Darwin and the origin of interspecific genetic incompatibilities

Darwin's Origin of Species is often criticized for having little to say about speciation. The complaint focuses in particular on Darwin's supposed failure to explain the evolution of the sterility and inviability of interspecific hybrids. But in his chapter on hybridism, Darwin, working without genetics, got as close to the modern understanding of the evolution of hybrid sterility and inviability as might reasonably be expected. In particular, after surveying what was then known about interspecific crosses and the resulting hybrids, he established two facts that, while now taken for granted, were at the time radical. First, the sterility barriers between species are neither specially endowed by a creator nor directly favored by natural selection but rather evolve as incidental by-products of interspecific divergence. Second, the sterility of species hybrids results when their development is "disturbed by two organizations having been compounded into one." Bateson, Dobzhansky, and Muller later put Mendelian detail to Darwin's inference that the species-specific factors controlling development (i.e., genes) are sometimes incompatible. In this article, I highlight the major developments in our understanding of these interspecific genetic incompatibilities--from Darwin to Muller to modern theory--and review comparative, genetic, and molecular rules that characterize the evolution of hybrid sterility and inviability.     

Sex chromosomes and speciation in Drosophila

Two empirical rules suggest that sex chromosomes play a special role in speciation. The first is Haldane's rule - the preferential sterility and inviability of species hybrids of the heterogametic (XY) sex. The second is the disproportionately large effect of the X chromosome in genetic analyses of hybrid sterility. Whereas the causes of Haldane's rule are well established, the causes of the 'large X-effect' have remained controversial. New genetic analyses in Drosophila confirm that the X is a hotspot for hybrid male sterility factors, providing a proximate explanation for the large X-effect. Several other new findings -- on faster X evolution, X chromosome meiotic drive and the regulation of the X chromosome in the male-germline -- provide plausible evolutionary explanations for the large X-effect.     

Telomerase activity coevolves with body mass not lifespan

In multicellular organisms, telomerase is required to maintain telomere length in the germline but is dispensable in the soma. Mice, for example, express telomerase in somatic and germline tissues, while humans express telomerase almost exclusively in the germline. As a result, when telomeres of human somatic cells reach a critical length the cells enter irreversible growth arrest called replicative senescence. Replicative senescence is believed to be an anticancer mechanism that limits cell proliferation. The difference between mice and humans led to the hypothesis that repression of telomerase in somatic cells has evolved as a tumor-suppressor adaptation in large, long-lived organisms. We tested whether regulation of telomerase activity coevolves with lifespan and body mass using comparative analysis of 15 rodent species with highly diverse lifespans and body masses. Here we show that telomerase activity does not coevolve with lifespan but instead coevolves with body mass: larger rodents repress telomerase activity in somatic cells. These results suggest that large body mass presents a greater risk of cancer than long lifespan, and large animals evolve repression of telomerase activity to mitigate that risk.     

Speciation genetics: search for the missing snowball

Theory predicts that, as species diverge from one another, the number of genetic incompatibilities causing sterility or inviability in interspecies hybrids grows faster than linearly, or snowballs. Two new genetic analyses now provide the first empirical support for this snowball effect.     

A fine-scale genetic analysis of hybrid incompatibilities in Drosophila

The sterility and inviability of species hybrids is thought to evolve by the accumulation of genes that cause generally recessive, incompatible epistatic interactions between species. Most analyses of the loci involved in such hybrid incompatibilities have suffered from low genetic resolution. Here I present a fine-resolution genetic screen that allows systematic counting, mapping, and characterizing of a large number of hybrid incompatibility loci in a model genetic system. Using small autosomal deletions from D. melanogaster and a hybrid rescue mutation from D. simulans, I measured the viability of hybrid males that are simultaneously hemizygous for a small region of the D. simulans autosomal genome and hemizygous for the D. melanogaster X chromosome. These hybrid males are exposed to the full effects of any recessive-recessive epistatic incompatibilities present in these regions. A screen of approximately 70% of the D. simulans autosomal genome reveals 20 hybrid-lethal and 20 hybrid-semilethal regions that are incompatible with the D. melanogaster X. In further crosses, I confirm the epistatic nature of hybrid lethality by showing that all of the incompatibilities are rescued when the D. melanogaster X is replaced with a D. simulans X. Combined with information from previous studies, these results show that the number of recessive incompatibilities is approximately eightfold larger than the number of dominant ones. Finally, I estimate that a total of approximately 191 hybrid-lethal incompatibilities separate D. melanogaster and D. simulans, indicating extensive functional divergence between these species' genomes.     

