Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation

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.

Parental dialectic: Epigenetic conversations in endosperm

Endosperm is a major evolutionary innovation of flowering plants, and its proper development critically impacts seed growth and viability. Epigenetic regulators have a key function in parental control of endosperm development. Notably, epigenetic regulation of parental genome dosage is a major determinant of seed development success, and disruption of this balance can produce inviable seed, as observed in some interploidy and interspecific crosses. These postzygotic reproduction barriers are also a potent driver of speciation. The molecular machinery and regulatory architecture governing endosperm development is proposed to have evolved under parental conflict. In this review, we emphasize parental conflict as a dialectic conflict and discuss recent findings about the epigenetic molecular machinery that mediates parental conflict in the endosperm.

Molecular basis and evolutionary drivers of endosperm-based hybridization barriers

The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.

Hybridization and gene expression: Beyond differentially expressed genes

Gene expression has a key role in reproductive isolation, and studies of hybrid gene expression have identified mechanisms causing hybrid sterility. Here, we review the evidence for altered gene expression following hybridization and outline the mechanisms shown to contribute to altered gene expression in hybrids. Transgressive gene expression, transcending that of both parental species, is pervasive in early generation sterile hybrids, but also frequently observed in viable, fertile hybrids. We highlight studies showing that hybridization can result in transgressive gene expression, also in established hybrid lineages or species. Such extreme patterns of gene expression in stabilized hybrid taxa suggest that altered hybrid gene expression may result in hybridization-derived evolutionary novelty. We also conclude that while patterns of misexpression in hybrids are well documented, the understanding of the mechanisms causing misexpression is lagging. We argue that jointly assessing differences in cell composition and cell-specific changes in gene expression in hybrids, in addition to assessing changes in chromatin and methylation, will significantly advance our understanding of the basis of altered gene expression. Moreover, uncovering to what extent evolution of gene expression results in altered expression for individual genes, or entire networks of genes, will advance our understanding of how selection moulds gene expression. Finally, we argue that jointly studying the dual roles of altered hybrid gene expression, serving both as a mechanism for reproductive isolation and as a substrate for hybrid ecological adaptation, will lead to significant advances in our understanding of the evolution of gene expression.

United by Conflict: Convergent Signatures of Parental Conflict in Angiosperms and Placental Mammals

Endosperm in angiosperms and placenta in eutherians are convergent innovations for efficient embryonic nutrient transfer. Despite advantages, this reproductive strategy incurs metabolic costs that maternal parents disproportionately shoulder, leading to potential inter-parental conflict over optimal offspring investment. Genomic imprinting-parent-of-origin-biased gene expression-is fundamental for endosperm and placenta development and has convergently evolved in angiosperms and mammals, in part, to resolve parental conflict. Here, we review the mechanisms of genomic imprinting in these taxa. Despite differences in the timing and spatial extent of imprinting, these taxa exhibit remarkable convergence in the molecular machinery and genes governing imprinting. We then assess the role of parental conflict in shaping evolution within angiosperms and eutherians using four criteria: (1) Do differences in the extent of sibling relatedness cause differences in the inferred strength of parental conflict? (2) Do reciprocal crosses between taxa with different inferred histories of parental conflict exhibit parent-of-origin growth effects? (3) Are these parent-of-origin growth effects caused by dosage-sensitive mechanisms and do these loci exhibit signals of positive selection? (4) Can normal development be restored by genomic perturbations that restore stoichiometric balance in the endosperm/placenta? Although we find evidence for all criteria in angiosperms and eutherians, suggesting that parental conflict may help shape their evolution, many questions remain. Additionally, myriad differences between the two taxa suggest that their respective biologies may shape how/when/where/to what extent parental conflict manifests. Lastly, we discuss outstanding questions, highlighting the power of comparative work in quantifying the role of parental conflict in evolution.

Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species

The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers, Mimulus guttatus and Mimulus nasutus, from the sympatric Catherine Creek population. We discover that the three M. guttatus founders differ dramatically in admixture history, with nearly a quarter of one founder's genome introgressed from M. nasutus. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the M. guttatus founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be explained by epistatic selection favouring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid pollen viability, including two interacting pairs that coincide with peaks of distortion. Remarkably, even with this limited sample of three M. guttatus lines, we discover abundant segregating variation for hybrid incompatibilities with M. nasutus, suggesting this population harbours diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities between Mimulus species persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system.

Genetic Cause of Hybrid Lethality Observed in Reciprocal Interspecific Crosses between Nicotiana simulans and N. tabacum

Hybrid lethality, a type of postzygotic reproductive isolation, is an obstacle to wide hybridization breeding. Here, we report the hybrid lethality that was observed in crosses between the cultivated tobacco, Nicotiana tabacum (section Nicotiana), and the wild tobacco species, Nicotiana simulans (section Suaveolentes). Reciprocal hybrid seedlings were inviable at 28 °C, and the lethality was characterized by browning of the hypocotyl and roots, suggesting that hybrid lethality is due to the interaction of nuclear genomes derived from each parental species, and not to a cytoplasmic effect. Hybrid lethality was temperature-sensitive and suppressed at 36 °C. However, when hybrid seedlings cultured at 36 °C were transferred to 28 °C, all of them showed hybrid lethality. After crossing between an N. tabacum monosomic line missing one copy of the Q chromosome and N. simulans, hybrid seedlings with or without the Q chromosome were inviable and viable, respectively. These results indicated that gene(s) on the Q chromosome are responsible for hybrid lethality and also suggested that N. simulans has the same allele at the Hybrid Lethality A1 (HLA1) locus responsible for hybrid lethality as other species in the section Suaveolentes. Haplotype analysis around the HLA1 locus suggested that there are at least six and two haplotypes containing Hla1-1 and hla1-2 alleles, respectively, in the section Suaveolentes.

The role of conflict in shaping plant biodiversity

Although intrinsic postzygotic reproductive barriers can play a fundamental role in speciation, their underlying evolutionary causes are widely debated. One hypothesis is that incompatibilities result from genomic conflicts. Here, I synthesize the evidence that conflict generates incompatibilities in plants, thus playing a creative role in plant biodiversity. While much evidence supports a role for conflict in several classes of incompatibility, integrating knowledge of incompatibility alleles with natural history can provide further essential tests. Moreover, comparative work can shed light on the relative importance of conflict in causing incompatibilities, including the extent to which their evolution is repeatable. Together, these approaches can provide independent lines of evidence that conflict causes incompatibilities, cementing its role in plant speciation.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Strong postmating reproductive isolation in Mimulus section Eunanus

Postmating reproductive isolation can help maintain species boundaries when premating barriers to reproduction are incomplete. The strength and identity of postmating reproductive barriers are highly variable among diverging species, leading to questions about their genetic basis and evolutionary drivers. These questions have been tackled in model systems but are less often addressed with broader phylogenetic resolution. In this study we analyse patterns of genetic divergence alongside direct measures of postmating reproductive barriers in an overlooked group of sympatric species within the model monkeyflower genus, Mimulus. Within this Mimulus brevipes species group, we find substantial divergence among species, including a cryptic genetic lineage. However, rampant gene discordance and ancient signals of introgression suggest a complex history of divergence. In addition, we find multiple strong postmating barriers, including postmating prezygotic isolation, hybrid seed inviability and hybrid male sterility. M. brevipes and M. fremontii have substantial but incomplete postmating isolation. For all other tested species pairs, we find essentially complete postmating isolation. Hybrid seed inviability appears linked to differences in seed size, providing a window into possible developmental mechanisms underlying this reproductive barrier. While geographic proximity and incomplete mating isolation may have allowed gene flow within this group in the distant past, strong postmating reproductive barriers today have likely played a key role in preventing ongoing introgression. By producing foundational information about reproductive isolation and genomic divergence in this understudied group, we add new diversity and phylogenetic resolution to our understanding of the mechanisms of plant speciation.

