Diverse paths to hybrid incompatibility in Arabidopsis

One of the most essential questions of biology is to understand how different species have evolved. Hybrid incompatibility, a phenomenon in which hybrids show reduced fitness in comparison with their parents, can result in reproductive isolation and speciation. Therefore, studying hybrid incompatibility provides an entry point in understanding speciation. Hybrid incompatibilities are known throughout taxa, and the underlying mechanisms have mystified scientists since the theory of evolution by means of natural selection was introduced. In plants, it is only in recent years that the high‐throughput genetic and molecular tools have become available for the Arabidopsis genus, thus helping to shed light on the different genes and molecular and evolutionary mechanisms that underlie hybrid incompatibilities. In this review, we highlight the current knowledge of diverse mechanisms that are known to contribute to hybrid incompatibility.     

Darwin's ‘mystery of mysteries’: the role of sexual selection in plant speciation

Sexual selection is considered one of the key processes that contribute to the emergence of new species. While the connection between sexual selection and speciation has been supported by comparative studies, the mechanisms that mediate this connection remain unresolved, especially in plants. Similarly, it is not clear how speciation processes within plant populations translate into large-scale speciation dynamics. Here, we review the mechanisms through which sexual selection, pollination, and mate choice unfold and interact, and how they may ultimately produce reproductive isolation in plants. We also overview reproductive strategies that might influence sexual selection in plants and illustrate how functional traits might connect speciation at the population level (population differentiation, evolution of reproductive barriers; i.e. microevolution) with evolution above the species level (macroevolution). We also identify outstanding questions in the field, and suitable data and tools for their resolution. Altogether, this effort motivates further research focused on plants, which might potentially broaden our general understanding of speciation by sexual selection, a major concept in evolutionary biology.     

The use of cytogenetic tools for studies in the crop-to-wild gene transfer scenario

Interspecific hybridization in plants is an important evolutionary phenomenon involved in the dynamics of speciation that receives increasing interest in the context of possible gene escapes from transgenic crop varieties. Crops are able to cross-pollinate with a number of wild related species and exchange chromosome segments through homoeologous recombination. In this paper, we review a set of cytogenetic techniques that are appropriate to document the different steps required for the stable introgression of a chromosome segment from a donor species (i.e., the crop) into a recipient species (i.e., the wild). Several examples in hybrids and derivatives are given to illustrate how these approaches may be used to evaluate the potential for gene transfer between crops and wild relatives. Different techniques, from classical chromosome staining methods to recent developments in molecular cytogenetics, can be used to differentiate genomes and identify the chromosome regions eventually involved in genetic exchanges. Some clues are also given for the study of fertility restoration in the interspecific hybrid forms.     

Extreme changes to gene expression associated with homoploid hybrid speciation

Hybridization is an important cause of abrupt speciation. Hybrid speciation without a change in ploidy (homoploid hybrid speciation) is well-established in plants but has also been reported in animals and fungi. A notable example of recent homoploid hybrid speciation is Senecio squalidus (Oxford ragwort), which originated in the UK in the 18th Century following introduction of hybrid material from a hybrid zone between S. chrysanthemifolius and S. aethnensis on Mount Etna, Sicily. To investigate genetic divergence between these taxa, we used complementary DNA microarrays to compare patterns of floral gene expression. These analyses revealed major differences in gene expression between the parent species and wild and resynthesized S. squalidus . Comparisons of gene expression between S. aethnensis , S. chrysanthemifolius and natural S. squalidus identified genes potentially involved in local environmental adaptation. The analysis also revealed non-additive patterns of gene expression in the hybrid relative to its progenitors. These expression changes were more dramatic and widespread in resynthesized hybrids than in natural S. squalidus , suggesting that a unique expression pattern may have been fixed during the allopatric divergence of British S. squalidus . We speculate that hybridization-induced gene-expression change may provide an immediate source of novel phenotypic variation upon which selection can act to facilitate homoploid hybrid speciation in plants.     

