Multilevel Organismal Diversity in an Ontogenetic Framework as a Solution for the Species Concept

doi:10.1017/9781009070553.004

4 - Multilevel Organismal Diversity in an Ontogenetic Framework as a Solution for the Species Concept

Published online by Cambridge University Press: 01 September 2022

Alexander Martynov and

Tatiana Korshunova

Edited by

Alexandre K. Monro and

Simon J. Mayo

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Alexandre K. Monro: Affiliation:
Royal Botanic Gardens, Kew
Simon J. Mayo: Affiliation:
Royal Botanic Gardens, Kew

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Summary

The concept of ‘species’ is a persistent biological problem. In discussions about the species phenomenon, the ‘cryptic species’ concept currently prevails. We propose that the ‘cryptic species’ concept as it is currently understood strongly emphasizes the distinctions between morphological and molecular levels and obscures multiple other biological levels and the organism itself. Therefore we suggest, instead of the term ‘species’, a multilevel organismal diversity concept (MOD) as an alternative that is well-supported by numerous data. We also highlight the central role of ontogeny in a broad sense (one that encompasses all major properties and traits of an organism as well as both genetic and epigenetic traits) for the future development of taxonomy and phylogenetics. Potential consequences of a new understanding of the species phenomenon for biological nomenclature are outlined. A general scheme for the future development of organism studies within the framework of MOD is presented.

Keywords

multilevel organismal diversity species concepts problem clonal organisms ontogeny periodic processes phylotopic periods PhyloPeriodic Table taxonomic decisions general properties

Information

Type: Chapter
Information: Cryptic Species
Morphological Stasis, Circumscription, and Hidden Diversity
, pp. 78 - 129
DOI: https://doi.org/10.1017/9781009070553.004 [Opens in a new window]
Publisher: Cambridge University Press
Print publication year: 2022

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References

Adams, M. J. et al. (2017) 50 years of the international committee on taxonomy of viruses: Progress and prospects. Archives of Virology 162: 1441–1446.Google Scholar

Agassiz, A. A. and Gould, A. A. (1857) Principles of Zoölogy. Gould and Lincoln, Boston, 250 pp.Google Scholar

Agosta, S. J and Brooks, D. R. (2020) The Major Metaphors of Evolution. Springer Intern. Publishing, Berlin, 273 pp.Google Scholar

Alberch, P. S., Gould, S. J., Oster, G. F., and Wake, D. B. (1979) Size and shape in ontogeny and phylogeny. Paleobiology 5: 296–317.CrossRef Google Scholar

Albert, V. A., Gustafsson., M. H. G., and Di Laurenzio, L. (1998) Ontogenetic systematics, molecular developmental genetics, and the angiosperm petal. In: Soltis, P. S., Soltis, D. E., and Doyle, J. J. (eds.) Molecular Systematics of Plants II. Kluwer Academic Publishing, Boston, pp. 349–374.Google Scholar

Amaral, A. R., Lovewell, G., Coelho, M. M., Amato, G., and Rosenbaum, H. C. (2014) Hybrid speciation in a marine mammal: The Clymene dolphin (Stenella clymene). PLoS ONE 9(1): e83645.Google Scholar

Amariei, C., Tomita, M., and Murray, D. B. (2014) Quantifying periodicity in omics data. Frontiers in Cell and Developmental Biology 2: 1–9.Google Scholar

Árnason, E. and Halldórsdóttir, K. (2019) Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids. Science Advance 5: eaat8788.Google Scholar

Arthur, W. (2002) The emerging conceptual framework of evolutionary developmental biology. Nature 415: 757–764.Google Scholar

Arthur, W. (2015) Internal factors in evolution: The morphogenetic tree, developmental bias, and some thoughts on the conceptual structure of evo-devo. In: Love, Alan C. (ed.) Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Springer Science & Business Media, Dordrecht, pp. 343–363.Google Scholar

Babaev, E. (2019) Periodic law in chemistry and other sciences. Pure and Applied Chemistry 91: 2023–2035.Google Scholar

Baer, K. E., von (1828–1837) Entwickelungsgeschichte der Thiere: Beobachtung und Reflexion. 2 Bd. Bornträger, Königsberg, 264 S.Google Scholar

Beer, G. R. de (1958) Embryos and Ancestors, 3rd ed. Oxford University Press, Oxford, 197 pp.Google Scholar

Beklemishev, V. N. (1969) Principles of Comparative Anatomy of Invertebrates, Vol 1. University of Chicago Press, Chicago, 490 pp.Google Scholar

Bellés, X. (2020) Insect Metamorphosis: From Natural History to Regulation of Development and Evolution. Elsevier, Academic Press, Amsterdam and New York, 304 pp.Google Scholar

Beurton, P. J. (2002) Ernst Mayr through time on the biological species concept: A conceptual analysis. Theory in Biosciences 121: 81–98.Google Scholar

Bierbach, D., Laskowski, K., and Wolf, M. (2017) Behavioural individuality in clonal fish arises despite near-identical rearing conditions. Nature Communications 8: 15361.Google Scholar

Blackstone, N. W. (2021) Evolutionary conflict and coloniality in animals. Journal of Experimental Zoology 336: 212–220.CrossRef Google Scholar PubMed

Bolnick, D. I., Barrett, R. D. H., Oke, K. B., Rennison, D. J., and Stuart, Y. E. (2019) (Non)parallel evolution. Annual Review of Ecology, Evolution, and Systematics 49: 303–330.Google Scholar

Brandt, A. et al. (2019) No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods. Scientific Reports 9: 5338.Google Scholar

Brehm, G. et al. (2016) Turning up the heat on a hotspot: DNA barcodes reveal 80% more species of geometrid moths along an Andean elevational gradient. PLoS ONE 11: e0150327.Google Scholar

Burggren, W. W. (2014) Epigenetics as a source of variation in comparative animal physiology – or – Lamarck is lookin’ pretty good these days. Journal of Experimental Biology 217: 682–689.Google Scholar

Burma, B. H. (1954) Reality, existence, and classification: A discussion of the species problem. Madroño 12: 193–209.Google Scholar

Burress, E. D., Alda, F., Duarte, A. et al. (2018) Phylogenomics of pike cichlids (Cichlidae: Crenicichla): The rapid ecological speciation of an incipient species flock. Journal of Evolutionary Biology 31: 14–30.Google Scholar

Burton, T. and Metcalfe, N. B. (2014) Can environmental conditions experienced in early life influence future generations? Proceedings of the Royal Society B 281: 20140311.CrossRef Google Scholar PubMed

Buss, L. (1987) The Evolution of Individuality. Princeton University Press, Princeton, NJ, 201 p.Google Scholar

Calcott, B. and Sterelny, K. (2011) The Major Transitions in Evolution Revisited. Vienna Series in Theoretical Biology, MIT Press, Cambridge, MA, 319 pp.Google Scholar

Cantino, P. D. and Queiroz, K. de (2010) International Code of Phylogenetic Nomenclature, Version 4c, 102 pp.Google Scholar

Capblancq, T., Després, L., Rioux, D., and Maváarez, J. (2015) Hybridization promotes speciation in Coenonympha butterflies. Molecular Ecology 24: 6209–6222.Google Scholar

