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

Ocean exposure and latitude drive multiple clines within the coastal perennial ecotype of the yellow monkeyflower, Mimulus guttatus

PREMISE

A key goal of evolutionary biologists is to understand how and why genetic variation is partitioned within species. In the yellow monkeyflower, Mimulus guttatus (syn. Erythranthe guttata), coastal perennial populations constitute a single genetically and morphologically differentiated ecotype compared to inland M. guttatus populations. While the coastal ecotype's distinctiveness has now been well documented, there is also environmental variation across the ecotype's range that could drive more continuous differentiation among its component populations.

METHODS

Based on previous observations of a potential cline within this ecotype, we quantified plant height, among other traits, across coastal perennial accessions from 74 populations in a greenhouse common garden experiment. To evaluate potential drivers of the relationship between trait variation and latitude, we regressed height against multiple climatic factors, including temperature, precipitation, and coastal wind speeds. We also accounted for exposure to the open ocean in all analyses.

RESULTS

Multiple traits were correlated with latitude of origin, but none more than plant height. Height was negatively correlated with latitude, and plants directly exposed to the open ocean were shorter than those protected from coastal winds. Further analyses revealed that height was correlated with climatic factors (precipitation, temperature, and wind speeds) that were autocorrelated with latitude. We hypothesize that one or more of these climatic factors drove the evolution of latitudinal clinal variation within the coastal ecotype.

CONCLUSIONS

Overall, our study illustrates the complexity of how the distribution of environmental variation can simultaneously drive the evolution of both distinct ecotypes and continuous clines within those ecotypes.

Patterns of genomic variation reveal a single evolutionary origin of the wild allotetraploid Mimulus sookensis

Polyploidy occurs across the tree of life and is especially common in plants. Because newly formed cytotypes are often incompatible with their progenitors, polyploidy is also said to trigger "instantaneous" speciation. If a polyploid can self-fertilize or reproduce asexually, it is even possible for one individual to produce an entirely new lineage, but how often this scenario occurs is unclear. Here, we investigate the evolutionary history of the wild allotetraploid Mimulus sookensis, which was formed through hybridization between self-compatible, diploid species in the Mimulus guttatus complex. We generate a chromosome-scale reference assembly for M. sookensis and define its distinct subgenomes. Despite previous reports suggesting multiple origins of this highly selfing polyploid, we discover patterns of population genomic variation that provide unambiguous support for a single origin. One M. sookensis subgenome is clearly derived from the selfer Mimulus nasutus, which organellar variation suggests is the maternal progenitor. The ancestor of the other subgenome is less certain, but it shares variation with both Mimulus decorus and M. guttatus, two outcrossing diploids with geographic ranges that overlap broadly with M. sookensis. This study establishes M. sookensis as an example of instantaneous speciation, likely facilitated by the polyploid's predisposition to self-fertilize.

The genetic basis of traits associated with the evolution of serpentine endemism in monkeyflowers

The floras on chemically and physically challenging soils, such as gypsum, shale, and serpentine, are characterized by narrowly endemic species. The evolution of edaphic endemics may be facilitated or constrained by genetic correlations among traits contributing to adaptation and reproductive isolation across soil boundaries. The yellow monkeyflowers in the Mimulus guttatus species complex are an ideal system in which to examine these evolutionary patterns. To determine the genetic basis of adaptive and prezygotic isolating traits, we performed genetic mapping experiments with F2 hybrids derived from a cross between a serpentine endemic, M. nudatus, and its close relative M. guttatus. Few large effect and many small effect QTL contribute to interspecific divergence in life history, floral, and leaf traits, and a history of directional selection contributed to trait divergence. Loci contributing to adaptive traits and prezygotic reproductive isolation overlap, and their allelic effects are largely in the direction of species divergence. These loci contain promising candidate genes regulating flowering time and plant organ size. Together, our results suggest that genetic correlations among traits can facilitate the evolution of adaptation and speciation and may be a common feature of the genetic architecture of divergence between edaphic endemics and their widespread relatives.

Recent parallel speciation in Antirrhinum involved complex haplotypes and multiple adaptive characters

A role of ecological adaptation in speciation can be obscured by stochastic processes and differences that species accumulate after genetic isolation. One way to identify adaptive characters and their underlying genes is to study cases of speciation involving parallel adaptations. Recently resolved phylogenies reveal that alpine morphology has evolved in parallel in the genus Antirrhinum (snapdragons): first in an early split of an alpine from a lowland lineage and, more recently, from within the lowland lineage to produce closely related sympatric species with contrasting alpine and lowland forms. Here, we find that two of these later diverged sympatric species are differentiated by only around 2% of nuclear loci. Though showing evidence of recent gene flow, the species remain distinct for a suite of morphological characters typical of earlier-diverged alpine or lowland lineages and their morphologies correlate with features of the local landscape, as expected of ecological adaptations. Morphological differences between the two species involve multiple, unlinked genes so that parental character combinations are readily broken up by recombination in hybrids. We detect little evidence for post-pollination barriers to gene flow or recombination, suggesting that genetic isolation related to ecological adaptation is important in maintaining character combinations and might have contributed to parallel speciation. We also find evidence that genes involved in the earlier alpine-lowland split were reused in parallel evolution of alpine species, consistent with introgressive hybridisation, and speculate that many non-ecological barriers to gene flow might have been purged during the process.

