Eukaryote hybrid genome#Glossary

File:Fig1v3_Potential_outcomes_of_hybridization.jpg

There are several potential evolutionary outcomes of hybridization. If early generation hybrids are not viable or sterile, hybridization may reduce the reproductive success of the parent species.{{cite journal | last1=Wolf|first1=Diana E.|last2=Takebayashi|first2=Naoki|last3=Rieseberg|first3=Loren H.| name-list-style = vanc |date=2001|title=Predicting the Risk of Extinction through Hybridization|journal=Conservation Biology|language=en|volume=15|issue=4|pages=1039–1053|doi=10.1046/j.1523-1739.2001.0150041039.x|bibcode=2001ConBi..15.1039W |s2cid=86704425 |issn=0888-8892}}{{cite journal | vauthors = Prentis PJ, White EM, Radford IJ, Lowe AJ, Clarke AR | title = Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis? | journal = The New Phytologist | volume = 176 | issue = 4 | pages = 902–12 | date = 2007 | pmid = 17850249 | doi = 10.1111/j.1469-8137.2007.02217.x | url = https://eprints.qut.edu.au/40148/1/c40148.pdf | doi-access = free }} This could potentially lead to reinforcement, selection to strengthen premating isolation{{cite journal | last1=Servedio|first1=Maria R.|last2=Noor|first2=Mohamed A.F.| name-list-style = vanc |date=2003|title=The Role of Reinforcement in Speciation: Theory and Data|journal=Annual Review of Ecology, Evolution, and Systematics|language=en|volume=34|issue=1|pages=339–364|doi=10.1146/annurev.ecolsys.34.011802.132412|issn=1543-592X}} or if the species fail to evolve premating isolation, it could increase their extinction risk due to wasted reproductive effort. If the fitness of early generation hybrids is non-zero and that of some later generation hybrids is as high or even higher than the fitness of one or both parent taxa, hybrids may displace the parent taxa and the hybridizing taxa may fuse (speciation reversal{{cite journal | last1=Rhymer|first1=Judith M.|last2=Simberloff|first2=Daniel | name-list-style = vanc |date=1996 |title=Extinction by hybridization and introgression |journal=Annual Review of Ecology and Systematics|language=en|volume=27|issue=1|pages=83–109|doi=10.1146/annurev.ecolsys.27.1.83|issn=0066-4162}}{{cite journal | vauthors = Seehausen O | title = Conservation: losing biodiversity by reverse speciation | journal = Current Biology | volume = 16 | issue = 9 | pages = R334-7 | date = May 2006 | pmid = 16682344 | doi = 10.1016/j.cub.2006.03.080 | s2cid = 17611278 | doi-access = free | bibcode = 2006CBio...16.R334S }}). If the fitness of early generation hybrids is reduced but non-zero, hybrid zones may emerge in the contact zone of the taxa.{{cite journal | last=Thompson| first=John D.| name-list-style = vanc | date=1994|title=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=Journal of Evolutionary Biology|volume=7|issue=5|pages=631–634|doi=10.1046/j.1420-9101.1994.7050631.x|issn=1010-061X}} If hybrids are fertile, hybridization may contribute novel variation through rare hybrids backcrossing with parental species. Such introgressive hybridization may enable neutral or selectively beneficial alleles to be transferred across species boundaries even in species pairs that remain distinct despite occasional gene flow.{{cite journal | vauthors = Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, etal | collaboration = Heliconius Genome Consortium | title = Butterfly genome reveals promiscuous exchange of mimicry adaptations among species | journal = Nature | volume = 487 | issue = 7405 | pages = 94–8 | date = July 2012 | pmid = 22722851 | pmc = 3398145 | doi = 10.1038/nature11041 | bibcode = 2012Natur.487...94T }}{{cite journal | vauthors = Hanemaaijer MJ, Collier TC, Chang A, Shott CC, Houston PD, Schmidt H, Main BJ, Cornel AJ, Lee Y, Lanzaro GC | display-authors = 6 | title = The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population | journal = Molecular Ecology | volume = 27 | issue = 24 | pages = 4978–4990 | date = December 2018 | pmid = 30447117 | doi = 10.1111/mec.14947 | bibcode = 2018MolEc..27.4978H | s2cid = 53568503 }} Hybrid fitness may vary with divergence time between the hybridizing taxa. This pattern has been shown for a variety of taxa including Drosophila,{{cite book|title=Speciation|last1=Coyne|first1=Jerry A.|last2=Orr|first2=H. Allen| name-list-style = vanc |date=2004|publisher=Sinauer Associates|isbn=0878930914|location=Sunderland|oclc=55078441}} birds{{cite journal | last1=Price|first1=Trevor D.|last2=Bouvier|first2=Michelle M.| name-list-style = vanc |date=2002|title=The evolution of F1 postzygotic incompatibilities in birds|journal=Evolution|volume=56|issue=10|pages=2083–9|doi=10.1554/0014-3820(2002)056[2083:teofpi]2.0.co;2|pmid=12449494|s2cid=24378606 |issn=0014-3820}} and fish.{{cite journal | vauthors = Stelkens RB, Young KA, Seehausen O | s2cid = 10319450 | title = The accumulation of reproductive incompatibilities in African cichlid fish | journal = Evolution; International Journal of Organic Evolution | volume = 64 | issue = 3 | pages = 617–33 | date = March 2010 | pmid = 19796149 | doi = 10.1111/j.1558-5646.2009.00849.x | url = https://serval.unil.ch/notice/serval:BIB_B288115772AD }} Hybrid fitness may also differ with cross direction,{{cite journal | vauthors = Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C | title = Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm | journal = PLOS Genetics | volume = 11 | issue = 6 | pages = e1005295 | date = June 2015 | pmid = 26086217 | pmc = 4472357 | doi = 10.1371/journal.pgen.1005295 | editor-first = Kirsten | editor-last = Bomblies | doi-access = free }} between first generation and later generation hybrids,{{cite journal | vauthors = Pritchard VL, Knutson VL, Lee M, Zieba J, Edmands S | s2cid = 10092426 | title = Fitness and morphological outcomes of many generations of hybridization in the copepod Tigriopus californicus | journal = Journal of Evolutionary Biology | volume = 26 | issue = 2 | pages = 416–33 | date = February 2013 | pmid = 23278939 | doi = 10.1111/jeb.12060 | doi-access = free }} and among individuals within generations of the same cross-type.{{cite journal | vauthors = Rieseberg LH, Archer MA, Wayne RK | title = Transgressive segregation, adaptation and speciation | journal = Heredity | volume = 83 ( Pt 4) | issue = 4 | pages = 363–72 | date = October 1999 | pmid = 10583537 | doi = 10.1038/sj.hdy.6886170 | doi-access = free }}{{cite journal | vauthors = Burke JM, Arnold ML | s2cid = 26683922 | title = Genetics and the fitness of hybrids | journal = Annual Review of Genetics | volume = 35 | issue = 1 | pages = 31–52 | date = 2001 | pmid = 11700276 | doi = 10.1146/annurev.genet.35.102401.085719 }} In some cases hybrids may evolve into new hybrid species with reproductive isolation to both parent taxa.{{cite journal | vauthors = Mallet J | title = Hybrid speciation | journal = Nature | volume = 446 | issue = 7133 | pages = 279–83 | date = March 2007 | pmid = 17361174 | doi = 10.1038/nature05706 | bibcode = 2007Natur.446..279M | s2cid = 1016526 }}{{cite journal | vauthors = Vallejo-Marín M, Hiscock SJ | title = Hybridization and hybrid speciation under global change | journal = The New Phytologist | volume = 211 | issue = 4 | pages = 1170–87 | date = September 2016 | pmid = 27214560 | doi = 10.1111/nph.14004 | hdl = 1893/23581 | doi-access = free | hdl-access = free }} Below is described the evolutionary outcomes of hybridisation that result in persistent hybrid genomes.

When rare hybrids backcross with parent species, alleles coding for traits that are beneficial for both parental species can be transferred across species boundaries, even if parent species remain distinct taxa. This process is referred to as adaptive introgression (a somewhat misleading term because backcrossing itself may not be adaptive, but some of the introgressed variants may be beneficial). Simulations suggest that adaptive introgression is possible unless hybrid fitness is substantially reduced,{{cite journal | vauthors = Barton N, Bengtsson BO | title = The barrier to genetic exchange between hybridising populations | journal = Heredity | volume = 57 ( Pt 3) | issue = 3 | pages = 357–76 | date = December 1986 | pmid = 3804765 | doi = 10.1038/hdy.1986.135 | doi-access = free }}{{cite journal | vauthors = Demon I, Haccou P, van den Bosch F | title = Introgression of resistance genes between populations: a model study of insecticide resistance in Bemisia tabaci | journal = Theoretical Population Biology | volume = 72 | issue = 2 | pages = 292–304 | date = September 2007 | pmid = 17658572 | doi = 10.1016/j.tpb.2007.06.005 }} or the adaptive loci are tightly linked to deleterious ones.{{cite journal | vauthors = Uecker H, Setter D, Hermisson J | title = Adaptive gene introgression after secondary contact | journal = Journal of Mathematical Biology | volume = 70 | issue = 7 | pages = 1523–80 | date = June 2015 | pmid = 24992884 | pmc = 4426140 | doi = 10.1007/s00285-014-0802-y }} Examples of adaptive traits that have been transferred via introgression include an insecticide resistance gene that was transferred from Anopheles gambiae to A. coluzzii and the red warning wing colouration trait in Heliconius butterflies that is under natural selection from predators which has been introgressed from e.g. H. melpomene to H. timareta{{cite journal | vauthors = Pardo-Diaz C, Salazar C, Baxter SW, Merot C, Figueiredo-Ready W, Joron M, McMillan WO, Jiggins CD | display-authors = 6 | title = Adaptive introgression across species boundaries in Heliconius butterflies | journal = PLOS Genetics | volume = 8 | issue = 6 | pages = e1002752 | date = 2012 | pmid = 22737081 | pmc = 3380824 | doi = 10.1371/journal.pgen.1002752 | editor-first = Marcus | editor-last = R. Kronforst | doi-access = free }} and other Heliconius species. In the plant Arabidopsis arenosa some of the alleles conferring adaptation to drought and phytotoxic levels of metal have been introgressed from A. lyrata.{{cite journal | vauthors = Arnold BJ, Lahner B, DaCosta JM, Weisman CM, Hollister JD, Salt DE, Bomblies K, Yant L | display-authors = 6 | title = Borrowed alleles and convergence in serpentine adaptation | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 29 | pages = 8320–5 | date = July 2016 | pmid = 27357660 | pmc = 4961121 | doi = 10.1073/pnas.1600405113 | bibcode = 2016PNAS..113.8320A | doi-access = free }} Even in humans there is evidence for adaptive introgression of e.g. immunity alleles, skin pigmentation alleles and alleles conferring adaptation to high altitude environments from Neanderthal and Denisovans.{{cite journal | vauthors = Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E | title = Evidence for archaic adaptive introgression in humans | journal = Nature Reviews. Genetics | volume = 16 | issue = 6 | pages = 359–71 | date = June 2015 | pmid = 25963373 | pmc = 4478293 | doi = 10.1038/nrg3936 }} If traits important for species recognition or reproductive isolation introgress into a population of another species, the introgressed population may become reproductively isolated against other populations of the same species. Examples of this include Heliconius butterflies, where selective introgression of wing pattern genes between diverged lineages occurs,{{cite journal | vauthors = Kronforst MR, Papa R | title = The functional basis of wing patterning in Heliconius butterflies: the molecules behind mimicry | journal = Genetics | volume = 200 | issue = 1 | pages = 1–19 | date = May 2015 | pmid = 25953905 | pmc = 4423356 | doi = 10.1534/genetics.114.172387 }} and wing patterns contribute to reproductive isolation in some species pairs with low (e.g. between H. t. florencia and H. t. linaresi) and intermediate levels (e.g. H. c. galanthus/H. pachinus) of divergence.{{cite journal | vauthors = Mérot C, Salazar C, Merrill RM, Jiggins CD, Joron M | title = Heliconius butterflies | journal = Proceedings. Biological Sciences | volume = 284 | issue = 1856 | pages = 20170335 | date = June 2017 | pmid = 28592669 | pmc = 5474069 | doi = 10.1098/rspb.2017.0335 }}