Carmel, Y. and Shavit, A. (2020) Operationalizing evolutionary transitions in individuality. Proceedings of the Royal Society B 287: 20192805.Google Scholar

Carroll, S. B. (2008) Evo-Devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25–36.CrossRef Google Scholar

Casadesús, J. and Low, D. A. (2013) Programmed heterogeneity: Epigenetic mechanisms in Bacteria. Journal of Biological Chemistry 288: 13929–13935.CrossRef Google Scholar PubMed

Cerca, J. Meyer, C., Purschke, G., and Struck, T. H. (2020) Delimitation of cryptic species drastically reduces the geographical ranges of marine interstitial ghost-worms (Stygocapitella, Annelida, Sedentaria). Molecular Phylogenetics and Evolution 143: 106663.Google Scholar

Chan, J. C. et al. (2020) Reproductive tract extracellular vesicles are sufficient to transmit intergenerational stress and program neurodevelopment. Nature Communications 11: 1499.Google Scholar

Chenuil, A., Cahill, A. E., Délémontey, N. et al. (2019) Problems and questions posed by cryptic species: A framework to guide future studies. In: Casetta, E., da Silva, M. J., and Vecchi, D. (eds.) From Assessing to Conserving Biodiversity. Springer Publishing, New York, pp. 77–107.Google Scholar

Chipman, A. D. (ed.) (2020) Cellular Processes in Segmentation. CRC Press, Taylor & Francis, Boca Raton, FL, 299 pp.Google Scholar

Chun, J. and Rainey, F. A. (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. International Journal of Systematic Evolutionary Microbiology 64: 316–324.Google Scholar

Claßen-Bockhoff, R., Franke, D., and Krähmer, H. (2020) Early ontogeny defines the diversification of primary vascular bundle systems in angiosperms. Botanical Journal of the Linnean Society 195: 281–307.Google Scholar

Coates, D. J., Byrne, M., and Moritz, C. (2018) Genetic diversity and conservation units: Dealing with the species-population continuum in the age of genomics. Frontiers Ecology and Evolution 6: 165.Google Scholar

Corlett, R. T. (2016) Plant diversity in a changing world: Status, trends, and conservation needs. Plant Diversity 38: 10–16.Google Scholar

Costa, S. G. D. S., Welbourn, C., Klimov, P., and Pepato, A. R. (2021). Integrating phylogeny, ontogeny and systematics of the mite family Smarididae (Prostigmata, Parasitengona): Classification, identification key, and description of new taxa. Systematic and Applied Acarology 26: 85–123.Google Scholar

Crossman, C. A., Taylor, E. B., and Barrett-Lennard, L. G. (2016) Hybridization in the Cetacea: Widespread occurrence and associated morphological, behavioral, and ecological factors. Ecology and Evolution 6: 1293–1303.Google Scholar

Daeschler, E., Shubin, N., and Jenkins, F. (2006) A Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440: 757–763.Google Scholar

Danchin, E., Charmantier, A., and Champagne, F. C. et al. (2011) Beyond DNA: Integrating inclusive inheritance into an extended theory of evolution. Nature Revue Genetics 12: 475–486.Google Scholar

Danchin, E., Pocheville, A., Rey, O., Pujol, B., and Blanchet, S. (2019) Epigenetically facilitated mutational assimilation: Epigenetics as a hub within the inclusive evolutionary synthesis. Biological Reviews 94: 259–282.Google Scholar

Darlington, C. D. (1940) Taxonomic species and genetic systems. In Huxley, J. (ed.) The New Systematics. Oxford University Press, Oxford, pp. 137–160.Google Scholar

Darwin, C. (1859) On the Origin of Species by Means of Natural Selection. John Murray, London.Google Scholar

Dayrat, B. (2005) Toward integrative taxonomy. Biological Journal of the Linnean Society 85: 407–415.Google Scholar

Deline, B. et al. (2020) Evolution and development at the origin of a phylum.Current Biology 30: 1672–1679.Google Scholar

DeSalle, R. and Goldstein, P. (2019) Review and interpretation of trends in DNA Barcoding. Frontiers Ecology and Evolution 7: 302.Google Scholar

De Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology 56: 879–886.Google Scholar

Diamond, J. (1991) The Rise and Fall of the Third Chimpanzee: How Our Animal Heritage Affects the Way We Live. Hutchinson Radius, London, 364 pp.Google Scholar

Dias, B. G. and Ressler, K. J. (2013) Parental olfactory experience influences behavior and neural structure in subsequent generations. Nature Neuroscience 17: 89–96.Google Scholar

DiFrisco, J. and Jaeger, J. (2021) Homology of process: Developmental dynamics in comparative biology. Interface Focus 11: 20210007.Google Scholar

Domazet-Lošo, T. and Tautz, D. (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468: 815–818.CrossRef Google Scholar PubMed

Duboule, D. (1994) Temporal colinearity and the phylotypic progression: A basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony. Development Suppl: 135–142.Google Scholar

Durvasula, A. and Sankararaman, S. (2020) Recovering signals of ghost archaic introgression in African populations. Science Advance 6: eaax5097.Google Scholar

Eldredge, N. and Gould, S. J. (1972) Punctuated equilibria: An alternative to phyletic gradualism. In: Schopf, T. J. M. (ed.) Models in Paleobiology. Freeman Cooper, San Francisco, pp. 82–115.Google Scholar

Ereshefsky, M. (1998) Species pluralism and ‘anti-realism’. Philosophy of Science 65: 103–120.Google Scholar

Evans, J. S., Erwin, P. M., Sihaloho, H. F., and López- Legentil, S. (2021) Cryptic genetic lineages of a colonial ascidian host distinct microbiomes. Zoologica Scripta, https://doi.org/10.1111/zsc.12482.Google Scholar

Faria, L. R. R., Pie, M. R., Salles, F. F., and Soares, E. D. G. (2020) The Haeckelian shortfall or the tale of the missing semaphoronts. Journal of Zoologcial Systematics and Evolutionary Research, 1–11.Google Scholar

Fei, X., Shi, J., Liu, Y., Niu, J., and Wei, A. (2019) The steps from sexual reproduction to apomixis. Planta 249: 1715–1730.Google Scholar

Ferretti, L., Krämer-Eis, A., and Schifferet, P. H. (2020) Conserved patterns in developmental processes and phases, rather than genes, unite the highly divergent Bilateria. Life (Basel) 10: 182.Google Scholar

Fišer, C., Robinson, C. T., and Malard, F. (2018) Cryptic species as a window into the paradigm shift of the species concept. Molecular Ecology 27: 613–635.Google Scholar

Fowler, D. R., Meinhardt, H., and Prusinkiewicz, P. (1992) Modeling seashells. Proceedings SIGGRAPH’92. Computer Graphics 26: 379–387.Google Scholar

Fraga, M. F. et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. PNAS 26: 10604–10609.Google Scholar

Fraïsse, C., Belkhir, K., Welch, J. J., and Bierne, N. (2016) Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Molecular Ecology and Evolution 25: 269–286.CrossRef Google Scholar PubMed

