Eukaryote hybrid genomes

English version

Autoři: Anna Runemark ^aff001; Mario Vallejo-Marin ^aff002; Joana I. Meier ^aff003
Působiště autorů: Department of Biology, Lund University, Lund, Sweden ^aff001; Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom ^aff002; St John's College, Cambridge, Cambridge, United Kingdom ^aff003; Department of Zoology, University of Cambridge, Cambridge, United Kingdom ^aff004
Vyšlo v časopise: Eukaryote hybrid genomes. PLoS Genet 15(11): e32767. doi:10.1371/journal.pgen.1008404
Kategorie: Topic Page
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1008404

Souhrn

Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.

Klíčová slova:

Plant genomics – Genome evolution – Mammalian genomics – Polyploidy – Invertebrate genomics – Hybridization – Introgression – Hybrid speciation

Zdroje

1. Abbott R, Albach D, Ansell S, Arntzen J, Baird S, Bierne N, et al. (2013), "Hybridization and speciation", Journal of Evolutionary Biology 26 (2): 229–246, doi: 10.1111/j.1420-9101.2012.02599.x http://doi.wiley.com/10.1111/j.1420-9101.2012.02599.x 23323997

2. Fisher R (1930), The genetical theory of natural selection., Oxford: Clarendon Press, doi: 10.5962/bhl.title.27468 http://www.biodiversitylibrary.org/bibliography/27468

3. Mayr E (1963), Animal Species and Evolution:, Cambridge, MA and London, England: Harvard University Press, doi: 10.4159/harvard.9780674865327 ISBN 9780674865327, http://www.degruyter.com/view/books/harvard.9780674865327/harvard.9780674865327/harvard.9780674865327.xml

4. Stebbins G (1959), "The Role of Hybridization in Evolution", Proceedings of the American Philosophical Society 103 (2): 231–251, ISSN 0003-049X, https://www.jstor.org/stable/985151

5. Anderson E, Stebbins G. (1954), "Hybridization as an evolutionary stimulus", Evolution 8 (4): 378–388, doi: 10.1111/j.1558-5646.1954.tb01504.x ISSN 0014-3820, http://dx.doi.org/10.1111/j.1558-5646.1954.tb01504.x

6. Arnold M (1997), Natural Hybridization and Evolution., Cary: Oxford University Press, ISBN 9780195356687, OCLC 960164734, https://www.worldcat.org/oclc/960164734

7. Mallet J, Besansky N, Hahn M. (2016), "How reticulated are species?", BioEssays 38 (2): 140–149, doi: 10.1002/bies.201500149 PMC PMC4813508, 26709836, http://doi.wiley.com/10.1002/bies.201500149

8. Lamichhaney S, Han F, Webster M, Andersson L, Grant R, Grant P. (2018), "Rapid hybrid speciation in Darwin’s finches", Science 359 (6372): 224–228, doi: 10.1126/science.aao4593 ISSN 0036-8075, http://www.sciencemag.org/lookup/doi/10.1126/science.aao4593 29170277

9. Meier J, Marques D, Mwaiko S, Wagner C, Excoffier L, Seehausen O (2017), "Ancient hybridization fuels rapid cichlid fish adaptive radiations", Nature Communications 8 (1), doi: 10.1038/ncomms14363 ISSN 2041-1723, PMC PMC5309898, 28186104, http://www.nature.com/articles/ncomms14363

10. Mavárez J, Salazar C, Bermingham E, Salcedo C, Jiggins C, Linares M (2006), "Speciation by hybridization in Heliconius butterflies", Nature 441 (7095): 868–871, doi: 10.1038/nature04738 ISSN 0028-0836, http://www.nature.com/articles/nature04738 16778888

11. Salazar C, Baxter S, Pardo-Diaz C, Wu G, Surridge A, Linares M, et al. (2010), "Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies", PLoS Genetics 6 (4): e1000930, doi: 10.1371/journal.pgen.1000930 ISSN 1553-7404, PMC PMC2861694, 20442862, https://dx.plos.org/10.1371/journal.pgen.1000930

12. Melo M, Salazar C, Jiggins C, Linares M (2009), "Assortative mating preferences among hybrids offers a route to hybrid speciation", Evolution 63 (6): 1660–1665, doi: 10.1111/j.1558-5646.2009.00633.x http://doi.wiley.com/10.1111/j.1558-5646.2009.00633.x 19492995

13. Tarweeds & silverswords: evolution of the Madiinae (Asteraceae), Carlquist, S, Baldwin, B, Carr, G, St. Louis: Missouri Botanical Garden Press, 2003, ISBN 1930723202, OCLC 52892451, https://www.worldcat.org/oclc/52892451

14. Wolf D, Takebayashi N, Rieseberg L. (2001), "Predicting the Risk of Extinction through Hybridization", Conservation Biology 15 (4): 1039–1053, doi: 10.1046/j.1523-1739.2001.0150041039.x ISSN 0888-8892, http://doi.wiley.com/10.1046/j.1523-1739.2001.0150041039.x

15. Prentis P, White E, Radford I, Lowe A, Clarke A. (2007), "Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis?", New Phytologist 176 (4): 902–912, doi: 10.1111/j.1469-8137.2007.02217.x ISSN 0028-646X, http://doi.wiley.com/10.1111/j.1469-8137.2007.02217.x 17850249

16. Servedio M, Noor M. (2003), "The Role of Reinforcement in Speciation: Theory and Data", Annual Review of Ecology, Evolution, and Systematics 34 (1): 339–364, doi: 10.1146/annurev.ecolsys.34.011802.132412 ISSN 1543-592X, http://www.annualreviews.org/doi/10.1146/annurev.ecolsys.34.011802.132412

17. Rhymer J, Simberloff D(1996), "EXTINCTION BY HYBRIDIZATION AND INTROGRESSION", Annual Review of Ecology and Systematics 27 (1): 83–109, doi: 10.1146/annurev.ecolsys.27.1.83 ISSN 0066-4162, http://www.annualreviews.org/doi/10.1146/annurev.ecolsys.27.1.83

18. Seehausen O (2006), "Conservation: Losing Biodiversity by Reverse Speciation", Current Biology 16 (9): R334–R337, doi: 10.1016/j.cub.2006.03.080 https://linkinghub.elsevier.com/retrieve/pii/S0960982206014138 16682344

19. Thompson J. (1994), " Harrison R. G. (ed.). Hybrid Zones and the Evolutionary Process. Oxford University Press Oxford. 364 pp. Price f45.00. ISBN: 0-19-506917-X.", Journal of Evolutionary Biology 7 (5): 631–634, doi: 10.1046/j.1420-9101.1994.7050631.x ISSN 1010-061X, http://dx.doi.org/10.1046/j.1420-9101.1994.7050631.x

