Skip to main content Accessibility help
×
Hostname: page-component-586b7cd67f-t7czq Total loading time: 0 Render date: 2024-11-26T00:03:12.778Z Has data issue: false hasContentIssue false

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

Published online by Cambridge University Press:  01 September 2022

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

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.

Type
Chapter
Information
Cryptic Species
Morphological Stasis, Circumscription, and Hidden Diversity
, pp. 78 - 129
Publisher: Cambridge University Press
Print publication year: 2022

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Adams, M. J. et al. (2017) 50 years of the international committee on taxonomy of viruses: Progress and prospects. Archives of Virology 162: 14411446.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: 296317.CrossRefGoogle 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. 349374.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: 19.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: 757764.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. 343363.Google Scholar
Babaev, E. (2019) Periodic law in chemistry and other sciences. Pure and Applied Chemistry 91: 20232035.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: 8198.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: 212220.CrossRefGoogle ScholarPubMed
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: 303330.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: 682689.Google Scholar
Burma, B. H. (1954) Reality, existence, and classification: A discussion of the species problem. Madroño 12: 193209.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: 1430.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.CrossRefGoogle ScholarPubMed
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: 62096222.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: 2536.CrossRefGoogle Scholar
Casadesús, J. and Low, D. A. (2013) Programmed heterogeneity: Epigenetic mechanisms in Bacteria. Journal of Biological Chemistry 288: 1392913935.CrossRefGoogle ScholarPubMed
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. 77107.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: 316324.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: 281307.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: 1016.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: 85123.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: 12931303.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: 757763.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: 475486.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: 259282.Google Scholar
Darlington, C. D. (1940) Taxonomic species and genetic systems. In Huxley, J. (ed.) The New Systematics. Oxford University Press, Oxford, pp. 137160.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: 407415.Google Scholar
Deline, B. et al. (2020) Evolution and development at the origin of a phylum.Current Biology 30: 16721679.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: 879886.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: 8996.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: 815818.CrossRefGoogle ScholarPubMed
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: 135142.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. 82115.Google Scholar
Ereshefsky, M. (1998) Species pluralism and ‘anti-realism’. Philosophy of Science 65: 103120.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, 111.Google Scholar
Fei, X., Shi, J., Liu, Y., Niu, J., and Wei, A. (2019) The steps from sexual reproduction to apomixis. Planta 249: 17151730.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: 613635.Google Scholar
Fowler, D. R., Meinhardt, H., and Prusinkiewicz, P. (1992) Modeling seashells. Proceedings SIGGRAPH’92. Computer Graphics 26: 379387.Google Scholar
Fraga, M. F. et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. PNAS 26: 1060410609.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: 269286.CrossRefGoogle ScholarPubMed
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: 396397.CrossRefGoogle 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: 61436161.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Garstang, W. (1922) The theory of recapitulation: A critical restatement of the biogenetic law. Proceeding of the Linnean Society, Zoology 35: 81101.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: 382388.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: 79113.Google Scholar
Ghiselin, M. (1974) A radical solution to the species problem. Systematic Zoology 23: 536544.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: 18.Google Scholar
Gilbert, S. F., Opitz, J. M., and Raff, R. A. (1996) Resynthesizing evolutionary and developmental biology. Developmental Biology 173: 357372.Google Scholar
Gladyshev, E. A., Meselson, M., and Arkhipova, I. R. (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320: 12101213.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: 303315.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: 127141.Google Scholar
Gogarten, J. P. and Townsend, J. P. (2005) Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology 3: 679687.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: 12371246.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: 812822.Google Scholar
Gregg, J. R. (1950) Taxonomy, language and reality. American Naturalist 84: 419435.Google Scholar
Guiry, M. D. (2012) How many species of algae are there? Journal of Phycology 48: 10571063.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: 795809.Google Scholar
Hauk, W. D. (1995) A molecular assessment of relationships among cryptic species of Botrychium subgenus Botrychium (Ophioglossaceae). American Fern Journal 85: 375394.Google Scholar
