Hybrid Incompatibility in Drosophila: An Updated Genetic and Evolutionary Analysis


Negative interactions between independently evolved genes in two species are responsible of incompatibility of their hybrid, manifested by sterility and inviability. The heterogametic sex (XY males in Drosophila) is the most affected and the X chromosome has the largest effect on hybrid incompatibility (HI). These rules of speciation depend on the genetic architecture of HI. Albeit some speciation genes have a major effect, this architecture shows a complex polygenic structure of multiple interactions. HI genes are frequently associated to genetic factors that evolved selfishly by favouring their preferential transmission. Genetic analyses show signatures of positive selection in speciation genes that may favour the role of adaptive evolution. Whether these signatures are compatible with evolution of selfish factors – an idea that is gaining support – still remains a contentious issue. Finally, there is also a current upsurge of evidences in favour of the importance of genetic regulation in the evolution of hybrid incompatibilities.

Key Concepts

  • Species must maintain their identity by isolation mechanisms that prevent gene flow among them.
  • In sexual species, hybrid incompatibility, evidenced by sterility and/or inviability, is an isolation mechanism of great importance.
  • The negative interaction in the hybrid between at least two genes that each evolved independently in two species (the BDM model) has been proved by multiple studies.
  • Several genes of major effect (speciation genes) are highly implicated, albeit interacting with other genetic factors, in hybrid incompatibilities.
  • A complex architecture of many genes with multiple interactions among them underlies the hybrid incompatibility.
  • The heterogametic sex is generally more affected by the hybrid incompatibility through interactions between X‐linked recessive genes and partially dominant autosomal genes (the dominant theory).
  • When substituted in a foreign genome, the X chromosome has a larger effect than any autosomal substitution, due to the greater density of speciation genes in the X chromosome.
  • Many speciation genes show signatures of positive selection in their DNA, which suggests, but not always, adaptive evolution.
  • Some speciation genes are associated to genetic factors evolved by genetic conflict, for example, meiotic drive, suggesting that a kind of evolutionary arms race between drivers and suppressors underlies the evolution of hybrid incompatibility.
  • Recently, regulatory divergence rather than divergence in coding sequences is gaining support as a main actor in hybrid incompatibilities.

Keywords: hybrid sterility; hybrid inviability; Drosophila; Haldane's rule; genetic conflict; speciation genes; large‐X effect; epistasis