Patterns of postzygotic isolation in Lepidoptera

I present patterns characterizing the evolution of intrinsic postzygotic isolation in Lepidoptera by analyzing data from the literature on genetic distance, strength of hybrid sterility and inviability, biogeography, and natural hybridization. Using genetic distance as a proxy for time, I investigate the time-course of the evolution of postzygotic isolation and the waiting times to particular hybrid fitness problems. The results show that postzygotic isolation increases gradually as species diverge, but that hybrid sterility evolves faster than hybrid inviability. The overwhelming preponderance of female-specific hybrid problems in Lepidoptera shows that Haldane's rule (the preferential sterility or inviability of the heterogametic sex) is well obeyed. Together the rates and patterns characterizing the accumulation of postzygotic isolation allow several tests of the composite theory of Haldane's rule. Interestingly, comparing these data with those from Drosophila reveals that Haldane's rule for sterility evolves as fast (if not faster) in Lepidoptera. Finally, I show that a substantial fraction of sympatric species hybridizes in nature and that the majority of these suffer some level of hybrid sterility or inviability.     

Hitchhiking to Speciation

The modern evolutionary synthesis codified the idea that species exist as distinct entities because intrinsic reproductive barriers prevent them from merging together. Understanding the origin of species therefore requires understanding the evolution and genetics of reproductive barriers between species. In most cases, speciation is an accident that happens as different populations adapt to different environments and, incidentally, come to differ in ways that render them reproductively incompatible. As with other reproductive barriers, the evolution and genetics of interspecific hybrid sterility and lethality were once also thought to evolve as pleiotripic side effects of adaptation. Recent work on the molecular genetics of speciation has raised an altogether different possibility—the genes that cause hybrid sterility and lethality often come to differ between species not because of adaptation to the external ecological environment but because of internal evolutionary arms races between selfish genetic elements and the genes of the host genome. Arguably one of the best examples supporting a role of ecological adaptation comes from a population of yellow monkey flowers, Mimulus guttatus, in Copperopolis, California, which recently evolved tolerance to soil contaminants from copper mines and simultaneously, as an incidental by-product, hybrid lethality in crosses with some off-mine populations. However, in new work, Wright and colleagues show that hybrid lethality is not a pleiotropic consequence of copper tolerance. Rather, the genetic factor causing hybrid lethality is tightly linked to copper tolerance and spread to fixation in Copperopolis by genetic hitchhiking.New species arise when populations gradually evolve intrinsic reproductive barriers to interbreeding with other populations [1]–[3]. Two species can be reproductively isolated from one another in ways that prevent the formation of interspecific hybrids—the species may, for instance, have incompatible courtship signals or occupy different ecological habitats. Two species can also be reproductively isolated from one another if interspecific hybrids are formed but are somehow unfit—the hybrids may be sterile, inviable, or may simply fall between parental ecological niches. All forms of reproductive isolation limit the genetic exchange between species, preventing their fusion and facilitating their further divergence. Understanding the genetic and evolutionary basis of speciation—a major cause of biodiversity—therefore involves understanding the genetics and evolutionary basis of the traits that mediate reproductive isolation.Most reproductive barriers arise as incidental by-products of selection—either ecological adaptation or sexual selection. For these cases, the genetic basis of speciation is, effectively, the genetics of adaptation. But hybrid sterility and lethality have historically posed two special problems. Darwin [4] devoted an entire chapter of his Origin of Species to the first problem: as the sterility or lethality of hybrids provides no advantage to parents, how could the genetic factors involved possibly evolve by natural selection? The second problem was recognized much later [5], after the rediscovery of Mendelian genetics: if two species (with genotypes AA and aa) produce, say, sterile hybrids (Aa) due to an incompatibility between the A and a alleles, then how could, e.g., the AA genotype have evolved from an aa ancestor in the first place without passing through a sterile intermediate genotype (Aa)? Not only does natural selection not directly favor the evolution of hybrid sterility or lethality, but there is reason to believe natural selection positively prevents its evolution.Together these problems stymied evolutionists and geneticists for decades. T.H. Huxley [6] and William Bateson [5], writing decades apart, each branded the evolution of hybrid sterility one of the most serious challenges for a then-young