Many empirical case studies start with exploratory detection of putative hybrid taxa or individuals with genomic clustering approaches, such as those used in the software STRUCTURE,{{cite journal | vauthors = Pritchard JK, Stephens M, Donnelly P | title = Inference of population structure using multilocus genotype data | journal = Genetics | volume = 155 | issue = 2 | pages = 945–59 | date = June 2000 | doi = 10.1093/genetics/155.2.945 | pmid = 10835412 | pmc = 1461096 }} ADMIXTURE{{cite journal | vauthors = Alexander DH, Novembre J, Lange K | title = Fast model-based estimation of ancestry in unrelated individuals | journal = Genome Research | volume = 19 | issue = 9 | pages = 1655–64 | date = September 2009 | pmid = 19648217 | pmc = 2752134 | doi = 10.1101/gr.094052.109 }} or fineSTRUCTURE.{{cite journal | vauthors = Lawson DJ, Hellenthal G, Myers S, Falush D | title = Inference of population structure using dense haplotype data | journal = PLOS Genetics | volume = 8 | issue = 1 | pages = e1002453 | date = January 2012 | pmid = 22291602 | pmc = 3266881 | doi = 10.1371/journal.pgen.1002453 | editor-first = Gregory P. | editor-last = Copenhaver | doi-access = free }} These methods infer a user-specified number of genetic groups from the data and assign each individual to one or a mix of these groups. They can be applied to closely related taxa without having to preassign individuals to taxa and may thus be particularly useful in the study of closely related taxa or species complexes. However, uneven sampling of the parental taxa or different amounts of drift in the included taxa may lead to erroneous conclusions about evidence for hybridization.{{cite journal | vauthors = Lawson DJ, van Dorp L, Falush D | title = A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots | journal = Nature Communications | volume = 9 | issue = 1 | pages = 3258 | date = August 2018 | pmid = 30108219 | pmc = 6092366 | doi = 10.1038/s41467-018-05257-7 | bibcode = 2018NatCo...9.3258L }}

If genomic data of multiple species is available, phylogenetic methods may be better suited to identify introgression. Introgressive hybridization leads to gene trees that are discordant from the species tree, whereby introgressed individuals are phylogenetically closer to the source of introgression than to their non-introgressed conspecifics. Such discordant gene trees can also arise by chance through incomplete lineage sorting, particularly if the species compared are still young. Therefore, discordant gene trees are only evidence of introgression if a gene tree produced by excess allele sharing between the hybridizing taxa is strongly overrepresented compared to alternative discordant gene trees. An entire suite of methods have been developed to detect such excess allele sharing between hybridizing taxa, including Patterson’s D statistics or ABBA-BABA tests{{cite journal | vauthors = Kulathinal RJ, Stevison LS, Noor MA | title = The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing | journal = PLOS Genetics | volume = 5 | issue = 7 | pages = e1000550 | date = July 2009 | pmid = 19578407 | pmc = 2696600 | doi = 10.1371/journal.pgen.1000550 | editor-first = Michael W. | editor-last = Nachman | doi-access = free }}{{cite journal | vauthors = Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S | display-authors = 6 | title = A draft sequence of the Neandertal genome | journal = Science | volume = 328 | issue = 5979 | pages = 710–722 | date = May 2010 | pmid = 20448178 | pmc = 5100745 | doi = 10.1126/science.1188021 | bibcode = 2010Sci...328..710G }}{{cite journal | vauthors = Durand EY, Patterson N, Reich D, Slatkin M | title = Testing for ancient admixture between closely related populations | journal = Molecular Biology and Evolution | volume = 28 | issue = 8 | pages = 2239–52 | date = August 2011 | pmid = 21325092 | pmc = 3144383 | doi = 10.1093/molbev/msr048 }} or f-statistics.{{cite journal | vauthors = Peter BM | title = Admixture, Population Structure, and F-Statistics | journal = Genetics | volume = 202 | issue = 4 | pages = 1485–501 | date = April 2016 | pmid = 26857625 | pmc = 4905545 | doi = 10.1534/genetics.115.183913 }}{{cite journal | vauthors = Reich D, Thangaraj K, Patterson N, Price AL, Singh L | title = Reconstructing Indian population history | journal = Nature | volume = 461 | issue = 7263 | pages = 489–94 | date = September 2009 | pmid = 19779445 | pmc = 2842210 | doi = 10.1038/nature08365 | bibcode = 2009Natur.461..489R }} Modified versions of these tests can be used to infer introgressed genomic regions,{{cite journal | vauthors = Martin SH, Davey JW, Jiggins CD | title = Evaluating the use of ABBA-BABA statistics to locate introgressed loci | journal = Molecular Biology and Evolution | volume = 32 | issue = 1 | pages = 244–57 | date = January 2015 | pmid = 25246699 | pmc = 4271521 | doi = 10.1093/molbev/msu269 }} the direction of gene flow{{cite journal | vauthors = Pease JB, Hahn MW | title = Detection and Polarization of Introgression in a Five-Taxon Phylogeny | journal = Systematic Biology | volume = 64 | issue = 4 | pages = 651–62 | date = July 2015 | pmid = 25888025 | doi = 10.1093/sysbio/syv023 | doi-access = free }}{{cite journal | vauthors = Eaton DA, Ree RH | title = Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae) | journal = Systematic Biology | volume = 62 | issue = 5 | pages = 689–706 | date = September 2013 | pmid = 23652346 | pmc = 3739883 | doi = 10.1093/sysbio/syt032 }} or the amount of gene flow.

For datasets with a large number of taxa it may be difficult to compute all possible test of hybridization. In such cases, graph construction methods may be better suited.{{cite journal | vauthors = Pickrell JK, Pritchard JK | title = Inference of population splits and mixtures from genome-wide allele frequency data | journal = PLOS Genetics | volume = 8 | issue = 11 | pages = e1002967 | date = 2012 | pmid = 23166502 | pmc = 3499260 | doi = 10.1371/journal.pgen.1002967 | editor-first = Hua | editor-last = Tang | bibcode = 2012arXiv1206.2332P | arxiv = 1206.2332 | doi-access = free }}{{cite journal | vauthors = Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D | display-authors = 6 | title = Ancient admixture in human history | journal = Genetics | volume = 192 | issue = 3 | pages = 1065–93 | date = November 2012 | pmid = 22960212 | pmc = 3522152 | doi = 10.1534/genetics.112.145037 }}{{cite journal | vauthors = Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B | title = Efficient moment-based inference of admixture parameters and sources of gene flow | journal = Molecular Biology and Evolution | volume = 30 | issue = 8 | pages = 1788–802 | date = August 2013 | pmid = 23709261 | pmc = 3708505 | doi = 10.1093/molbev/mst099 }} These methods reconstruct complex phylogenetic models with hybridization that best fit the genetic relationships among the sampled taxa and provide estimates for drift and introgression. Other phylogenetic network methods that account for incomplete lineage sorting and hybridization may also help.{{cite journal | vauthors = Yu Y, Barnett RM, Nakhleh L | title = Parsimonious inference of hybridization in the presence of incomplete lineage sorting | journal = Systematic Biology | volume = 62 | issue = 5 | pages = 738–51 | date = September 2013 | pmid = 23736104 | pmc = 3739885 | doi = 10.1093/sysbio/syt037 }}{{cite journal | vauthors = Wen D, Yu Y, Nakhleh L | title = Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent | journal = PLOS Genetics | volume = 12 | issue = 5 | pages = e1006006 | date = May 2016 | pmid = 27144273 | pmc = 4856265 | doi = 10.1371/journal.pgen.1006006 | editor-first = Scott | editor-last = Edwards | doi-access = free }} Methods based on linkage disequilibrium decay or methods inferring ancestry tracts can be used to date recent admixture or introgression events as over time ancestry tracts are continuously broken down by recombination.{{cite journal | vauthors = Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D | display-authors = 6 | title = The history of African gene flow into Southern Europeans, Levantines, and Jews | journal = PLOS Genetics | volume = 7 | issue = 4 | pages = e1001373 | date = April 2011 | pmid = 21533020 | pmc = 3080861 | doi = 10.1371/journal.pgen.1001373 | editor-first = Gil | editor-last = McVean | doi-access = free }}{{cite journal | vauthors = Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D | title = A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 20 | pages = 5652–7 | date = May 2016 | pmid = 27140627 | pmc = 4878468 | doi = 10.1073/pnas.1514696113 | bibcode = 2016PNAS..113.5652M | doi-access = free }}{{cite journal | vauthors = Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B | title = Inferring admixture histories of human populations using linkage disequilibrium | journal = Genetics | volume = 193 | issue = 4 | pages = 1233–54 | date = April 2013 | pmid = 23410830 | pmc = 3606100 | doi = 10.1534/genetics.112.147330 }}{{cite journal | vauthors = Sankararaman S, Patterson N, Li H, Pääbo S, Reich D | title = The date of interbreeding between Neandertals and modern humans | journal = PLOS Genetics | volume = 8 | issue = 10 | pages = e1002947 | date = 2012 | pmid = 23055938 | pmc = 3464203 | doi = 10.1371/journal.pgen.1002947 | editor-first = Joshua M. | editor-last = Akey | bibcode = 2012arXiv1208.2238S | arxiv = 1208.2238 | doi-access = free }} With increasing genome stabilization, individuals should vary less in local ancestry. Levels of genome stabilization can thus be assessed by computing the ancestry proportions (e.g. with fd) in genomic windows and testing if these correlate across individuals. Additionally, if hybridization is still ongoing, ancestry proportions should vary across individuals and in space.

