{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T04:02:25Z","timestamp":1773028945712,"version":"3.50.1"},"reference-count":224,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2020,7,5]],"date-time":"2020-07-05T00:00:00Z","timestamp":1593907200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005765","name":"Universidade de Lisboa","doi-asserted-by":"publisher","award":["DL57\/2016\/CP1479\/CT0066"],"award-info":[{"award-number":["DL57\/2016\/CP1479\/CT0066"]}],"id":[{"id":"10.13039\/501100005765","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/00678\/2020"],"award-info":[{"award-number":["UIDB\/00678\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["SFRH\/BPD\/89195\/2012"],"award-info":[{"award-number":["SFRH\/BPD\/89195\/2012"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UID\/FIL\/00678\/2019"],"award-info":[{"award-number":["UID\/FIL\/00678\/2019"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Information"],"abstract":"<jats:p>Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called \u201cDarwinian principles\u201d. Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. Because the \u201cDarwinian principles\u201d are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as \u201ctraits\u201d or \u201cproperties\u201d of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals.<\/jats:p>","DOI":"10.3390\/info11070352","type":"journal-article","created":{"date-parts":[[2020,7,6]],"date-time":"2020-07-06T03:19:27Z","timestamp":1594005567000},"page":"352","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Testing the \u201c(Neo-)Darwinian\u201d Principles against Reticulate Evolution: How Variation, Adaptation, Heredity and Fitness, Constraints and Affordances, Speciation, and Extinction Surpass Organisms and Species"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6382-7740","authenticated-orcid":false,"given":"Nathalie","family":"Gontier","sequence":"first","affiliation":[{"name":"Applied Evolutionary Epistemology Lab, Centro de Filosofia das Ci\u00eancias, Departamento de Hist\u00f3ria e Filosofia das Ci\u00eancias, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,7,5]]},"reference":[{"key":"ref_1","first-page":"104","article-title":"The epistemological roots of the \u2018Darwinian\u2019 principles: Changing motives in the foundation, hardening, and loosening of the Modern Synthesis","volume":"23","author":"Gontier","year":"2020","journal-title":"Kairos"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev.es.01.110170.000245","article-title":"The units of selection","volume":"1","author":"Lewontin","year":"1970","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"De Bary, A. (1879). Die Erscheinung der Symbiose: Vortrag, Gehalten auf der Versammlung Deutscher Natur-Forscher und Arzte zu Cassel, Verlag von Karl J. Tr\u00fcbner.","DOI":"10.1515\/9783111471839"},{"key":"ref_4","unstructured":"Van Beneden, P.J. (1875). Les Commensaux et les Parasites Dans le R\u00e8gne Animal, Biblio Sci Int."},{"key":"ref_5","first-page":"253","article-title":"Die Symbiose als Mittel der Synthese von Organismen","volume":"27","author":"Famintsyn","year":"1907","journal-title":"Biol. Zent."},{"key":"ref_6","unstructured":"Fet, V., and Margulis, L. (2010). Symbiogenesis: A New Principle of Evolution, Translated by V. Fet, Harvard University Press."},{"key":"ref_7","unstructured":"Margulis, L. (1998). The Symbiotic Planet, Basic Books."},{"key":"ref_8","first-page":"593","article-title":"\u00dcber Natur und Ursprung der Chromatophoren im Pflanzenreiche","volume":"25","author":"Merezhkowsky","year":"1905","journal-title":"Biol. Zent."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/0022-5193(67)90079-3","article-title":"On the origin of mitosing cells","volume":"14","author":"Sagan","year":"1967","journal-title":"J. Theor. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Wallin, I.E. (1927). Symbionticism and the Origin of Species, Williams and Wilkins.","DOI":"10.5962\/bhl.title.11429"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/nrg2386","article-title":"Horizontal gene transfer in eukaryotic evolution","volume":"9","author":"Keeling","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"R242","DOI":"10.1016\/j.cub.2011.01.045","article-title":"Lateral gene transfer","volume":"21","author":"Zhaxybayeva","year":"2011","journal-title":"Curr. Biol."},{"key":"ref_13","first-page":"27","article-title":"Infectious history","volume":"288","author":"Lederberg","year":"2003","journal-title":"Science"},{"key":"ref_14","unstructured":"Shapiro, J.A. (1983). Mobile Genetic Elements, Academic Press."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/nyas.14044","article-title":"No genome is an island: Toward a 21st century agenda for evolution","volume":"1447","author":"Shapiro","year":"2019","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/133462a0","article-title":"Origin of the angiosperms","volume":"133","author":"Anderson","year":"1934","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1086\/280872","article-title":"The significance of polyploidy in plant evolution","volume":"74","author":"Stebbins","year":"1940","journal-title":"Am. Nat."},{"key":"ref_18","first-page":"133","article-title":"Symbiogenesis: The holobiont as a unit of evolution","volume":"16","author":"Guerrero","year":"2013","journal-title":"Int. Microbiol."},{"key":"ref_19","unstructured":"Margulis, L., and Fester, R. (1991). Symbiogenesis and symbionticism. Symbiosis as a Source of Evolutionary Innovation, MIT Press."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Bapteste, E., and Huneman, P. (2018). Towards a dynamic interaction network of life to unify and expand the evolutionary theory. BMC Biol., 16.","DOI":"10.1186\/s12915-018-0531-6"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1126\/science.284.5423.2124","article-title":"Phylogenetic classification and the universal tree","volume":"284","author":"Doolittle","year":"1999","journal-title":"Science"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s12064-010-0100-1","article-title":"How symbiogenic is evolution?","volume":"129","year":"2010","journal-title":"Theor. Biosci."