Futuyma, D. J. and Kirkpatrick, M. (2017) Evolution. Fourth Edition. Sinauer, Associates, Inc., Publishers, Sunderland, MA, 599 pp.Google Scholar

Gante, H. F. (2018) How fish get their stripes-again and again. Science 362: 396–397.CrossRef Google Scholar

Gante, H. F., Matschiner, M., Malmstrøm, M. et al. (2016) Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Molecular Ecology 25: 6143–6161.CrossRef Google Scholar PubMed

Garcia-Dominguez, X., Marco-Jiménez, F., Peñaranda, D. S. et al. (2020) Long-term and transgenerational phenotypic, transcriptional and metabolic effects in rabbit males born following vitrified embryo transfer. Scientific Reports 10: 11313.CrossRef Google Scholar PubMed

Garstang, W. (1922) The theory of recapitulation: A critical restatement of the biogenetic law. Proceeding of the Linnean Society, Zoology 35: 81–101.Google Scholar

Gegenbaur, C. (1859) Grundzüge der vergleichenden Anatomie. Wilhelm Engelmann Verlag, Leipzig.Google Scholar

Gefaell, J., Varela, N., and Rolán-Alvarez, E. (2020) Comparing shape along growth trajectories in two marine snail ecotypes of Littorina saxatilis: A test of evolution by paedomorphosis. Journal of Molluscan Studies 86: 382–388.Google Scholar

Gee, B. M. (2020) Size matters: The effects of ontogenetic disparity on the phylogeny of Trematopidae (Amphibia: Temnospondyli). Zoological Journal of the Linnean Society 190: 79–113.Google Scholar

Ghiselin, M. (1974) A radical solution to the species problem. Systematic Zoology 23: 536–544.Google Scholar

Gilbert, S. F. (2010) Developmental Biology. Ninth ed. Sinauer Associates, Sunderland, MA, 711 pp.Google Scholar

Gilbert, S. F. (2019) Evolutionary transitions revisited: Holobiont evo‐devo. Journal of Experimental Zoology: 1–8.Google Scholar

Gilbert, S. F., Opitz, J. M., and Raff, R. A. (1996) Resynthesizing evolutionary and developmental biology. Developmental Biology 173: 357–372.Google Scholar

Gladyshev, E. A., Meselson, M., and Arkhipova, I. R. (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320: 1210–1213.Google Scholar

Glémin, S., François, C. M., and Galtier, N. (2019) Genome evolution in outcrossing vs. selfing vs. asexual species. In: Anisimova, M. (ed.) Evolutionary Genomics: Methods in Molecular Biology, vol. 1910. Humana, New York.Google Scholar

Glon, H., Haruka, Ya, Daly, M. et al. (2019) Temperature and salinity survival limits of the fluffy sea anemone, Metridium senile (L.), in Japan. Hydrobiologia 830: 303–315.Google Scholar

Göbbel, L. and Schultka, R. (2003) Meckel the Younger and his epistemology of organic form: morphology in the pre-Gegenbaurian age. Theory Bioscience 122: 127–141.Google Scholar

Gogarten, J. P. and Townsend, J. P. (2005) Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 3: 679–687.Google Scholar

Gómez Daglio, L. and Dawson, M. N. (2019). Integrative taxonomy: Ghosts of past, present and future. Journal of Marine Biological Association of United Kingdom 99: 1237–1246.Google Scholar

Gould, S. J. (1977) Ontogeny and Phylogeny. Harvard University Press, Cambridge, MA, 501 pp.Google Scholar

Graham, L. (2016) Lysenko’s Ghost: Epigenetics and Russia. Harvard University Press, Cambridge, MA, 224 pp.Google Scholar

Grant, P. R. and Grant, B. R. (2016) Introgressive hybridization and natural selection in Darwin’s finches. Biological Journal of the Linnean Society 117: 812–822.Google Scholar

Gregg, J. R. (1950) Taxonomy, language and reality. American Naturalist 84: 419–435.Google Scholar

Guiry, M. D. (2012) How many species of algae are there? Journal of Phycology 48: 1057–1063.Google Scholar

Haeckel, E. (1866) Generelle Morphologie der Organismen. Bd. 1–2. G. Reimer, Berlin, 574 S. 462 S.Google Scholar

Hall, B. K. (1999) Evolutionary Developmental Biology (2nd ed.). Kluwer Academic Publishers, Dordrecht, 491 pp.Google Scholar

Harrison, R. G. and Larson, E. L. (2014) Hybridization, introgression, and the nature of species boundaries. Journal of Heredity 105: 795–809.Google Scholar

Hauk, W. D. (1995) A molecular assessment of relationships among cryptic species of Botrychium subgenus Botrychium (Ophioglossaceae). American Fern Journal 85: 375–394.Google Scholar

Haupaix, N. and Manceau, M. (2020) The embryonic origin of periodic color patterns. Developmental Biology 460: 70–76.Google Scholar

Hawkins, J. (2002) Evolutionary developmental biology: Impact on systematic theory and practice, and the contribution of systematics. In: Developmental Genetics and Plant Evolution. Taylor and Francis, London, pp. 32–51.Google Scholar

Hawksworth, D. L. and Lücking, R. (2017) Fungal diversity revisited: 2.2 to 3.8 million species. Microbiology Spectrum 5: FUNK-0052-2016.Google Scholar

Henry, C. S. (1985) Sibling species, call differences, and speciation in green lacewings (Neuroptera: Chrysopidae: Chrysoperla). Evolution 39: 965–984.Google Scholar

Heethoff, M. (2018) Cryptic species: Conceptual or terminological chaos? Trends in Ecology & Evolution 33: 310.Google Scholar

Hennig, W. (1966) Phylogenetic Systematics. University of Illinois Press, Urbana, 263 pp.Google Scholar

Heratha, S. and Lobo, D. (2020) Cross-inhibition of Turing patterns explains the self-organized regulatory mechanism of planarian fission. Journal of Theoretical Biology 485: 110042.Google Scholar

Herrera, C. M. (2009) Multiplicity in Unity. University Chicago Press. 448 pp.Google Scholar

Herron, J. C. and Freeman, S. (2015) Evolutionary Analysis. Fifth Edition. Pearson Education Limited, London, 864 pp.Google Scholar

Hess, B. (2000) Periodic patterns in biology. Naturwissenschaften 87: 199–211.Google Scholar

Hey, J. (2001) The mind of the species problem. Trends in Ecology & Evolution 16: 326–329.Google Scholar

Hiebert, L. S., Simpson, C., and Tiozzo, S. (2020) Coloniality, clonality, and modularity in animals: The elephant in the room. Journal of Experimental Zoology Part B: 1–14.Google Scholar

Ho, M. W. (1992) Development, rational taxonomy and systematics. Rivista di Biologia-Biology Forum 85: 193–211.Google Scholar

Ho, W. K. W et al. (2019) Feather arrays are patterned by interacting signalling and cell density waves. PLoS Biology 17(2): e3000132.Google Scholar

Holeski, L. M., Jander, G., and Agrawal, A. A. (2012) Transgenerational defense induction and epigenetic inheritance in plants. Trends in Ecology & Evolution 27: 618–626.Google Scholar