A standardized and efficient technique to estimate seed traits in plants with numerous small propagules

Premise

Variation in seed traits is common within and among populations of plant species and often has ecological and evolutionary implications. However, due to the time-consuming nature of manual seed measurements and the level of variability in imaging techniques, quantifying and interpreting the extent of seed variation can be challenging.

Methods

We developed a standardized high-throughput technique to measure seed number, as well as individual seed area and color, using a derived empirical scale to constrain area in Arabidopsis thaliana, Brassica rapa, and Mimulus guttatus. We develop a specific rational model using seed area measured at various spatial scales relative to the pixel count, observing the asymptotic value of the seed area as the modeled number of pixels approaches infinity.

Results

We found that our model has high reliability in estimating seed traits and efficiently processes large numbers of images, facilitating the quantification of seed traits in studies with large sample sizes.

Discussion

This technique facilitates consistency between imaging sessions and standardizes the measurement of seed traits. These novel advances allow researchers to directly and reliably measure seed traits, which will enable tests of the ecological and evolutionary causes of their variation.

Understanding and overcoming hybrid lethality in seed and seedling stages as barriers to hybridization and gene flow

Hybrid lethality is a type of reproductive isolation barrier observed in two developmental stages, hybrid embryos (hybrid seeds) and hybrid seedlings. Hybrid lethality has been reported in many plant species and limits distant hybridization breeding including interspecific and intergeneric hybridization, which increases genetic diversity and contributes to produce new germplasm for agricultural purposes. Recent studies have provided molecular and genetic evidence suggesting that underlying causes of hybrid lethality involve epistatic interaction of one or more loci, as hypothesized by the Bateson-Dobzhansky-Muller model, and effective ploidy or endosperm balance number. In this review, we focus on the similarities and differences between hybrid seed lethality and hybrid seedling lethality, as well as methods of recovering seed/seedling activity to circumvent hybrid lethality. Current knowledge summarized in our article will provides new insights into the mechanisms of hybrid lethality and effective methods for circumventing hybrid lethality.

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.

Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication

Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.

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.

Genome-wide identification and characterization of lncRNAs in sunflower endosperm

BACKGROUND

Long non-coding RNAs (lncRNAs), as important regulators, play important roles in plant growth and development. The expression and epigenetic regulation of lncRNAs remain uncharacterized generally in plant seeds, especially in the transient endosperm of the dicotyledons.

RESULTS

In this study, we identified 11,840 candidate lncRNAs in 12 day-after-pollination sunflower endosperm by analyzing RNA-seq data. These lncRNAs were evenly distributed in all chromosomes and had specific features that were distinct from mRNAs including tissue-specificity expression, shorter and fewer exons. By GO analysis of protein coding genes showing strong correlation with the lncRNAs, we revealed that these lncRNAs potential function in many biological processes of seed development. Additionally, genome-wide DNA methylation analyses revealed that the level of DNA methylation at the transcription start sites was negatively correlated with gene expression levels in lncRNAs. Finally, 36 imprinted lncRNAs were identified including 32 maternally expressed lncRNAs and four paternally expressed lncRNAs. In CG and CHG context, DNA methylation levels of imprinted lncRNAs in the upstream and gene body regions were slightly lower in the endosperm than that in embryo tissues, which indicated that the maternal demethylation potentially induce the paternally bias expression of imprinted lncRNAs in sunflower endosperm.

CONCLUSION

Our findings not only identified and characterized lncRNAs on a genome-wide scale in the development of sunflower endosperm, but also provide novel insights into the parental effects and epigenetic regulation of lncRNAs in dicotyledonous seeds.