20. The Heliconius Genome Consortium (2012), "Butterfly genome reveals promiscuous exchange of mimicry adaptations among species", Nature 487(7405): 94–98, doi: 10.1038/nature11041 ISSN 0028-0836, PMC PMC3398145, 22722851, http://www.nature.com/articles/nature11041

21. Hanemaaijer M, Collier T, Chang A, Shott C, Houston P, Schmidt H, et al. (2018), "The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population", Molecular Ecology 27 (24): 4978–4990, doi: 10.1111/mec.14947 http://doi.wiley.com/10.1111/mec.14947 30447117

22. Coyne J, Orr A (2004), Speciation, Sunderland: Sinauer Associates, ISBN 0878930914, OCLC 55078441, https://www.worldcat.org/oclc/55078441

23. Price T, Bouvier M. (2002), [2083:teofpi2.0.co,2 "The evolution of F1 postzygotic incompatibilities in birds"], Evolution 56 (10): 2083, doi: 10.1554/0014-3820(2002)056[2083:teofpi]2.0.co,2 ISSN 0014-3820, http://dx.doi.org/10.1554/0014-3820(2002)056[2083:teofpi]2.0.co,2 12449494

24. Stelkens R, Young K, Seehausen O (2010), "The accumulation of reproductive incompatibilities in African cichlid fish", Evolution 64 (3): 617–633, doi: 10.1111/j.1558-5646.2009.00849.x http://doi.wiley.com/10.1111/j.1558-5646.2009.00849.x 19796149

25. Rebernig C, Lafon-Placette C, Hatorangan M, Slotte T, Köhler C (2015), "Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm", PLOS Genetics 11 (6): e1005295, doi: 10.1371/journal.pgen.1005295 ISSN 1553-7404, PMC PMC4472357, 26086217, https://dx.plos.org/10.1371/journal.pgen.1005295

26. Pritchard V, Knutson V, Lee M, Zieba J, Edmands S. (2013), "Fitness and morphological outcomes of many generations of hybridization in the copepod Tigriopus californicus", Journal of Evolutionary Biology 26 (2): 416–433, doi: 10.1111/jeb.12060 http://doi.wiley.com/10.1111/jeb.12060 23278939

27. Rieseberg L, Archer M, Wayne R. (1999), "Transgressive segregation, adaptation and speciation", Heredity 83 (4): 363–372, doi: 10.1038/sj.hdy.6886170 ISSN 0018-067X, http://dx.doi.org/10.1038/sj.hdy.6886170 10583537

28. Burke J, Arnold M. (2001), "Genetics and the Fitness of Hybrids", Annual Review of Genetics 35 (1): 31–52, doi: 10.1146/annurev.genet.35.102401.085719 ISSN 0066-4197, http://www.annualreviews.org/doi/10.1146/annurev.genet.35.102401.085719 11700276

29. Mallet J (2007), "Hybrid speciation", Nature 446 (7133): 279–283, doi: 10.1038/nature05706 ISSN 0028-0836, http://www.nature.com/articles/nature05706 17361174

30. Vallejo‐Marín M, Hiscock S. (2016), "Hybridization and hybrid speciation under global change", New Phytologist 211 (4): 1170–1187, doi: 10.1111/nph.14004 ISSN 0028-646X, https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.14004 27214560

31. Barton N, Bengtsson B (1986), "The barrier to genetic exchange between hybridising populations", Heredity 57 (3): 357–376, doi: 10.1038/hdy.1986.135 ISSN 0018-067X, http://www.nature.com/articles/hdy1986135 3804765

32. Demon I, Haccou P, van den Bosch F (2007), "Introgression of resistance genes between populations: A model study of insecticide resistance in Bemisia tabaci", Theoretical Population Biology 72 (2): 292–304, doi: 10.1016/j.tpb.2007.06.005 https://linkinghub.elsevier.com/retrieve/pii/S0040580907000731 17658572

33. Uecker H, Setter D, Hermisson J (2015), "Adaptive gene introgression after secondary contact", Journal of Mathematical Biology 70 (7): 1523–1580, doi: 10.1007/s00285-014-0802-y ISSN 0303-6812, PMC PMC4426140, 24992884, http://link.springer.com/10.1007/s00285-014-0802-y

34. Pardo-Diaz C, Salazar C, Baxter S, Merot C, Figueiredo-Ready W, Joron M, et al. (2012), "Adaptive Introgression across Species Boundaries in Heliconius Butterflies", PLoS Genetics 8 (6): e1002752, doi: 10.1371/journal.pgen.1002752 ISSN 1553-7404, PMC PMC3380824, 22737081, http://dx.plos.org/10.1371/journal.pgen.1002752

35. Arnold B, Lahner B, DaCosta J, Weisman C, Hollister J, Salt D, et al. (2016), "Borrowed alleles and convergence in serpentine adaptation", Proceedings of the National Academy of Sciences 113 (29): 8320–8325, doi: 10.1073/pnas.1600405113 ISSN 0027-8424, PMC PMC4961121, 27357660, http://www.pnas.org/lookup/doi/10.1073/pnas.1600405113

36. Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E (2015), "Evidence for archaic adaptive introgression in humans", Nature Reviews Genetics 16 (6): 359–371, doi: 10.1038/nrg3936 ISSN 1471-0056, PMC PMC4478293, 25963373, http://www.nature.com/articles/nrg3936

37. Kronforst M, Papa R. (2015), "The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry", Genetics 200 (1): 1–19, doi: 10.1534/genetics.114.172387 ISSN 0016-6731, PMC PMC4423356, 25953905, http://www.genetics.org/cgi/doi/10.1534/genetics.114.172387

38. Mérot C, Salazar C, Merrill R, Jiggins C, Joron M. (2017), "What shapes the continuum of reproductive isolation? Lessons from Heliconius butterflies", Proceedings of the Royal Society B: Biological Sciences 284 (1856): 20170335, doi: 10.1098/rspb.2017.0335 ISSN 0962-8452, PMC PMC5474069, 28592669, https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0335

39. Schumer M, Rosenthal G, Andolfatto P (2014), "How common is homoploid hybrid speciation", Evolution 68 (6): 1553–1560, doi: 10.1111/evo.12399 http://doi.wiley.com/10.1111/evo.12399 24620775

40. Feliner N, Álvarez I, Fuertes-Aguilar J, Heuertz M, Marques I, Moharrek Fet al. (2017), "Is homoploid hybrid speciation that rare? An empiricist’s view", Heredity 118 (6): 513–516, doi: 10.1038/hdy.2017.7 ISSN 0018-067X, PMC PMC5436029, 28295029, http://www.nature.com/articles/hdy20177

41. Rieseberg L. (2003), "Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization", Science 301 (5637): 1211–1216, doi: 10.1126/science.1086949 ISSN 0036-8075, http://www.sciencemag.org/cgi/doi/10.1126/science.1086949 12907807