From axenic spore germination to molecular farming

The first bryophyte tissue culture techniques were established almost a century ago. All of the techniques that have been developed for tissue culture of seed plants have also been adapted for bryophytes, and these range from mere axenic culture to molecular farming. However, specific characteristics of bryophyte biology—for example, a unique regeneration capacity—have also resulted in the development of methodologies and techniques different than those used for seed plants. In this review we provide an overview of the application of in vitro techniques to bryophytes, emphasising the differences as well as the similarities between bryophytes and seed plants. These are discussed within the framework of physiological and developmental processes as well as with respect to potential applications in plant biotechnology.     

Speciation genes in plants

Background

Analyses of speciation genes – genes that contribute to the cessation of gene flow between populations – can offer clues regarding the ecological settings, evolutionary forces and molecular mechanisms that drive the divergence of populations and species. This review discusses the identities and attributes of genes that contribute to reproductive isolation (RI) in plants, compares them with animal speciation genes and investigates what these genes can tell us about speciation.

Scope

Forty-one candidate speciation genes were identified in the plant literature. Of these, seven contributed to pre-pollination RI, one to post-pollination, prezygotic RI, eight to hybrid inviability, and 25 to hybrid sterility. Genes, gene families and genetic pathways that were frequently found to underlie the evolution of RI in different plant groups include the anthocyanin pathway and its regulators (pollinator isolation), S RNase-SI genes (unilateral incompatibility), disease resistance genes (hybrid necrosis), chimeric mitochondrial genes (cytoplasmic male sterility), and pentatricopeptide repeat family genes (cytoplasmic male sterility).

Conclusions

The most surprising conclusion from this review is that identities of genes underlying both prezygotic and postzygotic RI are often predictable in a broad sense from the phenotype of the reproductive barrier. Regulatory changes (both cis and trans) dominate the evolution of pre-pollination RI in plants, whereas a mix of regulatory mutations and changes in protein-coding genes underlie intrinsic postzygotic barriers. Also, loss-of-function mutations and copy number variation frequently contribute to RI. Although direct evidence of positive selection on speciation genes is surprisingly scarce in plants, analyses of gene family evolution, along with theoretical considerations, imply an important role for diversifying selection and genetic conflict in the evolution of RI. Unlike in animals, however, most candidate speciation genes in plants exhibit intraspecific polymorphism, consistent with an important role for stochastic forces and/or balancing selection in development of RI in plants.Key words: Speciation, reproductive isolation, mating system isolation, pollinator isolation, ecological isolation, unilateral incompatibility, hybrid necrosis, hybrid sterility, hybrid inviability, hybrid breakdown, cytoplasmic male sterility, restoration     

Island floras as model systems for studies of plant speciation: Prospects and challenges

Oceanic islands have long been called natural laboratories for studying evolution because they are geologically young, isolated, dynamic areas with diverse habitats over small spatial scales. Volcanic substrates of different ages permit the study of different stages of divergence and speciation within plant lineages. In addition to divergence, the dynamic island setting is conducive to hybridization. Discussion will focus on the potential of systematic/ecological studies, in combination with genomic data from high throughput sequencing and an ever‐increasing array of analytical techniques, for studying evolution in island plants. These studies may include: generation of highly resolved phylogenies to clarify the biogeography of speciation and whether divergence has occurred with or without gene flow; identification of the barriers to gene flow (extrinsic vs. intrinsic) of importance during divergence; documentation of historical and current hybridization events within island lineages; and elucidation of the genomic composition and ecology of hybrid populations in order to infer the evolutionary consequences of hybridization, such as the origin of stabilized homoploid hybrid species.     

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

Karst ecosystems in southern China are species‐rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid‐Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat.     