Figure 1. Depiction of results of the first genetic analysis of male hybrid sterility carried out by Dobzhansky (). Bar length denotes the testis length (a proxy for male hybrid fertility) of hybrid male genotypes obtained by backcrossing female F1 hybrids between Drosophila pseudoobscura and Drosophila persimilis to parental D. pseudoobscura males. Males with a D. pseudoobscura X chromosome (top half) often are fertile, but males carrying a D. persimilis X chromosome (bottom half) are almost completely sterile. These results show the disproportionately large effect of the X chromosome substitution on hybrid male sterility when compared to autosome substitution effects. Solid bar chromosomes denote D. persimilis, and open bar chromosomes denote D. pseudoobscura. Redrawn with permission from Dobzhansky, © Genetics Society of America.
Figure 2. Flowchart of the evolution of hybrid incompatibility following the BDM model. The ancestral species (aabb) is split into two populations, originating two lineages isolated from each other. In one lineage, allele a is substituted by allele A in two steps until fixation of genotype AA. Analogously, in the other lineage a similar substitution occurs for the allele B. During this evolutionary process, neither intermediate nor final genotype (Aabb → AAbb; or aaBb → aaBB) is sterile or inviable. If in a later stage, both evolved populations meet together and cross; the hybrid genotype (AaBb) may be sterile or inviable, depending on the strength of the negative epistatic interaction between A and B alleles. Notice that these alleles have never been together in the same genotype throughout their evolutionary substitution and natural selection had no chance to test their compatibility. In the hybrid, however, they co‐exist and may be incompatible with one another. The BDM model circumvents the impossibility of developing HI by one‐locus evolution, because in that case the intermediate stage (Aa or Bb) would already be inviable or sterile.
Figure 3. Flowchart of three strategies for mapping genetic factors (loci) associated to hybrid male sterility in Drosophila. The process starts by crossing two species (1 and 2) to generate hybrid fertile females, which are individually backcrossed (BC) to males of the host species (1) to yield a progeny of recombinant hybrids. In this first BC1 generation, male recombinant hybrids are sterile whereas hybrid females are fertile. Then individual hybrid females are backcrossed for several generations to host males (species 1) until introgressed sterile male phenotypes (BC) show to be associated to genetic markers of donor species 2 (strategies A and B) or progenies consists of both BC sterile and fertile males (strategy C). In strategy A, a set of morphological markers are used to detect the associated sterility factor by recombinant analysis, but usually the recombinant marker (represented by a four peak star) maps a wide region that must be further dissected using more specific markers (M1–M7) flanking the putative sterility factor depicted by a stared circle at M4 (in red). The figure shows (by a shaded bar column) how the introgressed fragments that yield fertile phenotypes do not contain the M4 marker, whereas those that yield sterile phenotypes do (see Perez et al., who used this strategy to map Ods gene). Strategy B applies to detect partially recessive autosomal alleles whose full effect on hybrid male sterility can be detected only in homozygosity. Using different techniques to introgress individual marker regions (five peak star) after many bakcrossings, crosses between BC hybrid heterozygotes for the same marker can yield a set of hybrid male homozygotes that can be tested for sterility. This procedure was used by Masly and Presgraves () to show that most sterility factors are recessive. Strategy C uses natural markers detected by dissecting the genome by means of DNA techniques such as AFLP. Markers specific to each species allows locating regions that are introgressed by the donor species in the BCn hybrid males. When the progeny of a BCn hybrid fertile female consists of both fertile and sterile males, one can detect the markers associated to sterility by comparing the marker patterns of siblings. Note that in the figure the chromosome of the BC hybrid sterile male contains a marker specific of species 2 (in the right extreme side) that is absent in its fertile sibling. By genome‐wide association studies for many markers, the genetic architecture of hybrid male sterility can be assessed as in Morán and Fontdevila's () work. Homologous chromosomes are depicted by bars: white and black bars for species 1 and 2, respectively. By recombination through backcrossing, chromosome fragments of species 2 (in black) are introgressed in homologous chromosomes of species 1 (in white). Note that the amount of introgressed fragments decreases with the number of backcrossing generations, until only one marked fragment is selected for its association to male sterility (strategies A and B) or until the combined introgressed fragments yield a progeny with fertile and sterile males (strategy C).