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/978-3-319-16345-1_3","article-title":"Can we understand evolution without symbiogenesis?","volume":"Volume 3","author":"Gontier","year":"2015","journal-title":"Reticulate Evolution"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Douglas, A.E. (2010). The Symbiotic Habit, Princeton University Press.","DOI":"10.1515\/9781400835430"},{"key":"ref_25","first-page":"272","article-title":"Symbiosis, History of","volume":"Volume 4","author":"Kliman","year":"2016","journal-title":"Encyclopedia of Evolutionary Biology"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"8627","DOI":"10.1073\/pnas.0611659104","article-title":"Symbiosis as an adaptive process and source of phenotypic complexity","volume":"104","author":"Moran","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Sapp, J. (1994). Evolution by Association: A History of Symbiosis, Oxford University Press.","DOI":"10.1093\/oso\/9780195088205.001.0001"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1139\/b04-055","article-title":"The dynamics of symbiosis: An historical overview","volume":"82","author":"Sapp","year":"2004","journal-title":"Can. J. Bot."},{"key":"ref_29","first-page":"250","article-title":"The classification of symbiotic phenomena","volume":"21","author":"McDougall","year":"1918","journal-title":"Plant. World"},{"key":"ref_30","unstructured":"Pfeffer, W. (1899). Physiology of Plants, English Edition Translated by AJ Ewart, Clarendon Press."},{"key":"ref_31","first-page":"779","article-title":"Un mot sur la vie sociale des animaux inf\u00e9rieurs","volume":"2","year":"1873","journal-title":"Bull. Acad. R. Belg."},{"key":"ref_32","unstructured":"Toynbee, A.J. (1947). A Study of History, Somervell Abridgement of Vols. I-VI., Oxford University Press."},{"key":"ref_33","unstructured":"Haskell, E. (1972). Generalization of the structure of Mendeleev\u2019s periodic table. Full Circle, The Moral Force of Unified Science, Gordon and Breach."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1086\/331473","article-title":"Hereditary symbiosis","volume":"59","author":"Cowles","year":"1915","journal-title":"Bot. Gaz."},{"key":"ref_35","first-page":"III","article-title":"Das erbliche Zusammenleben von Bakterien und tropischen Pflanzen","volume":"51","year":"1912","journal-title":"Jahrb. Wiss. Bot."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Buchner, P. (1921). Tier und Pflanze in Intrazellularer Symbiose, Gebr\u00fcder Borntraeger.","DOI":"10.5962\/bhl.title.1469"},{"key":"ref_37","unstructured":"Buchner, P. (1939). Symbiose der Tiere mit Pflanzlichen Mikroorganismen, De Gruyter."},{"key":"ref_38","first-page":"923","article-title":"The phenomena of symbiosis","volume":"1","author":"Schneider","year":"1897","journal-title":"Minn. Bot. Stud."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1071\/MA12111","article-title":"Even viruses can be beneficial microbes","volume":"33","author":"Roossinck","year":"2012","journal-title":"Microbiol. Aust."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1016\/j.jtbi.2009.10.014","article-title":"Viruses are essential agents within the roots and stem of the tree of life","volume":"262","author":"Villarreal","year":"2010","journal-title":"J. Theor. Biol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1126\/science.1675487","article-title":"Molecular biology of prion diseases","volume":"252","author":"Prusiner","year":"1991","journal-title":"Science"},{"key":"ref_42","unstructured":"Shapiro, J.A. (2011). Evolution: A View from the 21st Century, FT Press."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/sres.2191","article-title":"Systems theory and the role of synergy in the evolution of living systems","volume":"31","author":"Corning","year":"2014","journal-title":"Syst. Res."},{"key":"ref_44","first-page":"145","article-title":"Zur Kenntniss des Rhizoms von Corallorhiza und Epipogon","volume":"31","author":"Reinke","year":"1873","journal-title":"Flora"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Carrapi\u00e7o, F. (2006). The origins of life and the mechanisms of biological evolution. SPIE 6309, Instruments, Methods, and Missions for Astrobiology IX, Proceedings of the SPIE Optics + Photonics, San Diego, CA, USA, 14 September 2006, SPIE.Digital Library.","DOI":"10.1117\/12.681946"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Seckbach, J., and Grube, M. (2010). Azolla as a superorganism: Its implication in symbiotic studies. Symbioses and Stress, Springer.","DOI":"10.1007\/978-90-481-9449-0"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1152\/physrev.1952.32.4.403","article-title":"Cell genetics and hereditary symbiosis","volume":"32","author":"Lederberg","year":"1952","journal-title":"Physiol. Rev."},{"key":"ref_48","unstructured":"Koestler, A. (1967). The Ghost in the Machine, Penguin."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Sapp, J. (2003). Genesis: The Evolution of Biology, Oxford University Press.","DOI":"10.1093\/acprof:oso\/9780195156195.001.0001"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF01603792","article-title":"Beitr\u00e4ge zur Theorie der Evolution der Organismen I: Das typologische Grundgesetz und seine Folgerungen f\u00fcr Phylogenie und Entwicklungsphysiologie","volume":"7","year":"1943","journal-title":"Acta Biotheor."},{"key":"ref_51","unstructured":"Meyer-Abich, A. (1948). Naturphilosophie auf Neuen Wegen, Hippokrates-Verlag Marquardt."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Rosenberg, E., and Zilber-Rosenberg, I. (2013). The Hologenome Concept: Human, Animal and Plant Microbiota, Springer.","DOI":"10.1007\/978-3-319-13904-3"},{"key":"ref_53","first-page":"261","article-title":"Symbiogenesis, History of","volume":"Volume 4","author":"Kliman","year":"2016","journal-title":"Encyclopedia of Evolutionary Biology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"S164","DOI":"10.1086\/303291","article-title":"Tracing the thread of plastid diversity through the tapestry of life","volume":"154","author":"Delwiche","year":"1999","journal-title":"Am. Nat."