Dynamics of plant responses to combinations of air pollutants

The focus of this review is on how plants respond to combinations of multiple air pollutants. Global pollution trends, plant physiological responses and ecological perspectives in natural and agricultural systems are all discussed. In particular, we highlight the importance of studying sequential or simultaneous exposure of plants to pollutants, rather than exposure to individual pollutants in isolation, and explore how these responses may interfere with the way plants interact with their biotic community. Air pollutants can alter the normal physiology and metabolic functioning of plants. Here we describe how the phenotypic and molecular changes in response to multiple pollutants can differ compared to those elicited by single pollutants, and how different responses have been observed between plants in the field and in controlled laboratory conditions and between trees and crop plants. From an ecological perspective, we discuss how air pollution can result in greater susceptibility to biotic stressors and in direct or indirect effects on interactions with organisms that occupy higher trophic levels. Finally, we provide an overview of the potential uses of plants to mitigate air pollution, exploring the feasibility for pollution removal via the processes of bio‐accumulation and phytoremediation. We conclude by proposing some new directions for future research in the field.     

Molecular genetic and quantitative trait divergence associated with recent homoploid hybrid speciation: a study of Senecio squalidus (Asteraceae)

Hybridization is increasingly seen as a trigger for rapid evolution and speciation. To quantify and qualify divergence associated with recent homoploid hybrid speciation, we compared quantitative trait (QT) and molecular genetic variation between the homoploid hybrid species Senecio squalidus and its parental species, S. aethnensis and S. chrysanthemifolius, and also their naturally occurring Sicilian hybrids. S. squalidus originated and became invasive in the United Kingdom following the introduction of hybrid plants from Mount Etna, Sicily, about 300 years ago. We recorded considerable molecular genetic differentiation between S. squalidus and its parents and their Sicilian hybrids in terms of both reduced genetic diversity and altered allele frequencies, potentially due to the genetic bottleneck associated with introduction to the United Kingdom. S. squalidus is also distinct from its parents and Sicilian hybrids for QTs, but less so than for molecular genetic markers. We suggest that this is due to resilience of polygenic QTs to changes in allele frequency or lack of selection for hybrid niche divergence in geographic isolation. While S. squalidus is intermediate or parental-like for most QTs, some trangressively distinct traits were observed, which might indicate emerging local adaptation in its invasive range. This study emphasizes the important contribution of founder events and geographic isolation to successful homoploid hybrid speciation.     

Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna

Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome‐wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly‐differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs’ allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16–0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species – pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.     

Speciation by postzygotic isolation: forces, genes and molecules

New species arise as reproductive isolation evolves between diverging populations. Here we review recent work in the genetics of postzygotic reproductive isolation-the sterility and inviability of species hybrids. Over the last few years, research has taken two new directions. First, we have begun to learn a good deal about the population genetic forces driving the evolution of postzygotic isolation. It has, for instance, become increasingly clear that conflict-driven processes, like sexual selection and meiotic drive, may contribute to the evolution of hybrid sterility. Second, we have begun to learn something about the identity and molecular characteristics of the actual genes causing hybrid problems. Although molecular genetic data are limited, early findings suggest that "speciation genes" correspond to loci having normal functions within species and that these loci sometimes diverge as a consequence of evolution in gene regulation.     

Detection of DNA polymorphisms within the genusCattleya (Orchidaceae)

We have adapted methodology necessary for the detection of molecular polymorphisms in the orchid genusCattleya, namely, randomly amplified polymorphic DNA (RAPD). We report a high level of molecular variability among species; each of eight species examined exhibited a unique DNA fingerprint with nine out of ten arbitrary primers used in single-primer RAPD reactions. Among progeny of an intraspecificCattleya cross, 55 percent of major amplification products were found to segregate. Segregation of these markers facilitated the preliminary identification of several linkage intervals. The identification and mapping of DNA polymorphisms by the RAPD technique will facilitate the use of these taxa for the identification of species-specific and genus-specific traits, allow for the measurement of recombination and introgression in hybrid populations, and enable geneticists to address concordance (or lack thereof) in the processes of speciation, morphological evolution, and molecular change in a large and highly advanced plant family.     