42. Grant V. (1981), Plant speciation (2nd ed ed.), New York: Columbia University Press, ISBN 0231051123, OCLC 7552165, https://www.worldcat.org/oclc/7552165

43. Schumer M, Xu C, Powell D, Durvasula A, Skov L, Holland C, et al. (2018), "Natural selection interacts with recombination to shape the evolution of hybrid genomes", Science 360 (6389): 656–660, doi: 10.1126/science.aar3684 ISSN 0036-8075, PMC PMC6069607, 29674434, http://www.sciencemag.org/lookup/doi/10.1126/science.aar3684

44. Runemark A, Trier C, Eroukhmanoff F, Hermansen J, Matschiner M, Ravinet M et al. (2018), "Variation and constraints in hybrid genome formation", Nature Ecology & Evolution 2(3): 549–556, doi: 10.1038/s41559-017-0437-7 ISSN 2397-334X, http://dx.doi.org/10.1038/s41559-017-0437-7 29335572

45. Buerkle A, Rieseberg L. (2008), "The rate of genome stabilization in homoploid hybrid species", Evolution 62 (2): 266–275, doi: 10.1111/j.1558-5646.2007.00267.x ISSN 0014-3820, PMC PMC2442919, 18039323, http://doi.wiley.com/10.1111/j.1558-5646.2007.00267.x

46. Ungerer M, Baird S, Pan J, Rieseberg L. (1998), "Rapid hybrid speciation in wild sunflowers", Proceedings of the National Academy of Sciences 95 (20): 11757–11762, doi: 10.1073/pnas.95.20.11757 ISSN 0027-8424, PMC PMC21713, 9751738, http://www.pnas.org/cgi/doi/10.1073/pnas.95.20.11757

47. Lai Z, Nakazato T, Salmaso M, Burke J, Tang S, Knapp S, Rieseberg L (2005), "Extensive Chromosomal Repatterning and the Evolution of Sterility Barriers in Hybrid Sunflower Species", Genetics171 (1): 291–303, doi: 10.1534/genetics.105.042242 ISSN 0016-6731, PMC PMC1456521, 16183908, http://www.genetics.org/lookup/doi/10.1534/genetics.105.042242

48. Elgvin T, Trier C, Tørresen O, Hagen I, Lien S, Nederbragt A, et al. (2017), "The genomic mosaicism of hybrid speciation", Science Advances 3 (6): e1602996, doi: 10.1126/sciadv.1602996 ISSN 2375-2548, PMC PMC5470830, 28630911, http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1602996

49. Runemark A, Trier C, Eroukhmanoff F, Hermansen J, Matschiner M, Ravinet M et al. (2018), "Variation and constraints in hybrid genome formation", Nature Ecology & Evolution 2 (3): 549–556, doi: 10.1038/s41559-017-0437-7 ISSN 2397-334X, http://www.nature.com/articles/s41559-017-0437-7 29335572

50. Otto S, Whitton J (2000), "Polyploid Incidence and Evolution", Annual Review of Genetics 34 (1): 401–437, doi: 10.1146/annurev.genet.34.1.401, ISSN 0066-4197, http://www.annualreviews.org/doi/10.1146/annurev.genet.34.1.401 11092833

51. Abbott, R, Rieseberg, L (2012), John Wiley & Sons, Ltd, ed., "Hybrid Speciation", eLS (John Wiley & Sons, Ltd), doi: 10.1002/9780470015902.a0001753.pub2 ISBN 9780470016176, http://doi.wiley.com/10.1002/9780470015902.a0001753.pub2

52. Coyne J (1989), "Mutation rates in hybrids between sibling species of Drosophila", Heredity 63 (2): 155–162, doi: 10.1038/hdy.1989.87 ISSN 0018-067X, http://dx.doi.org/10.1038/hdy.1989.87 2553645

53. Chase M, Paun O, Fay M (2010), "Hybridization and speciation in angiosperms: arole for pollinator shifts?", Journal of Biology 9 (3): 21, doi: 10.1186/jbiol231 ISSN 1475-4924, http://jbiol.biomedcentral.com/articles/10.1186/jbiol231

54. Grant V (1949), "Pollination systems as isolating mechanisms in angiosperms", Evolution 3 (1): 82–97, doi: 10.1111/j.1558-5646.1949.tb00007.x http://doi.wiley.com/10.1111/j.1558-5646.1949.tb00007.x 18115119

55. Segraves K, Thompson J (1999), "Plant polyploidy and pollination: floral traits and insect visits to diploid and tetraploid Heuchera grossulariifolia", Evolution53 (4): 1114–1127, doi: 10.1111/j.1558-5646.1999.tb04526.x http://doi.wiley.com/10.1111/j.1558-5646.1999.tb04526.x 28565509

56. Moe A, Weiblen G. (2012), "Pollinator-mediated reproductive isolation among dioecious fig species (Ficus, Moraceae)", Evolution 66 (12): 3710–3721, doi: 10.1111/j.1558-5646.2012.01727.x http://doi.wiley.com/10.1111/j.1558-5646.2012.01727.x 23206130

57. Lowe A, Abbott R (2004), "Reproductive isolation of a new hybrid species, Senecio eboracensis Abbott & Lowe (Asteraceae)", Heredity 92 (5): 386–395, doi: 10.1038/sj.hdy.6800432 ISSN 0018-067X, http://www.nature.com/articles/6800432 15014422

58. Selz O, Thommen R, Maan M, Seehausen O. (2014), "Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish", Journal of Evolutionary Biology 27 (2): 275–289, doi: 10.1111/jeb.12287 http://doi.wiley.com/10.1111/jeb.12287 24372872

59. Schwarzbach A, Donovan L, Rieseberg L. (2001), "Transgressive character expression in a hybrid sunflower species", American Journal of Botany 88 (2): 270–277, doi: 10.2307/2657018 ISSN 0002-9122, http://dx.doi.org/10.2307/2657018 11222249

60. Mameli G, López-Alvarado J, Farris E, Alfonso S, Filigheddu R, Garcia-Jacas N (2014), "The role of parental and hybrid species in multiple introgression events: evidence of homoploid hybrid speciation in Centaurea (Cardueae, Asteraceae): Introgression in Centaurea", Botanical Journal of the Linnean Society 175 (3): 453–467, doi: 10.1111/boj.12177 https://academic.oup.com/botlinnean/article-lookup/doi/10.1111/boj.12177

61. Xie X, Michel A, Schwarz D, Rull J, Velez S, Forbes, et al. (2008), "Radiation and divergence in the Rhagoletis Pomonella species complex: inferences from DNA sequence data", Journal of Evolutionary Biology 21 (3): 900–913, doi: 10.1111/j.1420-9101.2008.01507.x ISSN 1010-061X, http://doi.wiley.com/10.1111/j.1420-9101.2008.01507.x 18312319