A different approach is to use demographic modelling to find the simplification of the evolutionary history of the studied taxa.{{cite journal | last1=Pinho|first1=Catarina|last2=Hey|first2=Jody|s2cid=45813707| name-list-style = vanc |date=2010|title=Divergence with Gene Flow: Models and Data|journal=Annual Review of Ecology, Evolution, and Systematics|language=en|volume=41|issue=1|pages=215–230|doi=10.1146/annurev-ecolsys-102209-144644|issn=1543-592X|doi-access=free}} Demographic modelling should only be applied to small sets of taxa because with increasing number of taxa, model complexity increases and the number of model parameters such as timing, amounts and direction of gene flow, and population sizes and split times can quickly become too high. The fit of the demographic models to the data can be assessed with the site frequency spectrum{{cite journal | vauthors = Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M | title = Robust demographic inference from genomic and SNP data | journal = PLOS Genetics | volume = 9 | issue = 10 | pages = e1003905 | date = October 2013 | pmid = 24204310 | pmc = 3812088 | doi = 10.1371/journal.pgen.1003905 | editor-first = Joshua M. | editor-last = Akey | doi-access = free }}{{cite journal | vauthors = Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD | title = Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data | journal = PLOS Genetics | volume = 5 | issue = 10 | pages = e1000695 | date = October 2009 | pmid = 19851460 | pmc = 2760211 | doi = 10.1371/journal.pgen.1000695 | editor-first = Gil | editor-last = McVean | bibcode = 2009arXiv0909.0925G | arxiv = 0909.0925 | doi-access = free }} or with summary statistics in an Approximate Bayesian Computation framework.{{cite journal | last=Beaumont|first=Mark A.| name-list-style = vanc |date=2010|title=Approximate Bayesian Computation in Evolution and Ecology|journal=Annual Review of Ecology, Evolution, and Systematics|volume=41|issue=1|pages=379–406|doi=10.1146/annurev-ecolsys-102209-144621}} It is also possible to gain more power by combining information from linkage disequilibrium decay patterns and the allele frequency spectrum.{{cite journal | vauthors = Theunert C, Slatkin M | title = Distinguishing recent admixture from ancestral population structure | journal = Genome Biology and Evolution | volume = 9 | issue = 3 | pages = 427–437 | date = February 2017 | pmid = 28186554 | pmc = 5381645 | doi = 10.1093/gbe/evx018 }}

One of the potential evolutionary outcomes of hybridisation is the establishment of a novel, reproductively isolated lineage, i.e., hybrid speciation. A hybrid species has an admixed genome and forms stable genetically distinct populations. Some researchers argue that evidence of a hybridization-derived basis for reproductive isolation should be an additional defining criterion for hybrid speciation,{{cite journal | vauthors = Schumer M, Rosenthal GG, Andolfatto P | s2cid = 22702297 | title = How common is homoploid hybrid speciation? | journal = Evolution; International Journal of Organic Evolution | volume = 68 | issue = 6 | pages = 1553–60 | date = June 2014 | pmid = 24620775 | doi = 10.1111/evo.12399 | doi-access = free }} but see Moharrek et al.{{cite journal | vauthors = Nieto Feliner G, Álvarez I, Fuertes-Aguilar J, Heuertz M, Marques I, Moharrek F, Piñeiro R, Riina R, Rosselló JA, Soltis PS, Villa-Machío I | display-authors = 6 | title = Is homoploid hybrid speciation that rare? An empiricist's view | journal = Heredity | volume = 118 | issue = 6 | pages = 513–516 | date = June 2017 | pmid = 28295029 | pmc = 5436029 | doi = 10.1038/hdy.2017.7 }} This stricter definition includes polyploid hybrid taxa but only encompasses a handful of well studied cases of homoploid hybrid speciation, e.g. Heliconius heurippa, Passer italiae, and three Helianthus sunflower species{{cite journal | vauthors = Rieseberg LH, Raymond O, Rosenthal DM, Lai Z, Livingstone K, Nakazato T, Durphy JL, Schwarzbach AE, Donovan LA, Lexer C | s2cid = 9232157 | display-authors = 6 | title = Major ecological transitions in wild sunflowers facilitated by hybridization | journal = Science | volume = 301 | issue = 5637 | pages = 1211–6 | date = August 2003 | pmid = 12907807 | doi = 10.1126/science.1086949 | bibcode = 2003Sci...301.1211R | doi-access = free }} because for most suggested examples of homoploid hybrid speciation, the genetic basis of reproductive isolation is still unknown.

Hybrid species can occupy an ecological niche different to those of the parents and may be isolated from the parent species primarily through pre-mating barriers (hybrid speciation with external barriers{{cite book|title=Plant speciation|last=Grant | first = Verne | name-list-style = vanc |date=1981|publisher=Columbia University Press|isbn=0231051123|edition=2nd|location=New York|oclc=7552165}}). Hybrid species may also be reproductively isolated from the parent species through sorting of incompatibilities leading to new combinations of parental alleles that are incompatible with both parent species but compatible within the hybrid taxon (recombinational hybrid speciation). A recombinational hybrid taxon typically also has a substantial proportion of the genome derived from the donor of introgressed material, although variation exists both between taxa and within lineages of hybrid taxa.{{cite journal | vauthors = Schumer M, Xu C, Powell DL, Durvasula A, Skov L, Holland C, Blazier JC, Sankararaman S, Andolfatto P, Rosenthal GG, Przeworski M | display-authors = 6 | title = Natural selection interacts with recombination to shape the evolution of hybrid genomes | journal = Science | volume = 360 | issue = 6389 | pages = 656–660 | date = May 2018 | pmid = 29674434 | pmc = 6069607 | doi = 10.1126/science.aar3684 | bibcode = 2018Sci...360..656S }}{{cite journal | vauthors = Runemark A, Trier CN, Eroukhmanoff F, Hermansen JS, Matschiner M, Ravinet M, Elgvin TO, Sætre GP | display-authors = 6 | title = Variation and constraints in hybrid genome formation | journal = Nature Ecology & Evolution | volume = 2 | issue = 3 | pages = 549–556 | date = March 2018 | pmid = 29335572 | doi = 10.1038/s41559-017-0437-7 | bibcode = 2018NatEE...2..549R | s2cid = 3375880 }}

File:Figure 2. Schematic representation of homoploid and allopolyploid hybrid speciation. Updated.svg

In general, hybrid species can arise from two major types of hybrid speciation, defined by whether the speciation event is associated with genome duplication (polyploidy) or not. Homoploid hybrid speciation is defined as the evolution of a new hybrid species with reproductive isolation to both parent taxa without change of ploidy, i.e. number of chromosome sets. The genomes of homoploid hybrid species are mosaics of the parent genomes as ancestry tracts from the parent species are broken up by recombination.{{cite journal | vauthors = Buerkle CA, Rieseberg LH | title = The rate of genome stabilization in homoploid hybrid species | journal = Evolution; International Journal of Organic Evolution | volume = 62 | issue = 2 | pages = 266–75 | date = February 2008 | pmid = 18039323 | pmc = 2442919 | doi = 10.1111/j.1558-5646.2007.00267.x }}{{cite journal | vauthors = Ungerer MC, Baird SJ, Pan J, Rieseberg LH | title = Rapid hybrid speciation in wild sunflowers | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 20 | pages = 11757–62 | date = September 1998 | pmid = 9751738 | pmc = 21713 | doi = 10.1073/pnas.95.20.11757 | bibcode = 1998PNAS...9511757U | doi-access = free }}{{cite journal | vauthors = Lai Z, Nakazato T, Salmaso M, Burke JM, Tang S, Knapp SJ, Rieseberg LH | title = Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species | journal = Genetics | volume = 171 | issue = 1 | pages = 291–303 | date = September 2005 | pmid = 16183908 | pmc = 1456521 | doi = 10.1534/genetics.105.042242 }}{{cite journal | vauthors = Elgvin TO, Trier CN, Tørresen OK, Hagen IJ, Lien S, Nederbragt AJ, Ravinet M, Jensen H, Sætre GP | display-authors = 6 | title = The genomic mosaicism of hybrid speciation | journal = Science Advances | volume = 3 | issue = 6 | pages = e1602996 | date = June 2017 | pmid = 28630911 | pmc = 5470830 | doi = 10.1126/sciadv.1602996 | bibcode = 2017SciA....3E2996E }} In the case of polyploid hybrid speciation, hybridisation is associated with genome duplication, resulting in an allopolyploid with increased ploidy compared to their parental taxa. In contrast to allopolyploids, autopolyploids are characterised by genome duplication within the same species and are thus not discussed further in the context of this review. Allopolyploid speciation is more common in plants than in animals.{{cite journal | vauthors = Otto SP, Whitton J | title = Polyploid incidence and evolution | journal = Annual Review of Genetics | volume = 34 | issue = 1 | pages = 401–437 | date = 2000 | pmid = 11092833 | doi = 10.1146/annurev.genet.34.1.401 }} Polyploid hybrids can be instantly isolated from their parental species through chromosome number differences.