Figure 4. Ordered representations of sterility‐associated markers present in each hybrid introgressed male obtained by backcrossing hybrid Drosophila buzzatii/Drosophila koepferae females to D. buzzatii males for three generations. (a) Ordered depiction of the fertile (F) and sterile (S) hybrid males in relation to the increasing number of sterility‐associated markers present in each hybrid male supports the cumulative action, with a threshold, of genes surrounding these sterility markers. The threshold number of sterility‐associated markers required to elicit sterility is approximately 14–16, whose limits are represented by two dotted lines that correspond to the transition from fertile to sterile hybrid phenotypes. Some outlier individuals exist, which shows that the effect on sterility of genes linked to markers is variable, and in some instances a particular mixture of a number of low‐effect (high‐effect) markers over (under) the threshold can produce a fertile (sterile) phenotype (see hybrid males F26, F11, and F14 over, and S19 under the threshold). Some of fertile outliers show a reduced fertility, such as F14 fertile individual (*) with an observed reduced offspring of only three adult flies. (b) Segregation matrix of sterility‐associated markers. Sterility‐associated markers (shown in columns) were scored in a binary matrix as 0 (white cells) when absent or 1 (grey cells) when present. To facilitate the matrix inspection all the fertile (F) males are grouped in the upper rows of the matrix and separated from the sterile (S) males by a straight black line. Inside each fertility class, (F, S) males (left margin) were organised by their increasing content of sterility‐associated markers (right margin). The figure shows that presence of a specific marker to produce sterility is not a necessity; rather, the presence of a minimum number of markers over a threshold induces sterility with high probability. In fact, some ubiquitous or highly present markers in sterile hybrids are also present in many fertile ones (e.g. GCGGG17, CAGCG8, TGCAT13 markers are present in all sterile males and in many fertile ones) and no marker exclusively occurs in sterile males. These data support the ample exchangeability of sterility‐associated markers. Reproduced with permission from Oxford University Press after Morán and Fontdevila ().
Figure 5. Distribution of hybrid incompatibilities of Drosophila mauritiana introgressions in the Drosophila sechellia genome. Above the X, second and third chromosomes, triangles show the insertion sites of different P‐elements used for introgressions: black indicates hybrid inviable; red indicates hybrid male‐sterile; white indicates hybrid fertile or untested. Below the chromosomes, arrows depict the estimated sizes of many introgressions. Black indicates hybrid inviable introgressions; red indicates hybrid male‐sterile; grey indicates hybrid fertile. This figure graphically depicts that the density of hybrid male sterility factors is >4 times higher on the X than on an average (and similarly sized) autosomal arm. These numbers are minimum estimates because each introgression might contain more than one incompatibility gene, hybrid inviable introgressions may mask tightly linked hybrid male steriles, and some regions of the genome that may contain hybrid incompatibility loci were not screened. Reproduced from Masly and Presgraves () © US National Library of Medicine, National Institutes of Health licensed under Creative Commons Attribution.
Figure 6. Genetic architecture of male sterility and segregation distortion in hybrid F1 males between D. pseudoobscura bogotana and D. pseudoobscura pseudoobscura. Hybrid male sterility is caused by loci (QTL regions) on the bogotana X chromosome, which interact with dominantly acting loci (QTL regions) on the pseudoobscura autosomes. Segregation distortion is caused by three loci on the bogotana X chromosome; bogotana 2_390 acts as an almost fully recessive suppressor of segregation distortion. The full expression of both phenotypes, however, requires 2_390 and 3001 regions (QTLs) from pseudoobscura sub‐species to be present simultaneously. Hybrid male sterility and segregation distortion show a partial overlap in their genetic bases (e.g. regions X23 and 2_390 act on both phenotypes). Solid (open) bars depict bogotana (pseudoobscura) chromosomes. The large metacentric X chromosome is denoted as a long bar with its centromere as an open oval, the Y chromosome as a hooked bar, and the autosomes as short bars. Thick arrow lines denote large‐effect regions, and thin arrow lines denote small‐effect regions. Republished with permission from Phadnis () © Genetics Society of America.


