Kalinka, A. T. & Tomancak, P. The evolution of early animal embryos: conservation or divergence? Trends Ecol. Evol. 27, 385â393 (2012).
Salazar-Ciudad, I. Morphological evolution and embryonic developmental diversity in metazoa. Development 137, 531â539 (2010).
Grau-Bové, X. et al. Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 6, e26036 (2017).
Ocaña-Pallarès, E. et al. Divergent genomic trajectories predate the origin of animals and fungi. Nature 609, 747â753 (2022).
Sebé-Pedrós, A., Degnan, B. M. & Ruiz-Trillo, I. The origin of Metazoa: a unicellular perspective. Nat. Rev. Genet. https://doi.org/10.1038/nrg.2017.21 (2017).
Brunet, T. & King, N. in The Evolution of Multicellularity (eds Herron, M. D. et al.) Ch. 13 (CRC, 2022).
Knoll, A. H. The multiple origins of complex multicellularity. Annu. Rev. Earth Planet Sci. 39, 217â239 (2011).
De Smet, I. & Beeckman, T. Asymmetric cell division in land plants and algae: the driving force for differentiation. Nat. Rev. Mol. Cell Biol. 12, 177â188 (2011).
Gönczy, P. Mechanisms of asymmetric cell division: flies and worms pave the way. Nat. Rev. Mol. Cell Biol. 9, 355â366 (2008).
Lechler, T. & Mapelli, M. Spindle positioning and its impact on vertebrate tissue architecture and cell fate. Nat. Rev. Mol. Cell Biol. 22, 691â708 (2021).
Tsai, T. Y. C., Garner, R. M. & Megason, S. G. Adhesion-based self-organization in tissue patterning. Annu. Rev. Cell Dev. Biol. 38, 349â374 (2022).
Wu, D., Yamada, K. M. & Wang, S. Tissue morphogenesis through dynamic cell and matrix interactions. Annu. Rev. Cell Dev. Biol. 39, 123â144 (2023).
Arendt, D. et al. The origin and evolution of cell types. Nat. Rev. Genet. 17, 744â757 (2016).
Bell, G. & Mooers, A. O. Size and complexity among multicellular organisms. Biol. J. Linn. Soc. 60, 345â363 (1997).
Márquez-ZacarÃas, P. et al. Evolution of cellular differentiation: from hypotheses to models. Trends Ecol. Evol. 36, 49â60 (2021).
Wolpert, L. Do we understand development? Science (1979) 266, 571â572 (1994).
Ruiz-Trillo, I. & de Mendoza, A. Towards understanding the origin of animal development. Development https://doi.org/10.1242/dev.192575 (2020).
Brunet, T. et al. A flagellate-to-amoeboid switch in the closest living relatives of animals. eLife 10, 1â73 (2021).
Brunet, T. et al. Light-regulated collective contractility in a multicellular choanoflagellate. Science https://doi.org/10.1126/science.aay2346 (2019).
Fairclough, S. R., Dayel, M. J. & King, N. Multicellular development in a choanoflagellate. Curr. Biol. https://doi.org/10.1016/j.cub.2010.09.014 (2010).
Parra-Acero, H. et al. Integrin-mediated adhesion in the unicellular holozoan Capsaspora owczarzaki. Curr. Biol. https://doi.org/10.1016/j.cub.2020.08.015 (2020).
Sebé-Pedrós, A. et al. Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife https://doi.org/10.7554/eLife.01287 (2013).
Pérez-Posada, A., Dudin, O., Ocaña-Pallarès, E., Ruiz-Trillo, I. & Ondracka, A. Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery. PLoS Genet. https://doi.org/10.1371/journal.pgen.1008584 (2020).
Xiao, S. et al. The Wengâan biota and the Ediacaran radiation of multicellular eukaryotes. Natl Sci. Rev. 1, 498â520 (2014).
Ros-Rocher, N. et al. Chemical factors induce aggregative multicellularity in a close unicellular relative of animals. Proc. Natl Acad. Sci. USA 120, e2216668120 (2023).
Woznica, A. et al. Bacterial lipids activate, synergize, and inhibit a developmental switch in choanoflagellates. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.1605015113 (2016).
Levin, T. C., Greaney, A. J., Wetzel, L. & King, N. The Rosetteless gene controls development in the choanoflagellate S. rosetta. eLife https://doi.org/10.7554/eLife.04070 (2014).
Levin, T. C. & King, N. Evidence for sex and recombination in the Choanoflagellate Salpingoeca rosetta. Curr. Biol. https://doi.org/10.1016/j.cub.2013.08.061 (2013).
Dayel, M. J. et al. Cell differentiation and morphogenesis in the colony-forming choanoflagellate Salpingoeca rosetta. Dev. Biol. 357, 73â82 (2011).
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).