62. Feder J, Xie X, Rull J, Velez S, Forbes A, Leung B, et al. (2005), "Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis", Proceedings of the National Academy of Sciences102 (Supplement 1): 6573–6580, doi: 10.1073/pnas.0502099102 ISSN 0027-8424, PMC PMC1131876, 15851672, http://www.pnas.org/cgi/doi/10.1073/pnas.0502099102

63. Schumer, Molly, Powell, Daniel L, Delclós, Pablo J, Squire, Mattie, Cui, Rongfeng, Andolfatto, Peter, Rosenthal, Gil G. (2017), "Assortative mating and persistent reproductive isolation in hybrids", Proceedings of the National Academy of Sciences 114 (41): 10936–10941, doi: 10.1073/pnas.1711238114 ISSN 0027-8424, PMC PMC5642718, 28973863, http://www.pnas.org/lookup/doi/10.1073/pnas.1711238114

64. Rieseberg L, Linder C, Seiler G. (1995), "Chromosomal and genic barriers to introgression in Helianthus", Genetics 141 (3): 1163–1171, ISSN 0016-6731, PMC 1206838, 8582621, https://www.ncbi.nlm.nih.gov/pubmed/8582621

65. Comeault A, Matute D. (2018), "Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation", Proceedings of the National Academy of Sciences 115 (39): 9761–9766, doi: 10.1073/pnas.1809685115 ISSN 0027-8424, PMC PMC6166845, 30209213, http://www.pnas.org/lookup/doi/10.1073/pnas.1809685115

66. Blanckaert A, Bank C (2018), "In search of the Goldilocks zone for hybrid speciation", PLOS Genetics 14 (9): e1007613, doi: 10.1371/journal.pgen.1007613 ISSN 1553-7404, PMC PMC6145587, 30192761, https://dx.plos.org/10.1371/journal.pgen.1007613

67. Schumer M, Cui R, Rosenthal G, Andolfatto P (2015), "Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities", PLOS Genetics 11 (3): e1005041, doi: 10.1371/journal.pgen.1005041 ISSN 1553-7404, PMC PMC4359097, 25768654, http://dx.plos.org/10.1371/journal.pgen.1005041

68. Vereecken N, Cozzolino S, Schiestl F (2010), "Hybrid floral scent novelty drives pollinator shift in sexually deceptive orchids", BMC Evolutionary Biology 10 (1): 103, doi: 10.1186/1471-2148-10-103 ISSN 1471-2148, PMC PMC2875231, 20409296, http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-103

69. Gaeta R, Chris P. (2010), "Homoeologous recombination in allopolyploids: the polyploid ratchet: Research review", New Phytologist 186(1): 18–28, doi: 10.1111/j.1469-8137.2009.03089.x http://doi.wiley.com/10.1111/j.1469-8137.2009.03089.x 20002315

70. Hvala J, Frayer M, Payseur B. (2018), "Signatures of hybridization and speciation in genomic patterns of ancestry", Evolution 72 (8): 1540–1552, doi: 10.1111/evo.13509 PMC PMC6261709, 29806154, http://doi.wiley.com/10.1111/evo.13509

71. Rieseberg L, Sinervo B, Linder C, Ungerer M, Arias D. (1996), "Role of Gene Interactions in Hybrid Speciation: Evidence from Ancient and Experimental Hybrids", Science 272 (5262): 741–745, doi: 10.1126/science.272.5262.741 ISSN 0036-8075, http://dx.doi.org/10.1126/science.272.5262.741 8662570

72. Stukenbrock E, Christiansen F, Hansen T, Dutheil J, Schierup M. (2012), "Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species", Proceedings of the National Academy of Sciences 109 (27): 10954–10959, doi: 10.1073/pnas.1201403109 ISSN 0027-8424, PMC PMC3390827, 22711811, http://www.pnas.org/cgi/doi/10.1073/pnas.1201403109

73. Schumer M, Cui R, Powell D, Rosenthal G, Andolfatto P. (2016), "Ancient hybridization and genomic stabilization in a swordtail fish", Molecular Ecology 25 (11): 2577–2591, doi: 10.1111/mec.13602

74. Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, et al. (2014), "The genomic landscape of Neanderthal ancestry in present-day humans", Nature 507 (7492): 354–357, doi: 10.1038/nature12961 ISSN 0028-0836, PMC PMC4072735, 24476815, http://www.nature.com/articles/nature12961

75. Eroukhmanoff F, Bailey R, Elgvin T, Hermansen J, Runemark A, Trier C, et al. (2017), "Resolution of conflict between parental genomes in a hybrid species", bioRxiv, doi: 10.1101/102970 http://biorxiv.org/lookup/doi/10.1101/102970

76. Ohta T (1971), "Associative overdominance caused by linked detrimental mutations", Genetical Research 18 (3): 277–286, doi: 10.1017/s0016672300012684, ISSN 0016-6723, http://dx.doi.org/10.1017/s0016672300012684 5158298

77. Zhao L, Charlesworth B (2016), "Resolving the Conflict Between Associative Overdominance and Background Selection", Genetics 203 (3): 1315–1334, doi: 10.1534/genetics.116.188912 ISSN 0016-6731, PMC PMC4937488, 27182952, http://www.genetics.org/lookup/doi/10.1534/genetics.116.188912

78. Faria R, Johannesson K, Butlin R, Westram A. (2019), "Evolving Inversions", Trends in Ecology & Evolution 34 (3): 239–248, doi: 10.1016/j.tree.2018.12.005 https://linkinghub.elsevier.com/retrieve/pii/S0169534718302866 30691998

79. Barton N. (2018), "The consequences of an introgression event", Molecular Ecology 27 (24): 4973–4975, doi: 10.1111/mec.14950 http://doi.wiley.com/10.1111/mec.14950 30599087

80. Martin S, Davey J, Salazar C, Jiggins C. (2019), "Recombination rate variation shapes barriers to introgression across butterfly genomes", PLOS Biology 17 (2): e2006288, doi: 10.1371/journal.pbio.2006288 ISSN 1545-7885, PMC PMC6366726, 30730876, http://dx.plos.org/10.1371/journal.pbio.2006288

81. Brandvain Y, Kenney A, Flagel L, Coop G, Sweigart A. (2014), "Speciation and Introgression between Mimulus nasutus and Mimulus guttatus", PLoS Genetics 10 (6): e1004410, doi: 10.1371/journal.pgen.1004410 ISSN 1553-7404, PMC PMC4072524, 24967630, http://dx.plos.org/10.1371/journal.pgen.1004410

82. Janoušek V, Munclinger P, Wang L, Teeter K, Tucker P. (2015), "Functional Organization of the Genome May Shape the Species Boundary in the House Mouse", Molecular Biology and Evolution 32 (5): 1208–1220, doi: 10.1093/molbev/msv011 ISSN 1537-1719, PMC PMC4408407, 25631927, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msv011

