Population genomic evidence of selection on structural variants in a natural hybrid zone

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.

Real-time geographic settling of a hybrid zone between the invasive winter moth (Operophtera brumata L.) and the native Bruce spanworm (O. bruceata Hulst)

Hybridization plays an important and underappreciated role in shaping the evolutionary trajectories of species. Following the introduction of a non-native organism to a novel habitat, hybridization with a native congener may affect the probability of establishment of the introduced species. In most documented cases of hybridization between a native and a non-native species, a mosaic hybrid zone is formed, with hybridization occurring heterogeneously across the landscape. In contrast, most naturally occurring hybrid zones are clinal in structure. Here we report on a long-term microsatellite dataset that monitored hybridization between the invasive winter moth, Operophtera brumata (Lepidoptera: Geometridae), and the native Bruce spanworm, O. bruceata, over a 12-year period. Our results document one of the first examples of the real-time formation and geographic settling of a clinal hybrid zone. In addition, by comparing one transect in Massachusetts where extreme winter cold temperatures have been hypothesized to restrict the distribution of winter moth, and one in coastal Connecticut, where winter temperatures are moderated by Long Island Sound, we find that the location of the hybrid zone appears to be independent of environmental variables and maintained under a tension model wherein the stability of the hybrid zone is constrained by population density, reduced hybrid fitness, and low dispersal rates. Documenting the formation of a contemporary clinal hybrid zone may provide important insights into the factors that shaped other well-established hybrid zones.

Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation

The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.

Enhanced Outcrossing, Directional Selection and Transgressive Segregation Drive Evolution of Novel Phenotypes in Hybrid Swarms of the Dutch Elm Disease Pathogen Ophiostoma novo-ulmi

In the 1970s, clones of the two subspecies of Ophiostoma novo-ulmi, subsp. americana (SSAM) and subsp. novo-ulmi (SSNU) began to overlap in Europe, resulting in hybrid swarms. By 1983–1986, hybrids with high, SSAM-like growth and pathogenic fitness comprised ~75% of popula-tions at Limburg, Netherlands and Orvieto, Italy. We resampled these populations in 2008 to examine trends in hybrid fitness traits. Since preliminary sampling in 1979–1980, MAT-1 locus frequency had increased from ~0% to ~32% at Orvieto and 5% to ~43% at Limburg, and vegeta-tive incompatibility type frequency had changed from near clonal to extremely diverse at both sites. This represents an enormous increase in outcrossing and recombination potential, due in part to selective acquisition (under virus pressure) of MAT-1 and vic loci from the resident O. ulmi and in part to SSAM × SSNU hybridisation. Overt virus infection in the 2008 samples was low (~4%), diagnostic SSAM and SSNU cu and col1 loci were recombinant, and no isolates exhib-ited a parental SSAM or SSNU colony pattern. At both sites, mean growth rate and mean patho-genicity to 3–5 m clonal elm were high SSAM-like, indicating sustained directional selection for these characters, though at Orvieto growth rate was slower. The once frequent SSNU-specific up-mut colony dimorphism was largely eliminated at both sites. Perithecia formed by Limburg isolates were mainly an extreme, long-necked SSNU-like form, consistent with transgressive segregation resulting from mismatch of SSAM and SSNU developmental loci. Orvieto isolates produced more parental-like perithecia, suggesting the extreme phenotypes may have been se-lected against. The novel phenotypes in the swarms are remodelling O. novo-ulmi in Europe. Locally adapted genotypes may emerge.

Rapid and recent allopatric speciation in firs from central Mexico: evidence for reinforcement?