The strength of reproductive isolating barriers in seed plants: Insights from studies quantifying premating and postmating reproductive barriers over the past 15 years

Speciation is driven by the evolution of reproductive isolating barriers that reduce, and ultimately prevent, substantial gene flow between lineages. Despite its central role in evolutionary biology, the process can be difficult to study because it proceeds differently among groups and may occur over long timescales. Due to this complexity, we typically rely on generalizations of empirical data to describe and understand the process. Previous reviews of reproductive isolation (RI) in flowering plants have suggested that prezygotic or extrinsic barriers generally have a stronger effect on reducing gene flow compared to postzygotic or intrinsic barriers. Past conclusions have rested on relatively few empirical estimates of RI; however, RI data have become increasingly abundant over the past 15 years. We analyzed data from recent studies quantifying multiple pre- and postmating barriers in plants and compared the strengths of isolating barriers across 89 taxa pairs using standardized RI metrics. Individual prezygotic barriers were on average stronger than individual postzygotic barriers, and the total strength of prezygotic RI was approximately twice that of postzygotic RI. These findings corroborate that ecological divergence and extrinsic factors, as opposed to solely the accumulation of genetic incompatibilities, are important to speciation and the maintenance of species boundaries in plants. Despite an emphasis in the literature on asymmetric postmating and postzygotic RI, we found that prezygotic barriers acted equally asymmetrically. Overall, substantial variability in the strengths of 12 isolating barriers highlights the great diversity of mechanisms that contribute to plant diversification.

Parental Genome Imbalance Causes Hybrid Seed Lethality as Well as Ovary Abscission in Interspecific and Interploidy Crosses in Nicotiana

Enhanced ovary abscission after pollination and hybrid seed lethality result in post-zygotic reproductive isolation in plant interspecific crosses. However, the connection between these barriers remains unclear. Here, we report that an imbalance in parental genomes or endosperm balance number (EBN) causes hybrid seed lethality and ovary abscission in both interspecific and intraspecific-interploidy crosses in the genus Nicotiana. Auxin treatment suppressed ovary abscission, but not hybrid seed lethality, in an interspecific cross between Nicotiana suaveolens and N. tabacum, suggesting that ovary abscission-related genes are located downstream of those involved in hybrid seed lethality. We performed interploidy crosses among N. suaveolens tetraploids, octoploids, and neopolyploids and revealed hybrid seed lethality and ovary abscission in interploid crosses. Furthermore, a higher maternal EBN than paternal EBN caused these barriers, as previously observed in N. suaveolens × N. tabacum crosses. Altogether, these results suggest that maternal excess of EBN causes hybrid seed lethality, which in turn leads to ovary abscission through the same mechanism in both interspecific and interploidy crosses.

Rapid evolution of post-zygotic reproductive isolation is widespread in Arctic plant lineages

BACKGROUND AND AIMS

The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbours one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific post-zygotic reproductive isolation (RI) in terms of hybrid sterility has frequently evolved within selfing Arctic species of the genus Draba. Here we assess whether incipient biological species are common in the Arctic flora.

METHODS

We conducted an extensive crossing experiment including six species representing four phylogenetically distant families collected across the circumpolar Arctic. We crossed conspecific parental populations representing different spatial scales, raised 740 F1 hybrids to maturity and measured fertility under laboratory conditions. We examined genetic divergence between populations for two of these species (Cardamine bellidifolia and Ranunculus pygmaeus).

KEY RESULTS

In five of the six species, we find extensive reduction in pollen fertility and seed set in F1 hybrids; 219 (46 %) of the 477 F1 hybrids generated between parents separated by ≥427 km had <20 % pollen fertility. Isolation with migration (IM) and *BEAST analyses of sequences of eight nuclear genes in C. bellidifolia suggests that reproductively isolated populations of this species diverged during, or even after, the last glaciation. Likewise, Arctic populations of R. pygmaeus were genetically very similar despite exhibiting strongly reduced fertility in crosses, suggesting that RI evolved recently also in this species.

CONCLUSION

We show that post-zygotic RI has developed multiple times within taxonomically recognized Arctic species belonging to several distantly related lineages, and that RI may have developed over just a few millennia. Rapid and widespread evolution of incipient biological species in the Arctic flora might be associated with frequent bottlenecks due to glacial cycles, and/or selfing mating systems, which are common in the harsh Arctic environment where pollinators are scarce.