The role of hybrid seed inviability in angiosperm speciation

Understanding which reproductive barriers contribute to speciation is essential to understanding the diversity of life on earth. Several contemporary examples of strong hybrid seed inviability (HSI) between recently diverged species suggest that HSI may play a fundamental role in plant speciation. Yet, a broader synthesis of HSI is needed to clarify its role in diversification. Here, I review the incidence and evolution of HSI. Hybrid seed inviability is common and evolves rapidly, suggesting that it may play an important role early in speciation. The developmental mechanisms that underlie HSI involve similar developmental trajectories in endosperm, even between evolutionarily deeply diverged incidents of HSI. In hybrid endosperm, HSI is often accompanied by whole-scale gene misexpression, including misexpression of imprinted genes which have a key role in endosperm development. I explore how an evolutionary perspective can clarify the repeated and rapid evolution of HSI. In particular, I evaluate the evidence for conflict between maternal and paternal interests in resource allocation to offspring (i.e., parental conflict). I highlight that parental conflict theory generates explicit predictions regarding the expected hybrid phenotypes and genes responsible for HSI. While much phenotypic evidence supports a role of parental conflict in the evolution of HSI, an understanding of the underlying molecular mechanisms of this barrier is essential to test parental conflict theory. Lastly, I explore what factors may influence the strength of parental conflict in natural plant populations as an explanation for why rates of HSI may differ between plant groups and the consequences of strong HSI in secondary contact.

Indirect Effects of Parental Conflict on Conspecific Offspring Development

AbstractHybrid seed inviability is a common reproductive barrier in angiosperms. Recent work suggests that the rapid evolution of hybrid seed inviability may, in part, be due to conflict between maternal and paternal optima for resource allocation to developing offspring (i.e., parental conflict). However, parental conflict requires that paternally derived resource-acquiring alleles impose a maternal cost. I test this requirement using three closely related species in the Mimulus guttatus species complex that exhibit significant hybrid seed inviability and differ in their inferred histories of parental conflict. I show that the presence of hybrid seeds significantly affects conspecific seed size for almost all crosses, such that conspecific seeds are smaller after developing with hybrids sired by fathers with a stronger history of conflict and are larger after developing with hybrids sired by fathers with a weaker history of conflict. This work demonstrates a potential maternal cost of paternally derived alleles and also has implications for species fitness in secondary contact.

Taking quantitative genomics into the wild

We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.

Developmental evidence for parental conflict in driving Mimulus species barriers

The endosperm, a tissue that nourishes the embryo in the seeds of flowering plants, is often disrupted in inviable hybrid seeds of closely related species. A key question is whether parental conflict is a major driver of this common form of reproductive isolation. Here, we performed reciprocal crosses between pairs of three monkeyflower species (Mimulus caespitosa, Mimulus tilingii, and Mimulus guttatus). The severity of hybrid seed inviability varies among these crosses, which we inferred to be due to species divergence in effective ploidy. By performing a time series experiment of seed development, we discovered parent-of-origin phenotypes that provide strong evidence for parental conflict in shaping endosperm evolution. We found that the chalazal haustorium, a tissue within the endosperm that is found at the maternal-filial boundary, shows pronounced differences between reciprocal hybrid seeds formed from Mimulus species that differ in effective ploidy. These parent-of-origin effects suggest that the chalazal haustorium might act as a mediator of parental conflict, potentially by controlling sucrose movement from the maternal parent into the endosperm. Our study suggests that parental conflict in the endosperm may function as a driver of speciation by targeting regions and developmental stages critical for resource allocation and thus proper seed development.

Adaptive significance of flowering time variation across natural seasonal environments in Arabidopsis thaliana

The relevance of flowering time variation and plasticity to climate adaptation requires a comprehensive empirical assessment. We investigated natural selection and the genetic architecture of flowering time in Arabidopsis through field experiments in Europe across multiple sites and seasons. We estimated selection for flowering time, plasticity and canalization. Loci associated with flowering time, plasticity and canalization by genome-wide association studies were tested for a geographic signature of climate adaptation. Selection favored early flowering and increased canalization, except at the northernmost site, but was rarely detected for plasticity. Genome-wide association studies revealed significant associations with flowering traits and supported a substantial polygenic inheritance. Alleles associated with late flowering, including functional FRIGIDA variants, were more common in regions experiencing high annual temperature variation. Flowering time plasticity to fall vs spring and summer environments was associated with GIGANTEA SUPPRESSOR 5, which promotes early flowering under decreasing day length and temperature. The finding that late flowering genotypes and alleles are associated with climate is evidence for past adaptation. Real-time phenotypic selection analysis, however, reveals pervasive contemporary selection for rapid flowering in agricultural settings across most of the species range. The response to this selection may involve genetic shifts in environmental cuing compared to the ancestral state.

Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (F_IS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent

Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.

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.