Sufficient reproductive isolation from both parental species is required for the successful establishment of a hybrid species.{{cite book | last1=Abbott|first1=Richard J|last2=Rieseberg|first2=Loren H| name-list-style = vanc |date=2012 |title=Hybrid Speciation|language=en|publisher=John Wiley & Sons, Ltd|doi=10.1002/9780470015902.a0001753.pub2|isbn=9780470016176|s2cid=242640180 }} Reproductive isolation against parent species is harder to achieve for homoploid hybrids where karyotype differences do not contribute to intrinsic isolation. Reproductive isolation between a hybrid species and its parental species can arise from a variety of reproductive barriers either before or after fertilization (prezygotic or postzygotic, respectively), which may themselves be dependent or independent of environmental conditions (extrinsic or intrinsic barriers, respectively).{{cite journal | vauthors = Coyne JA | title = Mutation rates in hybrids between sibling species of Drosophila | journal = Heredity | volume = 63 ( Pt 2) | issue = 2 | pages = 155–62 | date = October 1989 | pmid = 2553645 | doi = 10.1038/hdy.1989.87 | doi-access = free }} For example, intrinsic postzygotic barriers cause hybrid inviability or sterility regardless of the environment in which they occur, while extrinsic postzygotic barriers result in hybrids of low fitness due to maladaptation to specific environments.

Prezygotic intrinsic and extrinsic differences have also been shown to be important in isolating hybrids from their parent species. In plants, pollinator mediated isolation resulting from changes in floral characteristics may be an important extrinsic prezygotic ecological barrier.{{cite journal | last1=Chase|first1=Mark W|last2=Paun|first2=Ovidiu|last3=Fay|first3=Michael F| name-list-style = vanc |date=2010|title=Hybridization and speciation in angiosperms: arole for pollinator shifts?|journal=Journal of Biology|language=en|volume=9|issue=3|pages=21|doi=10.1186/jbiol231|issn=1475-4924|doi-access=free}}{{cite journal | vauthors = Grant V | title = Pollination systems as isolating mechanisms in angiosperms | journal = Evolution; International Journal of Organic Evolution | volume = 3 | issue = 1 | pages = 82–97 | date = March 1949 | pmid = 18115119 | doi = 10.1111/j.1558-5646.1949.tb00007.x | doi-access = free }}{{cite journal | vauthors = Segraves KA, Thompson JN | journal = Evolution; International Journal of Organic Evolution | volume = 53 | issue = 4 | pages = 1114–1127 | date = August 1999 | pmid = 28565509 | doi = 10.1111/j.1558-5646.1999.tb04526.x | title = Plant Polyploidy and Pollination: Floral Traits and Insect Visits to Diploid and Tetraploidheuchera Grossulariifolia | s2cid = 28429201 | doi-access = free }}{{cite journal | vauthors = Moe AM, Weiblen GD | title = Pollinator-mediated reproductive isolation among dioecious fig species (Ficus, Moraceae) | journal = Evolution; International Journal of Organic Evolution | volume = 66 | issue = 12 | pages = 3710–21 | date = December 2012 | pmid = 23206130 | doi = 10.1111/j.1558-5646.2012.01727.x | s2cid = 26585628 | doi-access = free }} Strong extrinsic pre-zygotic has been shown to isolate the hybrid species Senecio eboracensis from its parent species, where hybrids are virtually absent in the wild, although a fraction of hybrid offspring are fertile in lab experiments.{{cite journal | vauthors = Lowe AJ, Abbott RJ | title = Reproductive isolation of a new hybrid species, Senecio eboracensis Abbott & Lowe (Asteraceae) | journal = Heredity | volume = 92 | issue = 5 | pages = 386–95 | date = May 2004 | pmid = 15014422 | doi = 10.1038/sj.hdy.6800432 | doi-access = free }} Lowe & Abbott conclude that selfing, timing of flowering and characters involved in pollinator attraction likely contribute to this external isolation. Prezygotic mate preference driven isolation generated from intrinsic assortative mating between hybrids has also been reported in several taxa. In African cichlid fish, experimental hybrids displayed combinations of parental traits and preferences which resulted in hybrids predominantly mating with other hybrids.{{cite journal | vauthors = Selz OM, Thommen R, Maan ME, Seehausen O | title = Behavioural isolation may facilitate homoploid hybrid speciation in cichlid fish | journal = Journal of Evolutionary Biology | volume = 27 | issue = 2 | pages = 275–89 | date = February 2014 | pmid = 24372872 | doi = 10.1111/jeb.12287 | url = https://www.dora.lib4ri.ch/eawag/islandora/object/eawag%3A9027 | doi-access = free }} A similar pattern was found in Geospiza Galapagos finches where a specific hybrid song resulted from the transgressive beak morphology, and hybrid Heliconius butterflies preferred the hybrid wing patterning over that of both parent species. Intrinsic differences in habitat use{{cite journal | last1=Schwarzbach|first1=Andrea E.|last2=Donovan|first2=Lisa A.|last3=Rieseberg|first3=Loren H.| name-list-style = vanc |date=2001|title=Transgressive character expression in a hybrid sunflower species|journal=American Journal of Botany|volume=88|issue=2|pages=270–277|doi=10.2307/2657018|issn=0002-9122|jstor=2657018|pmid=11222249}} or in phenology{{cite journal | last1=Mameli|first1=Giulia|last2=López-Alvarado|first2=Javier|last3=Farris|first3=Emmanuele|last4=Susanna|first4=Alfonso|last5=Filigheddu|first5=Rossella|last6=Garcia-Jacas|first6=Núria| name-list-style = vanc |date=2014|title=The role of parental and hybrid species in multiple introgression events: evidence of homoploid hybrid speciation in Centaurea (Cardueae, Asteraceae): Introgression in Centaurea|journal=Botanical Journal of the Linnean Society|language=en|volume=175|issue=3|pages=453–467|doi=10.1111/boj.12177|doi-access=free}} may result in some degree of reproductive isolation against parent species if mating is time and habitat-specific. For example, the apple host race in Rhagoletis pomonella maggot flies evolved after introgression of diapause related genes from Mexican altiplano flies that allowed a switch from the ancestral host hawthorne to the later flowering apple {{cite journal | vauthors = Xie X, Michel AP, Schwarz D, Rull J, Velez S, Forbes AA, Aluja M, Feder JL | display-authors = 6 | title = Radiation and divergence in the Rhagoletis pomonella species complex: inferences from DNA sequence data | journal = Journal of Evolutionary Biology | volume = 21 | issue = 3 | pages = 900–13 | date = May 2008 | pmid = 18312319 | doi = 10.1111/j.1420-9101.2008.01507.x | doi-access = free }}{{cite journal | vauthors = Feder JL, Xie X, Rull J, Velez S, Forbes A, Leung B, Dambroski H, Filchak KE, Aluja M | display-authors = 6 | title = Mayr, Dobzhansky, and Bush and the complexities of sympatric speciation in Rhagoletis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 Suppl 1 | issue = Supplement 1 | pages = 6573–80 | date = May 2005 | pmid = 15851672 | pmc = 1131876 | doi = 10.1073/pnas.0502099102 | bibcode = 2005PNAS..102.6573F | doi-access = free }} and isolated the two host races via allochronic intrinsic pre-zygotic isolation. In Xiphophorus swordtail fish strong ancestry assortative mating maintained a hybrid genetic cluster separate for 25 generations, but disappeared under manipulated conditions.{{cite journal | vauthors = Schumer M, Powell DL, Delclós PJ, Squire M, Cui R, Andolfatto P, Rosenthal GG | title = Assortative mating and persistent reproductive isolation in hybrids | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 41 | pages = 10936–10941 | date = October 2017 | pmid = 28973863 | pmc = 5642718 | doi = 10.1073/pnas.1711238114 | bibcode = 2017PNAS..11410936S | doi-access = free }} Hence, prezygotic reproductive barriers to gene flow may be environment dependent.

Postzygotic isolating barriers have also been shown to be important in a variety of hybrid lineages. Work on Helianthus sunflowers has revealed that intrinsic postzygotic factors can cause reproductive isolation against the parent species. The postzygotic barriers consist in pre-existing structural differences,{{cite journal | vauthors = Rieseberg LH, Linder CR, Seiler GJ | title = Chromosomal and genic barriers to introgression in Helianthus | journal = Genetics | volume = 141 | issue = 3 | pages = 1163–71 | date = November 1995 | doi = 10.1093/genetics/141.3.1163 | pmid = 8582621 | pmc = 1206838 }} in combination with hybridization induced structural differences. Sorting of incompatibilities between parent species, where one subset of these isolates the hybrid taxon against one parent and a different subset isolates it against the other parent, has resulted in intrinsic postzygotic isolation between the Italian sparrow Passer italiae and its parent species. Simulation studies show that the likelihood of hybrid speciation through this mechanism depends on the divergence time between parent species,{{cite journal | vauthors = Comeault AA, Matute DR | title = Genetic divergence and the number of hybridizing species affect the path to homoploid hybrid speciation | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 115 | issue = 39 | pages = 9761–9766 | date = September 2018 | pmid = 30209213 | pmc = 6166845 | doi = 10.1073/pnas.1809685115 | bibcode = 2018PNAS..115.9761C | doi-access = free }} the population size of the hybrid species,{{cite journal | vauthors = Blanckaert A, Bank C | title = In search of the Goldilocks zone for hybrid speciation | journal = PLOS Genetics | volume = 14 | issue = 9 | pages = e1007613 | date = September 2018 | pmid = 30192761 | pmc = 6145587 | doi = 10.1371/journal.pgen.1007613 | editor-first = Jianzhi | editor-last = Zhang | doi-access = free }} the nature of selection acting on hybrids, and linkage among incompatibilities to each other and to adaptive variants.{{cite journal | vauthors = Schumer M, Cui R, Rosenthal GG, Andolfatto P | title = Reproductive isolation of hybrid populations driven by genetic incompatibilities | journal = PLOS Genetics | volume = 11 | issue = 3 | pages = e1005041 | date = March 2015 | pmid = 25768654 | pmc = 4359097 | doi = 10.1371/journal.pgen.1005041 | editor-first = Bret A. | editor-last = Payseur | doi-access = free }} Extrinsic ecological barriers against parent species may arise as by-products of ecological differentiation if mating is time and/or habitat specific. Hybrid species have been shown to adapt to novel ecological niches through transgressive phenotypes, or through novel combinations of ecological traits from the parent species,{{cite journal | vauthors = Vereecken NJ, Cozzolino S, Schiestl FP | title = Hybrid floral scent novelty drives pollinator shift in sexually deceptive orchids | journal = BMC Evolutionary Biology | volume = 10 | issue = 1 | pages = 103 | date = April 2010 | pmid = 20409296 | pmc = 2875231 | doi = 10.1186/1471-2148-10-103 | bibcode = 2010BMCEE..10..103V | doi-access = free }} and ecological selection against parent-hybrid cross phenotypes would result in extrinsic postzygotic isolation.