Sex-biased demography modulates male harm across the genome

Recent years have seen an explosion of theoretical and empirical interest in the role that kin selection plays in shaping patterns of sexual conflict, with a particular focus on male harming traits. However, this work has focused solely on autosomal genes, and as such it remains unclear how demography modulates the evolution of male harm loci occurring in other portions of the genome, such as sex chromosomes and cytoplasmic elements. To investigate this, we extend existing models of sexual conflict for application to these different modes of inheritance. We first analyse the general case, revealing how sex-specific relatedness, reproductive value and the intensity of local competition combine to determine the potential for male harm. We then analyse a series of demographically explicit models, to assess how dispersal, overlapping generations, reproductive skew and the mechanism of population regulation affect sexual conflict across the genome, and drive conflict between nuclear and cytoplasmic genes. We then explore the effects of sex biases in these demographic parameters, showing how they may drive further conflicts between autosomes and sex chromosomes. Finally, we outline how different crossing schemes may be used to identify signatures of these intragenomic conflicts.

Disentangling the components of triploid block and its fitness consequences in natural diploid-tetraploid contact zones of Arabidopsis arenosa

Hybrid seed inviability (HSI) is an important mechanism of reproductive isolation and speciation. HSI varies in strength among populations of diploid species but it remains to be tested whether similar processes affect natural variation in HSI within ploidy-variable species (triploid block). Here we used extensive endosperm, seed and F₁ -hybrid phenotyping to explore HSI variation within a diploid-autotetraploid species. By leveraging 12 population pairs from three ploidy contact zones, we tested for the effect of interploidy crossing direction (parent of origin), ploidy divergence and spatial arrangement in shaping reproductive barriers in a naturally relevant context. We detected strong parent-of-origin effects on endosperm development, F₁ germination and survival, which was also reflected in the rates of triploid formation in the field. Endosperm cellularization failure was least severe and F₁ -hybrid performance was slightly better in the primary contact zone, with genetically closest diploid and tetraploid lineages. We demonstrated overall strong parent-of-origin effects on HSI in a ploidy variable species, which translate to fitness effects and contribute to interploidy reproductive isolation in a natural context. Subtle intraspecific variation in these traits suggests the fitness consequences of HSI are predominantly a constitutive property of the species regardless of the evolutionary background of its populations.

A revival of effective ploidy: the asymmetry of parental roles in endosperm-based hybridization barriers

Interest in understanding hybrid seed failure (HSF) has mushroomed, both in terms of identifying underlying molecular processes and their evolutionary drivers. We review phenotypic and molecular advances with a focus on the 'effective ploidy' concept, witnessing a recent revival after long obscurity. Endosperm misdevelopment has now been shown to underlie HSF in many inter-specific, homoploid crosses. The consistent asymmetries in seed size and developmental trajectories likely reflect parental divergence in key, dosage-sensitive processes. Transcriptomic and epigenomic studies reveal genome-wide, polarized expression perturbations and shifts in parental expression proportions, consistent with small-RNA imbalances between parental roles. Among-species differences in levels of parental conflict over resource allocation enjoy strong support in explaining why differences in effective ploidy may evolve.

Endosperm and Seed Transcriptomes Reveal Possible Roles for Small RNA Pathways in Wild Tomato Hybrid Seed Failure

Crosses between the wild tomato species Solanum peruvianum and Solanum chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in the hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA (sRNA) expression levels. We identified 2,295 genes and 387 sRNA clusters as differentially expressed when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both hybrid cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resemble the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; differentially expressed sRNAs exhibit reduced transcript abundance in hybrid seeds of both cross directions. Moreover, sRNAs map to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that appear to be targets of sRNA-mediated gene silencing; in these cases, reduced sRNA abundance is concomitant with increased gene expression in hybrid seeds. Our analyses also show that S. peruvianum dominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.