evolutionary theory. Darwin had, in fact, offered a simple solution to the first problem. Namely, hybrid sterility and lethality are not advantageous per se but rather “incidental on other acquired differences" [4]. Then Bateson [5], in a few short, forgotten lines solved the second problem (see [7]). Later, Dobzhansky [2] and Muller [8] would arrive at the same solution, showing that hybrid sterility or lethality could evolve readily, unopposed by natural selection, under a two-locus model with epistasis. In particular, they imagined that separate populations diverge from a common ancestor (genotype aabb), with the A allele becoming established in one population (AAbb) and the B allele in the other (aaBB); while A and B alleles must function on their respective genetic backgrounds, there is no guarantee that the A and B alleles will be functionally compatible with one another. Hybrid sterility and lethality most likely result from incompatible complementary genetic factors that disrupt development when brought together in a common hybrid genome. Dobzhansky [2] and Muller [8] could point to a few supporting data in fish, flies, and plants. Notably, like Darwin, neither speculated on the forces responsible for the evolution of the genetic factors involved.Today, there is no doubt that the Dobzhansky-Muller model is correct, as the data for incompatible complementary genetic factors is now overwhelming [1],[9]. In the last decade, a fast-growing number of speciation genes involved in these genetic incompatibilities have been identified in mice, fish, flies, yeast, and plants [9]–[11]. Perhaps not surprisingly, these speciation genes often have histories of recurrent, adaptive protein-coding sequence evolution [10],[11]. The signature of selection at speciation genes has been taken by some as tacit evidence for the pervasive role of ecological adaptation in speciation, including the evolution of hybrid sterility and lethality [12]. What is surprising, however, from the modern molecular analysis of speciation genes is how often their rapid sequence evolution and functional divergence seems to have little to do with adaptation to external ecological circumstances. Instead, speciation genes often (but not always [9]–[11]) seem to evolve as by-products of evolutionary arms races between selfish genetic elements—e.g., satellite DNAs [13],[14], meiotic drive elements [15], cytoplasmic male sterility factors [16]—and the host genes that regulate or suppress them [9]–[11],[17]. The notion that selfish genes are exotic curiosities is now giving way to a realization that selfish genes are common and diverse, each generation probing for transmission advantages at the expense of their bearers, fueling evolutionary arms races and, not infrequently, contributing to the genetic divergence that drives speciation. Indeed, the case has become so strong that examples of hybrid sterility and lethality genes that have evolved in response to ecological challenges (other than pathogens) appear to be the exception [9],[11],[17].Perhaps the most clear-cut case in which a genetic incompatibility seems to have evolved as a by-product of ecological adaptation comes from populations of the yellow monkey flower, Mimulus guttatus, from Copperopolis (California, U.S.A.). In the last ∼150 years, the Copperopolis population has evolved tolerance to the tailings of local copper mines (Figure 1). These copper-tolerant M. guttatus plants also happen to be partially reproductively isolated from many off-mine M. guttatus plants, producing hybrids that suffer tissue necrosis and death. In classic work, Macnair and Christie showed that copper tolerance is controlled by a single major factor [18] and hybrid lethality, as expected under the Dobzhansky-Muller model, by complementary factors [19]. Surprisingly, in crosses between tolerant and nontolerant plants, hybrid lethality perfectly cosegregates with tolerance [19],[20]. The simplest explanation is that the copper tolerance allele that spread to fixation in the Copperopolis population also happens to cause hybrid lethality as a pleiotropic by-product. The alternative explanation is that the copper tolerance and hybrid lethality loci happen to be genetically linked; when the copper tolerance allele spread to fixation in Copperopolis, hybrid lethality hitchhiked to high frequency along with it [20]. But with 2n = 28 chromosomes, the odds that copper tolerance and hybrid lethality alleles happen to be linked would seem vanishingly small [20].Open in a separate windowFigure 1Yellow monkey flowers (Mimulus guttatus) growing in the heavy-metal contaminated soils of copper-mine tailings.In this issue, Wright and colleagues [21] revisit this classic case of genetic incompatibility as a by-product of ecological adaptation. They make two discoveries, one genetic and the other evolutionary. By conducting extensive crossing experiments and leveraging the M. guttatus genome sequence (www.mimulusevolution.org), Wright et al. [21] map copper tolerance and hybrid necrosis to tightly linked but genetically separable loci, Tol1 and Nec1, respectively. Hybrid lethality is not a pleiotropic consequence of copper tolerance. Instead, the tolerant Tol1 allele spread to fixation in Copperopolis, and