in the era of big data. Nature 556, 452456 (2018).

Article PubMed PubMed Central CAS Google Scholar

Thorley, J. L. & Wilkinson, M. Testing the phylogenetic stability of early tetrapods. J. Theor. Biol. 200, 343344 (1999).

Article PubMed CAS Google Scholar

Levy, C., Khaled, M. & Fisher, D. E. MITF: master regulator of melanocyte development and melanoma oncogene. Trends Mol. Med. 12, 406414 (2006).

Article PubMed CAS Google Scholar

van Zyl, T. et al. Cell atlas of the human ocular anterior segment: tissue-specific and shared cell types. Proc. Natl Acad. Sci. USA 119, e2200914119 (2022).

Article PubMed PubMed Central Google Scholar

Sokal, R. R. et al. Principles of Numerical Taxonomy (WH Freeman & Co, 1963).

Sokal, R. R. & Michener, C. D. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38, 14091438 (1958).

Google Scholar

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