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1046\/j.1529-8817.2001.01126.x","article-title":"Primary and secondary endosymbiosis and the origin of plastids","volume":"37","author":"McFadden","year":"2001","journal-title":"J. Phycol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"R514","DOI":"10.1016\/j.cub.2004.06.041","article-title":"Evolution: Red algal genome affirms a common origin of all plastids","volume":"14","author":"McFadden","year":"2004","journal-title":"Curr. Biol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"20140330","DOI":"10.1098\/rstb.2014.0330","article-title":"Endosymbiotic theories for eukaryote origin","volume":"370","author":"Martin","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1007\/s002390010215","article-title":"Viral eukaryogenesis: Was the ancestor of the nucleus a complex DNA virus?","volume":"53","year":"2001","journal-title":"J. Mol. Evol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.1126\/science.1142490","article-title":"Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes","volume":"317","author":"Clark","year":"2007","journal-title":"Science"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nrmicro.2017.137","article-title":"Functional horizontal gene transfer from bacteria to eukaryotes","volume":"16","author":"Husnik","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Ryan, F. (2009). Virolution, Harper Collins.","DOI":"10.1007\/978-3-8274-2542-3"},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Danchin, E. (2016). Lateral gene transfer in eukaryotes: Tip of the iceberg or of the ice cube?. BMC Biol., 14.","DOI":"10.1186\/s12915-016-0330-x"},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Ku, C., and Martin, W.F. (2016). A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: The 70% rule. BMC Biol., 14.","DOI":"10.1186\/s12915-016-0315-9"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1084\/jem.79.2.137","article-title":"Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a deoxyribonucleic acid fraction isolated from pneumococcus type III","volume":"79","author":"Avery","year":"1944","journal-title":"J. Exp. Med."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1017\/S0022172400031879","article-title":"The significance of pneumococcal types","volume":"27","author":"Griffith","year":"1928","journal-title":"J. Hyg. (Lond.)"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1128\/MMBR.67.2.277-301.2003","article-title":"Conjugative plasmid transfer in gram-positive bacteria","volume":"67","author":"Grohmann","year":"2003","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1038\/158558a0","article-title":"Gene recombination in E coli","volume":"158","author":"Lederberg","year":"1946","journal-title":"Nature"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/br.17.4.269-337.1953","article-title":"Lysogeny","volume":"17","author":"Lwoff","year":"1953","journal-title":"Bacteriol. Rev."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1093\/genetics\/41.1.142","article-title":"Transduction in Escherichia coli K-12","volume":"41","author":"Morse","year":"1956","journal-title":"Genetics"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1128\/jb.64.5.679-699.1952","article-title":"Genetic exchange in Salmonella","volume":"64","author":"Zinder","year":"1952","journal-title":"J. Bacteriol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/978-3-319-16345-1_5","article-title":"Historical and epistemological perspectives on what horizontal gene transfer mechanisms contribute to our understanding of evolution","volume":"Volume 3","author":"Gontier","year":"2015","journal-title":"Reticulate Evolution"},{"key":"ref_72","first-page":"68","article-title":"Disease and evolution","volume":"19","author":"Haldane","year":"1949","journal-title":"Ric. Sci. Suppl. A"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-3-319-16345-1_1","article-title":"Reticulate evolution everywhere","volume":"Volume 3","author":"Gontier","year":"2015","journal-title":"Reticulate Evolution"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1016\/j.cell.2009.11.042","article-title":"A Wolbachia symbiont in Aedes aegypti limits infection with dengue, Chikungunya, and Plasmodium","volume":"139","author":"Moreira","year":"2009","journal-title":"Cell"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1086\/668166","article-title":"A symbiotic view of life: We have never been individuals","volume":"87","author":"Gilbert","year":"2012","journal-title":"Q. Rev. Biol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1002\/(SICI)1099-1654(199904\/06)9:2<73::AID-RMV254>3.0.CO;2-5","article-title":"Time to consider the concept of a commensal virus?","volume":"9","author":"Griffiths","year":"1999","journal-title":"Rev. Med. Virol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1016\/j.tim.2013.07.001","article-title":"The human virome: New tools and concepts","volume":"21","author":"Lecuit","year":"2013","journal-title":"Trends Microbiol."},{"key":"ref_78","unstructured":"Sapp, J. (2009). The New Foundations of Evolution, Oxford University Press."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Tauber, A.I. (1994). The Immune Self: Theory or Metaphor?, Cambridge University Press.","DOI":"10.1017\/CBO9780511624957"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1086\/350398","article-title":"The species concept of Linnaeus","volume":"59","author":"Larson","year":"1969","journal-title":"Isis"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1094\/PHYTO-08-15-0184-RVW","article-title":"The role of hybridization in the evolution and emergence of new fungal plant pathogens","volume":"106","author":"Stukenbrock","year":"2016","journal-title":"Phytopathology"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/s41467-019-08809-7","article-title":"Hybridization is a recurrent evolutionary stimulus in wild yeast speciation","volume":"10","author":"Eberlein","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.tree.2015.04.010","article-title":"Hybrid zones: Windows on climate change","volume":"30","author":"Taylor","year":"2015","journal-title":"Trends Ecol. Evol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s40693-014-0016-0","article-title":"Genetic, morphological, and chemical patterns of plant hybridization","volume":"87","year":"2014","journal-title":"Rev. Chil. Hist. Nat."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nature05706","article-title":"Hybrid speciation","volume":"446","author":"Mallet","year":"2007","journal-title":"Nature"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1146\/annurev.ecolsys.28.1.359","article-title":"Hybrid origins of plant species","volume":"28","author":"Rieseberg","year":"1997","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Stebbins, G.L. (1950). Variation and Evolution in Plants, Columbia University Press.","DOI":"10.7312\/steb94536"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1111\/j.1420-9101.2012.02599.x","article-title":"Hybridization and speciation","volume":"26","author":"Abbott","year":"2013","journal-title":"J. Evol. Biol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Anderson, E. (1949). Introgressive Hybridization, Wiley.","DOI":"10.5962\/bhl.title.4553"},{"key":"ref_90","first-page":"278","article-title":"Theorie der zwei Plasmaarten als Grundlage der Symbiogenese, einer neuen Lehre von der Entstehung der Organismen","volume":"30","author":"Merezhkowsky","year":"1910","journal-title":"Biol. Zent."