File:The process of genome stabilization during hybrid speciation and introgression.tif

Hybridization can have many different outcomes. Hybrid speciation results in reproductive isolation against both parent species and genomes that evolve independently from those of the parent species. Introgressive hybridization can transfer important novel variants into genomes of a species that remains distinct from the other taxa in spite of occasional gene flow. In this article both types of hybridization-derived genomes are referred to as persistent hybrid genomes. Following initial hybridization, introgression tracts, the genetic blocks inherited from each parent species, are broken down with successive generations and recombination events. Recombination is more frequent in homoploid hybrid genomes than in allopolyploid hybrid genomes. In allopolyploids, recombination can destabilize the karyotype and lead to aberrant meiotic behaviour and reduced fertility, but may also generate novel gene combinations and advantageous phenotypic traits {{cite journal | vauthors = Gaeta RT, Chris Pires J | title = Homoeologous recombination in allopolyploids: the polyploid ratchet | journal = The New Phytologist | volume = 186 | issue = 1 | pages = 18–28 | date = April 2010 | pmid = 20002315 | doi = 10.1111/j.1469-8137.2009.03089.x | doi-access = free }} as in homoploid hybrids. Once hybridization between the hybrid taxon and its parent taxa ceases, different ancestry blocks or introgression tracts may become fixed, a process referred to as "genome stabilization". Some introgression tracts are removed by selection against incompatibilities and others are fixed. Theoretical models on hybrid zones suggest that the breakdown of ancestry blocks through recombination is suppressed near genes conferring reproductive isolation due to lower fitness of recombinant hybrids.{{cite journal | vauthors = Hvala JA, Frayer ME, Payseur BA | title = Signatures of hybridization and speciation in genomic patterns of ancestry | journal = Evolution; International Journal of Organic Evolution | volume = 72 | issue = 8 | pages = 1540–1552 | date = May 2018 | pmid = 29806154 | pmc = 6261709 | doi = 10.1111/evo.13509 }} The strength of the suppression is affected by the form of selection, dominance, and whether the locus was situated on an autosome or sex chromosome. The time to genome stabilization is variable. Fixation of ancestry blocks was found to be rapid in experimental hybrid Helianthus sunflower species genomes,{{cite journal | vauthors = Rieseberg LH, Sinervo B, Linder CR, Ungerer MC, Arias DM | s2cid = 39005242 | title = Role of Gene Interactions in Hybrid Speciation: Evidence from Ancient and Experimental Hybrids | journal = Science | volume = 272 | issue = 5262 | pages = 741–5 | date = May 1996 | pmid = 8662570 | doi = 10.1126/science.272.5262.741 | bibcode = 1996Sci...272..741R }} and the genome stabilization of hybrid sunflower species is estimated to take hundreds of generations. In Zymoseptoria fungi genomes were stabilized within ca. 400 generations,{{cite journal | vauthors = Stukenbrock EH, Christiansen FB, Hansen TT, Dutheil JY, Schierup MH | title = Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 109 | issue = 27 | pages = 10954–9 | date = July 2012 | pmid = 22711811 | pmc = 3390827 | doi = 10.1073/pnas.1201403109 | bibcode = 2012PNAS..10910954S | doi-access = free }} whereas in hybrid Xiphophorus swordtail genomes{{cite journal | vauthors = Schumer M, Brandvain Y | title = Determining epistatic selection in admixed populations | journal = Molecular Ecology | volume = 25 | issue = 11 | pages = 2577–91 | date = June 2016 | pmid = 27061282 | doi = 10.1111/mec.13641 | bibcode = 2016MolEc..25.2577S | s2cid = 10566380 }} genome stabilization was not achieved until after ca. 2000 and 2500 generations. Few Neanderthal regions have fixed in human genomes during the ca. 2000 generations after hybridization,{{cite journal | vauthors = Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D | display-authors = 6 | title = The genomic landscape of Neanderthal ancestry in present-day humans | journal = Nature | volume = 507 | issue = 7492 | pages = 354–7 | date = March 2014 | pmid = 24476815 | pmc = 4072735 | doi = 10.1038/nature12961 | bibcode = 2014Natur.507..354S }} and segregating incompatibilities are present in the hybrid Italian sparrow approximately 5000 generations after the initial hybridization event.{{cite journal | last1=Eroukhmanoff|first1=Fabrice|last2=Bailey|first2=Richard I.|last3=Elgvin|first3=Tore O.|last4=Hermansen|first4=Jo S.|last5=Runemark|first5=Anna R.|last6=Trier|first6=Cassandra N.|last7=Sætre|first7=Glenn-Peter| name-list-style = vanc |date=2017|title=Resolution of conflict between parental genomes in a hybrid species|journal=bioRxiv|doi=10.1101/102970|doi-access=free|hdl=20.500.11820/e14c46c6-ef76-41a4-a76d-88604ba5b30b|hdl-access=free}}

Given time, genetic drift will eventually stochastically fix blocks derived from the two parent species in finite isolated hybrid populations. Selection against incompatibility loci may accelerate the process of fixation of parental alleles as hybrids that possess alleles that are less likely to cause incompatibility will have higher fitness and favourable alleles will spread in the population. Fixation of recessive weakly deleterious alleles in the parent taxa may, however, also result in hybrids retaining both parental alleles: because hybrids with haplotypes from both parents are not homozygous for any weakly deleterious alleles, they have higher fitness than hybrids with only one parental haplotype. This associative overdominance,{{cite journal | last=Ohta|first=Tomoko| name-list-style = vanc |date=1971|title=Associative overdominance caused by linked detrimental mutations|journal=Genetical Research|volume=18|issue=3|pages=277–286|doi=10.1017/s0016672300012684|pmid=5158298|issn=0016-6723|doi-access=free}}{{cite journal | vauthors = Zhao L, Charlesworth B | title = Resolving the Conflict Between Associative Overdominance and Background Selection | journal = Genetics | volume = 203 | issue = 3 | pages = 1315–34 | date = July 2016 | pmid = 27182952 | pmc = 4937488 | doi = 10.1534/genetics.116.188912 }} may slow down the process of fixation of parental alleles through favouring retention of both parental haplotypes. The effect of associative overdominance is strongest in low recombination regions, including inversions.{{cite journal |author2-link=Kerstin Johannesson| vauthors = Faria R, Johannesson K, Butlin RK, Westram AM | title = Evolving Inversions | journal = Trends in Ecology & Evolution | volume = 34 | issue = 3 | pages = 239–248 | date = March 2019 | pmid = 30691998 | doi = 10.1016/j.tree.2018.12.005 | doi-access = free }} The balance between alleles and allelic combinations providing favourable phenotypic characters and the strength of selection against incompatibilities determine what introgression tracts will be inherited from which parent species upon hybridization.{{cite journal | vauthors = Barton NH | title = The consequences of an introgression event | journal = Molecular Ecology | volume = 27 | issue = 24 | pages = 4973–4975 | date = December 2018 | pmid = 30599087 | doi = 10.1111/mec.14950 | bibcode = 2018MolEc..27.4973B | doi-access = free }}{{cite journal | vauthors = Martin SH, Davey JW, Salazar C, Jiggins CD | title = Recombination rate variation shapes barriers to introgression across butterfly genomes | journal = PLOS Biology | volume = 17 | issue = 2 | pages = e2006288 | date = February 2019 | pmid = 30730876 | pmc = 6366726 | doi = 10.1371/journal.pbio.2006288 | editor-first = Leonie | editor-last = Moyle | doi-access = free }} An insecticide resistance region was retained following a hybridization event in Anopheles coluzzi, suggesting a role for selection in maintaining favourable introgressed regions. The local recombination rate is important for the likelihood of introgression because in the case of widespread incompatibilities, introgressed alleles are more likely to recombine away from incompatibilities in high recombination regions. This pattern has been detected in monkeyflowers Mimulus,{{cite journal | vauthors = Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL | title = Speciation and introgression between Mimulus nasutus and Mimulus guttatus | journal = PLOS Genetics | volume = 10 | issue = 6 | pages = e1004410 | date = June 2014 | pmid = 24967630 | pmc = 4072524 | doi = 10.1371/journal.pgen.1004410 | editor-first = Chris D. | editor-last = Jiggins | doi-access = free }} in Mus domesticus house mice,{{cite journal | vauthors = Janoušek V, Munclinger P, Wang L, Teeter KC, Tucker PK | title = Functional organization of the genome may shape the species boundary in the house mouse | journal = Molecular Biology and Evolution | volume = 32 | issue = 5 | pages = 1208–20 | date = May 2015 | pmid = 25631927 | pmc = 4408407 | doi = 10.1093/molbev/msv011 }} in Heliconius butterflies and in Xiphophorus swordtail fish.