83. Schumer M, Cui R, Powell D, Dresner R, Rosenthal G, Andolfatto P (2014), "High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species", eLife 3, doi: 10.7554/eLife.02535, ISSN 2050-084X, PMC PMC4080447, 24898754, https://elifesciences.org/articles/02535

84. Liu S, Luo J, Chai J, Ren L, Zhou Y, Huang F, et al. (2016), "Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross", Proceedings of the National Academy of Sciences 113 (5): 1327–1332, doi: 10.1073/pnas.1512955113 ISSN 0027-8424, PMC PMC4747765, 26768847, http://www.pnas.org/lookup/doi/10.1073/pnas.1512955113

85. Trier C, Hermansen J, Sætre G-P, Bailey R. (2014), "Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species", PLoS Genetics 10(1): e1004075, doi: 10.1371/journal.pgen.1004075 ISSN 1553-7404, PMC PMC3886922, 24415954, https://dx.plos.org/10.1371/journal.pgen.1004075

86. Giordano L, Sillo F, Garbelotto M, Gonthier P (2018), "Mitonuclear interactions may contribute to fitness of fungal hybrids", Scientific Reports 8 (1), doi: 10.1038/s41598-018-19922-w ISSN 2045-2322, PMC PMC5786003, 29374209, http://www.nature.com/articles/s41598-018-19922-w

87. Case A, Finseth F, Barr C, Fishman L (2016), "Selfish evolution of cytonuclear hybrid incompatibility in Mimulus", Proceedings of the Royal Society B: Biological Sciences 283 (1838): 20161493, doi: 10.1098/rspb.2016.1493 ISSN 0962-8452, PMC PMC5031664, 27629037, https://royalsocietypublishing.org/doi/10.1098/rspb.2016.1493

88. David W, Mitchell D, Walter R. (2004), "DNA repair in hybrid fish of the genus Xiphophorus", Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 138 (3): 301–309, doi: 10.1016/j.cca.2004.07.006 https://linkinghub.elsevier.com/retrieve/pii/S1532045604001322 15533788

89. Ávila V, Chavarrías D, Sánchez E, Manrique A, López-Fanjul C, García-Dorado A (2006), "Increase of the Spontaneous Mutation Rate in a Long-Term Experiment With Drosophila melanogaster", Genetics 173 (1): 267–277, doi: 10.1534/genetics.106.056200 ISSN 0016-6731, PMC PMC1461422, 16547099, http://www.genetics.org/lookup/doi/10.1534/genetics.106.056200

90. Bashir T, Sailer C, Gerber F, Loganathan N, Bhoopalan H, Eichenberger C, et al. (2014), "Hybridization Alters Spontaneous Mutation Rates in a Parent-of-Origin-Dependent Fashion in Arabidopsis", Plant Physiology 165 (1): 424–437, doi: 10.1104/pp.114.238451 ISSN 0032-0889, PMC PMC4012600, 24664208, http://www.plantphysiol.org/lookup/doi/10.1104/pp.114.238451

91. Dennenmoser S, Sedlazeck F, Iwaszkiewicz E, Li X-Y, Altmüller, J, Nolte, A. (2017), "Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin", Molecular Ecology 26 (18): 4712–4724, doi: 10.1111/mec.14134 PMC PMC5638112, 28390096, http://doi.wiley.com/10.1111/mec.14134

92. Dion-Côté A-M, Renaut S, Normandeau E, Bernatchez L(2014), "RNA-seq Reveals Transcriptomic Shock Involving Transposable Elements Reactivation in Hybrids of Young Lake Whitefish Species", Molecular Biology and Evolution 31 (5): 1188–1199, doi: 10.1093/molbev/msu069 ISSN 1537-1719, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu069 24505119

93. Senerchia N, Felber F, Parisod C (2015), "Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation", Proceedings of the Royal Society B: Biological Sciences 282 (1804): 20142874, doi: 10.1098/rspb.2014.2874 ISSN 0962-8452, PMC PMC4375867, 25716787, https://royalsocietypublishing.org/doi/10.1098/rspb.2014.2874

94. Ostberg C, Hauser L, Pritchard V, Garza J, Naish K (2013), "Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss)", BMC Genomics 14 (1): 570, doi: 10.1186/1471-2164-14-570 ISSN 1471-2164, PMC PMC3765842, 23968234, http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-570

95. Hirai H, Hirai Y, Morimoto M, Kaneko A, Kamanaka Y, Koga A (2017), "Night Monkey Hybrids Exhibit De Novo Genomic and Karyotypic Alterations: The First Such Case in Primates", Genome Biology and Evolution9 (4): 945–955, doi: 10.1093/gbe/evx058 ISSN 1759-6653, PMC PMC5388293, 28369492, https://academic.oup.com/gbe/article/9/4/945/3078090

96. Barkan A, Martienssen R. (1991), "Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1.", Proceedings of the National Academy of Sciences 88 (8): 3502–3506, doi: 10.1073/pnas.88.8.3502 ISSN 0027-8424, http://www.pnas.org/cgi/doi/10.1073/pnas.88.8.3502 1849660

97. Raizada M, Benito M-I, Walbot V(2008), "The MuDR transposon terminal inverted repeat contains a complex plant promoter directing distinct somatic and germinal programs: Transposon promoter expression pattern", The Plant Journal 25 (1): 79–91, doi: 10.1111/j.1365-313X.2001.00939.x http://doi.wiley.com/10.1111/j.1365-313X.2001.00939.x

98. Lim K, Matyasek R, Kovarik A, Leitch A. (2004), "Genome evolution in allotetraploid Nicotiana", Biological Journal of the Linnean Society82 (4): 599–606, doi: 10.1111/j.1095-8312.2004.00344.x https://academic.oup.com/biolinnean/article-lookup/doi/10.1111/j.1095-8312.2004.00344.x

99. Baack E, Whitney K, Rieseberg L. (2005), "Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species", New Phytologist 167 (2): 623–630, doi: 10.1111/j.1469-8137.2005.01433 http://doi.wiley.com/10.1111/j.1469-8137.2005.01433.x 15998412

100. Leitch I, Hanson L, Lim K, Kovarik A, Chase M, Clarkson J et al. (2008), "The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)", Annals of Botany 101 (6): 805–814, doi: 10.1093/aob/mcm326 ISSN 0305-7364, PMC PMC2710205, 18222910, https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mcm326

101. Wolfe K. (2001), "Yesterday's polyploids and the mystery of diploidization", Nature Reviews Genetics 2 (5): 333–341, doi: 10.1038/35072009 ISSN 1471-0056, http://www.nature.com/articles/35072009 11331899

102. Freeling M, Scanlon M, Fowler J (2015), "Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences", Current Opinion in Genetics & Development 35: 110–118, doi: 10.1016/j.gde.2015.11.002 https://linkinghub.elsevier.com/retrieve/pii/S0959437X15001173 26657818