Phillips, J. E., Santos, M., Konchwala, M., Xing, C. & Pan, D. Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis. eLife 11, e77598 (2022).
Glockling, S. L., Marshall, W. L. & Gleason, F. H. Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea). Fungal Ecol. 6, 237â247 (2013).
Mendoza, L., Taylor, J. W. & Ajello, L. The class Mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Annu. Rev. Microbiol. 56, 315â344 (2002).
Ondracka, A., Dudin, O. & Ruiz-Trillo, I. Decoupling of nuclear division cycles and cell size during the coenocytic growth of the Ichthyosporean Sphaeroforma arctica. Curr. Biol. 28, 1964â1969.e2 (2018).
Dudin, O., Wielgoss, S., New, A. M. & Ruiz-Trillo, I. Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals. PLoS Biol. 20, e3001551 (2022).
Dudin, O. et al. A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization. eLife 8, e49801 (2019).
McCartney, B. & Dudin, O. Cellularization across eukaryotes: conserved mechanisms and novel strategies. Curr. Opin. Cell Biol. 80, 102157 (2023).
Shah, H. et al. Life-cycle-coupled evolution of mitosis in close relatives of animals. Nature https://doi.org/10.1038/s41586-024-07430-z (2024).
Olivetta, M. & Dudin, O. The nuclear-to-cytoplasmic ratio drives cellularization in the close animal relative Sphaeroforma arctica. Curr. Biol. 33, 1597â1605.e3 (2023).
Vasudevan, S., Seli, E. & Steitz, J. A. Metazoan oocyte and early embryo development program: a progression through translation regulatory cascades. Genes Dev. 20, 138â146 (2006).
Levin, M. et al. The mid-developmental transition and the evolution of animal body plans. Nature https://doi.org/10.1038/nature16994 (2016).
Carvalho-Santos, Z., Azimzadeh, J., Pereira-Leal, J. B. & Bettencourt-Dias, M. Tracing the origins of centrioles, cilia, and flagella. J. Cell Biol. 194, 165â175 (2011).
Brunet, T. & Booth, D. S. Cell polarity in the protist-to-animal transition. Curr. Top. Dev. Biol. 154, 1â36 (2023).
Wright, B. A., Kvansakul, M., Schierwater, B. & Humbert, P. O. Cell polarity signalling at the birth of multicellularity: what can we learn from the first animals. Front. Cell. Dev. Biol. 10, 1024489 (2022).
Klapholz, B. & Brown, N. H. Talin – the master of integrin adhesions. J. Cell Sci. 130, 2435â2446 (2017).
Bays, J. L. & DeMali, K. A. Vinculin in cellâcell and cellâmatrix adhesions. Cell. Mol. Life Sci. 74, 2999â3009 (2017).
Sebé-Pedrós, A., De Mendoza, A., Lang, B. F., Degnan, B. M. & Ruiz-Trillo, I. Unexpected repertoire of metazoan transcription factors in the unicellular holozoan capsaspora owczarzaki. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msq309 (2011).
De Mendoza, A. et al. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.1311818110 (2013).
Serra, D. et al. Self-organization and symmetry breaking in intestinal organoid development. Nature 569, 66â72 (2019).
Palmer, A. R. Symmetry breaking and the evolution of development. Science 306, 828â833 (2004).
Brunet, T. & King, N. The origin of animal multicellularity and cell differentiation. Dev. Cell https://doi.org/10.1016/j.devcel.2017.09.016 (2017).
Raghu-kumar, S. Occurrence of the Thraustochytrid, Corallochytrium limacisporum gen. et sp. nov. in the coral reef lagoons of the Lakshadweep Islands in the Arabian Sea. Botanica Marina 30, 83â90 (1987).
Hehenberger, E. et al. Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signaling system in the ancestor of animals. Curr. Biol. 27, 2043â2050.e6 (2017).
Ros-Rocher, N., Pérez-Posada, A., Leger, M. M. & Ruiz-Trillo, I. The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition. Open Biol. 11, 200359 (2021).
Larson, B. T. et al. Biophysical principles of choanoflagellate self-organization. Proc. Natl Acad. Sci. USA 117, 1303â1311 (2020).
Yang, C. et al. The tempo of Ediacaran evolution. Sci. Adv. 7, 9643 (2021).
Cunningham, J. A., Vargas, K., Yin, Z., Bengtson, S. & Donoghue, P. C. J. The Wengâan Biota (Doushantuo Formation): an Ediacaran window on soft-bodied and multicellular microorganisms. J. Geol. Soc. London 174, 793â802 (2017).
Yin, Z. et al. Nuclei and nucleoli in embryo-like fossils from the Ediacaran Wengâan Biota. Precambrian Res. 301, 145â151 (2017).