Genome-wide incompatibilities have been identified in Xipophorous fish,{{cite journal | vauthors = Schumer M, Cui R, Powell DL, Dresner R, Rosenthal GG, Andolfatto P | title = High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species | journal = eLife | volume = 3 | date = June 2014 | pmid = 24898754 | pmc = 4080447 | doi = 10.7554/eLife.02535 | doi-access = free }} chimeric genes and mutations of orthologous genes cause incompatibilities in early generation experimental Cyprinidae goldfish - carp hybrids{{cite journal | vauthors = Liu S, Luo J, Chai J, Ren L, Zhou Y, Huang F, Liu X, Chen Y, Zhang C, Tao M, Lu B, Zhou W, Lin G, Mai C, Yuan S, Wang J, Li T, Qin Q, Feng H, Luo K, Xiao J, Zhong H, Zhao R, Duan W, Song Z, Wang Y, Wang J, Zhong L, Wang L, Ding Z, Du Z, Lu X, Gao Y, Murphy RW, Liu Y, Meyer A, Zhang YP | display-authors = 6 | title = Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 5 | pages = 1327–32 | date = February 2016 | pmid = 26768847 | pmc = 4747765 | doi = 10.1073/pnas.1512955113 | bibcode = 2016PNAS..113.1327L | doi-access = free }} and mito-nuclear incompatibilies are found to have a key role e.g. in Italian sparrows,{{cite journal | vauthors = Trier CN, Hermansen JS, Sætre GP, Bailey RI | title = Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species | journal = PLOS Genetics | volume = 10 | issue = 1 | pages = e1004075 | date = January 2014 | pmid = 24415954 | pmc = 3886922 | doi = 10.1371/journal.pgen.1004075 | editor-first = Chris D. | editor-last = Jiggins | doi-access = free }} fungus{{cite journal | vauthors = Giordano L, Sillo F, Garbelotto M, Gonthier P | title = Mitonuclear interactions may contribute to fitness of fungal hybrids | journal = Scientific Reports | volume = 8 | issue = 1 | pages = 1706 | date = January 2018 | pmid = 29374209 | pmc = 5786003 | doi = 10.1038/s41598-018-19922-w | bibcode = 2018NatSR...8.1706G }} and cyto-nuclear incompatibilities in Mimulus plants.{{cite journal | vauthors = Case AL, Finseth FR, Barr CM, Fishman L | title = Selfish evolution of cytonuclear hybrid incompatibility in Mimulus | journal = Proceedings. Biological Sciences | volume = 283 | issue = 1838 | pages = 20161493 | date = September 2016 | pmid = 27629037 | pmc = 5031664 | doi = 10.1098/rspb.2016.1493 }} Evidence from altered expression patterns in synthetic hybrids and missing gene combinations in a hybrid species also suggest that DNA-repair{{cite journal | vauthors = David WM, Mitchell DL, Walter RB | title = DNA repair in hybrid fish of the genus Xiphophorus | journal = Comparative Biochemistry and Physiology. Toxicology & Pharmacology | volume = 138 | issue = 3 | pages = 301–9 | date = July 2004 | pmid = 15533788 | doi = 10.1016/j.cca.2004.07.006 }} and genes involved in mutagenesis and cancer related pathways may cause incompatibilities in hybrids. Genome formation in hybrid species is shaped by selection against incompatible combinations.

The hybrid origin may affect genome structure and properties. It has been shown to increase mutation rates,{{cite journal | vauthors = Avila V, Chavarrías D, Sánchez E, Manrique A, López-Fanjul C, García-Dorado A | title = Increase of the spontaneous mutation rate in a long-term experiment with Drosophila melanogaster | journal = Genetics | volume = 173 | issue = 1 | pages = 267–77 | date = May 2006 | pmid = 16547099 | pmc = 1461422 | doi = 10.1534/genetics.106.056200 }}{{cite journal | vauthors = Bashir T, Sailer C, Gerber F, Loganathan N, Bhoopalan H, Eichenberger C, Grossniklaus U, Baskar R | display-authors = 6 | title = Hybridization alters spontaneous mutation rates in a parent-of-origin-dependent fashion in Arabidopsis | journal = Plant Physiology | volume = 165 | issue = 1 | pages = 424–37 | date = May 2014 | pmid = 24664208 | pmc = 4012600 | doi = 10.1104/pp.114.238451 }} to activate transposable elements,{{cite journal | vauthors = Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li XY, Altmüller J, Nolte AW | title = Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin | journal = Molecular Ecology | volume = 26 | issue = 18 | pages = 4712–4724 | date = September 2017 | pmid = 28390096 | pmc = 5638112 | doi = 10.1111/mec.14134 | bibcode = 2017MolEc..26.4712D }}{{cite journal | vauthors = Dion-Côté AM, Renaut S, Normandeau E, Bernatchez L | title = RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species | journal = Molecular Biology and Evolution | volume = 31 | issue = 5 | pages = 1188–99 | date = May 2014 | pmid = 24505119 | doi = 10.1093/molbev/msu069 | doi-access = free }}{{cite journal | vauthors = Senerchia N, Felber F, Parisod C | title = Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation | journal = Proceedings. Biological Sciences | volume = 282 | issue = 1804 | pages = 20142874 | date = April 2015 | pmid = 25716787 | pmc = 4375867 | doi = 10.1098/rspb.2014.2874 }} and to induce chromosomal rearrangements.{{cite journal | vauthors = Ostberg CO, Hauser L, Pritchard VL, Garza JC, Naish KA | title = Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss) | journal = BMC Genomics | volume = 14 | issue = 1 | pages = 570 | date = August 2013 | pmid = 23968234 | pmc = 3765842 | doi = 10.1186/1471-2164-14-570 | doi-access = free }}{{cite journal | vauthors = Hirai H, Hirai Y, Morimoto M, Kaneko A, Kamanaka Y, Koga A | title = Night Monkey Hybrids Exhibit De Novo Genomic and Karyotypic Alterations: The First Such Case in Primates | journal = Genome Biology and Evolution | volume = 9 | issue = 4 | pages = 945–955 | date = April 2017 | pmid = 28369492 | pmc = 5388293 | doi = 10.1093/gbe/evx058 }} Increased transposon activation, as proposed in McClintock's ‘genomic shock’ theory, could result in alterations to gene expression. Transposable elements may, in addition to altering gene products if inserted into a gene, also alter promoter activity for genes if inserted upstream of the coding regions, or may induce gene silencing as a result of gene disruption.{{cite journal | vauthors = Barkan A, Martienssen RA | title = Inactivation of maize transposon Mu suppresses a mutant phenotype by activating an outward-reading promoter near the end of Mu1 | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 88 | issue = 8 | pages = 3502–6 | date = April 1991 | pmid = 1849660 | pmc = 51476 | doi = 10.1073/pnas.88.8.3502 | bibcode = 1991PNAS...88.3502B | doi-access = free }}{{cite journal | last1=Raizada|first1=Manish N.|last2=Benito|first2=Maria-Ines|last3=Walbot|first3=Virginia|s2cid=26084899| name-list-style = vanc |date=2008|title=The MuDR transposon terminal inverted repeat contains a complex plant promoter directing distinct somatic and germinal programs: Transposon promoter expression pattern|journal=The Plant Journal|language=en|volume=25|issue=1|pages=79–91|doi=10.1111/j.1365-313X.2001.00939.x|doi-access=free}} For allopolyploid genomes chromosomal rearrangements may result from the "genomic shock" induced by hybridisation, with more distantly related species being more prone to genome reorganisations e.g. in Nicotiana.{{cite journal | last1=Lim|first1=Kar Yoong|last2=Matyasek|first2=Roman|last3=Kovarik|first3=Ales|last4=Leitch|first4=Andrew R.| name-list-style = vanc |date=2004|title=Genome evolution in allotetraploid Nicotiana|journal=Biological Journal of the Linnean Society|language=en|volume=82|issue=4|pages=599–606|doi=10.1111/j.1095-8312.2004.00344.x|doi-access=free}} Chromosomal rearrangements resulting from either genomic shock or recombination events between non-homologous subgenomes may cause genome sizes to either increase or decrease.{{cite journal | vauthors = Baack EJ, Whitney KD, Rieseberg LH | title = Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species | journal = The New Phytologist | volume = 167 | issue = 2 | pages = 623–30 | date = August 2005 | pmid = 15998412 | pmc = 2442926 | doi = 10.1111/j.1469-8137.2005.01433.x }} Both increases and decreases were found in the Nicotiana genus, and were not related to the age since hybridization.{{cite journal | vauthors = Leitch IJ, Hanson L, Lim KY, Kovarik A, Chase MW, Clarkson JJ, Leitch AR | title = The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae) | journal = Annals of Botany | volume = 101 | issue = 6 | pages = 805–14 | date = April 2008 | pmid = 18222910 | pmc = 2710205 | doi = 10.1093/aob/mcm326 }}

Following genome duplication in allopolyploids, the genome goes through diploidization, which is a process in which the genome is rearranged to act as a meiotic diploid.{{cite journal | vauthors = Wolfe KH | title = Yesterday's polyploids and the mystery of diploidization | journal = Nature Reviews. Genetics | volume = 2 | issue = 5 | pages = 333–41 | date = May 2001 | pmid = 11331899 | doi = 10.1038/35072009 | doi-access = free }}{{cite journal | vauthors = Freeling M, Scanlon MJ, Fowler JE | title = Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences | journal = Current Opinion in Genetics & Development | volume = 35 | pages = 110–8 | date = December 2015 | pmid = 26657818 | doi = 10.1016/j.gde.2015.11.002 }} After such diploidization, much of the genome is lost due to genome fractionation, the loss-of-function of one or the other of the newly duplicated genes.{{cite journal | vauthors = Sankoff D, Zheng C, Zhu Q | title = The collapse of gene complement following whole genome duplication | journal = BMC Genomics | volume = 11 | issue = 1 | pages = 313 | date = May 2010 | pmid = 20482863 | pmc = 2896955 | doi = 10.1186/1471-2164-11-313 | doi-access = free }} In a meta analysis, Sankoff and collaborators found evidence consistent with reduction-resistant pairs and a concentration of functional genes on a single chromosome and suggest that the reduction process partly is constrained.

A related allopolyploid specific phenomenon is subgenome dominance. For example, in the octoploid Fragaria strawberry, one of the four subgenomes is dominant and has significantly greater gene content, more frequently has its genes expressed, and exchanges between homologous chromosomes are biased in favour of this subgenome, as compared with the other subgenomes.{{cite journal | vauthors = Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson AD, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ | display-authors = 6 | title = Origin and evolution of the octoploid strawberry genome | journal = Nature Genetics | volume = 51 | issue = 3 | pages = 541–547 | date = March 2019 | pmid = 30804557 | doi = 10.1038/s41588-019-0356-4 | pmc = 6882729 | doi-access = free }} This study also showed that certain traits, e.g. disease-resistance, are controlled by the dominant subgenome to a high extent. A proposed mechanism of how subgenome dominance arises, suggests that relative dominance is related to the density of transposable elements in each subgenome. Subgenomes with higher transposable element density tend to behave submissively relative to the other subgenomes when brought together in the allopolyploid genome.{{cite journal | vauthors = Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan Y, Bewick AJ, Ji L, Platts AE, Bowman MJ, Childs KL, Washburn JD, Schmitz RJ, Smith GD, Pires JC, Puzey JR | display-authors = 6 | title = Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower | journal = The Plant Cell | volume = 29 | issue = 9 | pages = 2150–2167 | date = September 2017 | pmid = 28814644 | pmc = 5635986 | doi = 10.1105/tpc.17.00010 }} Interestingly, subgenome dominance can arise immediately in allopolyploids, as shown in synthetic and recently evolved monkeyflowers.