103. Sankoff D, Zheng C, Zhu Q (2010), "The collapse of gene complement following whole genome duplication", BMC Genomics 11 (1): 313, doi: 10.1186/1471-2164-11-313 ISSN 1471-2164, PMC PMC2896955, 20482863, http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-313

104. Edger P, Poorten T, VanBuren R, Hardigan M, Colle M, McKain M, et al. (2019), "Origin and evolution of the octoploid strawberry genome", Nature Genetics 51(3): 541–547, doi: 10.1038/s41588-019-0356-4 ISSN 1061-4036, http://www.nature.com/articles/s41588-019-0356-4 30804557

105. Edger P, Smith R, McKain M, Cooley A, Vallejo-Marin M, Yuan Y, et al. (2017), "Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower", The Plant Cell 29 (9): 2150–2167, doi: 10.1105/tpc.17.00010 ISSN 1040-4651, PMC PMC5635986, 28814644, http://www.plantcell.org/lookup/doi/10.1105/tpc.17.00010

106. Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, et al. (2014), "Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies", Molecular Biology and Evolution 31 (5): 1066–1076, doi: 10.1093/molbev/msu085 ISSN 1537-1719, PMC PMC3995341, 24577842, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu085

107. Renaut S, Nolte A, Bernatchez L. (2009), "Gene Expression Divergence and Hybrid Misexpression between Lake Whitefish Species Pairs (Coregonus spp. Salmonidae)", Molecular Biology and Evolution 26 (4): 925–936, doi: 10.1093/molbev/msp017 ISSN 1537-1719, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msp017 19174479

108. Buggs R, Zhang L, Miles N, Tate J, Gao L, Wei W, et al. (2011), "Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant", Current Biology 21 (7): 551–556, doi: 10.1016/j.cub.2011.02.016 https://linkinghub.elsevier.com/retrieve/pii/S0960982211002077 21419627

109. Ha M, Lu J, Tian L, Ramachandran V, Kasschau K. D, Chapman E. J, et al. (2009), "Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids", Proceedings of the National Academy of Sciences 106 (42): 17835–17840, doi: 10.1073/pnas.0907003106 ISSN 0027-8424, PMC PMC2757398, 19805056, http://www.pnas.org/cgi/doi/10.1073/pnas.0907003106

110. Mallet J (2005), "Hybridization as an invasion of the genome", Trends in Ecology & Evolution 20 (5): 229–237, doi: 10.1016/j.tree.2005.02.010 https://linkinghub.elsevier.com/retrieve/pii/S016953470500039X 16701374

111. Charlesworth D (2016), "Plant Sex Chromosomes", Annual Review of Plant Biology 67 (1): 397–420, doi: 10.1146/annurev-arplant-043015-111911 ISSN 1543-5008, http://www.annualreviews.org/doi/10.1146/annurev-arplant-043015-111911 26653795

112. Rieseberg L. (2001), "Chromosomal rearrangements and speciation", Trends in Ecology & Evolution 16 (7): 351–358, doi: 10.1016/s0169-5347(01)02187-5 ISSN 0169-5347, http://dx.doi.org/10.1016/s0169-5347(01)02187-5

113. Levin D. (2012), "The long wait for hybrid sterility in flowering plants", New Phytologist 196 (3): 666–670, doi: 10.1111/j.1469-8137.2012.04309.x http://doi.wiley.com/10.1111/j.1469-8137.2012.04309.x 22966819

114. Haldane J. (1922), "Sex ratio and unisexual sterility in hybrid animals", Journal of Genetics 12 (2): 101–109, doi: 10.1007/BF02983075 ISSN 0022-1333, http://link.springer.com/10.1007/BF02983075

115. Turelli M, Orr A. (1995), "The dominance theory of Haldane's rule", Genetics140 (1): 389–402, ISSN 0016-6731, PMC 1206564, 7635302, https://www.ncbi.nlm.nih.gov/pubmed/7635302

116. Runemark A, Eroukhmanoff F, Nava-Bolaños A, Hermansen J, Meier J. (2018), "Hybridization, sex-specific genomic architecture and local adaptation", Philosophical Transactions of the Royal Society B: Biological Sciences 373 (1757): 20170419, doi: 10.1098/rstb.2017.0419 ISSN 0962-8436, PMC PMC6125728, 30150218, https://royalsocietypublishing.org/doi/10.1098/rstb.2017.0419

117. Payseur B, Rieseberg L. (2016), "A genomic perspective on hybridization and speciation", Molecular Ecology 25 (11): 2337–2360, doi: 10.1111/mec.13557 PMC PMC4915564, 26836441, http://doi.wiley.com/10.1111/mec.13557

118. Lynch M (1998), Genetics and analysis of quantitative traits, Walsh, Bruce, 1957-, Sunderland, Mass.: Sinauer, ISBN 0878934812, OCLC 37030646, https://www.worldcat.org/oclc/37030646

119. Masly J, Presgraves D (2007), "High-Resolution Genome-Wide Dissection of the Two Rules of Speciation in Drosophila", PLoS Biology 5 (9): e243, doi: 10.1371/journal.pbio.0050243 ISSN 1545-7885, PMC PMC1971125, 17850182, https://dx.plos.org/10.1371/journal.pbio.0050243

120. Mank J, Hosken D, Wedell N. (2014), "Conflict on the Sex Chromosomes: Cause, Effect, and Complexity", Cold Spring Harbor Perspectives in Biology 6(12): a017715–a017715, doi: 10.1101/cshperspect.a017715 ISSN 1943-0264, PMC PMC4292157, 25280765, http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a017715

121. Brys R, Vanden Broeck A, Mergeay J, Jacquemyn H. (2014), "The contribution of mating system variation to reproductive isolation in two closely related Centaurium species (Gentianaceae) with a generalized flower morphology", Evolution 68 (5): 1281–1293, doi: 10.1111/evo.12345 http://doi.wiley.com/10.1111/evo.12345 24372301

122. Widmer A, Lexer C, Cozzolino S (2009), "Evolution of reproductive isolation in plants", Heredity 102 (1): 31–38, doi: 10.1038/hdy.2008.69 ISSN 0018-067X, http://www.nature.com/articles/hdy200869 18648386

123. Schardl C, Craven K. (2003), "Interspecific hybridization in plant-associated fungi and oomycetes: a review", Molecular Ecology 12 (11): 2861–2873, doi: 10.1046/j.1365-294x.2003.01965.x ISSN 0962-1083, http://dx.doi.org/10.1046/j.1365-294x.2003.01965.x 14629368

124. Levin D. (1975), "Minority Cytotype Exclusion in Local Plant Populations", Taxon 24 (1): 35–43, doi: 10.2307/1218997 http://doi.wiley.com/10.2307/1218997

125. McCarthy E, Asmussen M, Anderson W (1995), "A theoretical assessment of recombinational speciation", Heredity 74 (5): 502–509, doi: 10.1038/hdy.1995.71 ISSN 0018-067X, http://www.nature.com/articles/hdy199571

