Kenrick, P., Wellman, C. H., Schneider, H. & Edgecombe, G. D. A timeline for terrestrialization: consequences for the carbon cycle in the Palaeozoic. Philos. Trans. R. Soc. Lond. B. 367, 519–536 (2012).
Selden, P. A. Encyclopedia of Life Sciences: Terrestrialization (Precambrian–Devonian) (John Wiley & Sons, 2005).
Brusca, R. C., Giribet, G. & Moore, W. Invertebrates, 4th edn (Oxford Univ. Press, 2023).
Ashley-Ross, M. A., Hsieh, S. T., Gibb, A. C. & Blob, R. W. Vertebrate land invasions-past, present, and future: an introduction to the symposium. Integr. Comp. Biol. 53, 192–196 (2013).
Lozano-Fernandez, J. et al. A molecular palaeobiological exploration of arthropod terrestrialization. Philos. Trans. R. Soc. Lond. B 371, 20150133 (2016).
Barker, G. M. Naturalised terrestrial Stylommatophora (Mollusca: Gastropoda). Fauna N. Z. https://doi.org/10.7931/J2/FNZ.38 (1999).
Mobjerg, N. et al. Survival in extreme environments—on the current knowledge of adaptations in tardigrades. Acta Physiol. 202, 409–420 (2011).
Menter, D. G. et al. Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective. Cancer Metastasis Rev. 41, 147–172 (2022).
Carter, M. J., Cortes, P. A. & Rezende, E. L. Temperature variability and metabolic adaptation in terrestrial and aquatic ectotherms. J. Therm. Biol 115, 103565 (2023).
Nilsson, D. E. Evolution: an irresistibly clear view of land. Curr. Biol. 27, R715–R717 (2017).
Paps, J. & Holland, P. W. H. Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty. Nat. Commun. 9, 1730 (2018).
Fernandez, R. & Gabaldon, T. Gene gain and loss across the metazoan tree of life. Nat. Ecol. Evol. 4, 524–533 (2020).
Guijarro-Clarke, C., Holland, P. W. H. & Paps, J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat. Ecol. Evol. 4, 519–523 (2020).
Martinez-Redondo, G. I. et al. Parallel duplication and loss of aquaporin-coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization. Mol. Ecol. 32, 2022–2040 (2023).
Aristide, L. & Fernández, R. Genomic insights into mollusk terrestrialization: parallel and convergent gene family expansions as key facilitators in out-of-the-sea transitions. Genome Biol. Evol. 15, evad176 (2023).
Thomas, G. W. C. et al. Gene content evolution in the arthropods. Genome Biol. 21, 15 (2020).
Balart-Garcia, P. et al. Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nat. Commun. 14, 3842 (2023).
Vargas-Chavez, C. et al. An episodic burst of massive genomic rearrangements and the origin of non-marine annelids. Nat. Ecol. Evol. 9, 1263–1279 (2025).
Bowles, A. M. C., Bechtold, U. & Paps, J. The origin of land plants is rooted in two bursts of genomic novelty. Curr. Biol. 30, 530–536 e2 (2020).
WoRMS Editorial Board. World Register of Marine Species (WoRMS) (Flanders Marine Institute, 2024); https://www.marinespecies.org.
Fernández, R., Gabaldon, T. & Dessimoz, C. Phylogenetics in the Genomic Era: Orthology: Definitions, Prediction, and Impact on Species Phylogeny Inference (2020).
Mendes, F. K., Vanderpool, D., Fulton, B. & Hahn, M. W. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36, 5516–5518 (2021).
Natsidis, P., Kapli, P., Schiffer, P. H. & Telford, M. J. Systematic errors in orthology inference and their effects on evolutionary analyses. iScience 24, 102110 (2021).
Koonin, E. V. & Wolf, Y. I. Constraints and plasticity in genome and molecular-phenome evolution. Nat. Rev. Genet. 11, 487–498 (2010).
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000).
The Gene Ontology Consortium The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).
Steger, A. et al. The evolution of plant proton pump regulation via the R domain may have facilitated plant terrestrialization. Commun. Biol. 5, 1312 (2022).
Guna, A., Volkmar, N., Christianson, J. C. & Hegde, R. S. The ER membrane protein complex is a transmembrane domain insertase. Science 359, 470–473 (2018).
Thiel, M. & Watling, L. Lifestyles and Feeding Biology: The Natural History of the Crustacea (Oxford Univ. Press, 2015).
Snyder, M. J. Cytochrome P450 enzymes in aquatic invertebrates: recent advances and future directions. Aquat. Toxicol. 48, 529–547 (2000).
Naumann, C., Hartmann, T. & Ober, D. Evolutionary recruitment of a flavin-dependent monooxygenase for the detoxification of host plant-acquired pyrrolizidine alkaloids in the alkaloid-defended arctiid moth Tyria jacobaeae. Proc. Natl Acad. Sci. USA 99, 6085–6090 (2002).
Tian, R., Seim, I., Ren, W., Xu, S. & Yang, G. Contraction of the ROS scavenging enzyme glutathione S-transferase gene family in cetaceans. G3 9, 2303–2315 (2019).
Weis, W. I. & Kobilka, B. K. The molecular basis of G protein-coupled receptor activation. Annu. Rev. Biochem. 87, 897–919 (2018).