Early evolution of reproductive isolation: A case of weak inbreeder/strong outbreeder leads to an intraspecific hybridization barrier in Arabidopsis lyrata

Reproductive strategies play a major role in plant speciation. Notably, transitions from outcrossing to selfing may lead to relaxed sexual selection and parental conflict. Shifts in mating systems can affect maternal and paternal interests, and thus parent-specific influence on endosperm development, leading to reproductive isolation: if selfing and outcrossing species hybridize, the resulting seeds may not be viable due to endosperm failure. Nevertheless, it remains unclear how the switch in mating systems can impact reproductive isolation between recently diverged lineages, that is, during the process of speciation. We investigated this question using Arabidopsis lyrata, which recently transitioned to selfing (10,000 years ago) in certain North American populations, where European populations remain outcrossing. We performed reciprocal crosses between selfers and outcrossers, and measured seed viability and endosperm development. We show that parental genomes in the hybrid seed negatively interact, as predicted by parental conflict. This leads to extensive hybrid seed lethality associated with endosperm cellularization disturbance. Our results suggest that this is primarily driven by divergent evolution of the paternal genome between selfers and outcrossers. In addition, we observed other hybrid seed defects, suggesting that sex-specific interests are not the only processes contributing to postzygotic reproductive isolation.

Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance

The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

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.

Comparative studies on speciation: 30 years since Coyne and Orr

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.

X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters

Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.

Evolution of multiple postzygotic barriers between species of the Mimulus tilingii complex

Species are often defined by their ability to interbreed (i.e., Biological Species Concept), but determining how and why reproductive isolation arises between new species can be challenging. In the Mimulus tilingii species complex, three species (M. caespitosa, M. minor, and M. tilingii) are largely allopatric and grow exclusively at high elevations (>2000 m). The extent to which geographic separation has shaped patterns of divergence among the species is not well understood. In this study, we determined that the three species are morphologically and genetically distinct, yet recently diverged. Additionally, we performed reciprocal crosses within and between the species and identified several strong postzygotic reproductive barriers, including hybrid seed inviability, F1 hybrid necrosis, and F1 hybrid male and female sterility. In this study, such postzygotic barriers are so strong that a cross between any species pair in the M. tilingii complex would cause nearly complete reproductive isolation. We consider how geographical and topographical patterns may have facilitated the evolution of several postzygotic barriers and contributed to speciation of closely related members within the M. tilingii species complex.

Population Genomics of the "Arcanum" Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the "Arcanum" group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological "selfing syndrome." Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species' geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as "var. marañón" has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.

Two cryptic species of California mustard within Caulanthus lasiophyllus

PREMISE

Cryptic species are evolutionarily distinct lineages lacking distinguishing morphological traits. Hidden diversity may be lurking in widespread species whose distributions cross phylogeographic barriers. This study investigates molecular and morphological variation in the widely distributed Caulanthus lasiophyllus (Brassicaceae) in comparison to its closest relatives.

METHODS

Fifty-two individuals of C. lasiophyllus from across the species' range were sequenced for the nuclear ribosomal internal transcribed spacer region (ITS) and the chloroplast trnL-F region. A subset of these samples were examined for the chloroplast ndhF gene. All 52 individuals were scored for 13 morphological traits, as well as monthly and annual climate conditions at the collection locality. Morphological and molecular results are compared with the closest relatives-C. anceps and C. flavescens-in the "Guillenia Clade." To test for polyploidy, genome size estimates were made for four populations.

RESULTS

Caulanthus lasiophyllus consists of two distinct lineages separated by eight ITS differences-eight times more variation than what distinguishes C. anceps and C. flavescens. Fewer variable sites were detected in trnL-F and ndhF regions, yet these data are consistent with the ITS results. The two lineages of C. lasiophyllus are geographically and climatically distinct; yet morphologically overlapping. Their genome sizes are not consistently different.

CONCLUSIONS

Two cryptic species within C. lasiophyllus are distinguished at the molecular, geographic, and climatic scales. They have similar genome sizes and are morphologically broadly overlapping, but an ephemeral basal leaf character may help distinguish the species.

Effect of Whole-Genome Duplication on the Evolutionary Rescue of Sterile Hybrid Monkeyflowers

Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.