Holland, P. W. H. (2013) Evolution of homeobox genes. WIREs Developmental Biology 2: 31–45.Google Scholar

Holliday, R. (2006) Epigenetics: A historical overview. Epigenetics 1: 76–80.Google Scholar

Horsáková, V., Nekola, J. C., and Horsák, M. (2019) When is a ‘cryptic’ species not a cryptic species: A consideration from the Holarctic micro-land snail genus Euconulus (Gastropoda: Stylommatophora). Molecular Phylogenetics and Evolution 132: 307–320.Google Scholar

Hörandl, E. et al. (2020) Genome evolution of asexual organisms and paradox of sex in eukaryotes. In: Pontarotti, P. (eds.) Evolutionary Biology: A Transdisciplinary Approach. Springer, Champaign, IL, pp. 133–167.Google Scholar

Huxley, J. (1942) Evolution: The Modern Synthesis. George Allen & Unwin Ltd., London, 645 pp.Google Scholar

ICTV. (2020) International Committee on Taxonomy of Viruses. www.ictvonline.org Google Scholar

ICZN. (1999) International Code of Zoological Nomenclature. The International Trust for Zoological Nomenclature, London.Google Scholar

Inaba, M. and Chuong, C. M. (2020) Avian pigment pattern formation: Developmental control of macro- (across the body) and micro- (within a feather) level of pigment patterns. Frontiers in Cellular and Developmental Biology 8: 620.Google Scholar

Irie, N. and Kuratani, S. (2011) Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis. Nature Communications 2: 248.Google Scholar

Irie, N. and Kuratani, S. (2014) The developmental hourglass model: A predictor of the basic body plan? Development 141: 4649–4655.Google Scholar

Irie, N. and Sehara-Fujisawa, A. (2007) The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information. BMC Biology 5: 1.Google Scholar

Jablonka, E. and Lamb, M. J. (2010) Transgenerational epigenetic inheritance. In: Pigliucci, M. and Müller, G. B. (eds.) Evolution, the Extended Synthesis. The MIT Press, Cambridge, MA, pp. 137–174.Google Scholar

Jacobs, G. S. et al. (2019) Multiple deeply divergent denisovan ancestries in Papuans. Cell 177: 1010–1021.Google Scholar

Jakob, W. and Schierwater, B. (2007) Changing hydrozoan bauplans by silencing hox-like genes. PLoS ONE 2(8): e69.Google Scholar

Jančúchová-Lásková, J., Landová, E., and Frynta, D. (2015) Experimental crossing of two distinct species of leopard geckos, Eublepharis angramainyu and E. macularius: Viability, fertility and phenotypic variation of the hybrids. PLoS ONE 10(12): e0143630.CrossRef Google Scholar

Jaron, K. S., Bast, J., Nowell, R. W. et al. (2021) Genomic features of parthenogenetic animals. Journal of Heredity 112: 19–33.Google Scholar

Jaspers, C. et al. (2020) Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 133: 81–87.Google Scholar

Jékely, G., Paps, J., and Nielsen, C. (2015) The phylogenetic position of ctenophores and the origin(s) of nervous systems. EvoDevo 6: 1.Google Scholar

Jirapatrasilp, P. et al. (2019) Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms. Molecular Phylogenetics and Evolution 139: 1–20.Google Scholar

Johnson, M. R., Barsh, G. S., and Mallarino, R. (2019) Periodic patterns in Rodentia: Development and evolution. Experimental Dermatology 28: 509–551.Google Scholar

Jorgensen, D. R., Wu, C. M., and Hariharan, S. (2020) Epidemiology of end‐stage renal failure among twins and diagnosis, management, and current outcomes of kidney transplantation between identical twins. American Journal of Transplantation 20: 761–768.Google Scholar

Jörger, K. M. and Schrödl, M. (2013) How to describe a cryptic species? Practical challenges of molecular taxonomy. Frontiers in Zoology 10: 59.Google Scholar

Jung, H. S. et al. (1998) Local inhibitory action of BMPs and their relationships with activators in feather formation: Implications for periodic patterning. Developmental Biology 196: 11–23.Google Scholar

Kalinka, A. T., Varga, K. M., Gerrard, D. T. et al. (2010) Gene expression divergence recapitulates the developmental hourglass model. Nature 468: 811–814.Google Scholar

Kapitanova, D. V. and Shkil, F. N. (2014) Effects of thyroid hormone level alterations on the development of supraneural series in zebrafish, Danio rerio. Journal of Applied Ichthyology 30: 821–824.Google Scholar

Karp, D. (2020) Detecting small and cryptic animals by combining thermography and a wildlife detection dog. Scientific Reports 10: 5220.Google Scholar

Kijewski, T. K., Zbawicka, M., Väinölä, R., and Wenne, R. (2006) Introgression and mitochondrial DNA heteroplasmy in the Baltic populations of mussels Mytilus trossulus and M. edulis. Marine Biology 149: 1371–1385.Google Scholar

Klingenberg, C. P. and Marugán-Lobón, J. (2013) Evolutionary covariation in geometric morphometric data: analyzing integration, modularity, and allometry in a phylogenetic context. Systematic Biology 62: 591–610.Google Scholar

Kluge, A. G. (1985) Ontogeny and phylogenetic systematics. Cladistics 1: 13–27.Google Scholar

Kluge, A. G. and Strauss, R. E. (1985) Ontogeny and systematics. Annual Review of Ecology Systematics 16: 247–268.Google Scholar

Knowlton, N. (1986) Cryptic and sibling species among the decapod Crustacea. Journal of Crustacean Biology 6: 356–363.Google Scholar

Knowlton, N. (1993) Sibling species in the sea. Annual Review of Ecology and Systematics 24: 189–216.Google Scholar

Koĉi, J. et al. (2020) No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets. Molecular Ecology 29: 3038–3055.CrossRef Google Scholar PubMed

Kocot, K. M., Poustka, A. J., Stöger, I., Halanych, K. M., and Schrödl, M. (2020) New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Scientific Reports 10: 101.Google Scholar

Kondo, S. and Miura, T. (2010) Reaction-diffusion model as a framework for understanding biological pattern formation. Science 329: 1616–1620.Google Scholar

Kondrashov, A. S. (2018) Through sex, nature is telling us something important. Trends in Genetics 34: 352–361.Google Scholar

Koonin, E. V. and Wolf, Yu. I. (2008) Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Research 36: 6688–6719.Google Scholar

Korshunova, T. A. and Martynov, A. V. (2020) Consolidated data on the phylogeny and evolution of the family Tritoniidae (Gastropoda: Nudibranchia) contribute to genera reassessment and clarify the taxonomic status of the neuroscience models Tritonia and Tochuina. PLoS ONE 15: e0242103.CrossRef Google Scholar PubMed

Korshunova, T. A., Martynov, A. V., and Picton, B. E (2017a) Ontogeny as an important part of integrative taxonomy in tergipedid aeolidaceans (Gastropoda: Nudibranchia) with a description of a new genus and species from the Barents Sea. Zootaxa 4324: 1–22.Google Scholar

Korshunova, T. A., Martynov, A. V., Bakken, T., and Picton, B. E. (2017b) External diversity is restrained by internal conservatism: New nudibranch mollusc contributes to the cryptic species problem. Zoologica Scripta 46: 683–692.Google Scholar

