Early Stages Of Speciation Research Articles

Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea).

Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I.lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I.lacunosa to I.cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I.cordatotriloba being substantially more different than sympatric and allopatric I.lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I.cordatotriloba traits become much more like those of I.lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.

Behavioural syndromes as a link between ecology and mate choice: a field study in a reef fish population

The link between ecology and reproductive isolation constitutes the cornerstone of the ecological hypothesis of speciation. Such a link can arise when traits under ecologically based selection are also used as cues for mating (‘magic traits’) or as a by-product of habitat choice when mating takes place within habitats. Here, we propose that behavioural syndromes may also constitute such a link. We illustrate this mechanism in the butter hamlet, Hypoplectrus unicolor, a reef fish from the wider Caribbean, with aggressive mimicry as the focal ecological trait. Aggressive mimicry is of particular interest in hamlets since it has been proposed to play a key role in the radiation of Hypoplectrus. Individuals from a natural population in Bocas del Toro, Panama, were tagged and their diurnal and spawning behaviours observed over 2 years. The results indicate that aggressive mimicry behaviour differed consistently between individuals and formed two discrete behavioural types that also differed with respect to territoriality. Differences in territoriality between the two behavioural types translated into different use of space in spawning contexts, which generated a tendency for assortative mating by behavioural type. This case study illustrates how behavioural syndromes may form a link between ecologically relevant behavioural traits and mate choice, suggesting that they might play an underappreciated role in the early stages of speciation.

Mate Choice versus Mate Preference: Inferences about Color-Assortative Mating Differ between Field and Lab Assays of Poison Frog Behavior.

Codivergence of mating traits and mate preferences can lead to behavioral isolation among lineages in early stages of speciation. However, mate preferences limit gene flow only when expressed as mate choice, and numerous factors might be more important than preferences in nature. In the extremely color polytypic strawberry poison frog (Oophaga pumilio), female mate preferences have codiverged with color in most allopatric populations tested. Whether these lab-assayed preferences predict mating (gene flow) in the wild remains unclear. We observed courting pairs in a natural contact zone between red and blue lineages until oviposition or courtship termination. We found color-assortative mating in a disturbed habitat with high population density but not in a secondary forest with lower density. Our results suggest color-assortative O. pumilio mate choice in the wild but also mating patterns that do not match those predicted by lab-assayed preferences.

Current geography masks dynamic history of gene flow during speciation in northern Australian birds.

Genome divergence is greatly influenced by gene flow during early stages of speciation. As populations differentiate, geographic barriers can constrain gene flow and so affect the dynamics of divergence and speciation. Current geography, specifically disjunction and continuity of ranges, is often used to predict the historical gene flow during the divergence process. We test this prediction in eight meliphagoid bird species complexes codistributed in four regions. These regions are separated by known biogeographical barriers across northern Australia and Papua New Guinea. We find that bird populations currently separated by terrestrial habitat barriers within Australia and marine barriers between Australia and Papua New Guinea have a range of divergence levels and probability of gene flow not associated with current range connectivity. Instead, geographic distance and historical range connectivity better predict divergence and probability of gene flow. In this dynamic environmental context, we also find support for a nonlinear decrease of the probability of gene flow during the divergence process. The probability of gene flow initially decreases gradually after a certain level of divergence is reached. Its decrease then accelerates until the probability is close to zero. This implies that although geographic connectivity may have more of an effect early in speciation, other factors associated with higher divergence may play a more important role in influencing gene flow midway through and later in speciation. Current geographic connectivity may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.

Dialects of Metrioptera bicolor (Orthoptera: Tettigonioidea): Intraspecific Acoustic Signal Divergence in a Small-Scale Geographical Distribution

We present an analysis of the calling songs of species Metrioptera bicolor isolated from different locations within Northeast China illustrating the intraspecies calling song divergence. Recording and analysis of the male calling songs of some acoustic characters were performed and five morphological traits of M. bicolor were examined under stereoscope microscope and scanning electron microscope. A cluster analysis was made based on the song properties and the morphology of stridulatory organs. All the song traits, except the pulse number per pulse group, differ distinctly within species collected at different localities, while the pulse number of each pulse group and all the five morphological characters were consistent across locations. The cluster analysis showed that M. bicolor collected from eight sampling sites grouped into two branches and were consistent with geographical distribution.The dialect phenomenon exists in insects and the divergence of acoustic signals occurs in a small-scale geographical region and may be an early stage of speciation. We inferred that the divergence of intraspecific acoustic signals on a small-scale may result from different habitats. This study provides evidence for insect acoustic signal divergence, speciation, and insect acoustic signal evolution.