126. Charlton N, Craven K, Afkhami M, Hall B, Ghimire S, Young C. (2014), "Interspecific hybridization and bioactive alkaloid variation increases diversity in endophytic Epichloë species of Bromus laevipes", FEMS Microbiology Ecology 90 (1): 276–289, doi: 10.1111/1574-6941.12393 https://academic.oup.com/femsec/article-lookup/doi/10.1111/1574-6941.12393 25065688

127. Janko K, Pačes J, Wilkinson-Herbots H, Costa R, Roslein J, Drozd P, et al. (2018), "Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation", Molecular Ecology 27 (1): 248–263, doi: 10.1111/mec.14377 http://doi.wiley.com/10.1111/mec.14377 28987005

128. Neaves W, Baumann P (2011), "Unisexual reproduction among vertebrates", Trends in Genetics 27 (3): 81–88, doi: 10.1016/j.tig.2010.12.002, https://linkinghub.elsevier.com/retrieve/pii/S0168952510002295 21334090

129. Brochmann C, Brysting A, Alsos I, Borgen L, Grundt H, Scheen A-C, et al. (2004), "Polyploidy in arctic plants", Biological Journal of the Linnean Society 82 (4): 521–536, doi: 10.1111/j.1095-8312.2004.00337.x https://academic.oup.com/biolinnean/article-lookup/doi/10.1111/j.1095-8312.2004.00337.x

130. Norris L, Main B, Lee Y, Collier T, Fofana A, Cornel A et al. (2015), "Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets", Proceedings of the National Academy of Sciences 112 (3): 815–820, doi: 10.1073/pnas.1418892112 ISSN 0027-8424, PMC PMC4311837, 25561525, http://www.pnas.org/lookup/doi/10.1073/pnas.1418892112

131. Marques D, Meier J, Seehausen O (2019), "A Combinatorial View on Speciation and Adaptive Radiation", Trends in Ecology & Evolution 34 (6): 531–544, doi: 10.1016/j.tree.2019.02.008 ISSN 0169-5347, http://dx.doi.org/10.1016/j.tree.2019.02.008 30885412

132. Maheshwari S, Barbash D (2011), "The Genetics of Hybrid Incompatibilities", Annual Review of Genetics 45 (1): 331–355, 10.1146/annurev-genet-110410-132514, ISSN 0066-4197, http://www.annualreviews.org/doi/10.1146/annurev-genet-110410-132514

133. Buggs R, Doust A, Tate J, Koh J, Soltis K, Feltus F, et al. (2009), "Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids", Heredity103 (1): 73–81, doi: 10.1038/hdy.2009.24 ISSN 0018-067X, http://www.nature.com/articles/hdy200924 19277058

134. Jiggins C, Salazar C, Linares M, Mavarez J (2008), "Hybrid trait speciation and Heliconius butterflies", Philosophical Transactions of the Royal Society B: Biological Sciences 363 (1506): 3047–3054, doi: 10.1098/rstb.2008.0065 ISSN 0962-8436, PMC PMC2607310, 18579480, https://royalsocietypublishing.org/doi/10.1098/rstb.2008.0065

135. Fontaine M, Pease J, Steele A, Waterhouse R, Neafsey D, Sharakhov I, et al. (2015), "Extensive introgression in a malaria vector species complex revealed by phylogenomics", Science 347 (6217): 1258524, doi: 10.1126/science.1258524 ISSN 0036-8075, PMC PMC4380269, 25431491, http://www.sciencemag.org/lookup/doi/10.1126/science.1258524

136. Jay P, Whibley A, Frézal L, Rodríguez de Cara M, Nowell R, Mallet J, et al. (2018), "Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion", Current Biology 28 (11): 1839–1845.e3, doi: 10.1016/j.cub.2018.04.072 https://linkinghub.elsevier.com/retrieve/pii/S096098221830544X 29804810

137. Yeaman S. (2013), "Genomic rearrangements and the evolution of clusters of locally adaptive loci", Proceedings of the National Academy of Sciences 110 (19): E1743–E1751, doi: 10.1073/pnas.1219381110 ISSN 0027-8424, PMC PMC3651494, 23610436, http://www.pnas.org/cgi/doi/10.1073/pnas.1219381110

138. Wu C-I (2001), "The genic view of the process of speciation: Genic view of the process of speciation", Journal of Evolutionary Biology 14 (6): 851–865, doi: 10.1046/j.1420-9101.2001.00335.x http://doi.wiley.com/10.1046/j.1420-9101.2001.00335.x

139. Harrison R, Larson E. (2014), "Hybridization, Introgression, and the Nature of Species Boundaries", Journal of Heredity 105 (S1): 795–809, doi: 10.1093/jhered/esu033 ISSN 0022-1503, https://academic.oup.com/jhered/jhered/article/2961884/Hybridization, 25149255

140. Teeter K, Payseur B, Harris L, Bakewell M, Thibodeau L, O'Brien J, et al. (2007), "Genome-wide patterns of gene flow across a house mouse hybrid zone", Genome Research 18 (1): 67–76, doi: 10.1101/gr.6757907 ISSN 1088-9051, PMC PMC2134771, 18025268, http://www.genome.org/cgi/doi/10.1101/gr.6757907

141. Hooper D, Griffith S, Price T. (2019), "Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone", Molecular Ecology 28 (6): 1246–1262, doi: 10.1111/mec.14874 ISSN 0962-1083, https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14874 30230092

142. Pritchard J, Stephens M, Donnelly P. (2000), "Inference of population structure using multilocus genotype data", Genetics 155 (2): 945–959, ISSN 0016-6731, PMC 1461096, 10835412, https://www.ncbi.nlm.nih.gov/pubmed/10835412

143. Alexander D, Novembre J, Lange K. (2009), "Fast model-based estimation of ancestry in unrelated individuals", Genome Research 19 (9): 1655–1664, doi: 10.1101/gr.094052.109 ISSN 1088-9051, PMC PMC2752134, 19648217, http://genome.cshlp.org/cgi/doi/10.1101/gr.094052.109

144. Lawson D, Hellenthal G, Myers S, Falush D (2012), "Inference of Population Structure using Dense Haplotype Data", PLoS Genetics 8 (1): e1002453, doi: 10.1371/journal.pgen.1002453 ISSN 1553-7404, PMC PMC3266881, 22291602, http://dx.plos.org/10.1371/journal.pgen.1002453

145. Lawson D, van Dorp L, Falush D (2018), "A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots", Nature Communications 9 (1), doi: 10.1038/s41467-018-05257-7 ISSN 2041-1723, PMC PMC6092366, 30108219, http://www.nature.com/articles/s41467-018-05257-7

146. Kulathinal R, Stevison L, Noor M. (2009), "The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing", PLoS Genetics 5 (7): e1000550, doi: 10.1371/journal.pgen.1000550 ISSN 1553-7404, PMC PMC2696600, 19578407, https://dx.plos.org/10.1371/journal.pgen.1000550

