Rapid speciation with gene flow following the formation of Mt. Etna

Documenting homoploid hybrid speciation

Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo-species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that - given the ubiquity of admixture and the polygenic basis of reproductive isolation - homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies.

Genomics of plant speciation

Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.

Rapid evolution of hybrid breakdown following recent divergence with gene flow in Senecio species on Mount Etna, Sicily

How do nascent species evolve reproductive isolation during speciation with on-going gene flow? How do hybrid lineages become stabilised hybrid species? While commonly used genomic approaches provide an indirect way to identify species incompatibility factors, synthetic hybrids generated from interspecific crosses allow direct pinpointing of phenotypic traits involved in incompatibilities and the traits that are potentially adaptive in hybrid species. Here we report the analysis of phenotypic variation and hybrid breakdown in crosses between closely-related Senecio aethnensis and S. chrysanthemifolius, and their homoploid hybrid species, S. squalidus. The two former species represent a likely case of recent (<200 ky) speciation with gene flow driven by adaptation to contrasting conditions of high- and low-elevations on Mount Etna, Sicily. As these species form viable and fertile hybrids, it remains unclear whether they have started to evolve reproductive incompatibility. Our analysis represents the first study of phenotypic variation and hybrid breakdown involving multiple Senecio hybrid families. It revealed wide range of variation in multiple traits, including the traits previously unrecorded in synthetic hybrids. Leaf shape, highly distinct between S. aethnensis and S. chrysanthemifolius, was extremely variable in F₂ hybrids, but more consistent in S. squalidus. Our study demonstrates that interspecific incompatibilities can evolve rapidly despite on-going gene flow between the species. Further work is necessary to understand the genetic bases of these incompatibilities and their role in speciation with gene flow.

Adaptive divergence generates distinct plastic responses in two closely related Senecio species

The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variations they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled 40 representative genotypes of each species from their native range on Mt. Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation, we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content, and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little changes in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is, therefore, associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.

The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio

Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.

Senecio as a model system for integrating studies of genotype, phenotype and fitness

Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.

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 in Howea Palms Occurred in Sympatry, Was Preceded by Ancestral Admixture, and Was Associated with Edaphic and Phenological Adaptation

Howea palms are viewed as one of the most clear-cut cases of speciation in sympatry. The sister species Howea belmoreana and H. forsteriana are endemic to the oceanic Lord Howe Island, Australia, where they have overlapping distributions and are reproductively isolated mainly by flowering time differences. However, the potential role of introgression from Australian mainland relatives had not previously been investigated, a process that has recently put other examples of sympatric speciation into question. Furthermore, the drivers of flowering time-based reproductive isolation remain unclear. We sequenced an RNA-seq data set that comprehensively sampled Howea and their closest mainland relatives (Linospadix, Laccospadix), and collected detailed soil chemistry data on Lord Howe Island to evaluate whether secondary gene flow had taken place and to examine the role of soil preference in speciation. D-statistics analyses strongly support a scenario whereby ancestral Howea hybridized frequently with its mainland relatives, but this only occurred prior to speciation. Expression analysis, population genetic and phylogenetic tests of selection, identified several flowering time genes with evidence of adaptive divergence between the Howea species. We found expression plasticity in flowering time genes in response to soil chemistry as well as adaptive expression and sequence divergence in genes pleiotropically linked to soil adaptation and flowering time. Ancestral hybridization may have provided the genetic diversity that promoted their subsequent adaptive divergence and speciation, a process that may be common for rapid ecological speciation.

Completing the hybridization triangle: the inheritance of genetic incompatibilities during homoploid hybrid speciation in ragworts (Senecio)

A new homoploid hybrid lineage needs to establish a degree of reproductive isolation from its parent species if it is to persist as an independent entity, but the role hybridization plays in this process is known in only a handful of cases. The homoploid hybrid ragwort species, Senecio squalidus (Oxford ragwort), originated following the introduction of hybrid plants to the UK approximately 320 years ago. The source of the hybrid plants was from a naturally occurring hybrid zone between S. aethnensis and S. chrysanthemifolius on Mount Etna, Sicily. Previous studies of the parent species found evidence for multiple incompatibility loci causing transmission ratio distortion of genetic markers in their hybrid progeny. This study closes the hybridization triangle by reporting a genetic mapping analysis of the remaining two paired cross combinations between S. squalidus and its parents. Genetic maps produced from F₂ mapping families were generally collinear but with half of the linkage groups showing evidence of genomic reorganization between genetic maps. The new maps produced from crosses between S. squalidus and each parent showed multiple incompatibility loci distributed across the genome, some of which co-locate with previously reported incompatibility loci between the parents. These findings suggest that this young homoploid hybrid species has inherited a unique combination of genomic rearrangements and incompatibilities from its parents that contribute to its reproductive isolation.

Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna

Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow - a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialization to a particular host plant. Genomewide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genomewide divergence associated with both geographic distance and ecological divergence. However, a hybridization assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different host-associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.

Can genomic data alone tell us whether speciation happened with gene flow?

The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.

Hybridization and hybrid speciation under global change

Contents 1170 I. 1170 II. 1172 III. 1175 IV. 1180 V. 1183 1184 References 1184 SUMMARY: An unintended consequence of global change is an increase in opportunities for hybridization among previously isolated lineages. Here we illustrate how global change can facilitate the breakdown of reproductive barriers and the formation of hybrids, drawing on the flora of the British Isles for insight. Although global change may ameliorate some of the barriers preventing hybrid establishment, for example by providing new ecological niches for hybrids, it will have limited effects on environment-independent post-zygotic barriers. For example, genic incompatibilities and differences in chromosome numbers and structure within hybrid genomes are unlikely to be affected by global change. We thus speculate that global change will have a larger effect on eroding pre-zygotic barriers (eco-geographical isolation and phenology) than post-zygotic barriers, shifting the relative importance of these two classes of reproductive barriers from what is usually seen in naturally produced hybrids where pre-zygotic barriers are the largest contributors to reproductive isolation. Although the long-term fate of neo-hybrids is still to be determined, the massive impact of global change on the dynamics and distribution of biodiversity generates an unprecedented opportunity to study large numbers of unpredicted, and often replicated, hybridization 'experiments', allowing us to peer into the birth and death of evolutionary lineages.

Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses

Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.

Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient

Knowledge of the genetic basis of phenotypic divergence between species and how such divergence is caused and maintained is crucial to an understanding of speciation and the generation of biodiversity. The hybrid zone between Senecio aethnensis and S. chrysanthemifolius on Mount Etna, Sicily, provides a well-studied example of species divergence in response to conditions at different elevations, despite hybridization and gene flow. Here, we investigate the genetic architecture of divergence between these two species using a combination of quantitative trait locus (QTL) mapping and genetic differentiation measures based on genetic marker analysis. A QTL architecture characterized by physical QTL clustering, epistatic interactions between QTLs, and pleiotropy was identified, and is consistent with the presence of divergent QTL complexes resistant to gene flow. A role for divergent selection between species was indicated by significant negative associations between levels of interspecific genetic differentiation at mapped marker gene loci and map distance from QTLs and hybrid incompatibility loci. Within-species selection contributing to interspecific differentiation was evidenced by negative associations between interspecific genetic differentiation and genetic diversity within species. These results show that the two Senecio species, while subject to gene flow, maintain divergent genomic regions consistent with local selection within species and selection against hybrids between species which, in turn, contribute to the maintenance of their distinct phenotypic differences.

Demographic history of speciation in a Senecio altitudinal hybrid zone on Mt. Etna

Hybrid zones typically form as a result of species coming into secondary contact, but can also be established in situ as an ecotonal hybrid zone, a situation which has been reported far less frequently. An altitudinal hybrid zone on Mount Etna between two ragwort species (the low elevation Senecio chrysanthemifolius and high elevation S. aethnensis) could potentially represent either of these possibilities. However, a scenario of secondary contact vs. speciation with gene flow has not been explicitly tested. Here, we test these alternatives and demonstrate that the data do not support secondary contact. Furthermore, we report that the previous analyses of speciation history of these species were based on admixed populations, which has led to inflated estimates of ongoing, interspecific gene flow. Our new analyses, based on 'pure' S. aethnensis and S. chrysanthemifolius populations, reveal gene exchange of less than one effective migrant per generation, a level low enough to allow the species to accumulate neutral, genomewide differences. Overall, our results are consistent with a scenario of speciation with gene flow and a divergence time which coincides with the rise of Mt. Etna to altitudes above 2000 m (~150 KY). Further work to quantify the role of adaptation to contrasting environments of high and low altitudes will be needed to support the scenario of recent ecological speciation in this system.