Pelagic–littoral resource polymorphism in Hovsgol grayling Thymallus nigrescens from Lake Hovsgol, Mongolia

AbstractResource polymorphism is a widespread phenomenon in post‐glacial fishes where multiple morphotypes of a species occur sympatrically and exhibit distinct resource use. Availability of open niches and high levels of within and among species competition are thought to drive differences in morphology and may provide insights into early stages of speciation. Hovsgol grayling (Thymallus nigrescens) are endemic to Lake Hovsgol, a lake colonised by fish following the Pleistocene, and are threatened with habitat loss due to climate change and illegal harvest. Previous analysis of Hovsgol grayling diet inferred through C and N stable isotopes suggested the presence of littoral and pelagic foraging groups. We hypothesised that morphology of the two foraging groups would reflect predictions of functional morphology, indicating the presence of resource polymorphism. To test this hypothesis, we evaluated evidence from C and N stable isotopes, stomach contents, fish ages, capture location and morphology. Two foraging groups of Hovsgol grayling were identified through stomach content and C and N stable isotope analysis. Individuals with greater zooplankton consumption were more frequently captured in the pelagic zone, exhibited higher gill raker counts, larger orbit (eye) sizes, longer paired fins, narrower head width, larger maxilla and smaller size at age than the group with greater reliance on benthic invertebrate prey. These differences were generally consistent with those described in other fish species exhibiting littoral–pelagic resource polymorphism. Our study provides the first example of littoral–pelagic resource polymorphism in the salmonid subfamily Thymallinae and highlights the potential influence of competition on fish evolution.

Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation?

BackgroundGeographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals.ResultsThe results reveal a low level of genetic differentiation and relatively simple phylogeographic structure for this species, but two independent clades corresponding to geographically isolated populations were recognised. Genetic and geographical distances were significantly correlated among lineages. Results of divergence-time estimation are consistent with a scenario of isolation due to glacial refugia and interglacial climate oscillation in northwestern China. Significant genetic divergence was found between the population occurring in the Helan Mountains and other populations, and recent population expansion has occurred in the Helan Mountains and/or adjacent areas. This population is also significantly different in calling song structure from other populations.ConclusionsGeographical barriers (i.e., the deserts and semi-deserts surrounding the Helan Mountains), possibly coupled with related ecological differences, may have driven population divergence and allopatric speciation. This provides a possible example of incipient speciation in Cicadidae, improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this rare cicada species of conservation concern, and informs future studies on population differentiation, speciation and phylogeography of other insects with a high degree of endemism in the Helan Mountains and adjacent areas.

Consistent seasonal polyphenism in male genitalia of threeLeptideabutterfly species (Lepidoptera: Pieridae)

Insect genitalia are important for species identification and taxonomy and are key traits for the evolution of reproductive isolation through their 'lock-And-key mechanism'. Nevertheless, few studies have evaluated intraspecific variation and the impact of seasonal environmental variation on genital morphology. We used geometric morphometric analysis to quantify male genital morphology within and among the three taxa in the Leptidea sinapis cryptic species complex (Lepidoptera: Pieridae). We focused on the potential presence of seasonal polyphenism, i.e. consistent differences among temporally separated generations. As predicted, our analysis revealed that male genitalia differed in size, shape and form (the joint effect of size and shape) among species. More surprisingly, all species harboured consistent genital variation between the spring and summer generations. The interspecific variation in genital structures could function as a mechanical reproductive barrier, although contemporary populations of these butterflies do not engage in heterospecific matings. We suggest that the smaller, but significant, genital differences among conspecific generations provide an opportunity to test empirically whether a seasonal polyphenism in genital morphology could generate raw material for the build-up of reproductive isolation at an early stage of speciation. Collectively, our results provide evidence demonstrating that insect genitalia can indeed harbour ample intraspecific variation. (Less)

Behavioral Isolation and Incipient Speciation in Birds

Behavioral changes, such as those involved in mating, foraging, and migration, can generate reproductive barriers between populations. Birds, in particular, are known for their great diversity in these behaviors, and so behavioral isolation is often proposed to be the major driver of speciation. Here, we review empirical evidence to evaluate the importance of behavioral isolation in the early stages of avian speciation. Experimentally measured mating preferences indicate that changes in mating behavior can result in premating barriers, with their strength depending on the extent of divergence in mating signals. Differences in migratory and foraging behavior also can play important roles in generating reproductive barriers in the early stages of speciation. However, because premating behavioral isolation is imperfect, extrinsic postzygotic barriers, in the form of selection against hybrids having intermediate phenotypes, also play an important role in avian diversification, especially in completing the speciation process.

Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus

The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation. Here, we report a high-quality reference genome for one population (~190 megabases across 12 scaffolds, and ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific to T. californicus, with an apparent proliferation of genes involved in ion transport and receptor activity. Beyond the reference population, we report re-sequenced genomes of seven additional populations, spanning the continuum of reproductive isolation. Populations show extreme mitochondrial DNA divergence, with higher levels of amino acid differentiation than observed in other taxa. Across the nuclear genome, we find elevated protein evolutionary rates and positive selection in genes predicted to interact with mitochondrial DNA and the proteins and RNA it encodes in multiple pathways. Together, these results support the hypothesis that rapid mitochondrial evolution drives compensatory nuclear evolution within isolated populations, thereby providing a potentially important mechanism for causing intrinsic reproductive isolation.

Transgressive phenotypes and evidence of weak postzygotic isolation in F1 hybrids between closely related capuchino seedeaters.

Postzygotic reproductive isolation may become strong only once the process of speciation is in its advanced stages. For taxa in the early stages of speciation, prezygotic reproductive isolation barriers may play a predominant role in maintaining species boundaries. Here, we study the recent capuchino seedeater biological radiation, a group of highly sympatric species from the genus Sporophila that have diversified during the Pleistocene in Neotropical grasslands. Capuchinos can be diagnosed by adult male coloration patterns and song, two sets of characters known to contribute to pre-mating reproductive isolation. However, it remains unknown whether potzygotic incompatibilities contribute to maintaining species limits in this group. Here we use existing breeding records from captive individuals to test for patterns consistent with F1 inviability. We compare hatching success, fledging success, and the sex ratio at adulthood between conspecific and hybrid capuchino pairs. We observed a trend towards lower numbers of the heterogametic sex among adult hybrids, consistent Haldane's rule, but this was supported by only one of our statistical tests. Our study is the first to document hybrid male capuchino phenotypes based on known crosses. We observed phenotypes that were similar or intermediate to those of the parental species, as well as novel plumage patterns that have not been described in the wild. One cross produced a plumage pattern that has been observed at low frequencies in natural populations. We discuss the implications of our results for understanding the relative importance of the mechanisms of reproductive isolation in capuchino seedeaters.

Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds.

Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST) and absolute (dXY) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window‐based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.

Mechanical and tactile incompatibilities cause reproductive isolation between two young damselfly species.

External male reproductive structures have received considerable attention as a cause of reproductive isolation (RI), because the morphology of these structures often evolves rapidly between populations. This rapid evolution presents the potential for mechanical incompatibilities with heterospecific female structures during mating and could thus prevent interbreeding between nascent species. Although such mechanical incompatibilities have received little empirical support as a common cause of RI, the potential for mismatch of reproductive structures to cause RI due to incompatible species-specific tactile cues has not been tested. We tested the importance of mechanical and tactile incompatibilities in RI between Enallagma anna and E. carunculatum, two damselfly species that diverged within the past ∼250,000 years and currently hybridize in a sympatric region. We quantified 19 prezygotic and postzygotic RI barriers using both naturally occurring and laboratory-reared damselflies. We found incomplete mechanical isolation between the two pure species and between hybrid males and pure species females. Interestingly, in mating pairs for which mechanical isolation was incomplete, females showed greater resistance and refusal to mate with hybrid or heterospecific males compared to conspecific males. This observation suggests that tactile incompatibilities involving male reproductive structures can influence female mating decisions and form a strong barrier to gene flow in early stages of speciation.

Divergent competitive phenotypes between females of two sex-role-reversed species

Divergent phenotypes between lineages in the early stages of speciation can promote or impede reproductive isolation. Although divergence in male competitive morphology and behavior has been explored for many hybridizing lineages, it is less known how divergence between females influences hybridization. Here, I compare competitive phenotypes between females of two hybridizing, sex-role-reversed jacana species in Panama. Previous work suggests Jacana spinosa females monopolize mating in the hybrid zone, potentially through a competitive advantage. I tested whether J. spinosa females have a more competitive phenotype than Jacana jacana females. I compared morphological traits related to territoriality and measured aggressive behavior using territorial intrusion simulations: the first aggression assay in a shorebird. I also quantified these traits in males, to confirm previous studies reporting males as smaller and less aggressive than females in both species. As predicted, J. spinosa females had larger body mass and longer wing spurs than J. jacana females. J. spinosa females were also more aggressive than J. jacana females. Male J. spinosa had longer wing spurs than male J. jacana, but there was no difference in male body mass between the species, and J. spinosa males were more aggressive than J. jacana males. Additionally, male J. spinosa was more aggressive than female J. spinosa, suggesting mixed support for females as competitively dominant to males and indicating the need for additional experimental work on sex differences in Jacana. Historically, research on the role of mating behavior in hybridization has focused on competitive males and choosy females. Although female-female competition is widespread and has important fitness consequences for many species across numerous taxa, little is known about the role of female competition in mediating hybridization between closely related lineages. I compare morphological and behavioral traits related to competition between two hybridizing species of jacanas, tropical shorebirds with sex-role reversal. I find that J. spinosa females have a more competitive morphological phenotype and higher aggression than J. jacana females, which may allow them a competitive advantage in obtaining and defending territories and mates in the hybrid zone. These patterns align with a pattern of asymmetrical introgression of J. spinosa mitochondrial DNA previously described in the hybrid zone, as well as findings from other hybrid zones in which male-male competition can potentially explain asymmetric patterns of gene flow from the more dominant species into the less dominant species.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel‐web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62, 285–392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110‐kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders’ behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Genomic evidence for convergent evolution of a key trait underlying divergence in island birds.