Sakai, Y. et al. The integrin signaling network promotes axon regeneration via the Src–Ephexin–RhoA GTPase signaling axis. J. Neurosci. 41, 4754–4767 (2021).
You, J. S. et al. ARHGEF3 regulates skeletal muscle regeneration and strength through autophagy. Cell Rep. 34, 108731 (2021).
Nakamura, M., Verboon, J. M. & Parkhurst, S. M. Prepatterning by RhoGEFs governs Rho GTPase spatiotemporal dynamics during wound repair. J. Cell Biol. 216, 3959–3969 (2017).
Tsuchiya, T. et al. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Proc. Natl Acad. Sci. USA 96, 15362–15367 (1999).
Orth, M. et al. Shugoshin is a Mad1/Cdc20-like interactor of Mad2. EMBO J. 30, 2868–2880 (2011).
Bradley, T. J. Terrestrial Animals: Animal Osmoregulation (Oxford Univ. Press, 2008).
Bowman, K. G. & Bertozzi, C. R. Carbohydrate sulfotransferases: mediators of extracellular communication. Chem. Biol. 6, R9–R22 (1999).
Reiter, R. J. The melatonin rhythm: both a clock and a calendar. Experientia 49, 654–664 (1993).
Stout, J. The terrestrial plankton. Tuatara 11, 57 (1963).
Kameda, Y. & Kato, M. Terrestrial invasion of pomatiopsid gastropods in the heavy-snow region of the Japanese Archipelago. BMC Evol. Biol. 11, 118 (2011).
Locke, M. Secretion of wax through the cuticle of insects. Nature 184, 1967–1967 (1959).
Wang, T. & Montell, C. Rhodopsin formation in Drosophila is dependent on the PINTA retinoid-binding protein. J. Neurosci. 25, 5187–5194 (2005).
Lillywhite, H. B. Water relations of tetrapod integument. J. Exp. Biol. 209, 202–226 (2006).
Riera Romo, M., Perez-Martinez, D. & Castillo Ferrer, C. Innate immunity in vertebrates: an overview. Immunology 148, 125–139 (2016).
Morris, J. L. et al. The timescale of early land plant evolution. Proc. Natl Acad. Sci. USA 115, E2274–E2283 (2018).
Carlisle, E., Yin, Z., Pisani, D. & Donoghue, P. C. J. Ediacaran origin and Ediacaran–Cambrian diversification of Metazoa. Sci. Adv. 10, eadp7161 (2024).
Qing, X. et al. Phylogenomic insights into the evolution and origin of nematoda. Syst. Biol. 74, 349–358 (2025).
Mitchell, R. L. et al. Cryptogamic ground covers as analogues for early terrestrial biospheres: initiation and evolution of biologically mediated proto-soils. Geobiology 19, 292–306 (2021).
Kearsey, T. I. et al. The terrestrial landscapes of tetrapod evolution in earliest Carboniferous seasonal wetlands of SE Scotland. Palaeogeogr. Palaeoclimatol. Palaeoecol. 457, 52–69 (2016).
Selles Vidal, L., Kelly, C. L., Mordaka, P. M. & Heap, J. T. Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application. Biochim. Biophys. Acta 1866, 327–347 (2018).
Benton, M. J., Wilf, P. & Sauquet, H. The angiosperm terrestrial revolution and the origins of modern biodiversity. New Phytol. 233, 2017–2035 (2022).
Alibardi, L. Regeneration among animals: an evolutionary hypothesis related to aquatic versus terrestrial environment. Dev. Biol. 501, 74–80 (2023).
Lozano-Fernandez, J. et al. Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida. Nat. Commun. 10, 2295 (2019).
Ballesteros, J. A. & Sharma, P. P. A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error. Syst. Biol. 68, 896–917 (2019).
Martínez-Redondo, G. I. et al. FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life. Commun. Biol. 8, 1227 (2025).
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).
UniProt, C. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 51, D523–D531 (2023).
Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Res. 51, D29–D38 (2023).
Martin, F. J. et al. Ensembl 2023. Nucleic Acids Res. 51, D933–D941 (2023).
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Manni, M., Berkeley, M. R., Seppey, M., Simao, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Laumer, C. E. et al. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proc. Biol. Sci. 286, 20190831 (2019).
Pett, W. et al. The role of homology and orthology in the phylogenomic analysis of metazoan gene content. Mol. Biol. Evol. 36, 643–649 (2019).
Redmond, A. K. & McLysaght, A. Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat. Commun. 12, 1783 (2021).
Simion, P. et al. A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals. Curr. Biol. 27, 958–967 (2017).
Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Kuck, P. & Longo, G. C. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool. 11, 81 (2014).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Bealer, K. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016).
Cantalapiedra, C. P., Hernandez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Thomas, P. D. et al. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 31, 8–22 (2022).
Alvarez-Carretero, S. et al. A species-level timeline of mammal evolution integrating phylogenomic data. Nature 602, 263–267 (2022).
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Álvarez-Carretero, S., Kapli, P. & Yang, Z. Beginner’s guide on the use of PAML to detect positive selection. Mol. Biol. Evol. 40, msad041 (2023).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics Using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