A high maternal genome excess causes severe seed abortion leading to ovary abscission in Nicotiana interploidy-interspecific crosses

Seed abortion and ovary abscission, two types of postzygotic reproductive barriers, are often observed in interspecific and/or interploidy crosses in plants. However, the mechanisms underlying these reproductive barriers remain unclear. Here, we show that the distinct types of seed developmental abnormalities (type I and type II seed abortion) occur in a phased manner as maternal to paternal genome dosage increases and that type II seed abortion is followed by ovary abscission. We revealed that these two types of seed developmental abnormalities are observed during seed development in the interploidy-interspecific crosses of Nicotiana suaveolens and N. tabacum. Moreover, in the cross showing type II seed abortion, several events, such as changes in abscission-related gene expression and lignin deposition, occurred in the ovary abscission zone, eventually leading to ovary abscission. Notably, successive increases in maternal ploidy using ploidy manipulated lines resulted in successive type I and type II seed abortions, and the latter was accompanied by ovary abscission. Conversely, both types of seed abortion and ovary abscission could be overcome with a ploidy manipulation technique that balances parental ploidy levels. We thus concluded that a high maternal genome excess cross may cause severe seed developmental defects and ovary abscission. Based on our findings, we propose a model explaining the abortion phenomena, where an interaction between the promotive and inhibitive effects of the parental genomes determines the developmental destiny of seeds.

SIGNIFICANCE STATEMENT

We demonstrate that a stepwise increase in maternal ploidy results in a stepwise increase in seed abortion severity, leading to ovary abscission in plants. We propose a model explaining the abortion phenomena, where an interaction between the promotive and inhibitive effects of the parental genomes determines the developmental destiny of seeds.

The importance of intrinsic postzygotic barriers throughout the speciation process

Intrinsic postzygotic barriers can play an important and multifaceted role in speciation, but their contribution is often thought to be reserved to the final stages of the speciation process. Here, we review how intrinsic postzygotic barriers can contribute to speciation, and how this role may change through time. We outline three major contributions of intrinsic postzygotic barriers to speciation. (i) reduction of gene flow: intrinsic postzygotic barriers can effectively reduce gene exchange between sympatric species pairs. We discuss the factors that influence how effective incompatibilities are in limiting gene flow. (ii) early onset of species boundaries via rapid evolution: intrinsic postzygotic barriers can evolve between recently diverged populations or incipient species, thereby influencing speciation relatively early in the process. We discuss why the early origination of incompatibilities is expected under some biological models, and detail how other (and often less obvious) incompatibilities may also serve as important barriers early on in speciation. (iii) reinforcement: intrinsic postzygotic barriers can promote the evolution of subsequent reproductive isolation through processes such as reinforcement, even between relatively recently diverged species pairs. We incorporate classic and recent empirical and theoretical work to explore these three facets of intrinsic postzygotic barriers, and provide our thoughts on recent challenges and areas in the field in which progress can be made. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Developmental Analysis of Mimulus Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes

The double fertilization of the female gametophyte initiates embryogenesis and endosperm development in seeds via the activation of genes involved in cell differentiation, organ patterning, and growth. A subset of genes expressed in endosperm exhibit imprinted expression, and the correct balance of gene expression between parental alleles is critical for proper endosperm and seed development. We use a transcriptional time series analysis to identify genes that are associated with key shifts in seed development, including genes associated with secondary cell wall synthesis, mitotic cell cycle, chromatin organization, auxin synthesis, fatty acid metabolism, and seed maturation. We relate these genes to morphological changes in Mimulus seeds. We also identify four endosperm-expressed transcripts that display imprinted (paternal) expression bias. The imprinted status of these four genes is conserved in other flowering plants, suggesting that they are functionally important in endosperm development. Our study explores gene regulatory dynamics in a species with ab initio cellular endosperm development, broadening the taxonomic focus of the literature on gene expression in seeds. Moreover, it is the first to validate genes with imprinted endosperm expression in Mimulus guttatus, and will inform future studies on the genetic causes of seed failure in this model system.