In addition to these changes to genome structure and properties, studies of allopolyploid rice and whitefish suggest that patterns of gene expression may be disrupted in hybrid species.{{cite journal | vauthors = Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B | display-authors = 6 | title = Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies | journal = Molecular Biology and Evolution | volume = 31 | issue = 5 | pages = 1066–76 | date = May 2014 | pmid = 24577842 | pmc = 3995341 | doi = 10.1093/molbev/msu085 }}{{cite journal | vauthors = Renaut S, Nolte AW, Bernatchez L | title = Gene expression divergence and hybrid misexpression between lake whitefish species pairs (Coregonus spp. Salmonidae) | journal = Molecular Biology and Evolution | volume = 26 | issue = 4 | pages = 925–36 | date = April 2009 | pmid = 19174479 | doi = 10.1093/molbev/msp017 | doi-access = free }} Studies of synthetic and natural allopolyploids of Tragopogon miscellus show that gene expression is less strictly regulated directly after hybridization, and that novel patterns of expression emerge and are stabilized during 40 generations.{{cite journal | vauthors = Buggs RJ, Zhang L, Miles N, Tate JA, Gao L, Wei W, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE | display-authors = 6 | title = Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant | journal = Current Biology | volume = 21 | issue = 7 | pages = 551–6 | date = April 2011 | pmid = 21419627 | doi = 10.1016/j.cub.2011.02.016 | s2cid = 18417406 | doi-access = free | bibcode = 2011CBio...21..551B }} While expression variation in miRNAs alters gene expression and affects growth in the natural allopolyploid Arabidopsis suecica and experimental lineages, inheritance of siRNAs is stable and maintains chromatin and genome stability,{{cite journal | vauthors = Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ, Chen ZJ | display-authors = 6 | title = Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 42 | pages = 17835–40 | date = October 2009 | pmid = 19805056 | pmc = 2757398 | doi = 10.1073/pnas.0907003106 | bibcode = 2009PNAS..10617835H | doi-access = free }} potentially buffering against a transcriptomic shock.

Whereas hybridization is required for the generation of persistent hybrid genomes, it is not sufficient. For the persistence of hybrid genomes in hybrid species they need to be sufficiently reproductively isolated from their parent species to avoid species fusion. Selection on introgressed variants allows the persistence of hybrid genomes in introgressed lineages. Frequency of hybridization, viability of hybrids, and the ease at which reproductive isolation against the parent species arises or strength of selection to maintain introgressed regions are hence factors influencing the rate of formation of stable hybrid lineages.

Few general conclusions about the relative prevalence of hybridization can be drawn, as sampling is not evenly distributed, even if there is evidence for hybridization in an increasing number of taxa. One pattern that emerges is that hybridization is more frequent in plants where it occurs in 25% of the species, whereas it only occurs in 10% of animal species.{{cite journal | vauthors = Mallet J | title = Hybridization as an invasion of the genome | journal = Trends in Ecology & Evolution | volume = 20 | issue = 5 | pages = 229–37 | date = May 2005 | pmid = 16701374 | doi = 10.1016/j.tree.2005.02.010 }} Most plants, as well as many groups of animals, lack heteromorphic sex chromosomes.{{cite journal | vauthors = Charlesworth D | title = Plant Sex Chromosomes | journal = Annual Review of Plant Biology | volume = 67 | issue = 1 | pages = 397–420 | date = April 2016 | pmid = 26653795 | doi = 10.1146/annurev-arplant-043015-111911 }} The absence of heteromorphic sex chromosomes results in slower accumulation of reproductive isolation,{{cite journal | last=Rieseberg|first=Loren H.| name-list-style = vanc |date=2001|title=Chromosomal rearrangements and speciation|journal=Trends in Ecology & Evolution|volume=16|issue=7|pages=351–358|doi=10.1016/s0169-5347(01)02187-5|pmid=11403867|issn=0169-5347}}{{cite journal | vauthors = Levin DA | title = The long wait for hybrid sterility in flowering plants | journal = The New Phytologist | volume = 196 | issue = 3 | pages = 666–70 | date = November 2012 | pmid = 22966819 | doi = 10.1111/j.1469-8137.2012.04309.x | doi-access = free }} and may hence enable hybridization between phylogenetically more distant taxa. Haldane's rule{{cite journal | last=Haldane|first=J. B. S.| name-list-style = vanc |date=1922|title=Sex ratio and unisexual sterility in hybrid animals|journal=Journal of Genetics|language=en|volume=12|issue=2|pages=101–109|doi=10.1007/BF02983075|s2cid=32459333|issn=0022-1333|url=https://zenodo.org/record/1428440}} states that "when F1 offspring of two different animal races one sex is absent, rare, or sterile, that sex is the heterozygous sex". Empirical evidence supports a role for heteromorphic sex chromosomes in hybrid sterility and inviability. A closely related observation is the large X effect stating that there is a disproportionate contribution of the X/Z-chromosome in fitness reduction of heterogametic hybrids. These patterns likely arise as recessive alleles with deleterious effects in hybrids have a stronger impacts on the heterogametic than the homogametic sex, due to hemizygous expression.{{cite journal | vauthors = Turelli M, Orr HA | title = The dominance theory of Haldane's rule | journal = Genetics | volume = 140 | issue = 1 | pages = 389–402 | date = May 1995 | doi = 10.1093/genetics/140.1.389 | pmid = 7635302 | pmc = 1206564 }} In taxa with well-differentiated sex chromosomes, Haldane’s rule has shown to be close to universal, and heteromorphic sex chromosomes show reduced introgression on the X in XY.{{cite journal | vauthors = Runemark A, Eroukhmanoff F, Nava-Bolaños A, Hermansen JS, Meier JI | title = Hybridization, sex-specific genomic architecture and local adaptation | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 373 | issue = 1757 | pages = 20170419 | date = October 2018 | pmid = 30150218 | pmc = 6125728 | doi = 10.1098/rstb.2017.0419 }} In line with a role for heteromorphic sex chromosomes in constraining hybrid genome formation, elevated differentiation on sex chromosomes has been observed in both ZW and XY systems.{{cite journal | vauthors = Payseur BA, Rieseberg LH | title = A genomic perspective on hybridization and speciation | journal = Molecular Ecology | volume = 25 | issue = 11 | pages = 2337–60 | date = June 2016 | pmid = 26836441 | pmc = 4915564 | doi = 10.1111/mec.13557 | bibcode = 2016MolEc..25.2337P }} This pattern may reflect the lower effective population sizes and higher susceptibility to drift on the sex chromosomes,{{cite book|title=Genetics and analysis of quantitative traits|last=Lynch|first=Michael| name-list-style = vanc |date=1998|publisher=Sinauer|others=Walsh, Bruce, 1957-|isbn=0878934812|location=Sunderland, Mass.|oclc=37030646}} the elevated frequency of loci involved in reproductive isolation{{cite journal | vauthors = Masly JP, Presgraves DC | title = High-resolution genome-wide dissection of the two rules of speciation in Drosophila | journal = PLOS Biology | volume = 5 | issue = 9 | pages = e243 | date = September 2007 | pmid = 17850182 | pmc = 1971125 | doi = 10.1371/journal.pbio.0050243 | editor-first = Nick H | editor-last = Barton | doi-access = free }} and/or the heightened conflict on sex chromosomes.{{cite journal | vauthors = Mank JE, Hosken DJ, Wedell N | title = Conflict on the sex chromosomes: cause, effect, and complexity | journal = Cold Spring Harbor Perspectives in Biology | volume = 6 | issue = 12 | pages = a017715 | date = October 2014 | pmid = 25280765 | pmc = 4292157 | doi = 10.1101/cshperspect.a017715 }} Findings of selection for uniparental inheritance of e.g. mitonuclear loci residing on the Z chromosome in hybrid Italian sparrows is consistent with compatible sex chromosomes being important for the formation of a viable hybrid genomes.

There are also several ecological factors that affect the probability of hybridization. Generally, hybridization is more frequently observed in species with external fertilization including plants but also fishes, than in internally fertilized clades. In plants, high rates of selfing in some species may prevent hybridization, and breeding system may also affect the frequency of heterospecific pollen transfer.{{cite journal | vauthors = Brys R, Vanden Broeck A, Mergeay J, Jacquemyn H | title = The contribution of mating system variation to reproductive isolation in two closely related Centaurium species (Gentianaceae) with a generalized flower morphology | journal = Evolution; International Journal of Organic Evolution | volume = 68 | issue = 5 | pages = 1281–93 | date = May 2014 | pmid = 24372301 | doi = 10.1111/evo.12345 | doi-access = free }}{{cite journal | vauthors = Widmer A, Lexer C, Cozzolino S | title = Evolution of reproductive isolation in plants | journal = Heredity | volume = 102 | issue = 1 | pages = 31–8 | date = January 2009 | pmid = 18648386 | doi = 10.1038/hdy.2008.69 | doi-access = free }} In fungi, hybrids can be generated by ameiotic fusion of cells or hyphae{{cite journal | vauthors = Schardl CL, Craven KD | title = Interspecific hybridization in plant-associated fungi and oomycetes: a review | journal = Molecular Ecology | volume = 12 | issue = 11 | pages = 2861–73 | date = November 2003 | pmid = 14629368 | doi = 10.1046/j.1365-294x.2003.01965.x | bibcode = 2003MolEc..12.2861S | s2cid = 25879264 | doi-access = free }} in addition to mechanisms available to plants and animals. Such fusion of vegetative cells and subsequent parasexual mating with mitotic crossover may generate recombined hybrid cells.