Yin, Z. et al. Developmental biology of Helicoforamina reveals holozoan affinity, cryptic diversity, and adaptation to heterogeneous environments in the early Ediacaran Wengâan biota (Doushantuo Formation, South China). Sci. Adv. 6, 83â95 (2020).
Sun, W., Yin, Z., Liu, P., Zhu, M. & Donoghue, P. Developmental biology of Spiralicellula and the Ediacaran origin of crown metazoans. Proc. R. Soc. Lond. B Biol. Sci. 291, 20240101 (2024).
Yin, Z. et al. The early Ediacaran Caveasphaera foreshadows the evolutionary origin of animal-like embryology. Curr. Biol. 29, 4307â4314.e2 (2019).
Yin, Z. et al. Diverse and complex developmental mechanisms of early Ediacaran embryo-like fossils from the Wengâan Biota, southwest China. Phil. Trans. R. Soc. Lond. B Biol. Sci. 377, 20210032 (2022).
Xiao, S. Mitotic topologies and mechanics of Neoproterozoic algae and animal embryos. Paleobiology 28, 244â250 (2002).
Shuhai, X. et al. Fossil preservation in the Neoproterozoic Doushantuo phosphorite Lagerstätte, South China. Lethaia 32, 219â238 (1999).
Chen, L., Xiao, S., Pang, K., Zhou, C. & Yuan, X. Cell differentiation and germ-soma separation in Ediacaran animal embryo-like fossils. Nature 516, 238â241 (2014).
Huldtgren, T. et al. Fossilized nuclei and germination structures identify ediacaran âanimal embryosâ as encysting protists. Science 334, 1696â1699 (2011).
Alexa, A. & Rahnenfuhrer, J. topGO: enrichment analysis for gene ontology. R package version 2.42.0 https://rdrr.io/bioc/topGO/ (2020).
Gambarotto, D. et al. Imaging cellular ultrastructures using expansion microscopy (U-ExM). Nat. Methods 16, 71â74 (2018).
Machado, S., Mercier, V. & Chiaruttini, N. LimeSeg: a coarse-grained lipid membrane simulation for 3D image segmentation. BMC Bioinf. 20, 1â12 (2019).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676â682 (2012).
Multicellgenome Lab. Genome – Chromosphaera perkinsii. Figshare https://figshare.com/articles/dataset/Genome_-_Chromosphaera_perkinsii/5426494 (2024).
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417â419 (2017).
Soneson, C., Love, M. I. & Robinson, M. D. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 4, 1521 (2016).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139â140 (2010).
McCarthy, D. J., Chen, Y. & Smyth, G. K. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 40, 4288 (2012).
Chen, Y., Lun, A. T. L. & Smyth, G. K. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Res. 5, 1438 (2016).
Meyer, D. et al. e1071: misc functions of the Department of Statistics, Probability Theory Group (formerly: E1071), TU Wien. R package version 1.7-15 https://rdrr.io/rforge/e1071/ (2024).
Garnier, S. et al. viridis: colorblind-friendly color maps for R. R package version 0.6.4 https://rdrr.io/cran/viridis/ (2024).
Barter, R. & Yu, B. superheat: a graphical tool for exploring complex datasets using heatmaps. R package version 0.1.0 https://rdrr.io/cran/superheat/ (2019).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 1â9 (2009).
Boutet, E. et al. UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Methods Mol. Biol. 1374, 23â54 (2016).
Rost, B. Enzyme function less conserved than anticipated. J. Mol. Biol. 318, 595â608 (2002).
Burns, J. A., Paasch, A., Narechania, A. & Kim, E. Comparative genomics of a bacterivorous green alga reveals evolutionary causalities and consequences of phago-mixotrophic mode of nutrition. Genome Biol. Evol. 7, 3047â3061 (2015).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 1â14 (2019).
Haas, B. J. et al. TransDecoder source. GitHub https://github.com/TransDecoder/TransDecoder (2024).
Engel, S. R. et al. New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. Genetics 220, iyab224 (2022).
Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871â880 (2002).
Eichinger, I. et al. The genome of the social amoeba Dictyostelium discoideum. Nature 435, 43â57 (2005).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772â780 (2013).
Wei, T. & Simko, V. corrplot: visualization of a correlation matrix. R package version 0.92. https://rdocumentation.org/packages/corrplot/versions/0.94 (2024).
Gearty, W. & Jones, L. A. rphylopic: an R package for fetching, transforming, and visualising PhyloPic silhouettes. Methods Ecol. Evol. 14, 2700â2708 (2023).
Olivetta, M. et al. Source data for âA multicellular developmental program in a close animal relativeâ. Figshare https://figshare.com/s/f20f6d471c719990471c (2024).
Olivetta, M. et al. Code for âA multicellular developmental program in a close animal relativeâ. Zenodo https://doi.org/10.5281/zenodo.13352464 (2024).