Maintenance of Species Boundaries Despite Ongoing Gene Flow in Ragworts

The role of hybridization between diversifying species has been the focus of a huge amount of recent evolutionary research. While gene flow can prevent speciation or initiate species collapse, it can also generate new hybrid species. Similarly, while adaptive divergence can be wiped out by gene flow, new adaptive variation can be introduced via introgression. The relative frequency of these outcomes, and indeed the frequency of hybridization and introgression in general are largely unknown. One group of closely-related species with several documented cases of hybridization is the Mediterranean ragwort (genus: Senecio) species-complex. Examples of both polyploid and homoploid hybrid speciation are known in the clade, although their evolutionary relationships and the general frequency of introgressive hybridization among them remain unknown. Using a whole genome gene-space dataset comprising eight Senecio species we fully resolve the phylogeny of these species for the first time despite phylogenetic incongruence across the genome. Using a D-statistic approach, we demonstrate previously unknown cases of introgressive hybridization between multiple pairs of taxa across the species tree. This is an important step in establishing these species as a study system for diversification with gene flow, and suggests that introgressive hybridization may be a widespread and important process in plant evolution.

The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae)

Ecological speciation, driven by adaptation to contrasting environments, provides an attractive opportunity to study the formation of distinct species, and the role of selection and genomic divergence in this process. Here, we focus on a particularly clear-cut case of ecological speciation to reveal the genomic bases of reproductive isolation and morphological differences between closely related Senecio species, whose recent divergence within the last ~200,000 years was likely driven by the uplift of Mt. Etna (Sicily). These species form a hybrid zone, yet remain morphologically and ecologically distinct, despite active gene exchange. Here, we report a high-density genetic map of the Senecio genome and map hybrid breakdown to one large and several small quantitative trait loci (QTL). Loci under diversifying selection cluster in three 5 cM regions which are characterized by a significant increase in relative (F(ST)), but not absolute (d(XY)), interspecific differentiation. They also correspond to some of the regions of greatest marker density, possibly corresponding to 'cold-spots' of recombination, such as centromeres or chromosomal inversions. Morphological QTL for leaf and floral traits overlap these clusters. We also detected three genomic regions with significant transmission ratio distortion (TRD), possibly indicating accumulation of intrinsic genetic incompatibilities between these recently diverged species. One of the TRD regions overlapped with a cluster of high species differentiation, and another overlaps the large QTL for hybrid breakdown, indicating that divergence of these species may have occurred due to a complex interplay of ecological divergence and accumulation of intrinsic genetic incompatibilities.

Genetic structure is associated with phenotypic divergence in floral traits and reproductive investment in a high-altitude orchid from the Iron Quadrangle, southeastern Brazil

Knowledge of the role of Neotropical montane landscapes in shaping genetic connectivity and local adaptation is essential for understanding the evolutionary processes that have shaped the extraordinary species diversity in these regions. In the present study, we examined the landscape genetics, estimated genetic diversity, and explored genetic relationships with morphological variability and reproductive strategies in seven natural populations of Cattleya liliputana (Orchidaceae). Nuclear microsatellite markers were used for genetic analyses. Spatial Bayesian clustering and population-based analyses revealed significant genetic structuring and high genetic diversity (He = 0.733 ± 0.03). Strong differentiation was found between populations over short spatial scales (FST = 0.138, p < 0.001), reflecting the landscape discontinuity and isolation. Monmonier´s maximum difference algorithm, Bayesian analysis on STRUCTURE and principal component analysis identified one major genetic discontinuity between populations. Divergent genetic groups showed phenotypic divergence in flower traits and reproductive strategies. Increased sexual reproductive effort was associated with rock outcrop type and may be a response to adverse conditions for growth and vegetative reproduction. Here we discuss the effect of restricted gene flow, local adaptation and phenotypic plasticity as drivers of population differentiation in Neotropical montane rock outcrops.

Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox)

We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic structure across the range of the Western Diamondback Rattlesnake (Crotalus atrox), a widely distributed North American pit viper. We also tested hypotheses of population structure using double-digest restriction site associated DNA (ddRADseq) data, incorporating thousands of nuclear genome-wide SNPs from 42 individuals. We found strong mitochondrial support for a deep divergence between eastern and western C. atrox populations, and subsequent intermixing of these populations in the Inter-Pecos region of the United States and Mexico. Our nuclear RADseq data also identify these two distinct lineages of C. atrox, and provide evidence for nuclear admixture of eastern and western alleles across a broad geographic region. We identified contrasting patterns of mitochondrial and nuclear genetic variation across this genetic fusion zone that indicate partially restricted patterns of gene flow, which may be due to either pre- or post-zygotic isolating mechanisms. The failure of these two lineages to maintain complete genetic isolation, and evidence for partially-restricted gene flow, imply that these lineages were in the early stages of speciation prior to secondary contact.

Morphological differentiation despite gene flow in an endangered grasshopper

BACKGROUND

Gene flow is traditionally considered a limitation to speciation because selection is required to counter the homogenising effect of allele exchange. Here we report on two sympatric short-horned grasshoppers species in the South Island of New Zealand; one (Sigaus australis) widespread and the other (Sigaus childi) a narrow endemic.

RESULTS

Of the 79 putatively neutral markers (mtDNA, microsatellite loci, ITS sequences and RAD-seq SNPs) all but one marker we examined showed extensive allele sharing, and similar or identical allele frequencies in the two species where they co-occur. We found no genetic evidence of deviation from random mating in the region of sympatry. However, analysis of morphological and geometric traits revealed no evidence of morphological introgression.

CONCLUSIONS

Based on phenotype the two species are clearly distinct, but their genotypes thus far reveal no divergence. The best explanation for this is that some loci associated with the distinguishing morphological characters are under strong selection, but exchange of neutral loci is occurring freely between the two species. Although it is easier to define species as requiring a barrier between them, a dynamic model that accommodates gene flow is a biologically more reasonable explanation for these grasshoppers.

Useful insights from evolutionary biology for developing perennial grain crops

Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding.

Models of selection, isolation, and gene flow in speciation

Many marine ecologists aspire to use genetic data to understand how selection and demographic history shape the evolution of diverging populations as they become reproductively isolated species. I propose combining two types of genetic analysis focused on this key early stage of the speciation process to identify the selective agents directly responsible for population divergence. Isolation-with-migration (IM) models can be used to characterize reproductive isolation between populations (low gene flow), while codon models can be used to characterize selection for population differences at the molecular level (especially positive selection for high rates of amino acid substitution). Accessible transcriptome sequencing methods can generate the large quantities of data needed for both types of analysis. I highlight recent examples (including our work on fertilization genes in sea stars) in which this confluence of interest, models, and data has led to taxonomically broad advances in understanding marine speciation at the molecular level. I also highlight new models that incorporate both demography and selection: simulations based on these theoretical advances suggest that polymorphisms shared among individuals (a key source of information in IM models) may lead to false-positive evidence of selection (in codon models), especially during the early stages of population divergence and speciation that are most in need of study. The false-positive problem may be resolved through a combination of model improvements plus experiments that document the phenotypic and fitness effects of specific polymorphisms for which codon models and IM models indicate selection and reproductive isolation (such as genes that mediate sperm-egg compatibility at fertilization).

Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data

Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean = 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.

Altitudinal gradients, plant hybrid zones and evolutionary novelty

Altitudinal gradients are characterized by steep changes of the physical and biotic environment that present challenges to plant adaptation throughout large parts of the world. Hybrid zones may form where related species inhabit different neighbouring altitudes and can facilitate interspecific gene flow and potentially the breakdown of species barriers. Studies of such hybrid zones can reveal much about the genetic basis of adaptation to environmental differences stemming from changes in altitude and the maintenance of species divergence in the face of gene flow. Furthermore, owing to recombination and transgressive effects, such hybrid zones can be sources of evolutionary novelty. We document plant hybrid zones associated with altitudinal gradients and emphasize similarities and differences in their structure. We then focus on recent studies of a hybrid zone between two Senecio species that occur at high and low altitude on Mount Etna, Sicily, showing how adaptation to local environments and intrinsic selection against hybrids act to maintain it. Finally, we consider the potential of altitudinal hybrid zones for generating evolutionary novelty through adaptive introgression and hybrid speciation. Examples of homoploid hybrid species of Senecio and Pinus that originated from altitudinal hybrid zones are discussed.

Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily

Studies of hybridizing species can reveal much about the genetic basis and maintenance of species divergence in the face of gene flow. Here we report a genetic segregation and linkage analysis conducted on F2 progeny of a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius that form a hybrid zone on Mount Etna, Sicily, aimed at determining the genetic basis of intrinsic hybrid barriers between them. Significant transmission ratio distortion (TRD) was detected at 34 (∼27%) of 127 marker loci located in nine distinct clusters across seven of the ten linkage groups detected, indicating genomic incompatibility between the species. TRD at these loci could not be attributed entirely to post-zygotic selective loss of F2 individuals that failed to germinate or flower (16.7%). At four loci tests indicated that pre-zygotic events, such as meiotic drive in F1 parents or gametophytic selection, contributed to TRD. Additional tests revealed that cytonuclear incompatibility contributed to TRD at five loci, Bateson-Dobzhansky-Muller (BDM) incompatibilities involving epistatic interactions between loci contributed to TRD at four loci, and underdominance (heterozygote disadvantage) was a possible cause of TRD at one locus. Major chromosomal rearrangements were probably not a cause of interspecific incompatibility at the scale that could be examined with current map marker density. Intrinsic genomic incompatibility between S. aethnensis and S. chrysanthemifolius revealed by TRD across multiple genomic regions in early-generation hybrids is likely to impact the genetic structure of the natural hybrid zone on Mount Etna by limiting introgression and promoting divergence across the genome.

Evidence for isolation-by-habitat among populations of an epiphytic orchid species on a small oceanic island

Identifying factors that promote population differentiation is of interest for understanding the early stages of speciation. Gene flow among populations inhabiting different environments can be reduced by geographical distance (isolation-by-distance) or by divergent selection resulting from local adaptation (isolation-by-ecology). Few studies have investigated the influence of these factors in small oceanic islands where the influence of geographic distance is expected to be null but where habitat diversity could have a strong effect on population differentiation. In this study, we tested for the spatial divergence of phenotypes (floral morphology and floral scent) and genotypes (microsatellites) among ten populations of Jumellea rossii, an epiphytic orchid endemic to Réunion growing in three different habitats. We found a significant genetic differentiation between populations that is structured by habitat heterogeneity rather than by geographic distance between populations. These results suggest that ecological factors might reduce gene flow among populations located in different habitats. This pattern of isolation-by-habitat may be the result of both isolation-by-ecology by habitat filtering and asynchrony in flowering phenology. Furthermore, data on floral morphology match these findings, with multivariate analysis grouping populations by habitat type but could be only due to phenotypic plasticity. Indeed floral scent compounds were not significantly different between populations indicating that specific plant-pollinator mutualism does not seem to play a major role in the population differentiation of J. rossii. In conclusion, the results from our study emphasize the importance of habitat diversity of small oceanic islands as a factor of population differentiation.

Short Reads Phasing to Construct Haplotypes in Genomic Regions That Are Associated with Body Mass Index in Korean Individuals

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

Genomic divergence during speciation driven by adaptation to altitude

Even though Darwin's "On the Origin of Species" implied selection being the main driver of species formation, the role of natural selection in speciation remains poorly understood. In particular, it remains unclear how selection at a few genes can lead to genomewide divergence and the formation of distinct species. We used a particularly attractive clear-cut case of recent plant ecological speciation to investigate the demography and genomic bases of species formation driven by adaptation to contrasting conditions. High-altitude Senecio aethnensis and low-altitude S. chrysanthemifolius live at the extremes of a mountain slope on Mt. Etna, Sicily, and form a hybrid zone at intermediate altitudes but remain morphologically distinct. Genetic differentiation of these species was analyzed at the DNA polymorphism and gene expression levels by high-throughput sequencing of transcriptomes from multiple individuals. Out of ≈ 18,000 genes analyzed, only a small number (90) displayed differential expression between the two species. These genes showed significantly elevated species differentiation (FST and Dxy), consistent with diversifying selection acting on these genes. Genomewide genetic differentiation of the species is surprisingly low (FST = 0.19), while ≈ 200 genes showed significantly higher (false discovery rate < 1%; mean outlier FST > 0.6) interspecific differentiation and evidence for local adaptation. Diversifying selection at only a handful of loci may be enough for the formation and maintenance of taxonomically well-defined species, despite ongoing gene flow. This provides an explanation of why many closely related species (in plants, in particular) remain phenotypically and ecologically distinct despite ongoing hybridization, a question that has long puzzled naturalists and geneticists alike.