the tightly linked incompatible Nec1 allele spread with it by genetic hitchhiking. In a turn of bad luck, the loci happen to fall in a heterochromatic pericentric region, where genome assemblies are often problematic, putting identification of the Tol1 and Nec1 genes out of immediate reach. Wright et al. [21] were, however, able to identify linked markers within ∼0.3 cM of Tol1 and place Nec1 within a 10-kb genomic interval that contains a Gypsy3 retrotransposon, raising two possibilities. First, the Gypsy3 element is unlikely to cause hybrid lethality directly; instead, as transposable elements are often epigenetically silenced in plants, it seems possible that the Nec1-associated Gypsy3 is silenced with incidental consequences for gene expression on a gene (or genes) in the vicinity [22]. Second, although the Nec1 interval is 10-kb in the reference genome of M. guttatus, it could be larger in the (not-yet-sequenced) Copperopolis population, perhaps harboring additional genes.With Tol1 and Nec1 mapped near and to particular genomic scaffolds, respectively, Wright et al. were able to investigate the evolutionary history of the genomic region. Given the clear adaptive significance of copper tolerance in Copperopolis plants, we might expect to see the signatures of a strong selective sweep in the Tol1 region—a single Tol1 haplotype may have spread to fixation so quickly that all Copperopolis descendant plants bear the identical haplotype and thus show strongly reduced population genetic variability in the Tol1-Nec1 region relative to the rest of the genome [23],[24]. After the selective sweep is complete, variability in the region ought to recover gradually as new mutations arise and begin to fill out the mutation-drift equilibrium frequency spectrum expected for neutral variation in the Copperopolis population [25],[26]. Given that Tol1 reflects an adaptation to mine tailings established just ∼150 generations ago, there would have been little time for such a recovery. And yet, while Wright et al. find evidence of moderately reduced genetic variability in the Tol1-Nec1 genomic region, the magnitude of the reduction is hardly dramatic relative to the genome average.How, then, is it possible that the Tol1-Nec1 region swept to fixation in Copperopolis in fewer than ∼150 generations and yet left no strong footprint of a hitchhiking event? One possibility is that rather than a single, unique Tol1-Nec1 haplotype contributing to fixation, causing a “hard sweep," multiple Tol1-Nec1 haplotypes sampled from previously standing genetic variation contributed to fixation, causing a “soft sweep" [27]. A soft sweep would be plausible if Tol1 and Nec1 both segregate in the local off-mine ancestral population and if the two were, coincidentally, found on the same chromosome more often than expected by chance (i.e., in linkage disequilibrium). Then, after the copper mines were established, multiple plants with multiple Tol1 haplotypes (and, by association, Nec1) could have colonized the newly contaminated soils of the mine tailings. Tol1 segregates at ∼9% in surrounding populations, suggesting that standing genetic variation for copper tolerance may well have been present in the ancestral populations.Two big questions remain for the Tol1-Nec1 story, and both would be readily advanced by identification of Tol1 and Nec1. The first question concerns the history of Tol1 haplotypes in Copperopolis and surrounding off-mine populations. As Nec1-mediated hybrid lethality is incomplete, the ∼9% Tol1 frequency in surrounding populations could reflect its export via gene flow from the Copperopolis populations. Conversely, if there was a soft sweep from standing Tol1 variation in surrounding off-mine populations, then Tol1 and Nec1 may still be in linkage disequilibrium in those populations (assuming ∼150 years of recombination has not broken up the association). Resolving these alternative possibilities is a matter of establishing the history of movement of Tol1 haplotypes into or out of the Copperopolis population. The soft sweep scenario, if correct, presents a population genetics puzzle: during the historical time that mutations accumulated among the multiple tolerant but incompatible Tol1-Nec1 haplotypes in the ancestral off-mine populations, why did recombination fail to degrade the association, giving rise to tolerant but compatible haplotypes?The second question concerns the identity of Nec1 (or if it really is a Gypsy3 element, the identity of the nearby gene whose expression is disrupted as a consequence). The answer bears on one of the new emerging generalizations about genetic incompatibilities in plants [9]. Recently, Bomblies and Weigel [28] synthesized a century''s worth of observations on the commonly seen necrosis phenotype in plant hybrids and, based on their own genetic analyses in Arabidopsis [29], suggested that many of these cases may have a common underlying basis: incompatibilities between plant pathogen resistance genes can cause autoimmune responses that result in tissue necrosis and hybrid lethality. Hybrid necrosis, indeed, appears to involve pathogen resistance genes across multiple plants groups [9],[28]. It remains to be seen if the Nec1-mediated lethality provides yet another instance.