Bateson W (1909) Heredity and variation in modern lights. In: Seward AC (ed) Darwin and Modern Science, pp. 85–101. Cambridge: Cambridge University Press.

Britten RJ and Davidson EH (1969) Gene regulation for higher cells: a theory. Science 165: 349–357.

Butlin R et al. (2012) What do we need to know about speciation? Trends in Ecology & Evolution 27: 27–39.

Cabot EL, Davis AW, Johnson NA and Wu CI (1994) Genetics of reproductive isolation in the Drosophila simulans clade: complex epistasis underlying hybrid male sterility. Genetics 137: 175–189.

Chae E, Bomblies K, Kim S‐T, et al. (2014) Species‐wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 159: 1341–1351.

Chang AS, Bennett SM and Noor MAF (2010) Epistasis among Drosophila persimilis factors conferring hybrid male sterility with D. pseudoobscura bogotana. PLoS One 5 (10). DOI: 10.1371/journal.pone.0015377.

Chang AS and Noor MAF (2010) Epistasis modifies the dominance of loci causing hybrid male sterility in the Drosophila pseudoobscura species group. Evolution 64: 253–260.

Charlesworth B, Coyne JA and Barton NH (1987) The relative rates of evolution of sex chromosomes and autosomes. American Naturalist 130: 113–146.

Coyne JA and Charlesworth B (1989) Genetic analysis of X‐linked sterility in hybrids between three sibling species of Drosophila. Heredity 62 (Pt 1): 97–106.

Coyne JA (1992) Genetics and speciation. Nature 355: 511–515.

Crespi B and Nosil P (2013) Conflictual speciation: species formation via genomic conflict. Trends in Ecology & Evolution 28: 48–57.

Cronshaw JM and Matunis MJ (2004) The nuclear pore complex: disease associations and functional correlations. Trends in Endocrinology & Metabolism 15: 34–39.

Demuth JP and Wade MJ (2007) Population differentiation in the beetle Tribolium castaneum. II. Haldane's rule and incipient speciation. Evolution 61: 694–699.

Dobzhansky T (1935) A critique of the species concept in biology. Philosophy of Science 2: 344.

Dobzhansky T (1936) Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 21: 113–135.

Dobzhansky T (1937) Genetics and the Origin of Species. New York: Columbia University Press (Reprinted in 1982).

Dzur‐Gejdosova M, Simecek P, Gregorova S, Bhattacharyya T and Forejt J (2012) Dissecting the genetic architecture of F1 hybrid sterility in house mice. Evolution 66: 3321–3335.

Fontdevila A (2011) The Dynamic Genome: A Darwinian approach. Oxford: Oxford University Press.

Garrigan D, Kingan SB, Geneva AJ, Vedanayagam JP and Presgraves DC (2014) Genome diversity and divergence in Drosophila mauritiana: multiple signatures of faster X evolution. Genome Biology and Evolution 6: 2444–2458.

Haerty W and Singh RS (2006) Gene regulation divergence is a major contributor to the evolution of Dobzhansky‐Muller incompatibilities between species of Drosophila. Molecular Biology and Evolution 23: 1707–1714.

Hollocher H and Wu CI (1996) The genetics of reproductive isolation in the Drosophila simulans clade: X vs. autosomal effects and male vs. female effects. Genetics 143: 1243–1255.

Hurst LD and Pomiankowski A (1991) Causes of sex ratio bias may account for unisexual sterility in hybrids: a new explanation of Haldane's rule and related phenomena. Genetics 128: 841–858.

Johnson NA (2010) Hybrid incompatibility genes: remnants of a genomic battlefield? Trends in Genetics 26: 317–325.

King MC and Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107–116.

Llopart A (2012) The rapid evolution of X‐linked male‐biased gene expression and the large‐X effect in Drosophila yakuba, D. santomea, and their hybrids. Molecular Biology and Evolution 29: 3873–3886.

Maheshwari S and Barbash D (2011) The genetics of hybrid incompatibilities. Annual Review of Genetics 45: 331–355.

Mank JE, Vicoso B, Berlin S and Charlesworth B (2010) Effective population size and the Faster‐X effect: empirical results and their interpretation. Evolution 64: 663–674.

Masly JP, Jones CD, Noor MAF, Locke J and Orr HA (2006) Gene transposition as a novel cause of hybrid male sterility. Science 313: 1448–1450.

Masly JP and Presgraves DC (2007) High‐resolution genome‐wide dissection of the two rules of speciation in Drosophila. PLoS Biology 5: 1890–1898.

McDermott SR and Noor MAF (2012) Mapping of within‐ species segregation distortion in Drosophila persimilis and hybrid sterility between D. persimilis and D. pseudoobscura. Journal of Evolutionary Biology 25: 2023–2032.

Meiklejohn CD and Tao Y (2010) Genetic conflict and sex chromosome evolution. Trends in Ecology &Evolution 25: 215–223.

Meiklejohn CD, Coolon JD, Hartl DL and Wittkopp PJ (2014) The roles of cis‐ and trans‐regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Research 24: 84–95.

