Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment

Pericentromeric recombination suppression and the 'large X effect' in plants

X chromosome was reported to be a major contributor to isolation between closely related species-the 'large X' effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plant Silene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE in S. latifolia is caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression in S. latifolia and its close cross-compatible relative S. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE in S. latifolia and S. dioica.

The diverse effects of phenotypic dominance on hybrid fitness

When divergent populations interbreed, their alleles are brought together in hybrids. In the initial F1 cross, most divergent loci are heterozygous. Therefore, F1 fitness can be influenced by dominance effects that could not have been selected to function well together. We present a systematic study of these F1 dominance effects by introducing variable phenotypic dominance into Fisher's geometric model. We show that dominance often reduces hybrid fitness, which can generate optimal outbreeding followed by a steady decline in F1 fitness, as is often observed. We also show that "lucky" beneficial effects sometimes arise by chance, which might be important when hybrids can access novel environments. We then show that dominance can lead to violations of Haldane's Rule (reduced fitness of the heterogametic F1) but strengthens Darwin's Corollary (F1 fitness differences between cross directions). Taken together, results show that the effects of dominance on hybrid fitness can be surprisingly difficult to isolate, because they often resemble the effects of uniparental inheritance or expression. Nevertheless, we identify a pattern of environment-dependent heterosis that only dominance can explain, and for which there is some suggestive evidence. Our results also show how existing data set upper bounds on the size of dominance effects. These bounds could explain why additive models often provide good predictions for later-generation recombinant hybrids, even when dominance qualitatively changes outcomes for the F1.

Drosophila melanogaster hosts coevolving with Pseudomonas entomophila pathogen show sex-specific patterns of local adaptation

Background

In spatially structured populations, local adaptation improves organisms’ fitness in their native environment. Hosts and pathogens can rapidly adapt to their local antagonist. Since males and females can differ in their immunocompetence, the patterns of local adaptation can be different between the sexes. However, there is little information about sex differences in local adaptation in host–pathogen systems.

Results

In the current study, we experimentally coevolved four different replicate populations of Drosophila melanogaster (host) and Pseudomonas entomophila (pathogen) along with appropriate controls. We used the four host–pathogen coevolution populations to investigate the occurrence of local adaptation separately in males and females of the coevolving hosts. We also assessed local adaptation in pathogens. We set up a reciprocal infection experiment where we infected each of the four coevolving hosts with their local pathogen or non-local pathogens from the other three replicate populations. We found that overall, male and female hosts had better survivorship when infected with local pathogens, indicating that they were locally adapted. Interestingly, males were more susceptible to non-local pathogens compared to females. In addition, we found no fecundity cost in females infected with either local or non-local pathogens. We found no evidence of local adaptation among the pathogens.

Conclusion

Our study showed sex-specific adaptation in the coevolving hosts where female hosts had a broader response against allopatric coevolving pathogens with no cost in fecundity. Thus, our results might suggest a novel mechanism that can maintain variation in susceptibility in spatially structured populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02031-8.

A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene

Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and Silene latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian sparse linear mixed models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a polygenic architecture of cumulative flowering. Allelic effects were mostly beneficial or deleterious in one habitat and neutral in the other. Positive-effect alleles often were derived from the native species, whereas negative-effect alleles, at other loci, tended to originate from the non-native species. We conclude that ecological differentiation is governed and maintained by many loci with small, habitat-dependent effects consistent with conditional neutrality. This pattern may result from differences in selection targets in the two habitats and from environmentally dependent deleterious load. Our results further suggest that selection for native alleles and against non-native alleles acts as a barrier to gene flow between species.

Towards a unified framework to study causality in Earth-life systems

There is considerable interest in better understanding how earth processes shape the generation and distribution of life on Earth. This question, at its heart, is one of causation. In this article I propose that at a regional level, earth processes can be thought of as behaving somewhat deterministically and may have an organized effect on the diversification and distribution of species. However, the study of how landscape features shape biology is challenged by pseudocongruent or collinear variables. I demonstrate that causal structures can be used to depict the cause–effect relationships between earth processes and biological patterns using recent examples from the literature about speciation and species richness in montane settings. This application shows that causal diagrams can be used to better decipher the details of causal relationships by motivating new hypotheses. Additionally, the abstraction of this knowledge into structural equation metamodels can be used to formulate theory about relationships within Earth–life systems more broadly. Causal structures are a natural point of collaboration between biologists and Earth scientists, and their use can mitigate against the risk of misassigning causality within studies. My goal is that by applying causal theory through application of causal structures, we can build a systems‐level understanding of what landscape features or earth processes most shape the distribution and diversification of species, what types of organisms are most affected, and why.

Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island

Polyploidy is pervasive in angiosperm evolution and plays important roles in adaptation and speciation. However, polyploid groups are understudied due to complex sequence homology, challenging genome assembly, and taxonomic complexity. Here, we study adaptive divergence in taxonomically complex eyebrights (Euphrasia), where recent divergence, phenotypic plasticity, and hybridization blur species boundaries. We focus on three closely related tetraploid species with contrasting ecological preferences that are sympatric on Fair Isle, a small isolated island in the British Isles. Using a common garden experiment, we show a genetic component to the morphological differences present between these species. Using whole-genome sequencing and a novel k-mer approach we call "Tetmer", we demonstrate that the species are of allopolyploid origin, with a sub-genome divergence of approximately 5%. Using ∼2 million SNPs, we show sub-genome homology across species, with a very low sequence divergence characteristic of recent speciation. This genetic variation is broadly structured by species, with clear divergence of Fair Isle heathland Euphrasia micrantha, while grassland Euphrasia arctica and coastal Euphrasia foulaensis are more closely related. Overall, we show that tetraploid Euphrasia is a system of allopolyploids of postglacial species divergence, where adaptation to novel environments may be conferred by old variants rearranged into new genetic lineages.

Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (F_ST) and sequence divergence (d_XY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.

Potential adaptive divergence between subspecies and populations of snapdragon plants inferred from QST -FST comparisons

Phenotypic divergence among natural populations can be explained by natural selection or by neutral processes such as drift. Many examples in the literature compare putatively neutral (F_ST ) and quantitative genetic (Q_ST ) differentiation in multiple populations to assess their evolutionary signature and identify candidate traits involved with local adaptation. Investigating these signatures in closely related or recently diversified species has the potential to shed light on the divergence processes acting at the interspecific level. Here, we conducted this comparison in two subspecies of snapdragon plants (eight populations of Antirrhinum majus pseudomajus and five populations of A. m. striatum) in a common garden experiment. We also tested whether altitude was involved with population phenotypic divergence. Our results identified candidate phenological and morphological traits involved with local adaptation. Most of these traits were identified in one subspecies but not the other. Phenotypic divergence increased with altitude for a few biomass-related traits, but only in A. m. striatum. These traits therefore potentially reflect A. m. striatum adaptation to altitude. Our findings imply that adaptive processes potentially differ at the scale of A. majus subspecies.

Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species

The evolution of sexual dimorphism in species with separate sexes is influenced by the resolution of sexual conflicts creating sex differences through genetic linkage or sex-biased expression. Plants with different degrees of sexual dimorphism are thus ideal to study the genetic basis of sexual dimorphism. In this study we explore the genetic architecture of sexual dimorphism between Silene latifolia and Silene dioica. These species have chromosomal sex determination and differ in the extent of sexual dimorphism. To test whether QTL for sexually dimorphic traits have accumulated on the sex chromosomes and to quantify their contribution to species differences, we create a linkage map and performed QTL analysis of life history, flower and vegetative traits using an unidirectional interspecific F2 hybrid cross. We found support for an accumulation of QTL on the sex chromosomes and that sex differences explained a large proportion of the variance between species, suggesting that both natural and sexual selection contributed to species divergence. Sexually dimorphic traits that also differed between species displayed transgressive segregation. We observed a reversal in sexual dimorphism in the F2 population, where males tended to be larger than females, indicating that sexual dimorphism is constrained within populations but not in recombinant hybrids. This study contributes to the understanding of the genetic basis of sexual dimorphism and its evolution in Silene.

Sex differences in local adaptation: what can we learn from reciprocal transplant experiments?

Local adaptation is of fundamental interest to evolutionary biologists. Traditionally, local adaptation has been studied using reciprocal transplant experiments to quantify fitness differences between residents and immigrants in pairwise transplants between study populations. Previous studies have detected local adaptation in some cases, but others have shown lack of adaptation or even maladaptation. Recently, the importance of different fitness components, such as survival and fecundity, to local adaptation have been emphasized. Here, we address another neglected aspect in studies of local adaptation: sex differences. Given the ubiquity of sexual dimorphism in life histories and phenotypic traits, this neglect is surprising, but may be partly explained by differences in research traditions and terminology in the fields of local adaptation and sexual selection. Studies that investigate differences in mating success between resident and immigrants across populations tend to be framed in terms of reproductive and behavioural isolation, rather than local adaptation. We briefly review the published literature that bridges these areas and suggest that reciprocal transplant experiments could benefit from quantifying both male and female fitness components. Such a more integrative research approach could clarify the role of sex differences in the evolution of local adaptations.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana)

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.

Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene)

New species arise through the evolution of reproductive barriers between formerly interbreeding lineages. Yet, comprehensive assessments of potential reproductive barriers, which are needed to make inferences on processes driving speciation, are only available for a limited number of systems. In this study, we estimated individual and cumulative strengths of seven prezygotic and six postzygotic reproductive barriers between the recently diverged taxa Silene dioica (L.) Clairv. and S. latifolia Poiret using both published and new data. A combination of multiple partial reproductive barriers resulted in near-complete reproductive isolation between S. dioica and S. latifolia, consistent with earlier estimates of gene flow between the taxa. Extrinsic barriers associated with adaptive ecological divergence were most important, while intrinsic postzygotic barriers had moderate individual strength but contributed only little to total reproductive isolation. These findings are in line with ecological divergence as driver of speciation. We further found extensive variation in extrinsic reproductive isolation, ranging from sites with very strong selection against migrants and hybrids to intermediate sites where substantial hybridization is possible. This situation may allow for, or even promote, heterogeneous genetic divergence.

The two "rules of speciation" in species with young sex chromosomes

The two "rules of speciation," Haldane's rule (HR) and the large-X effect (LXE), are thought to be caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. Thus, the reports of HR and the LXE in species with recently evolved non- or partially degenerate Y-chromosomes, such as Silene latifolia and its relatives, were surprising. Here, I argue that rapid species-specific degeneration of Y-linked genes and associated adjustment of expression of X-linked gametologs (dosage compensation) may lead to rapid evolution of sex-linked species incompatibilities. This process is likely to be too slow in species with old degenerate Y-chromosomes (e.g., in mammals), but Y-degeneration in species with young gene-rich sex chromosomes may be fast enough to play a significant role in speciation. To illustrate this point, I report the analysis of Y-degeneration and the associated evolution of gene expression on the X-chromosome of S. latifolia and Silene dioica, a close relative that shares the same recently evolved sex chromosomes. Despite the recent (≤1MY) divergence of the two species, ~7% of Y-linked genes have undergone degeneration in one but not the other species. This species-specific degeneration appears to drive faster expression divergence of X-linked genes, which may account for HR and the LXE reported for these species. Furthermore, I suggest that "exposure" of autosomal or sex-linked recessive species incompatibilities in the haploid plant gametophyte may mimic the presence of HR in plants. Both haploid expression and species-specific Y-degeneration need to receive more attention if we are to understand the role of these processes in speciation.

Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation

The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F₂ crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F₂ crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.

Interspecific Divergence of Two Sinalliaria (Brassicaceae) Species in Eastern China

How endemic species originated in eastern Asia has interested botanists for a long time. In this study, we combined experimental and computational modeling approaches to examine the morphological and genetic divergence and reproductive isolation of two tentative species of Sinalliaria (Brassicaceae) endemic to eastern China, S. limprichtiana and S. grandifolia. Most of the examined morphological characters (including hairs of leaf blades and stems, corolla length and width, and flower stalk length) were well-delineated between two species at the same ploidy level, and there was clear evidence of reproductive isolation between them (mainly due to post-pollination barriers) in the common garden environment. There were also strong and consistent divergences in the population genetic data. Coalescent simulations based on sequence variation of the nuclear genes suggest that interspecific divergence began during the Pleistocene when the climate oscillated in eastern Asia. Gene flow between two species appears to have been very limited and asymmetrical. Our results suggested that both species are well-differentiated and that the fast divergence between them might have been together shaped by both stochastic processes and habitat selection pressures.

Sequence diversity patterns suggesting balancing selection in partially sex-linked genes of the plant Silene latifolia are not generated by demographic history or gene flow

DNA sequence diversity in genes in the partially sex-linked pseudoautosomal region (PAR) of the sex chromosomes of the plant Silene latifolia is higher than expected from within-species diversity of other genes. This could be the footprint of sexually antagonistic (SA) alleles that are maintained by balancing selection in a PAR gene (or genes) and affect polymorphism in linked genome regions. SA selection is predicted to occur during sex chromosome evolution, but it is important to test whether the unexpectedly high sequence polymorphism could be explained without it, purely by the combined effects of partial linkage with the sex-determining region and the population's demographic history, including possible introgression from Silene dioica. To test this, we applied approximate Bayesian computation-based model choice to autosomal sequence diversity data, to find the most plausible scenario for the recent history of S. latifolia and then to estimate the posterior density of the most relevant parameters. We then used these densities to simulate variation to be expected at PAR genes. We conclude that an excess of variants at high frequencies at PAR genes should arise in S. latifolia populations only for genes with strong associations with fully sex-linked genes, which requires closer linkage with the fully sex-linked region than that estimated for the PAR genes where apparent deviations from neutrality were observed. These results support the need to invoke selection to explain the S. latifolia PAR gene diversity, and encourage further work to test the possibility of balancing selection due to sexual antagonism.