Haupaix, N. and Manceau, M. (2020) The embryonic origin of periodic color patterns. Developmental Biology 460: 7076.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. 3251.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: 965984.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: 199211.Google Scholar
Hey, J. (2001) The mind of the species problem. Trends in Ecology & Evolution 16: 326329.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: 114.Google Scholar
Ho, M. W. (1992) Development, rational taxonomy and systematics. Rivista di Biologia-Biology Forum 85: 193211.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: 618626.Google Scholar
Holland, P. W. H. (2013) Evolution of homeobox genes. WIREs Developmental Biology 2: 3145.Google Scholar
Holliday, R. (2006) Epigenetics: A historical overview. Epigenetics 1: 7680.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: 307320.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. 133167.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.orgGoogle 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: 46494655.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. 137174.Google Scholar
Jacobs, G. S. et al. (2019) Multiple deeply divergent denisovan ancestries in Papuans. Cell 177: 10101021.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.CrossRefGoogle Scholar
Jaron, K. S., Bast, J., Nowell, R. W. et al. (2021) Genomic features of parthenogenetic animals. Journal of Heredity 112: 1933.Google Scholar
Jaspers, C. et al. (2020) Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. Zoology 133: 8187.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: 120.Google Scholar
Johnson, M. R., Barsh, G. S., and Mallarino, R. (2019) Periodic patterns in Rodentia: Development and evolution. Experimental Dermatology 28: 509551.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: 761768.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: 1123.Google Scholar
Kalinka, A. T., Varga, K. M., Gerrard, D. T. et al. (2010) Gene expression divergence recapitulates the developmental hourglass model. Nature 468: 811814.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: 821824.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: 13711385.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: 591610.Google Scholar
Kluge, A. G. (1985) Ontogeny and phylogenetic systematics. Cladistics 1: 1327.Google Scholar
Kluge, A. G. and Strauss, R. E. (1985) Ontogeny and systematics. Annual Review of Ecology Systematics 16: 247268.Google Scholar
Knowlton, N. (1986) Cryptic and sibling species among the decapod Crustacea. Journal of Crustacean Biology 6: 356363.Google Scholar
Knowlton, N. (1993) Sibling species in the sea. Annual Review of Ecology and Systematics 24: 189216.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: 30383055.CrossRefGoogle ScholarPubMed
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: 16161620.Google Scholar
Kondrashov, A. S. (2018) Through sex, nature is telling us something important. Trends in Genetics 34: 352361.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: 66886719.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.CrossRefGoogle ScholarPubMed
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: 122.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: 683692.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: 1139.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: 123.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: 762827.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: 93153.Google Scholar
Korshunova, T. A. et al. (2020c) Fine-scale species delimitation: Speciation in process and periodic patterns in nudibranch diversity. ZooKeys 917: 1550.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: 168.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: 457472.Google Scholar
Kupferschmidt, K. and Cohen, J. (2020) Will novel virus go pandemic or be contained? Science 367: 610611.Google Scholar
Lamsdell, J. C. (2020) A new method for quantifying heterochrony in evolutionary lineages. Paleobiology: 122.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: 161169.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: 679698.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: 565604.Google Scholar
Levin, M., Hashimshony, T., Wagner, F., and Yanai, I. (2012) Developmental milestones punctuate gene expression in the Caenorhabditis embryo. Developmental Cell 22: 11011108.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: 21052124.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: 19401955.Google Scholar
Mallet, J. (2005) Hybridization as an invasion of the genome. Trends Ecology and Evolution 20: 229237.Google Scholar
Martynov, A. V. (1994) Materials for revision of nudibranch molluscs of the family Corambidae (Gastropoda, Opisthobranchia). Part II. Origin. Zoologichesky Zhurnal 73: 3643.Google Scholar
Martynov, A. V. (2009) From ontogeny to evolution: An expectation for changing current systematic paradigm. Trudy Zoologicheskogo Muzeya Moskovskogo Gosudarstvennogo Universiteta 50: 145229.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: 193224.Google Scholar
Martynov, A. V. (2012a) Ontogenetic systematics: The synthesis of taxonomy, phylogenetics, and evolutionary developmental biology. Paleontological Journal 46: 833864.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: 393401.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: 201240.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: 365379.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: 495513.Google Scholar
Mayer, F. and von Helversen, O. (2001) Cryptic diversity in European bats. Proceedings of the Royal Society London B 268: 18251832.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. 160.Google Scholar
Mehnert, E. (1897) Kainogenese. Morphologische Arbeiten 7: 1156.Google Scholar
Mendeleev, D. (1869) Über die Beziehungen der Eigenschaften zu den Atomgewichten der Elemente. Zeitschrift für Chemie 12: 405406.Google Scholar