Morán T and Fontdevila A (2014) Genome‐wide dissection of hybrid sterility in Drosophila confirms a polygenic threshold architecture. The Journal of Heredity 105: 381–396.

Muller HJ (1942) Isolating mechanisms, evolution and temperature. In: Dobzhansky T (ed) Temperature, Evolution, Development, vol. 6, Biological Symposia: A Series of Volumes Devoted to Current Symposia in the Field of Biology, pp. 71–125. Lancaster, PA: Jaques Cattell.

Naveira H and Fontdevila A (1986) The evolutionary history of Drosophila buzzatii. Xii. The genetic basis of sterility in hybrids between D. buzzatii and its sibling D. serido from Argentina. Genetics 114: 841–857.

Naveira H and Fontdevila A (1991a) The evolutionary history of D. buzzatii. XXII. Chromosomal and genic sterility in male hybrids of Drosophila buzzatii and Drosophila koepferae. Heredity (Edinburg) 66: 233–239.

Naveira H and Fontdevila A (1991b) The evolutionary history of Drosophila buzzatii. XXI. Cumulative action of multiple sterility factors on spermatogenesis in hybrids of D. buzzatii and D. koepferae. Heredity (Edinburg) 67: 57–72.

Naveira HF (1992) Location of X‐linked polygenic effects causing sterility in male hybrids of Drosophila simulans and D. mauritiana. Heredity (Edinburg) 68: 211–217.

Naveira H and Maside X (1998) The genetics of hybrid male sterility in Drosophila. In: Howard DJ and Berlocher SH (eds) Endless Forms: Species and Speciation, pp. 330–338. Oxford: Oxford University Press.

Nosil P and Schluter D (2011) The genes underlying the process of speciation. Trends in Ecology & Evolution 26: 160–167.

Orr HA (1989) Localization of genes causing postzygotic isolation in two hybridizations involving Drosophila pseudoobscura. Heredity 63 (Pt 2): 231–237.

Orr HA and Turelli MM (2001) The evolution of postzygotic isolation: accumulating Dobzhansky‐Muller incompatibilities. Evolution 55: 1085–1094.

Orr HA and Irving S (2005) Segregation distortion in hybrids between the Bogota and USA subspecies of Drosophila pseudoobscura. Genetics 169: 671–682.

Orr HA, Masly JP and Phadnis N (2007) Speciation in Drosophila: from phenotypes to molecules. Journal of Heredity 98: 103–110.

Perez DE, Wu CI, Johnson NA and Wu ML (1993) Genetics of reproductive isolation in the Drosophila simulans clade: DNA marker‐assisted mapping and characterization of a hybrid‐male sterility gene, Odysseus (Ods). Genetics 134: 261–275.

Phadnis N and Orr HA (2009) A single gene causes male sterility and segregation distortion in Drosophila hybrids. Science 323: 376–379.

Phadnis N (2011) Genetic architecture of male sterility and segregation distortion in Drosophila pseudoobscura bogota‐USA hybrids. Genetics 189: 1001–1009.

Presgraves DC (2003) A fine‐scale genetic analysis of hybrid incompatibilities in Drosophila. Genetics 163: 955–972.

Presgraves DC, Balagopalan L, Abmayr SM and Orr HA (2003) Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila. Nature 423: 715–719.

Presgraves DC and Stephan W (2007) Pervasive adaptive evolution among interactors of the Drosophila hybrid inviability gene, Nup96. Molecular Biology and Evolution 24: 306–314.

Presgraves DC (2010) The molecular evolutionary basis of species formation. Nature Reviews Genetics 11: 175–180.

Reed LK and Markow TA (2004) Early events in speciation: polymorphism for hybrid male sterility in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 101: 9009–9012.

Schluter D (2009) Evidence for ecological speciation and its alternative. Science 323: 737–741.

Schilthuizen M, Giesbers MCWG and Beukeboom LW (2011) Haldane's rule in the 21st century. Heredity 107: 95–102.