The role of plastids in plant speciation

Understanding the molecular basis of how new species arise is a central question and prime challenge in evolutionary biology and includes understanding how genomes diversify. Eukaryotic cells possess an integrated compartmentalized genetic system of endosymbiotic ancestry. The cellular subgenomes in nucleus, mitochondria and plastids communicate in a complex way and co-evolve. The application of hybrid and cybrid technologies, most notably those involving interspecific exchanges of plastid and nuclear genomes, has uncovered a multitude of species-specific nucleo-organelle interactions. Such interactions can result in plastome-genome incompatibilities, which can phenotypically often be recognized as hybrid bleaching, hybrid variegation or disturbance of the sexual phase. The plastid genome, because of its relatively low number of genes, can serve as a valuable tool to investigate the origin of these incompatibilities. In this article, we review progress on understanding how plastome-genome co-evolution contributes to speciation. We genetically classify incompatible phenotypes into four categories. We also summarize genetic, physiological and environmental influence and other possible selection forces acting on plastid-nuclear co-evolution and compare taxa providing molecular access to the underlying loci. It appears that plastome-genome incompatibility can establish hybridization barriers, comparable to the Dobzhansky-Muller model of speciation processes. Evidence suggests that the plastid-mediated hybridization barriers associated with hybrid bleaching primarily arise through modification of components in regulatory networks, rather than of complex, multisubunit structures themselves that are frequent targets.     

Influences of gene flow on adaptive speciation in the Dubautia arborea--D. ciliolata complex

Mechanisms of reproductive isolation during plant speciation are often unclear because distinct species often experience high levels of gene flow and hybridization. Adaptive radiations such as the Hawaiian silversword alliance (HSA) provide unique opportunities to study the interactions of selection, gene flow and isolating mechanisms during the speciation process. We examined patterns of phenotypic and genetic differentiation in Dubautia arborea and Dubautia ciliolata, two parapatric HSA taxa that show marked morphological divergence but evidence of weak molecular differentiation, in order to estimate genome-wide differentiation and gene flow patterns. We scored 166 amplified fragment length polymorphism markers in a set of 89 plants from two populations each of D. arborea and D. ciliolata and phenotypically D. arborea-like and D. ciliolata-like plants from a natural hybrid zone. Analyses of population subdivision showed low levels of differentiation between the two species (F(ST) = 0.089) and evidence that the phenotypically parental hybrid zone plants were largely of parental species rather than of hybrid origin. A Bayesian analysis of population ancestry identified a number of plants with admixed D. arborea and D. ciliolata ancestry, even in nonhybrid-zone populations. These results suggest that genome-wide low levels of differentiation between D. arborea and D. ciliolata are in part due to gene flow, and favour models of genic speciation and collective evolution in which gene flow has different effects on selected loci vs. nonselected genomic regions. We discuss ecological and climatic factors that may have shaped patterns of differentiation in this species complex.     

Advances in the genetics of reproductive isolation in Drosophila

Speciation genetics is defined as the study of genetic events and processes that differentiate the probabilities that genetic material from individual members of a population will co-occur in individuals of some future generation. It follows that phenotypic attributes that contribute to this differentiation of probabilities (e.g., mating preferences, sterility, or infertility of individuals from certain types of matings) constitute the phenotype of speciation, and genetic loci that may affect these phenotypic attributes can be considered as speciation genes. The literature on genetic differences between hybridizable species of Drosophila that are responsible for morphological differences, mating preferences, hybrid inviability, and hybrid sterility are reviewed with special reference to the species pair D. mojavensis - D. arizonensis. The case for the involvement of karyotypic changes in speciation in rodents is briefly discussed. It is concluded that no major advance has been made in the speciation genetics of Drosophila since Dobzhansky initiated the field 40 years ago. Yet, the identification of several gene loci that cause hybrid inviability or sterility may open the way to the understanding of reproductive isolation at the molecular level. It is not clear whether this approach will lead to general molecular mechanisms underlying the speciation process.     