For hybrid species to evolve, reproductive isolation against the parent species is required. The ease by which such reproductive isolation arises is thus also important for the rate at which stable hybrid species arise. Polyploidisation and asexuality are both mechanisms that result in instantaneous isolation and may increase the rate of hybrid lineage formation. The ability to self-pollinate may also act in favour of stabilising allopolyploid taxa by providing a compatible mate (itself) in the early stages of allopolyploid speciation when rare cytotypes are at a reproductive disadvantage due to inter-cytotype mating.{{cite journal | last=Levin|first=Donald A.| name-list-style = vanc |date=1975|title=Minority Cytotype Exclusion in Local Plant Populations|journal=Taxon|language=en|volume=24|issue=1|pages=35–43|doi=10.2307/1218997|jstor=1218997}} Selfing is also expected to increase the likelihood of establishment for homoploid hybrids according to a modelling study,{{cite journal | last1=McCarthy|first1=Eugene M|last2=Asmussen|first2=Marjorie A|last3=Anderson|first3=Wyatt W| name-list-style = vanc |date=1995|title=A theoretical assessment of recombinational speciation|journal=Heredity|language=en|volume=74|issue=5|pages=502–509|doi=10.1038/hdy.1995.71|issn=0018-067X|doi-access=free}} and the higher probability of selfing may contribute to the higher frequency of hybrid species in plants. Fungal hybridization may result in asexual hybrid species, as Epichloe fungi where hybrids species are asexual while nonhybrids include both asexual and sexual species.{{cite journal | vauthors = Charlton ND, Craven KD, Afkhami ME, Hall BA, Ghimire SR, Young CA | title = Interspecific hybridization and bioactive alkaloid variation increases diversity in endophytic Epichloë species of Bromus laevipes | journal = FEMS Microbiology Ecology | volume = 90 | issue = 1 | pages = 276–89 | date = October 2014 | pmid = 25065688 | doi = 10.1111/1574-6941.12393 | bibcode = 2014FEMME..90..276C | doi-access = free }} Hybridization between strongly divergent animal taxa may also generate asexual hybrid species, as shown e.g. in the European spined loaches, Cobitis,{{cite journal | vauthors = Janko K, Pačes J, Wilkinson-Herbots H, Costa RJ, Roslein J, Drozd P, Iakovenko N, Rídl J, Hroudová M, Kočí J, Reifová R, Šlechtová V, Choleva L | display-authors = 6 | title = Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation | journal = Molecular Ecology | volume = 27 | issue = 1 | pages = 248–263 | date = January 2018 | pmid = 28987005 | pmc = 6849617 | doi = 10.1111/mec.14377 | bibcode = 2018MolEc..27..248J }} and most if not all asexual vertebrate species are of hybrid origin.{{cite journal | vauthors = Neaves WB, Baumann P | title = Unisexual reproduction among vertebrates | journal = Trends in Genetics | volume = 27 | issue = 3 | pages = 81–8 | date = March 2011 | pmid = 21334090 | doi = 10.1016/j.tig.2010.12.002 }} Interestingly, Arctic floras harbour an unusually high proportion of allopolyploid plants,{{cite journal | vauthors = Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen AC, Elven R |date=2004|title=Polyploidy in arctic plants|journal=Biological Journal of the Linnean Society|language=en|volume=82|issue=4|pages=521–536|doi=10.1111/j.1095-8312.2004.00337.x|doi-access=free}} suggesting that these hybrid taxa could have an advantage in extreme environments, potentially through reducing the negative effects of inbreeding. Hence both genomic architecture and ecological properties may affect the probability of hybrid species formation.

For introgressed taxa, the strength of selection on introgressed variants decides whether introgressed sections will spread in the population and stable introgressed genomes will be formed. Strong selection for insecticide resistance has been shown to increase introgression of an Anopheles gambiae resistance allele into A. coluzzi malaria mosquitoes.{{cite journal | vauthors = Norris LC, Main BJ, Lee Y, Collier TC, Fofana A, Cornel AJ, Lanzaro GC | title = Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 3 | pages = 815–20 | date = January 2015 | pmid = 25561525 | pmc = 4311837 | doi = 10.1073/pnas.1418892112 | bibcode = 2015PNAS..112..815N | doi-access = free }} In Heliconius butterflies, strong selection on having the locally abundant wing colour patterns repeatedly led to fixation of alleles that introgressed from locally adapted butterflies into newly colonizing species or subspecies. Chances of fixation of beneficial introgressed variants depend on the type and strength of selection on the introgressed variant and linkage with other introgressed variants that are selected against.

Genetic exchange can occur between populations or incipient species diverging in geographical proximity or between divergent taxa that come into secondary contact. Hybridization between more diverged lineages is expected to have a greater potential to contribute beneficial alleles or generate novelty than hybridization between less diverged populations because more divergent alleles are combined, and are thus more likely to have a large fitness effect, to generate transgressive phenotypes.{{cite journal | vauthors = Marques DA, Meier JI, Seehausen O | title = A Combinatorial View on Speciation and Adaptive Radiation | journal = Trends in Ecology & Evolution | volume = 34 | issue = 6 | pages = 531–544 | date = June 2019 | pmid = 30885412 | doi = 10.1016/j.tree.2019.02.008 | s2cid = 83462549 | url = https://www.dora.lib4ri.ch/eawag/islandora/object/eawag%3A18534 }} Hybridization between more diverged lineages is also more likely to generate incompatible allele combinations, reducing initial hybrid fitness{{cite journal | vauthors = Maheshwari S, Barbash DA | title = The genetics of hybrid incompatibilities | journal = Annual Review of Genetics | volume = 45 | issue = 1 | pages = 331–55 | date = 2011 | pmid = 21910629 | doi = 10.1146/annurev-genet-110410-132514 }} but potentially also contributing to hybrid speciation if they are sorted reciprocally as described above. An intermediate genetic distance may thus be most conducive to hybrid speciation. Experimental lab crosses support this hypothesis.

The proportion of the genome that is inherited from the recipient of introgressed material varies strongly among and within species. After the initial hybridization event the representation is 50% in many polyploid taxa, although parental gene copies are successively lost and might bias the contribution to one majority parent genome.{{cite journal | vauthors = Buggs RJ, Doust AN, Tate JA, Koh J, Soltis K, Feltus FA, Paterson AH, Soltis PS, Soltis DE | display-authors = 6 | title = Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids | journal = Heredity | volume = 103 | issue = 1 | pages = 73–81 | date = July 2009 | pmid = 19277058 | doi = 10.1038/hdy.2009.24 | doi-access = free }} Relatively equal parental contributions are also found in some homoploid hybrid species but in other cases they are highly unequal such as in some Heliconius species.{{cite journal | vauthors = Jiggins CD, Salazar C, Linares M, Mavarez J | title = Review. Hybrid trait speciation and Heliconius butterflies | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 363 | issue = 1506 | pages = 3047–54 | date = September 2008 | pmid = 18579480 | pmc = 2607310 | doi = 10.1098/rstb.2008.0065 }} The majority ancestry may even be that from the donor of introgressed material, as was shown for Anopheles gambiae mosquitoes.{{cite journal | vauthors = Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ | display-authors = 6 | title = Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics | journal = Science | volume = 347 | issue = 6217 | pages = 1258524 | date = January 2015 | pmid = 25431491 | pmc = 4380269 | doi = 10.1126/science.1258524 }} Interestingly there may also be variation in parental contribution within a hybrid species. In both swordtail fish and Italian sparrows there are populations which differ strongly in what proportions of the parent genomes they have inherited.

Patterns of introgression can vary strongly across the genome, even over short chromosomal distances. Examples of adaptive introgression of well defined regions, include an inversed region containing genes involved in insecticide resistance and introgression of a divergent, inverted chromosomal segment has resulted in a "super gene" that encodes mimicry polymorphism in the butterfly Heliconius numata.{{cite journal | vauthors = Jay P, Whibley A, Frézal L, Rodríguez de Cara MÁ, Nowell RW, Mallet J, Dasmahapatra KK, Joron M | display-authors = 6 | title = Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion | journal = Current Biology | volume = 28 | issue = 11 | pages = 1839–1845.e3 | date = June 2018 | pmid = 29804810 | doi = 10.1016/j.cub.2018.04.072 | doi-access = free | bibcode = 2018CBio...28E1839J }} These findings are consistent with models suggesting that genomic rearrangements are important for the coupling of locally adaptive loci.{{cite journal | vauthors = Yeaman S | title = Genomic rearrangements and the evolution of clusters of locally adaptive loci | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 19 | pages = E1743-51 | date = May 2013 | pmid = 23610436 | pmc = 3651494 | doi = 10.1073/pnas.1219381110 | bibcode = 2013PNAS..110E1743Y | doi-access = free }} Genes and genomic regions that are adaptive may be readily introgressed between species e.g. in hybrid zones if they are not linked to incompatibility loci. This often referred to semi-permeable species boundaries,{{cite journal | last=Wu|first=Chung-I|s2cid=54863357| name-list-style = vanc |date=2001|title=The genic view of the process of speciation: Genic view of the process of speciation|journal=Journal of Evolutionary Biology|language=en|volume=14|issue=6|pages=851–865|doi=10.1046/j.1420-9101.2001.00335.x}}{{cite journal | vauthors = Harrison RG, Larson EL | title = Hybridization, introgression, and the nature of species boundaries | journal = The Journal of Heredity | volume = 105 Suppl 1 | issue = S1 | pages = 795–809 | date = 2014 | pmid = 25149255 | doi = 10.1093/jhered/esu033 | doi-access = free }} and examples include e.g. genes involved in olfaction that are introgressed across a Mus musculus and M. domesticus hybrid zone.{{cite journal | vauthors = Teeter KC, Payseur BA, Harris LW, Bakewell MA, Thibodeau LM, O'Brien JE, Krenz JG, Sans-Fuentes MA, Nachman MW, Tucker PK | display-authors = 6 | title = Genome-wide patterns of gene flow across a house mouse hybrid zone | journal = Genome Research | volume = 18 | issue = 1 | pages = 67–76 | date = January 2008 | pmid = 18025268 | pmc = 2134771 | doi = 10.1101/gr.6757907 }} In hybrid zones with mainly permeable species boundaries, patterns of introgressed regions enable deducing what genomic regions involved in incompatibilities and reproductive isolation.{{cite journal | vauthors = Hooper DM, Griffith SC, Price TD | title = Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone | journal = Molecular Ecology | volume = 28 | issue = 6 | pages = 1246–1262 | date = March 2019 | pmid = 30230092 | doi = 10.1111/mec.14874 | bibcode = 2019MolEc..28.1246H | doi-access = free }}

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