Sobel JM, Chen GF, Watt LR and Schemske DW (2010) The biology of speciation. Evolution 64: 295–315.

Sturtevant AH (1920) Genetic studies on Drosophila simulans. I. Introduction: hybrids with Drosophila melanogaster. Genetics 5: 488–500.

Tang S and Presgraves DC (2009) Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323: 779–782.

Tao Y and Hartl DL (2003) Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. III. Heterogeneous accumulation of hybrid incompatibilities, degree of dominance, and implications for Haldane's rule. Evolution 57: 2580–2598.

Tao Y, Chen S, Hartl DL and Laurie CC (2003a) Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. I. Differential accumulation of hybrid male sterility effects on the X and autosomes. Genetics 164: 1383–1397.

Tao Y, Zeng ZB, Li J, Hartl DL and Laurie CC (2003b) Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome. Genetics 164: 1399–1418.

Thornton K, Bachtrog D and Andolfatto P (2006) X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster‐X protein evolution. Genome Research 16: 498–504.

Ting CT, Tsaur SC, Wu ML and Wu CI (1998) A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282: 1501–1504.

True JR, Weir BS and Laurie CC (1996) A genome‐wide survey of hybrid incompatibility factors by the introgression of marked segments of Drosophila mauritiana chromosomes into Drosophila simulans. Genetics 142: 819–837.

Turelli M and Orr HA (1995) The dominance theory of HALDANE's rule. Genetics 140: 389–402.

Turner LM and Harr B (2014) Genome‐wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky‐Muller interactions. eLife 3: 1–25.

Turner LM, White MA, Tautz D and Payseur BA (2014) Genomic networks of hybrid sterility. PLoS Genetics 10: 18–22.

Vicoso B and Charlesworth B (2009) Effective population size and the faster‐X effect: an extended model. Evolution 63: 2413–2426.

White MA, Stubbings M, Dumont BL and Payseur BA (2012) Genetics and evolution of hybrid male sterility in house mice. Genetics 191: 917–934.

Wolf JBW, Lindell J and Backström N (2010) Speciation genetics: current status and evolving approaches. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 365: 1717–1733.

Wright KM, Lloyd D, Lowry DB, Macnair MR and Willis JH (2013) Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus. PLoS Biology 11: e1001497. DOI: 10.1371/journal.pbio.1001497.

Wu CI and Davis AW (1993) Evolution of postmating reproductive isolation: the composite nature of Haldane's rule and its genetic bases. The American Naturalist 142: 187–212.

Wu CI, Johnson NA and Palopoli MF (1996) Haldane's rule and its legacy: why are there so many sterile males? Trends in Ecology & Evolution 11: 281–284.

Wu CI and Hollocher H (1998) Subtle is nature: the genetics of differentiation and speciation. In: Howard DJ and Berlocher ST (eds) Endless Forms: Species and Speciation, pp. 339–351. Oxford: Oxford University Press.

Further Reading

Coyne JA and Orr A (2004) Speciation. Sunderland, MA: Sinauer Associates.

Mayr E (1942) Systematics and the Origin of Species. New York: Columbia University Press (Reprinted in 1999 by Harvard University Press).

Noor MAF and Feder JL (2006) Speciation genetics: evolving approaches. Nature Reviews. Genetics 7: 851–861. DOI: 10.1038/nrg1968.

Presgraves DC (2010b) Darwin and the origin of interspecific genetic incompatibilities. American Naturalist 176 (Suppl 1): S45–S60.

Sobel JM, Chen GF, Watt LR and Schemske DW (2010b) The biology of speciation. Evolution 64: 295–315.

Wolf JBW, Lindell J and Backström N (2010b) Speciation genetics: current status and evolving approaches. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 365: 1717–1733.

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Fontdevila, Antonio(Feb 2016) Hybrid Incompatibility in Drosophila: An Updated Genetic and Evolutionary Analysis. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020896.pub2]