Secondary contact of species that have evolved partial reproductive isolation in allopatry may result in several outcomes, which range from rampant hybridization to barrier reinforcement. Reinforcement arises from reduced hybrid fitness, which promotes assortative mating and hence speciation. In plants, self-fertilization and disjunctions in reproductive-phenology are often invoked as evidence of reinforcement. However, local adaptation and pleiotropic effects during colonization can also lead to reproductive isolation without reinforcement. We explored these possibilities in a fir species complex (Abies flinckii - A. religiosa) distributed in ‘sky-islands’ along the Trans-Mexican Volcanic Belt (TMVB), in central Mexico. Despite co-occurring in two independent sympatric regions (west and center), these two taxa seem to rarely interbreed because of disjunct reproductive phenologies. We genotyped 1,147 SNPs, generated by GBS across 23 populations, and compared multiple demographic scenarios, built based on the geological history of the TMVB. The best-fitting model suggested a recent species split (for a conifer), dating back to ~1.2 Ma, together with early asymmetric gene flow (mostly from A. flinckii into A. religiosa), limited to the central sympatric region. Coupled with the lack of support for colonization models, the summary statistics (f, Hobs, FST, θπ, etc.) and historical demographic inferences made herein point to a rapid speciation with an early development of reinforcement, as a putative mechanism for avoiding hybridization. The role of reinforcement should be thus further explored in the (sub)tropics, as likely explanation for how species diversity is generated and maintained.

The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex

Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.

Hybridization and the coexistence of species

It is thought that two species can coexist if they use different resources present in the environment, yet this assumes that species are completely reproductively isolated. Closely related species often interbreed, raising the question of how this might affect coexistence. We model coexistence outcomes for two sympatric species that are ecologically differentiated but have incomplete reproductive isolation. Results show that the consequences of interbreeding depend crucially on hybrid fitness. When hybrid fitness is high, just a small rate of hybridization can lead to collapse of two species into one. Low hybrid fitness can cause population declines, making extinction of one or both species likely. The intrinsic growth rate of the population has an important influence on the outcome. High intrinsic growth rates result in higher reproductive rates when populations are below carrying capacity, reducing the probability of extinction and increasing the likelihood of stable coexistence at moderate levels of assortative mating and hybrid fitness. Very strong but incomplete assortative mating can induce low hybrid fitness via a mating disadvantage to rare genotypes, and this can stabilize coexistence of two species at high but incomplete levels of assortative mating. Given these results and evidence that it may take many millions of years of divergence before related species become sympatric, we postulate that coexistence of closely-related species is more often limited by insufficient assortative mating than by insufficient ecological differentiation.

Predicting distributions of Wolbachia strains through host ecological contact -- who's manipulating whom?

Barriers to gene-flow within populations, typically in response to divergent selection, are often mediated via third-party interactions. Under these conditions speciation is inextricably linked to ecological context. We present a novel framework for studying arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI) via alternative strain associations. Building on empirical findings, our model predicts that sympatric host sister-species harbour paraphyletic strains that provide CI, while well-defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia may provide an adaptive advantage when coupled with reduced hybrid fitness (via trait mismatching), by facilitating assortative mating between co-occurring divergent phenotypes – the contact contingency hypothesis. To test this, we applied a custom-built predictive algorithm to empirical data from host-specific pollinating fig wasps, achieving ≤88.46% accuracy. We then considered post-zygotic offspring mortality during CI matings by developing a model featuring fitness clines across oviposition resources. This oviposition trade-off model, tested through simulation, favoured CI at realistic conspecific mating frequencies despite fecundity losses. We demonstrate that a rules-based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely-related sympatric species encounter adaptive disadvantage through hybridisation.

Predicting distributions of Wolbachia strains through host ecological contact -- who's manipulating whom?

Barriers to gene-flow within populations, typically in response to divergent selection, are often mediated via third-party interactions. Under these conditions speciation is inextricably linked to ecological context. We present a novel framework for studying arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI) via alternative strain associations. Building on empirical findings, our model predicts that sympatric host sister-species harbour paraphyletic strains that provide CI, while well-defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia may provide an adaptive advantage when coupled with reduced hybrid fitness (via trait mismatching), by facilitating assortative mating between co-occurring divergent phenotypes – the contact contingency hypothesis. To test this, we applied a custom-built predictive algorithm to empirical data from host-specific pollinating fig wasps, achieving ≤88.46% accuracy. We then considered post-zygotic offspring mortality during CI matings by developing a model featuring fitness clines across oviposition resources. This oviposition trade-off model, tested through simulation, favoured CI at realistic conspecific mating frequencies despite fecundity losses. We demonstrate that a rules-based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely-related sympatric species encounter adaptive disadvantage through hybridisation.