147. Green R, Krause J, Briggs A, Maricic T, Stenzel U, Kircher M, et al. (2010), "A Draft Sequence of the Neandertal Genome", Science328 (5979): 710–722, doi: 10.1126/science.1188021 ISSN 0036-8075, PMC PMC5100745, 20448178, http://www.sciencemag.org/cgi/doi/10.1126/science.1188021

148. Durand E, Patterson N, Reich D, Slatkin M (2011), "Testing for Ancient Admixture between Closely Related Populations", Molecular Biology and Evolution 28 (8): 2239–2252, doi: 10.1093/molbev/msr048 ISSN 1537-1719, PMC PMC3144383, 21325092, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msr048

149. Peter B. (2016), "Admixture, Population Structure, and F -Statistics", Genetics 202 (4): 1485–1501, doi: 10.1534/genetics.115.183913 ISSN 0016-6731, PMC PMC4905545, 26857625, http://www.genetics.org/lookup/doi/10.1534/genetics.115.183913

150. Reich D, Thangaraj K, Patterson N, Price A, Singh L. (2009), "Reconstructing Indian population history", Nature 461 (7263): 489–494, doi: 10.1038/nature08365 ISSN 0028-0836, PMC PMC2842210, 19779445, http://www.nature.com/articles/nature08365

151. Martin S, Davey J, Jiggins C. (2015), "Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci", Molecular Biology and Evolution 32 (1): 244–257, doi: 10.1093/molbev/msu269 ISSN 1537-1719, PMC PMC4271521, 25246699, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu269

152. Pease J, Hahn M. (2015), "Detection and Polarization of Introgression in a Five-Taxon Phylogeny", Systematic Biology 64 (4): 651–662, doi: 10.1093/sysbio/syv023 ISSN 1076-836X, https://academic.oup.com/sysbio/article/64/4/651/1650669 25888025

153. Eaton D, Ree, Richard H. (2013), "Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)", Systematic Biology 62 (5): 689–706, doi: 10.1093/sysbio/syt032 ISSN 1076-836X, PMC PMC3739883, 23652346, https://academic.oup.com/sysbio/article/62/5/689/1684460

154. Pickrell J, Pritchard J. (2012), "Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data", PLoS Genetics 8 (11): e1002967, doi: 10.1371/journal.pgen.1002967 ISSN 1553-7404, PMC PMC3499260, 23166502, https://dx.plos.org/10.1371/journal.pgen.1002967

155. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, et al. (2012), "Ancient Admixture in Human History", Genetics 192 (3): 1065–1093, doi: 10.1534/genetics.112.145037 ISSN 0016-6731, PMC PMC3522152, 22960212, http://www.genetics.org/lookup/doi/10.1534/genetics.112.145037

156. Lipson M, Loh P-R, Levin A, Reich D, Patterson N, Berger B(2013), "Efficient Moment-Based Inference of Admixture Parameters and Sources of Gene Flow", Molecular Biology and Evolution 30 (8): 1788–1802, doi: 10.1093/molbev/mst099 ISSN 1537-1719, PMC PMC3708505, 23709261, https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mst099

157. Yu Y, Barnett M, Nakhleh L (2013), "Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting", Systematic Biology 62 (5): 738–751, doi: 10.1093/sysbio/syt037 ISSN 1076-836X, PMC PMC3739885, 23736104, https://academic.oup.com/sysbio/article/62/5/738/1685537

158. Wen D, Yu Y, Nakhleh L (2016), "Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent", PLOS Genetics 12 (5): e1006006, doi: 10.1371/journal.pgen.1006006 ISSN 1553-7404, PMC PMC4856265, 27144273, https://dx.plos.org/10.1371/journal.pgen.1006006

159. Moorjani P, Patterson N, Hirschhorn J, Keinan A, Hao L, Atzmon G, et al. (2011), "The History of African Gene Flow into Southern Europeans, Levantines, and Jews", PLoS Genetics 7(4): e1001373, doi: 10.1371/journal.pgen.1001373 ISSN 1553-7404, PMC PMC3080861, 21533020, http://dx.plos.org/10.1371/journal.pgen.1001373

160. Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D (2016), "A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years", Proceedings of the National Academy of Sciences 113 (20): 5652–5657, doi: 10.1073/pnas.1514696113 ISSN 0027-8424, PMC PMC4878468, 27140627, http://www.pnas.org/lookup/doi/10.1073/pnas.1514696113

161. Loh P-R, Lipson M, Patterson N, Moorjani P, Pickrell J, Reich D, Berger B(2013), "Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium", Genetics 193 (4): 1233–1254, doi: 10.1534/genetics.112.147330 ISSN 0016-6731, http://www.genetics.org/lookup/doi/10.1534/genetics.112.147330 23410830

162. Sankararaman S, Patterson N, Li H, Pääbo S, Reich D (2012), "The Date of Interbreeding between Neandertals and Modern Humans", PLoS Genetics 8 (10): e1002947, doi: 10.1371/journal.pgen.1002947 ISSN 1553-7404, PMC PMC3464203, 23055938, https://dx.plos.org/10.1371/journal.pgen.1002947

163. Pinho C, Hey J (2010), "Divergence with Gene Flow: Models and Data", Annual Review of Ecology, Evolution, and Systematics 41 (1): 215–230, doi: 10.1146/annurev-ecolsys-102209-144644 ISSN 1543-592X, http://www.annualreviews.org/doi/10.1146/annurev-ecolsys-102209-144644

164. Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa V, Foll M (2013), "Robust Demographic Inference from Genomic and SNP Data", PLoS Genetics 9 (10): e1003905, doi: 10.1371/journal.pgen.1003905 ISSN 1553-7404, PMC PMC3812088, 24204310, https://dx.plos.org/10.1371/journal.pgen.1003905

165. Gutenkunst R, Hernandez R, Williamson S, Bustamante C. (2009), "Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data", PLoS Genetics 5(10): e1000695, doi: 10.1371/journal.pgen.1000695 ISSN 1553-7404, PMC PMC2760211, 19851460, https://dx.plos.org/10.1371/journal.pgen.1000695

166. Beaumont M A. (2010), "Approximate Bayesian Computation in Evolution and Ecology", Annual Review of Ecology, Evolution, and Systematics 41 (1): 379–406, doi: 10.1146/annurev-ecolsys-102209-144621 https://doi.org/10.1146/annurev-ecolsys-102209-144621

167. Theunert C, Slatkin M (2017), "Distinguishing Recent Admixture from Ancestral Population Structure", Genome Biology and Evolution 9 (3): 427–437, doi: 10.1093/gbe/evx018 ISSN 1759-6653, PMC PMC5381645, 28186554, https://academic.oup.com/gbe/article/2982377/Distinguishing