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/0303-2647(78)90023-0","article-title":"Protist classification and the kingdoms of organisms","volume":"10","author":"Whittaker","year":"1978","journal-title":"Biosystems"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/35082053","article-title":"Major fungal lineages are derived from lichen symbiotic ancestors","volume":"411","author":"Lutzoni","year":"2001","journal-title":"Nature"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.1095-8339.1988.tb00623.x","article-title":"The variety of fungal\u2013algal symbioses, their evolutionary significance, and the nature of lichens","volume":"96","author":"Hawksworth","year":"1988","journal-title":"Bot. J. Linn. Soc."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1146\/annurev.pp.42.060191.003005","article-title":"Functional aspects of Lichen symbiosis","volume":"42","author":"Honegger","year":"1991","journal-title":"Annu. Rev. Plant. Physiol. Plant. Mol. Biol."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Archibald, J.M., and Richards, T.A. (2010). Gene transfer: Anything goes in plant mitochondria. BMC Biol., 8.","DOI":"10.1186\/1741-7007-8-147"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1104\/pp.118.1.9","article-title":"Gene transfer from organelles to the nucleus: How much, what happens, and Why?","volume":"118","author":"Martin","year":"1998","journal-title":"Plant. Physiol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1093\/genetics\/38.1.51","article-title":"Genetic studies of lysogenicity in Escherichia coli","volume":"38","author":"Lederberg","year":"1953","journal-title":"Genetics"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1128\/jb.177.5.1247-1253.1995","article-title":"bor gene of phage lambda, involved in serum resistance, encodes a widely conserved outer membrane lipoprotein","volume":"177","author":"Barondess","year":"1995","journal-title":"J. Bacteriol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/1574-6968.12419","article-title":"Bacterial self-defense: How Escherichia coli evades serum killing","volume":"354","author":"Miajlovic","year":"2014","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1146\/annurev-pathmechdis-012419-032633","article-title":"Our conflict with transposable elements and its implications for human disease","volume":"15","author":"Burns","year":"2020","journal-title":"Annu. Rev. Pathol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1126\/science.69.1798.629","article-title":"Chromosome morphology of Zey mays","volume":"69","author":"McClintock","year":"1929","journal-title":"Science"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1073\/pnas.36.6.344","article-title":"The origin and behavior of mutable loci in maize","volume":"36","author":"McClintock","year":"1950","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0168-9525(89)90039-5","article-title":"Eukaryotic transposable elements and genome evolution","volume":"5","author":"Finnegan","year":"1989","journal-title":"Trends Genet."},{"key":"ref_104","unstructured":"Gregory, R. (2020, January 01). A Word about \u2018Junk DNA\u2019. Evolver Zone Genomicron. Available online: http:\/\/www.genomicron.evolverzone.com\/2007\/04\/word-about-junk-dna."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1038\/sj.cgt.7700493","article-title":"Viruses as gene delivery vectors: Application to gene function, target validation, and assay development","volume":"9","author":"Lotze","year":"2002","journal-title":"Cancer Gene Ther."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/hdy.2011.65","article-title":"Hybrid fitness, adaptation and evolutionary diversification: Lessons learned from Louisiana Irises","volume":"108","author":"Arnold","year":"2012","journal-title":"Heredity (Edinb.)"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"710","DOI":"10.1126\/science.1188021","article-title":"A draft sequence of the Neanderthal genome","volume":"328","author":"Green","year":"2010","journal-title":"Science"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1126\/science.aao1887","article-title":"A high-coverage Neandertal genome from Vindija Cave in Croatia","volume":"358","author":"Grote","year":"2017","journal-title":"Science"},{"key":"ref_109","first-page":"43","article-title":"The complete genome sequence of a Neanderthal from the Altai Mountains","volume":"505","author":"Racimo","year":"2013","journal-title":"Nature"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1016\/j.ajhg.2015.01.006","article-title":"Complex History of Admixture between Modern Humans and Neandertals","volume":"96","author":"Vernot","year":"2015","journal-title":"Am. J. Hum. Gene"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1534\/genetics.112.148213","article-title":"Higher Levels of Neanderthal Ancestry in East Asians than in Europeans","volume":"194","author":"Wall","year":"2013","journal-title":"Genetics"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.cell.2020.01.012","article-title":"Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals","volume":"180","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1126\/science.1245938","article-title":"Resurrecting Surviving Neandertal Lineages from Modern Human Genomes","volume":"343","author":"Vernot","year":"2014","journal-title":"Science"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.ajhg.2017.09.010","article-title":"The Contribution of Neanderthals to Phenotypic Variation in Modern Humans","volume":"101","author":"Dannemann","year":"2017","journal-title":"Am. J. Hum. Genet."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1242\/dev.120.7.1719","article-title":"Bacterial symbionts induce host organ morphogenesis during early postembryonic development of the squid Euprymna scolopes","volume":"120","author":"Montgomery","year":"1994","journal-title":"Development"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1146\/annurev-micro-091313-103654","article-title":"The importance of microbes in animal development: Lessons from the squid-vibrio symbiosis","volume":"68","year":"2014","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_117","first-page":"1394","article-title":"Emerging model systems: The Hawaiian bobtail squid (Euprymna scolopes) as a model to study the molecular basis of eukaryote-prokaryote mutualism and the development and evolution of morphological novelties in cephalopods","volume":"4","author":"Lee","year":"2009","journal-title":"Cold Spring Harb."