Korshunova, T. A. et al. (2017c) Polyphyly of the traditional family Flabellinidae affects a major group of Nudibranchia: aeolidacean taxonomic reassessment with descriptions of several new families, genera, and species (Mollusca, Gastropoda). ZooKeys 717: 1–139.Google Scholar

Korshunova, T. A., Lundin, K., Malmberg, K., Picton, B., and Martynov, A. V. (2018) First true brackish water nudibranch mollusc provides new insights for phylogeny and biogeography and reveals paedomorphosis-driven evolution. PLoS ONE 13(3): e0192177.Google Scholar

Korshunova, T. A. et al. (2019) Multilevel fine-scale diversity challenges the ‘cryptic species’ concept. Scientific Reports 9: 1–23.Google Scholar

Korshunova, T. A. et al. (2020a) The Emperor Cadlina, hidden diversity and gill cavity evolution: new insights for taxonomy and phylogeny of dorid nudibranchs (Mollusca: Gastropoda). Zoological Journal of the Linnean Society 189: 762–827.Google Scholar

Korshunova, T. A., Bakken, T., Grøtan, V. et al. (2020b). A synoptic review of the family Dendronotidae (Mollusca: Nudibranchia): A multilevel organismal diversity approach. Contribution to Zoology 90: 93–153.Google Scholar

Korshunova, T. A. et al. (2020c) Fine-scale species delimitation: Speciation in process and periodic patterns in nudibranch diversity. ZooKeys 917: 15–50.Google Scholar

Korshunova, T. A., Sanamyan, N. P., Sanamyan, K. E. et al. (2021) Biodiversity hotspot in cold waters: A review of the genus Cuthonella with descriptions of seven new species (Mollusca, Nudibranchia). Contributions to Zoology: 1–68.Google Scholar

Kumar, S., Filipski, A. J., Battistuzzi, F. U., Kosakovsky Pond, S. J., and Tamura, K. (2012) Statistics and truth in phylogenomics. Molecular Biology and Evolution 29: 457–472.Google Scholar

Kupferschmidt, K. and Cohen, J. (2020) Will novel virus go pandemic or be contained? Science 367: 610–611.Google Scholar

Lamsdell, J. C. (2020) A new method for quantifying heterochrony in evolutionary lineages. Paleobiology: 1–22.Google Scholar

Laskowski, K. L., Doran, C., Bierbach, D., Krause, J., and Wolf, M. (2019) Naturally clonal vertebrates are an untapped resource in ecology and evolution research. Nature Ecology and Evolution 3: 161–169.Google Scholar

Laumer, C. E. et al. (2019) Revisiting metazoan phylogeny with genomic sampling of all phyla. Proceedings of the Royal Society B 286: 20190831.Google Scholar

Lecointre, G., Schnell, N. K., and Teletchea, F. (2020) Hierarchical analysis of ontogenetic time to describe heterochrony and taxonomy of developmental stages. Scientific Reports 10: 19732.Google Scholar

Leebens-Mack, J. H. et al. (2019) One thousand plant transcriptomes and phylogenomics of green plants. Nature 574: 679–698.Google Scholar

León-Martínez, G. and Vielle-Calzada, J. P. (2019) Apomixis in flowering plants: Developmental and evolutionary considerations. Current Topics in Developmental Biology 131: 565–604.Google Scholar

Levin, M., Hashimshony, T., Wagner, F., and Yanai, I. (2012) Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell 22: 1101–1108.Google Scholar

Lherminier, P. and Solignac, M. (2005) De l’espèce. Syllepse. Paris, 694 pp.Google Scholar

Louca, S., Mazel, F., Doebeli, M., and Parfrey, L. W. (2019) A census-based estimate of Earth’s bacterial and archaeal diversity. PLoS Biology 17: e3000106.Google Scholar

Lotsy, J. P. (1906) Vorlesungen uber Deszendenztheorien mit besonderer Berücksichtigung der Botanischen Seite der Frage gehalten an der Reichsuniversität zu Leiden. Gustav Fischer, Jena, 384 S.Google Scholar

Majeský, L., Vašut, R. J., and Kitner, M. (2015) Genotypic diversity of apomictic microspecies of Taraxacum scanicum group (Taraxacum sect. Erythrosperma). Plant Systematics and Evolution 301: 2105–2124.Google Scholar

Malinsky, M., Svardal, H., Tyers, A. et al. (2018) Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nature Ecology and Evolution 2: 1940–1955.Google Scholar

Mallet, J. (2005) Hybridization as an invasion of the genome. Trends Ecology and Evolution 20: 229–237.Google Scholar

Martynov, A. V. (1994) Materials for revision of nudibranch molluscs of the family Corambidae (Gastropoda, Opisthobranchia). Part II. Origin. Zoologichesky Zhurnal 73: 36–43.Google Scholar

Martynov, A. V. (2009) From ontogeny to evolution: An expectation for changing current systematic paradigm. Trudy Zoologicheskogo Muzeya Moskovskogo Gosudarstvennogo Universiteta 50: 145–229.Google Scholar

Martynov, A. V. (2011a) Ontogenetic Systematics and a New Model of Evolution of Bilateria. KMK, Moscow, 286 pp.Google Scholar

Martynov, A. V. (2011b) From ‘tree-thinking’ to ‘cycle-thinking’: Ontogenetic systematics of nudibranch molluscs. Thalassas 27: 193–224.Google Scholar

Martynov, A. V. (2012a) Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology. Paleontological Journal 46: 833–864.Google Scholar

Martynov, A. V. (2012b) Ontogeny, systematics, and phylogenetics: Perspectives of future synthesis and a new model of evolution of Bilateria. Biological Bulletin 39: 393–401.Google Scholar

Martynov, A. V. (2013) Evolutionary history of Metazoa, ancestral status of Bilateria clonal reproduction, and semicolonial origin of Mollusca. Zhurnal Obshei Biologii 74: 201–240.Google Scholar

Martynov, A. V. (2014) Ontogeny as a Central Paradigm of Biology: Declarative Importance and Practical Underestimation. 3rd International Congress on Invertebrate Morphology, Berlin. Program and Abstract Book, pp. 128.Google Scholar

Martynov, A. V. and Korshunova, T. A. (2015) A new deep-sea genus of the family Polyceridae (Nudibranchia) possesses a gill cavity, with implications for cryptobranch condition and a ‘Periodic Table’ approach to taxonomy. Journal of Molluscan Studies 81: 365–379.Google Scholar

Martynov, A. V., Ishida, Y., Irimura, S. et al. (2015) When ontogeny matters: A new Japanese species of brittle star illustrates importance of considering both adult and juvenile characters in taxonomic practice. PLoS ONE 10: e0139463.Google Scholar

Martynov, A. V., Lundin, K., Picton, B. et al. (2020a) Multiple paedomorphic lineages of soft-substrate burrowing invertebrates: Parallels in the origin of Xenocratena and Xenoturbella. PLoS ONE 15(1): e0227173.Google Scholar