Miller, W. et al. (2012) Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. PNAS 109: E2382E2390.Google Scholar
Minelli, A. (2007) Invertebrate taxonomy and evolutionary developmental biology. Zootaxa 1668: 5560.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: 918.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. 110122.Google Scholar
Mishler, B. D. and Budd, A. F. (1990) Species and evolution in clonal organisms: Introduction. Systematic Botany 15: 7985.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: 109114.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: 605615.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: 589600.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. 281306.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: 24592467.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: 415430.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: 951969.Google Scholar
Orton, G. R. (1955) The role of ontogeny in systematics and evolution. Evolution 9: 7583.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: 259265.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: 17661771.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: 215229.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. 2129.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: 59085921.Google Scholar
Perez, M. and Lehner, B. (2019) Intergenerational and transgenerational epigenetic inheritance in animals. Nature Cell Biology 21: 143151.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: 29963010.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: 809822.Google Scholar
Pleijel, F. (1999) Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Systematic Biology 48: 755789.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: 11191128.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: 110.Google Scholar
Queller, D. C. and Strassmann, J. E. (2009) Beyond society: The evolution of organismality. Philosophical Transactions of the Royal Society B 364: 31433155.Google Scholar
Quint, M. et al. (2012) A transcriptomic hourglass in plant embryogenesis. Nature 490: 98101.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: 925940.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: 15951600.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: 119143.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: 99112.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: 623636.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: 147154.Google Scholar
Richter, S. and Wirkner, C. S. (2014). A research program for evolutionary morphology. Journal of Zoological Systematics and Evolutionary Research 52: 338350.Google Scholar
Rieppel, O. (2006) The PhyloCode: A critical discussion of its theoretical foundation. Cladistics 22: 186197.Google Scholar
Robilliard, G. A. (1970) The systematics and some aspects of the ecology of the genus Dendronotus (Gastropoda: Nudibranchia). The Veliger 12: 433479.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: 115273.Google Scholar
Sáez, A. G., Probert, I., Geisen, M. et al. (2003) Pseudo-cryptic speciation in coccolithophores. PNAS 100: 71637168.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: 265278.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: 501510.Google Scholar
Schimkewitsch, W. (1906) Über die Periodizität in den System der Pantopoda. Zoologischer Anzeiger 30: 122.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: 421438.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: 93108.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: 751757.Google Scholar
Simmonds, P. and Aiewsakun, P. (2018) Virus classification: Where do you draw the line? Archives of Virology 163: 20372046.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: 490492.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: 30813098.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: 101113.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. 139152.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: 665675.Google Scholar
Steyer, J. S. (2000) Ontogeny and phylogeny in temnospondyls: A new method of analysis. Zoological Journal of the Linnean Society 130: 449467.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: 647667.Google Scholar
Sweatt, J. D. (2019) The epigenetic basis of individuality. Current Opinion in Behavioral Sciences 25: 5156.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. 327.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: 16161628.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: 363397.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: 2732.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: 111.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: 7461758.Google Scholar
Vavilov, N. I. (1922) The law of homologous series in variation. Journal of Genetics 12: 4789.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: 6772.Google Scholar
Wägele, H. and Willan, R. C. (2000) Phylogeny of the Nudibranchia. Zoological Journal of the Linnean Society 130: 83181.Google Scholar
Walker, T. J. (1964) Cryptic species among sound-producing ensiferan Orthoptera (Gryllidae and Tettigoniidae). Quarterly Review of Biology 39: 345355.Google Scholar
Wang, S. S. and Ellington, A. D. (2019) Pattern generation with nucleic acid chemical reaction networks. Chemical Reviewers 119: 63706383.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. 101118.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: 138147.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: 27.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: 366390.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: 372380.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: 188193.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: 811815.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: 636644.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×