},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1128\/JB.05926-11","article-title":"Sensor Kinase RscS Induces the Production of Antigenically Distinct Outer Membrane Vesicles That Depend on the Symbiosis Polysaccharide Locus in Vibrio fischeri","volume":"194","author":"Shibata","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1128\/JB.182.16.4578-4586.2000","article-title":"Vibrio fischeri lux Genes Play an Important Role in Colonization and Development of the Host Light Organ","volume":"182","author":"Visick","year":"2000","journal-title":"J. Bacteriol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1111\/1462-2920.12179","article-title":"The first engagement of partners in the Euprymna scolopes-Vibrio fischeri symbiosis is a two-step process initiated by a few environmental symbiont cells","volume":"15","author":"Altura","year":"2013","journal-title":"Environ. Microbiol."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.mib.2019.09.002","article-title":"The impact of Vibrio fischeri strain variation on host colonization","volume":"50","author":"Bongrand","year":"2019","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"e00165-18","DOI":"10.1128\/mSystems.00165-18","article-title":"Persistent Interactions with Bacterial Symbionts Direct Mature-Host Cell Morphology and Gene Expression in the Squid-Vibrio Symbiosis","volume":"3","author":"Kremer","year":"2018","journal-title":"mSystems"},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.chom.2013.07.006","article-title":"Initial symbiont contact orchestrates host-organ-wide transcriptional changes that prime tissue colonization","volume":"14","author":"Kremer","year":"2013","journal-title":"Cell Host Microbe"},{"key":"ref_124","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1128\/br.27.1.87-115.1963","article-title":"Infective Heredity of Multiple Drug Resistance in Bacteria","volume":"27","author":"Watanabe","year":"1963","journal-title":"Bacteriol. Rev."},{"key":"ref_125","doi-asserted-by":"crossref","unstructured":"Iwasaki, W., and Takagi, T. (2009). Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages. PLoS Genet., 5.","DOI":"10.1371\/journal.pgen.1000402"},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1093\/oxfordjournals.aje.a010288","article-title":"Sickle hemoglobin (HbS) allele and sickle cell disease: A HuGE review","volume":"151","author":"Yang","year":"2000","journal-title":"Am. J. Epidemiol."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Dieterich, W., Schink, M., and Zopf, Y. (2018). Microbiota in the Gastrointestinal Tract. Med. Sci., 6.","DOI":"10.3390\/medsci6040116"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"93","DOI":"10.2307\/1224513","article-title":"Natural hybridisation and fitness","volume":"50","author":"Arnold","year":"2001","journal-title":"TAXON"},{"key":"ref_129","first-page":"131","article-title":"\u00dcber Nichtmendelnde Vererbung","volume":"I","author":"Correns","year":"1928","journal-title":"Z. Indukt. Abstamm. Vererb."},{"key":"ref_130","first-page":"435","article-title":"Erwin Baur or Carl Correns: Who really created the theory of plastid inheritance?","volume":"91","author":"Hagemann","year":"2001","journal-title":"Am. Genet. Assoc."},{"key":"ref_131","first-page":"453","article-title":"Are bacteria the third partner of the Azolla-Anabaena symbiosis?","volume":"Volume 48","author":"Polsinelli","year":"1991","journal-title":"Advanced Structural Safety Studies"},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Shropshire, J.D., and Bordenstein, S. (2016). Speciation by Symbiosis: The Microbiome and Behavior. mBio, 7.","DOI":"10.1128\/mBio.01785-15"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1093\/genetics\/144.3.1063","article-title":"Wolbachia Infection and Cytoplasmic Incompatibility in Drosophila Species","volume":"144","author":"Bourtzis","year":"1996","journal-title":"Genetics"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1093\/genetics\/162.3.1313","article-title":"Interspecific transfer of Wolbachia between two lepidopteran insects expressing cytoplasmic incompatibility: A Wolbachia variant naturally infecting Cadra cautella causes male killing in Ephestia kuehniella","volume":"162","author":"Sasaki","year":"2002","journal-title":"Genetics"},{"key":"ref_135","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.1098\/rspb.1998.0402","article-title":"Evidence for widespread Wolbachia infection in isopod crustaceans: Molecular identification and host feminization","volume":"265","author":"Bouchon","year":"1998","journal-title":"Proc. R. Soc. B Boil. Sci."},{"key":"ref_136","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1038\/hdy.2008.126","article-title":"Mobile male-killer: Similar Wolbachia strains kill males of divergent Drosophila hosts","volume":"102","author":"Sheeley","year":"2009","journal-title":"Heredity"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1098\/rspb.1997.0052","article-title":"Horizontal transmission of parthenogenesis-inducing microbes in Trichogramma wasps","volume":"264","author":"Schilthuizen","year":"1997","journal-title":"Proc. R. Soc. B Boil. Sci."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1093\/oxfordjournals.molbev.a026084","article-title":"Phylogenetic evidence for horizontal transmission of Wolbachia in host-parasitoid associations","volume":"16","author":"Vavre","year":"1999","journal-title":"Mol. Boil. Evol."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1146\/annurev.micro.53.1.71","article-title":"Wolbachia Pipientis: Microbial Manipulator of Arthropod Reproduction","volume":"53","author":"Stouthamer","year":"1999","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/978-3-319-16345-1_4","article-title":"Novel Endosymbioses as a Catalyst of Fast Speciation","volume":"Volume 3","author":"Gontier","year":"2015","journal-title":"Reticulate Evolution"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1098\/rspb.1999.0698","article-title":"Male\u2014killingwolbachiain two species of insect","volume":"266","author":"Hurst","year":"1999","journal-title":"Proc. R. Soc. B Boil. Sci."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/nrmicro1969","article-title":"Wolbachia: Master manipulators of invertebrate biology","volume":"6","author":"Werren","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"ref_143","unstructured":"Archibald, J. (2014). One Plus One Equals One: Symbiosis and the Evolution of Complex Life, Oxford University Press."