Martynov, A. V. et al. (2020b) Three new species of the genus Dendronotus from Japan and Russia (Mollusca, Nudibranchia). Zootaxa 4747: 495–513.Google Scholar

Mayer, F. and von Helversen, O. (2001) Cryptic diversity in European bats. Proceedings of the Royal Society London B 268: 1825–1832.Google Scholar

Maynard Smith, J. and Szathmáry, E. (1995) The Major Transitions in Evolution. Freeman, Oxford, 343 pp.Google Scholar

Mayr, E. (1942) Systematics and the Origin of Species. Columbia University Press, New York, 372 pp.Google Scholar

Mayr, E. (1963) Animal Species and Evolution. Harvard University Press, Cambridge, MA, 797 pp.Google Scholar

Meckel, J. F. (1811) Entwurf einer Darstellung der zwischen dem Embryozustände der höheren Tiere und dem permanenten der niederen stattfindenden Parallele. Carl Heinrich Reclam, Leipzig, pp. 1–60.Google Scholar

Mehnert, E. (1897) Kainogenese. Morphologische Arbeiten 7: 1–156.Google Scholar

Mendeleev, D. (1869) Über die Beziehungen der Eigenschaften zu den Atomgewichten der Elemente. Zeitschrift für Chemie 12: 405–406.Google Scholar

Miller, W. et al. (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. PNAS 109: E2382–E2390.Google Scholar

Minelli, A. (2007) Invertebrate taxonomy and evolutionary developmental biology. Zootaxa 1668: 55–60.Google Scholar

Minelli, A. (2009) Perspectives in Animal Phylogeny and Evolution. Oxford University Press, Oxford, 336 pp.Google Scholar

Minelli, A. (2015) EvoDevo and its significance for animal evolution and phylogeny. In: Wanninger, A. (ed.) Evolutionary Developmental Biology of Invertebrates, Vol. 1. Introduction, Non-Bilateria, Acoelomorpha, Xenoturbellida, Chaetognatha. Springer-Verlag, Vienna.Google Scholar

Minelli, A. (2020) Taxonomy needs pluralism, but a controlled and manageable one. Megataxa 1: 9–18.Google Scholar

Mishler, B. D. (2010) Species are not uniquely real biological entities. In: Ayala, F. and Arp, R. (eds.) Contemporary Debates in Philosophy of Biology. Wiley Blackwell, Weinheim, pp. 110–122.Google Scholar

Mishler, B. D. and Budd, A. F. (1990) Species and evolution in clonal organisms: Introduction. Systematic Botany 15: 79–85.Google Scholar

Mora, C., Tittensor, D. P., Adl, S. et al. (2011) How many species are there on Earth and in the Ocean? PLoS Biology 9: e1001127.Google Scholar

Moroz, L. et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510: 109–114.Google Scholar

Müller, F. (1864) Für Darwin. Verlag von Wilhelm Engelmann, Leipzig.Google Scholar

Müller, G. B. (1991) Experimental strategies in evolutionary embryology. American Zoologist 31: 605–615.Google Scholar

Neelapu, N. R. R., Dutta, T., and Challaet, S. (2019) Role of horizontal gene transfer in evolution of the plant genome. In: Villa, T. G. and Viñas, M. (eds.) Horizontal Gene Transfer. Springer Publishing, Champaign, IL, pp. 425.Google Scholar

Neiman, M., Lively, C. M., and Meirmans, S. (2017) Why sex? A pluralist approach revisited. Trends in Ecology and Evolution 32: 589–600.Google Scholar

Newman, S. A. (2010) Dynamical patterning modules. In: Pigliucci, M. and Müller, G. B. (eds.) Evolution, the Extended Synthesis. The MIT Press, Cambridge, MA, pp. 281–306.Google Scholar

Ninova, M., Ronshaugen, M., and Griffiths-Jones, S. (2014) Conserved temporal patterns of microRNA expression in Drosophila support a developmental hourglass model. Genome Biology and Evolution 6: 2459–2467.Google Scholar

O’Hara, T. D., Hugall, A. F., Thuy, B., Stöhr, S., and Martynov, A. V. (2017) Restructuring higher taxonomy using broadscale phylogenomics: The living Ophiuroidea. Molecular Phylogenetic and Evolution 107: 415–430.Google Scholar

Olsson, L., Levit, G. S., and Hossfeld, U. (2010) Evolutionary developmental biology: Its concepts and history with a focus on Russian and German contributions. Naturwissenschaften 97: 951–969.Google Scholar

Orton, G. R. (1955) The role of ontogeny in systematics and evolution. Evolution 9: 75–83.Google Scholar

Ottenburghs, J. (2020) Ghost introgression: Spooky gene flow in the distant past. BioEssays 42: 2000012.Google Scholar

Pääbo, S. (2014). Neanderthal Man: In Search of Lost Genomes. Basic Books, New York, 275 pp.Google Scholar

Pabst, E. A. and Kocot, K. M. (2018) Phylogenomics confirms monophyly of Nudipleura (Gastropoda: Heterobranchia). Journal of Molluscan Studies 84: 259–265.Google Scholar

Packard, A., Smotherman, C., and Jovanovic, N. (2020) Effect of circadian rhythm on the pain associated with preventive onabotulinumtoxinA injections for migraines. Chronobiology International 37: 1766–1771.Google Scholar

Padula, V., Bahia, J., Stöger, I. et al. (2016) A test of color-based taxonomy in nudibranchs: Molecular phylogeny and species delimitation of the Felimida clenchi (Mollusca: Chromodorididae) species complex. Molecular Phylogenetics and Evolution 103: 215–229.Google Scholar

Paterson, H. E. H. (1985) The recognition concept of species. In: Vrba, E. S. (ed.) Species and Speciation. Transvaal Museum Monograph No. 4., pp. 21–29.Google Scholar

Pellino, M. et al. (2013) Asexual genome evolution in apomictic Ranunculus auricomus complex: Examining the effects of hybridization and mutation accumulation. Molecular Ecology 22: 5908–5921.Google Scholar

Perez, M. and Lehner, B. (2019) Intergenerational and transgenerational epigenetic inheritance in animals. Nature Cell Biology 21: 143–151.Google Scholar

Phillips, J. D., Gillis, D. J., and Hanner, R. H. (2019) Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecology and Evolution 9: 2996–3010.Google Scholar

Piasecka, B. et al. (2013) The hourglass and the early conservation models: Co-existing patterns of developmental constraints in vertebrates. PLoS Genetics 9(4): e1003476.Google Scholar

Platania, L., Vodă, R., Dincă, V. et al. (2020) Integrative analyses on Western Palearctic Lasiommata reveal a mosaic of nascent butterfly species. Journal of Zoological Systematics and Evolutionary Research 58: 809–822.Google Scholar

Pleijel, F. (1999) Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Systematic Biology 48: 755–789.Google Scholar

Pollock, L. J., O’Connor, M. J., Mokany, K. et al. (2020) Protecting biodiversity (in all its complexity): New models and methods. Trends in Ecology and Evolution 35: 1119–1128.Google Scholar

Pradeu, T. (2012) The Limits of the Self: Immunology and Biological Identity. Oxford University Press, Oxford, 302 pp.Google Scholar