Integrating ancient patterns and current dynamics of insect–plant interactions: Taxonomic and geographic variation in herbivore specialization

Abstract The search for pattern in the ecology and evolutionary biology of insect–plant associations has fascinated biologists for centuries. High levels of tropical (low-latitude) plant and insect diversity relative to poleward latitudes and the disproportionate abundance of host-specialized insect herbivores have been noted. This review addresses several aspects of local insect specialization, host use abilities (and loss of these abilities with specialization), host-associated evolutionary divergence, and ecological (including “hybrid”) speciation, with special reference to the generation of biodiversity and the geographic and taxonomic identification of “species borders” for swallowtail butterflies (Papilionidae). From ancient phytochemically defined angiosperm affiliations that trace back millions of years to recent and very local specialized populations, the Papilionidae (swallowtail butterflies) have provided a model for enhanced understanding of localized ecological patterns and genetically based evolutionary processes. They have served as a useful group for evaluating the feeding specialization/physiological efficiency hypothesis. They have shown how the abiotic (thermal) environment interacts with host nutrirional suitability to generate “voltinism/suitability” gradients in specialization or preference latitudinally, and geographical mosaics locally. Several studies reviewed here suggest strongly that the oscillation hypothesis for speciation does have considerable merit, but at the same time, some species-level host specializations may lead to evolutionary dead-ends, especially with rapid environmental/habitat changes involving their host plants. Latitudinal gradients in species richness and degree of herbivore feeding specialization have been impacted by recent developments in ecological genetics and evolutionary ecology. Localized insect–plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious, with simple definitions still debated. However, molecular analyses combined with ecological, ethological and physiological studies, have already begun to unveil some answers for many important ecological/evolutionary questions.     

Impacts of climate warming on hybrid zone movement: Geographically diffuse and biologically porous “species borders”

Abstract The ecology and evolutionary biology of insect–plant associations has realized extensive attention, especially during the past 60 years. The classifications (categorical designations) of continuous variation in biodiversity, ranging from global patterns (e.g., latitudinal gradients in species richness/diversity and degree of herbivore feeding specialization) to localized insect–plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious. Semantic and biosystematic (taxonomical) disagreements sometimes detract from more important ecological and evolutionary processes that drive diversification, the dynamics of gene flow and local extinctions. This review addresses several aspects of insect specialization, host‐associated divergence and ecological (including “hybrid”) speciation, with special reference to the climate warming impacts on species borders of hybridizing swallowtail butterflies (Papilionidae). Interspecific hybrid introgression may result in collapse of multi‐species communities or increase species numbers via homoploid hybrid speciation. We may see diverging, merging, or emerging genotypes across hybrid zones, all part of the ongoing processes of evolution. Molecular analyses of genetic mosaics and genomic dynamics with “divergence hitchhiking”, combined with ecological, ethological and physiological studies of “species porosity”, have already begun to unveil some answers for some important ecological/evolutionary questions. (i) How rapidly can host‐associated divergence lead to new species (and why doesn't it always do so, e.g., resulting in “incomplete” speciation)? (ii) How might “speciation genes” function, and how/where would we find them? (iii) Can oscillations from specialists to generalists and back to specialists help explain global diversity in herbivorous insects? (iv) How could recombinant interspecific hybridization lead to divergence and speciation? From ancient phytochemically defined angiosperm affiliations to recent and very local geographical mosaics, the Papilionidae (swallowtail butterflies) have provided a model for enhanced understanding of ecological patterns and evolutionary processes, including host‐associated genetic divergence, genomic mosaics, genetic hitchhiking and sex‐linked speciation genes. Apparent homoploid hybrid speciation in Papilio appears to have been catalyzed by climate warming‐induced interspecific introgression of some, but not all, species diagnostic traits, reflecting strong divergent selection (discordant), especially on the Z (= X) chromosome. Reproductive isolation of these novel recombinant hybrid genotypes appears to be accomplished via a delayed post‐diapause emergence or temporal isolation, and is perhaps aided by the thermal landscape. Changing thermal landscapes appear to have created (and may destroy) novel recombinant hybrid genotypes and hybrid species.