},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1073\/pnas.23.7.378","article-title":"Sex, Sex Inheritance and Sex Determination in Paramecium Aurelia","volume":"23","author":"Sonneborn","year":"1937","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1128\/br.38.2.113-163.1974","article-title":"Kappa and other endosymbionts in Paramecium aurelia","volume":"38","author":"Preer","year":"1974","journal-title":"Bacteriol. Rev."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"a023051","DOI":"10.1101\/cshperspect.a023051","article-title":"The Perinatal Microbiome and Pregnancy: Moving Beyond the Vaginal Microbiome","volume":"5","author":"Prince","year":"2015","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_147","first-page":"237ra65","article-title":"The Placenta Harbors a Unique Microbiome","volume":"6","author":"Aagaard","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"ref_148","doi-asserted-by":"crossref","unstructured":"Mesa, M.-D., Loureiro, B., Iglesia, I., Gonzalez, S.F., Oliv\u00e9, E.L., Garcia-Algar, O., Solana, M.J., Perez, M.J.C., Sainz, T., and Martinez, L. (2020). The Evolving Microbiome from Pregnancy to Early Infancy: A Comprehensive Review. Nutrients, 12.","DOI":"10.3390\/nu12010133"},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1055\/s-0029-1199190","article-title":"Bemerkungen \u00fcber die Immunit\u00e4t durch Vererbung und S\u00e4ugung","volume":"18","author":"Ehrlich","year":"1892","journal-title":"Deut. Med. Wochenschr."},{"key":"ref_150","doi-asserted-by":"crossref","unstructured":"Kordy, K., Gaufin, T., Mwangi, M., Li, F., Cerini, C., Lee, D.J., Adisetiyo, H., Woodward, C., Pannaraj, P.S., and Tobin, N.H. (2020). Contributions to human breast milk microbiome and enteromammary transfer of Bifidobacterium breve. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0219633"},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"e22994","DOI":"10.1002\/ajp.22994","article-title":"Diversity and temporal dynamics of primate milk microbiomes","volume":"81","author":"Kurata","year":"2019","journal-title":"Am. J. Primatol."},{"key":"ref_152","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1128\/JVI.73.2.1175-1185.1999","article-title":"Molecular Characterization and Placental Expression of HERV-W, a New Human Endogenous Retrovirus Family","volume":"73","author":"Blond","year":"1999","journal-title":"J. Virol."},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1128\/JVI.74.7.3321-3329.2000","article-title":"An Envelope Glycoprotein of the Human Endogenous Retrovirus HERV-W Is Expressed in the Human Placenta and Fuses Cells Expressing the Type D Mammalian Retrovirus Receptor","volume":"74","author":"Blond","year":"2000","journal-title":"J. Virol."},{"key":"ref_154","unstructured":"Darwin, C. (1876). The Effects of Cross- and Self-Fertilization in the Vegetable Kingdom, John Murrey."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/genetics\/33.5.439","article-title":"What Is \u2018Heterosis\u2019?","volume":"33","author":"Shull","year":"1948","journal-title":"Genetics"},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/genetics\/148.3.923","article-title":"90 years ago: The beginning of hybrid maize","volume":"148","author":"Crow","year":"1998","journal-title":"Genetics"},{"key":"ref_157","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.tplants.2009.12.003","article-title":"Molecular mechanisms of polyploidy and hybrid vigor","volume":"15","author":"Chen","year":"2010","journal-title":"Trends Plant Sci."},{"key":"ref_158","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1038\/1831654a0","article-title":"Canalization of Development and Genetic Assimilation of Acquired Characters","volume":"183","author":"Waddington","year":"1959","journal-title":"Nature"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1666\/0094-8373(2005)031[0133:TDOES]2.0.CO;2","article-title":"The dynamics of evolutionary stasis","volume":"31","author":"Eldredge","year":"2005","journal-title":"Paleobiology"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1002\/bdrc.20196","article-title":"Symbiosis and development: The hologenome concept","volume":"93","author":"Rosenberg","year":"2011","journal-title":"Birth Defects Res. Part C Embryo Today Rev."},{"key":"ref_161","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/374227a0","article-title":"The major evolutionary transitions","volume":"374","author":"Smith","year":"1995","journal-title":"Nature"},{"key":"ref_162","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/BF00140962","article-title":"Assessing evolutionary epistemology","volume":"1","author":"Bradie","year":"1986","journal-title":"Boil. Philos."},{"key":"ref_163","first-page":"1193","article-title":"Evolutionary Epistemology","volume":"I","author":"Buri","year":"2012","journal-title":"Encycl. Sci. Learn."},{"key":"ref_164","first-page":"515","article-title":"Evolutionary epistemology as a scientific method: A new look upon the units and levels of evolution debate","volume":"4","author":"Gontier","year":"2011","journal-title":"Theor. Biosci."},{"key":"ref_165","unstructured":"Wuppuluri, S., and Doria, F.A. (2018). On How Epistemology and Ontology Converge Through Evolution: The Applied Evolutionary Epistemological Approach. Extreme Events in Nature and Society, Springer."},{"key":"ref_166","first-page":"31","article-title":"Genome degeneration affects both extracellular and intracellular bacterial endosymbionts","volume":"8","author":"Feldhaar","year":"2009","journal-title":"J. Boil."},{"key":"ref_167","doi-asserted-by":"crossref","unstructured":"Fitzpatrick, D.A., E Logue, M., and Butler, G. (2008). Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol. Boil., 8.","DOI":"10.1186\/1471-2148-8-181"},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"186","DOI":"10.4161\/rna.27506","article-title":"Constraint and opportunity in genome innovation","volume":"11","author":"Shapiro","year":"2013","journal-title":"RNA Boil."},{"key":"ref_169","doi-asserted-by":"crossref","first-page":"797","DOI":"10.3389\/fmicb.2016.00797","article-title":"Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile \u201cFerrovum\u201d","volume":"7","author":"Ullrich","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_170","doi-asserted-by":"crossref","unstructured":"Caragata, E.P., Rocha, M.N., Pereira, T.N., Mansur, S.B., Dutra, H.L.C., and Moreira, L.A. (2019). Pathogen blocking in Wolbachia-infected Aedes aegypti is not affected by Zika and dengue virus co-infection. PLOS Negl. Trop. Dis., 13.","DOI":"10.1371\/journal.pntd.0007443"},{"key":"ref_171","unstructured":"Mayr, E. (1982). The Growth of Biological Thought, Harvard University Press."