Pyykkö, P. (2019) An essay on periodic tables. Pure and Applied Chemistry 91: 1–10.Google Scholar

Queller, D. C. and Strassmann, J. E. (2009) Beyond society: The evolution of organismality. Philosophical Transactions of the Royal Society B 364: 3143–3155.Google Scholar

Quint, M. et al. (2012) A transcriptomic hourglass in plant embryogenesis. Nature 490: 98–101.Google Scholar

Raff, R. A. (1996) The Shape of Life. University of Chicago Press, Chicago, 520 pp.Google Scholar

Raff, R. A. and Kaufman, T. C. (1983) Embryos, Genes, and Evolution. Indiana University Press, Bloomington, 395 pp.Google Scholar

Ralston, A. and Shaw, K. (2008) Environment controls gene expression: Sex determination and the onset of genetic disorders. Nature Education 1: 203.Google Scholar

Raphaël, M. et al. (2016) Nomenclature for the nameless: A proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic Foraminifera. Systematic Biology 65: 925–940.Google Scholar

Raso, L. et al. (2014) Molecular identification of adult and juvenile linyphiid and theridiid spiders in Alpine glacier foreland communities. PLoS ONE 9(7): e101755.Google Scholar

Ratcliff, W. C., Denison, R. F., Borrello, M., and Travisano, M. (2012) Experimental evolution of multicellularity. PNAS 109: 1595–1600.Google Scholar

Redmond, A. K. and McLysaght, A. (2021) Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nature Communications 12: 1783.Google Scholar

Reilly, S. M., Wiley, E. O., and Meinhardt, D. J. (1997) An integrative approach to heterochrony: The distinction between interspecific and intraspecific phenomena. Biological Journal of the Linnean Society 60: 119–143.Google Scholar

Reiss, D. et al. (2019) Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot. PLoS Genetics 15(2): e1007965.Google Scholar

Reitzel, A. M., Burton, P. M., Krone, C., and Finnerty, J. R. (2007) Comparison of developmental trajectories in the starlet sea anemone Nematostella vectensis: Embryogenesis, regeneration, and two forms of asexual fission. Invertebrate Biology 126: 99–112.Google Scholar

Reydon, T. A. C. and Kunz, W. (2019) Species as natural entities, instrumental units and ranked taxa: New perspectives on the grouping and ranking problems. Biological Journal of the Linnean Society 126: 623–636.Google Scholar

Richards, R. A. (2010) The Species Problem. A Philosophical Analysis. Cambridge University Press, Cambridge, 236 pp.Google Scholar

Richards, R. J. (2009) Haeckel’s embryos: Fraud not proven. Biological Philosophy 24: 147–154.Google Scholar

Richter, S. and Wirkner, C. S. (2014). A research program for evolutionary morphology. Journal of Zoological Systematics and Evolutionary Research 52: 338–350.Google Scholar

Rieppel, O. (2006) The PhyloCode: A critical discussion of its theoretical foundation. Cladistics 22: 186–197.Google Scholar

Robilliard, G. A. (1970) The systematics and some aspects of the ecology of the genus Dendronotus (Gastropoda: Nudibranchia). The Veliger 12: 433–479.Google Scholar

Robson, G. C. and Richards, O. W. (1936) The Variation of Animals in Nature. Longmans, Green and Co, London, 425 pp.Google Scholar

Ros-Rocher, N., Pérez-Posada, A., Leger, M. M., and Ruiz-Trillo, I. (2021) The origin of animals: An ancestral reconstruction of the unicellular-to-multicellular transition. Open Biology 11: 200359.Google Scholar

Rosslenbroich, B. (2014) On the Origin of Autonomy: A New Look at the Major Transitions in Evolution. Springer International Publishing, Switzerland, 302 pp.Google Scholar

Rudman, W. B. (1984) The Chromodorididae (Opisthobranchia: Mollusca) of the Indo-West Pacific: A review of the genera. Zoological Journal of the Linnean Society 81: 115–273.Google Scholar

Sáez, A. G., Probert, I., Geisen, M. et al. (2003) Pseudo-cryptic speciation in coccolithophores. PNAS 100: 7163–7168.Google Scholar

Salis, P., Lorin, T., Laudet, V., and Frédérich, B. (2019) Magic traits in magic fish: Understanding color pattern evolution using reef fish. Trends in Genetics 35: 265–278.Google Scholar

Scerri, E. (2020) Recent attempts to change the periodic table. Philosophical Transactions of the Royal Society A 378: 20190300Google Scholar

Scheffers, B. R. et al. (2012) What we know and don’t know about Earth’s missing biodiversity. Trends in Ecology and Evolution, 27: 501–510.Google Scholar

Schimkewitsch, W. (1906) Über die Periodizität in den System der Pantopoda. Zoologischer Anzeiger 30: 1–22.Google Scholar

Schlick-Steiner, B. C., Steiner, F. M., Seifert, B. et al. (2010) Integrative taxonomy: A multisource approach to exploring biodiversity. Annual Review of Entomology 55: 421–438.Google Scholar

Scornavacca, C., Delsuc, F., and Galtier, N. (eds.) (2020) Phylogenetics in the Genomic Era. Authors open access book, hal-02535070, 568 pp.Google Scholar

Sharma, P. P., Clouse, R. M., and Wheeler, W. C. (2017) Hennig’s semaphoront concept and the use of ontogenetic stages in phylogenetic reconstruction. Cladistics 33: 93–108.Google Scholar

Sharma, R. and Bhat, V. (2020) Role of apomixis in perpetuation of flowering plants: ecological perspective. In: Tandon, R., Shivanna, K., and Koul, M. (eds.) Reproductive Ecology of Flowering Plants: Patterns and Processes. Springer, Singapore.Google Scholar

Sharp, N. P. and Otto, S. P. (2016) Evolution of sex: Using experimental genomics to select among competing theories. Bioessays 38: 751–757.Google Scholar

Simmonds, P. and Aiewsakun, P. (2018) Virus classification: Where do you draw the line? Archives of Virology 163: 2037–2046.Google Scholar

Simpson, C., Herrera-Cubilla, A., and Jackson, J. B. C. (2020) How colonial animals evolve. Science Advances 6: eaaw9530.Google Scholar

Slack, J. M. W., Holland, P. W. H., and Graham, C. F. (1993) The zootype and the phylotypic stage. Nature 361: 490–492.Google Scholar

Slater, M. (2013) Are Species Real? An Essay on the Metaphysics of Species. Palgrave Macmillan, London, 214 pp.Google Scholar

Smaczniak, C., Immink, R. G. H., and Angenent, G. C. (2012) Developmental and evolutionary diversity of plant MADS-domain factors: Insights from recent studies. Development 139: 3081–3098.Google Scholar

Stanton, D. W. G. et al. (2019) More grist for the mill? Species delimitation in the genomic era and its implications for conservation. Conservation Genetics 20: 101–113.Google Scholar

Stamos, D. N. (2003). The Species Problem: Biological Species, Ontology, and the Metaphysics of Biology. Lexington Press, 380 pp.Google Scholar

Stebbins, G. L. (1950) Variation and Evolution in Plants. Columbia University Press, New York, 643 pp.Google Scholar