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.tree.2012.03.011","article-title":"Speciation by symbiosis","volume":"27","author":"Brucker","year":"2012","journal-title":"Trends Ecol. Evol."},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/s00248-002-0012-9","article-title":"Estimating Population Size and Transmission Bottlenecks in Maternally Transmitted Endosymbiotic Bacteria","volume":"44","author":"Mira","year":"2002","journal-title":"Microb. Ecol."},{"key":"ref_174","first-page":"1607","article-title":"The effect of Wolbachia versus genetic incompatibilities on reinforcement and speciation","volume":"59","author":"Telschow","year":"2005","journal-title":"Evolution"},{"key":"ref_175","unstructured":"Hoard, D., and Berlocher, S. (1998). Wolbachia and speciation. Endless Forms: Species and Speciation, Oxford University Press."},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.2307\/2409365","article-title":"Reproductive Isolation as a Consequence of Adaptive Divergence in Drosophila Pseudoobscura","volume":"43","author":"Dodd","year":"1989","journal-title":"Evolution"},{"key":"ref_177","doi-asserted-by":"crossref","first-page":"20051","DOI":"10.1073\/pnas.1009906107","article-title":"Commensal bacteria play a role in mating preference of Drosophila melanogaster","volume":"107","author":"Sharon","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_178","first-page":"173","article-title":"Axillary malodor production: A new mechanism","volume":"41","author":"Froebe","year":"1990","journal-title":"J. Soc. Cosmet. Chem."},{"key":"ref_179","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s40168-014-0064-3","article-title":"Mapping axillary microbiota responsible for body odours using a culture-independent approach","volume":"3","author":"Troccaz","year":"2015","journal-title":"Microbiome"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nrgastro.2015.137","article-title":"Gut microbiota: Ganoderma lucidum, a new prebiotic agent to treat obesity?","volume":"12","author":"Delzenne","year":"2015","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1007\/s11914-015-0287-7","article-title":"The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities","volume":"13","author":"Inglis","year":"2015","journal-title":"Curr. Osteoporos. Rep."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nm.4358","article-title":"Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention","volume":"23","author":"Liu","year":"2017","journal-title":"Nat. Med."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nature05414","article-title":"An obesity-associated gut microbiome with increased capacity for energy harvest","volume":"444","author":"Turnbaugh","year":"2006","journal-title":"Nature"},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.bbi.2018.09.026","article-title":"Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives","volume":"75","author":"Coello","year":"2019","journal-title":"Brain Behav. Immun."},{"key":"ref_185","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.jad.2017.11.063","article-title":"A meta-analysis of the use of probiotics to alleviate depressive symptoms","volume":"228","author":"Ng","year":"2018","journal-title":"J. Affect. Disord."},{"key":"ref_186","doi-asserted-by":"crossref","first-page":"S12","DOI":"10.1038\/518S13a","article-title":"Mental health: Thinking from the Gut","volume":"518","author":"Schmidt","year":"2015","journal-title":"Nature"},{"key":"ref_187","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1034\/j.1600-0706.2001.920103.x","article-title":"Nestmate recognition mediated by intestinal bacteria in a termite, Reticulitermes speratus","volume":"92","author":"Matsuura","year":"2001","journal-title":"Oikos"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"19832","DOI":"10.1073\/pnas.1306477110","article-title":"Symbiotic bacteria appear to mediate hyena social odors","volume":"110","author":"Theis","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"e05224","DOI":"10.7554\/eLife.05224","article-title":"Social networks predict gut microbiome composition in wild baboons","volume":"4","author":"Tung","year":"2015","journal-title":"eLife"},{"key":"ref_190","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.3390\/life5021405","article-title":"Horizontal Gene Transfer, Dispersal and Haloarchaeal Speciation","volume":"5","author":"Papke","year":"2015","journal-title":"Life"},{"key":"ref_191","doi-asserted-by":"crossref","first-page":"1514","DOI":"10.1093\/gbe\/evu123","article-title":"The extent of genome flux and its role in the differentiation of bacterial lineages","volume":"6","author":"Nowell","year":"2014","journal-title":"Genome Boil. Evol."},{"key":"ref_192","doi-asserted-by":"crossref","unstructured":"Serrato-Capuchina, A., and Matute, D.R. (2018). The Role of Transposable Elements in Speciation. Genes, 9.","DOI":"10.3390\/genes9050254"},{"key":"ref_193","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1111\/mec.13089","article-title":"Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species","volume":"24","author":"Stapley","year":"2015","journal-title":"Mol. Ecol."},{"key":"ref_194","doi-asserted-by":"crossref","first-page":"11171","DOI":"10.1128\/JVI.00021-12","article-title":"Cross-Species Transmission in the Speciation of the Currently Known Murinae-Associated Hantaviruses","volume":"86","author":"Lin","year":"2012","journal-title":"J. Virol."},{"key":"ref_195","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virol.2017.03.019","article-title":"Extensive diversity of coronaviruses in bats from China","volume":"507","author":"Lin","year":"2017","journal-title":"Virology"},{"key":"ref_196","doi-asserted-by":"crossref","first-page":"1967","DOI":"10.1056\/NEJMoa030747","article-title":"Identification of a Novel Coronavirus in Patients with Severe Acute Respiratory Syndrome","volume":"348","author":"Drosten","year":"2003","journal-title":"N. Engl. J. Med."},{"key":"ref_197","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1126\/science.1118391","article-title":"Bats Are Natural Reservoirs of SARS-Like Coronaviruses","volume":"310","author":"Li","year":"2005","journal-title":"Science"},{"key":"ref_198","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1056\/NEJMoa1211721","article-title":"Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia","volume":"367","author":"Zaki","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref_199","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1021\/acs.jproteome.0c00129","article-title":"Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1","volume":"19","author":"Zhang","year":"2020","journal-title":"J. Proteome Res."},{"key":"ref_200","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"ref_201","doi-asserted-by":"crossref","unstructured":"Arnold, M.L. (2014). Hybrid Speciation. Oxford Bibliographies Online Datasets, Oxford University Press (OUP).","DOI":"10.1093\/obo\/9780199941728-0005"},{"key":"ref_202","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1146\/annurev.arplant.043008.092039","article-title":"The Role of Hybridization in Plant Speciation","volume":"60","author":"Soltis","year":"2009","journal-title":"Annu. Rev. Plant Boil."},{"key":"ref_203","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/j.tree.2005.07.008","article-title":"Genome duplication and the origin of angiosperms","volume":"20","author":"Debodt","year":"2005","journal-title":"Trends Ecol. Evol."},{"key":"ref_204","doi-asserted-by":"crossref","first-page":"13875","DOI":"10.1073\/pnas.0811575106","article-title":"The frequency of polyploid speciation in vascular plants","volume":"106","author":"Wood","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_205","doi-asserted-by":"crossref","first-page":"6991","DOI":"10.1093\/jxb\/erv432","article-title":"Whole genome duplications in plants: An overview fromArabidopsis","volume":"66","year":"2015","journal-title":"J. Exp. Bot."},{"key":"ref_206","first-page":"82","article-title":"Solanum dulcamara and its inflorescence","volume":"11","author":"Turrill","year":"1935","journal-title":"Rep. Bot. Soc. Exch. Club Brit. Isles"},{"key":"ref_207","doi-asserted-by":"crossref","first-page":"262","DOI":"10.2307\/1438156","article-title":"Evolution the Modern Synthesis","volume":"1943","author":"Schmidt","year":"1943","journal-title":"Copeia"},{"key":"ref_208","first-page":"1","article-title":"A new evolutionary law","volume":"1","year":"1973","journal-title":"Evol. Theor."},{"key":"ref_209","unstructured":"Benton, M. (2005). When Life Nearly Died: The Greatest Mass Extinction of All Time, Thames and Hudson."},{"key":"ref_210","doi-asserted-by":"crossref","first-page":"10792","DOI":"10.1073\/pnas.94.20.10792","article-title":"Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death","volume":"94","author":"Min","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_211","doi-asserted-by":"crossref","first-page":"284","DOI":"10.3402\/tellusb.v35i4.14616","article-title":"Biological homeostasis of the global environment: The parable of Daisyworld","volume":"4","author":"Watson","year":"1983","journal-title":"Tellus B Chem. Phys. Meteorol."},{"key":"ref_212","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/j.jtbi.2010.12.042","article-title":"Symbiotic physiology promotes homeostasis in Daisyworld","volume":"274","author":"Boyle","year":"2011","journal-title":"J. Theor. Boil."},{"key":"ref_213","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1126\/science.1206360","article-title":"Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex","volume":"333","author":"Morran","year":"2011","journal-title":"Science"},{"key":"ref_214","doi-asserted-by":"crossref","first-page":"205","DOI":"10.3354\/esr003205","article-title":"Review: Extinction of microbes: Evidence and potential consequences","volume":"3","author":"Weinbauer","year":"2007","journal-title":"Endanger. Species Res."},{"key":"ref_215","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.1038\/s41559-018-0625-0","article-title":"Bacterial diversification through geological time","volume":"2","author":"Louca","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"ref_216","first-page":"93","article-title":"Emerging Disease and the Evolution of Virulence: The Case of the 1918\u20131919 Influenza Pandemic","volume":"Volume 7","author":"Huneman","year":"2014","journal-title":"Classification, Disease and Evidence"},{"key":"ref_217","unstructured":"World Health Organization (2019). Progress Report on HIV, Viral Hepatitis and Sexually Transmitted Infections 2019: Accountability for the Global Health Sector Strategies, 2016\u20132021, World Health Organization. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/324797."},{"key":"ref_218","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1177\/014107680409701202","article-title":"Human endogenous retroviruses in health and disease: A symbiotic perspective","volume":"97","author":"Ryan","year":"2004","journal-title":"J. R. Soc. Med."},{"key":"ref_219","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1146\/annurev.ecolsys.27.1.83","article-title":"Extinction by Hybridization and Introgression","volume":"27","author":"Rhymer","year":"1996","journal-title":"Annu. Rev. Ecol. Syst."},{"key":"ref_220","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1146\/annurev-genet-110410-132514","article-title":"The Genetics of Hybrid Incompatibilities","volume":"45","author":"Maheshwari","year":"2011","journal-title":"Annu. Rev. Genet."},{"key":"ref_221","doi-asserted-by":"crossref","unstructured":"Ereshefsky, M. (2001). The Poverty of the Linnaean Hierarchy: A Philosophical Study of Biological Taxonomy, Cambridge University Press.","DOI":"10.1017\/CBO9780511498459"},{"key":"ref_222","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1007\/s12052-011-0355-0","article-title":"Depicting the Tree of Life: The Philosophical and Historical Roots of Evolutionary Tree Diagrams","volume":"4","author":"Gontier","year":"2011","journal-title":"Evol. Educ. Outreach"},{"key":"ref_223","first-page":"345","article-title":"Tracking the Rules of Transmission and Introgression with Networks","volume":"6","author":"Vigliotti","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_224","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1007\/s12041-017-0792-9","article-title":"Co-niche construction between hosts and symbionts: Ideas and evidence","volume":"96","author":"Borges","year":"2017","journal-title":"J. Genet."}],"container-title":["Information"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2078-2489\/11\/7\/352\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:47:38Z","timestamp":1760176058000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2078-2489\/11\/7\/352"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,5]]},"references-count":224,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2020,7]]}},"alternative-id":["info11070352"],"URL":"https:\/\/doi.org\/10.3390\/info11070352","relation":{},"ISSN":["2078-2489"],"issn-type":[{"value":"2078-2489","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,5]]}}}