Stebbins, G. L. (1980) Botany and the synthetic theory of evolution. In: Mayr, E. and Provine, W. B., The Evolutionary Synthesis: Perspectives on the Unification of Biology. Harvard University Press, Cambridge, MA, pp. 139–152.Google Scholar

Stenz, L., Schechter, D. S., Serpa, S. R. et al. (2018) Intergenerational transmission of DNA methylation signatures associated with early life stress. Current Genomics 19: 665–675.Google Scholar

Steyer, J. S. (2000) Ontogeny and phylogeny in temnospondyls: A new method of analysis. Zoological Journal of the Linnean Society 130: 449–467.Google Scholar

Stöhr, S. and Martynov, A. V. (2016) Paedomorphosis as an evolutionary driving force: Insights from deep-sea brittle stars. PLOS ONE 11: e0164562.Google Scholar

Stuefer, J. F., Gómez, S., and Van Mölken, T. (2004) Clonal integration beyond resource sharing: Implications for defence signalling and disease transmission in clonal plant networks. Evolution and Ecology 18: 647–667.Google Scholar

Sweatt, J. D. (2019) The epigenetic basis of individuality. Current Opinion in Behavioral Sciences 25: 51–56.Google Scholar

Templeton, A. R. (1989) The meaning of species and speciation: A genetic perspective. In: Otte, D. and Endler, J. A. (eds.) Speciation and Its Consequences. Sinauer Associates, Sunderland, MA, pp. 3–27.Google Scholar

Thielsch, A., Brede, N., Petrusek, A., de Meester, L., and Schwenk, K. (2009) Contribution of cyclic parthenogenesis and colonization history to population structure in Daphnia. Molecular Ecology 18: 1616–1628.Google Scholar

Thomson, W. (1st Baron Kelvin) (1900) Nineteenth century clouds over the dynamical theory of heat and light. Notices of Proceedings at Meetings of Members of Royal Institution of Great Britain 16: 363–397.Google Scholar

Thorpe, J. P., Beardmore, J. A., and Ryland, J. S. (1978) Genetic evidence for cryptic speciation in the marine bryozoan Alcyonidium gelatinosum. Marine Biology 49: 27–32.Google Scholar

Tikhomirova, A. L. (1990) Alteration of Ontogeny as Mechanism of Insect Evolution. Nauka, Moscow, 168 pp.Google Scholar

Turland, N. J. et al. (eds.) (2018) International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code). Regnum Vegetabile 159, Koeltz Botanical Books, Glashütten.Google Scholar

Uesaka, M., Kuratani, S., and Irie, N. (2021) The developmental hourglass model and recapitulation: An attempt to integrate the two models. Journal of Experimental Zoology: 1–11.Google Scholar

Vannier, N., Mony, C., Bittebiere, A. K. et al. (2019) Clonal plants as meta-holobionts. mSystems 4: e00213–18.Google Scholar

Varki, A. and Altheide, T. K. (2005) Comparing the human and chimpanzee genomes: Searching for needles in a haystack. Genome Research 151: 746–1758.Google Scholar

Vavilov, N. I. (1922) The law of homologous series in variation. Journal of Genetics 12: 47–89.Google Scholar

Vrba, E. (ed.) (1985) Species and speciation. Transvaal Museum Monograph No. 4: 73 pp.Google Scholar

Vrana, P. and Wheeler, W. (1992) Individual organisms as terminal entities: Laying the species problem to rest. Cladistics 8: 67–72.Google Scholar

Wägele, H. and Willan, R. C. (2000) Phylogeny of the Nudibranchia. Zoological Journal of the Linnean Society 130: 83–181.Google Scholar

Walker, T. J. (1964) Cryptic species among sound-producing ensiferan Orthoptera (Gryllidae and Tettigoniidae). Quarterly Review of Biology 39: 345–355.Google Scholar

Wang, S. S. and Ellington, A. D. (2019) Pattern generation with nucleic acid chemical reaction networks. Chemical Reviewers 119: 6370–6383.Google Scholar

Wanninger, A. (2015) Morphology is dead – long live morphology! Integrating MorphoEvoDevo into molecular EvoDevo and phylogenomics. Frontiers of Ecology and Evolution 3: 54.Google Scholar

West-Eberhard, M. J. (2003) Developmental Plasticity and Evolution. Oxford University Press, New York.Google Scholar

Wheeler, Q. D. and Meier, R. (eds.) (2000) Species Concepts and Phylogenetic Theory: A Debate. Columbia University Press, New York, 230 pp.Google Scholar

Willmann, R. and Meier, R. (2000) A critique from the Hennigian species concept perspective. In: Wheeler, Q. D. and Meier, R. (eds.) Species Concept and Phylogenetic Theory: A Debate. Columbia University Press, New York, pp. 101–118.Google Scholar

Wilding, C. S., Fletcher, N., Smith, E. et al. (2020) The genome of the sea anemone Actinia equina (L.): Meiotic toolkit genes and the question of sexual reproduction. Marine Genomics 53: 100753.Google Scholar

Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., and Embley, T. M. (2020) Phylogenomics provides robust support for a two-domains tree of life. Nature Ecology & Evolution 4: 138–147.Google Scholar

Wilkins, J. S. (2009) Species: A History of the Idea. University of California Press, Berkeley.Google Scholar

Willis, S. C. (2017) One species or four? Yes!…and, no. Or, arbitrary assignment of lineage to species obscures the diversification processes of Neotropical fishes. PLoS ONE 12: e0172349.Google Scholar

Winsor, M. P. (2006) Linnaeus’s biology was not essentialist. Annals of the Missouri Botanical Garden 93: 2–7.Google Scholar

Wolfe, J. M. and Hegna, T. A. (2013) Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages. Cladistics 30: 366–390.Google Scholar

Yang, Z. (2014). Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford, 492 pp.Google Scholar

Yehuda, R. et al. (2016) Holocaust exposure induced intergenerational effects on FKBP5 methylation. Biological Psychiatry 80: 372–380.Google Scholar

Yoshida, Yu., Nowell, R. W., Arakawa, K., and Blaxter, M. (2019) Horizontal gene transfer in Metazoa: examples and methods. In: Villa, T. G. and Viñas, M. (eds.) Horizontal Gene Transfer, Springer Nature, Switzerland, Cham, 220 pp.Google Scholar

Yoshikawa, H. et al. (2020) Effects of the global coronavirus disease-2019 pandemic on early childhood development: Short- and long-term risks and mitigating program and policy actions. The Journal of Pediatrics 223: 188–193.Google Scholar

Zachos, F. E. (2016) Species concepts in biology. Historical Development, Theoretical Foundations and Practical Relevance. Springer Nature, Switzerland, Cham, 220 pp.Google Scholar

Zachos, F. E. (2018) (New) Species concepts, species delimitation and the inherent limitations of taxonomy. Journal of Genetics 97: 811–815.Google Scholar

Zimmermann, W. (1959) Die Phylogenie der Pflanzen. Gustav Fischer Verlag, Stuttgart, 777 S.Google Scholar

Zirkle, C. (1959) Species before Darwin. Proceedings of the American Philosophical Society 103: 636–644.Google Scholar

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