Reproductive isolation can be initiated by changes in one or a few key traits that prevent random mating among individuals in a population. During the early stages of speciation, when isolation is often incomplete, there will be a heterogeneous pattern of differentiation across regions of the genome between diverging populations, with loci controlling these key traits appearing the most distinct as a result of strong diversifying selection. In this study, we used Illumina-sequenced ddRAD tags to identify genomewide patterns of differentiation in three recently diverged island populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. Populations of this species have diverged in plumage colour, and these differences in plumage colour, in turn, are used in conspecific recognition and likely important in reproductive isolation. Previous candidate gene sequencing identified point mutations in MC1R and ASIP, both known pigmentation genes, to be associated with the difference in plumage colour between islands. Here, we show that background levels of genomic differentiation based on over 70,000 SNPs are extremely low between populations of distinct plumage colour, with no loci reaching the level of differentiation found in either candidate gene. Further, we found that a phylogenetic analysis based on these SNPs produced a taxonomy wherein the two melanic populations appear to have evolved convergently, rather than from a single common ancestor, in contrast to their original classification as a single subspecies. Finally, we found evidence that the pattern of low genomic differentiation is the result of both incomplete lineage sorting and gene flow between populations.

Complex songs and cryptic ethospecies: the case of the Ducetia japonica group (Orthoptera: Tettigonioidea: Phaneropteridae: Phaneropterinae)

In many groups of animals, especially insects, genital morphology is species distinctive. This is true of bush-crickets or katydids (Tettigonioidea). The calling songs produced by males are species distinctive and do not change significantly during the early stages of speciation. Their patterns are usually relatively simple. We present an example where none of these assumptions is true. Since the last revision of the genus Ducetia in 1961, one widespread species, Ducetia japonica (Thunberg, 1815) has been thought to be morphologically uniform. It is represented by tens of specimens from south and eastern Asia and Australasia on both sides of Wallace's Line. The male genitalic appendages vary little over the extent of its range. In contrast, the calling songs differ considerably from place to place. Examination of the stridulatory organs of both sexes (located on the first set of wings) reflects the differences in song. The teeth, which produce the sound, differ in shape, number, and size. We present details of the song patterns and the stridulatory organs that produce them. As a result, some synonyms are re-established, and new species are described. Chromosomal information is presented for two species. The origins and the distribution and expansion of the group are detailed. Duets between courting pairs have played an important role in the evolution of this song structure where efforts to trick eavesdropping rivals are common.

Assessing the Potential Contributions of Reduced Immigrant Viability and Fecundity to Reproductive Isolation.

Reduced fitness of immigrants from alternative environments is thought to be an important reproductive isolating barrier. Most studies evaluating the importance of the relative fitness of immigrants to speciation have focused on reduced survival of immigrants (i.e., immigrant inviability). However, variation in fecundity appears to have a greater impact on variation in fitness than does variation in viability, suggesting that reduced fecundity of immigrants could act as an important yet largely overlooked reproductive isolating barrier. Using a model and a survey of studies of local adaptation, we evaluate the relative strength of reduced immigrant viability and fecundity as potential causes of reproductive isolation. We found that reduced fecundity as compared to reduced viability as a reproductive isolating barrier should increase in importance as the relative costs of reproduction increase. Consistent with the elevated demands of reproduction reported in the literature, we found that reproductive isolation from reduced immigrant fecundity was of similar magnitude or greater than that from reduced immigrant viability, particularly in the early stages of speciation. These results suggest that the important role of differential fecundity in local adaptation extends to speciation.

Divergence in brain composition during the early stages of ecological specialization in Heliconius butterflies.

During speciation across ecological gradients, diverging populations are exposed to contrasting sensory and spatial information that present new behavioural and perceptive challenges. These challenges may be met by heritable or environmentally induced changes in brain function which mediate behaviour. However, few studies have investigated patterns of neural divergence at the early stages of speciation, inhibiting our understanding of the relative importance of these processes. Here, we provide a novel case study. The incipient species pair, Heliconius erato and H.himera, are parapatric across an environmental and altitudinal gradient. Despite ongoing gene flow, these species have divergent ecological, behavioural and physiological traits. We demonstrate that these taxa also differ significantly in brain composition, in particular in the relative levels of investment in structures that process sensory information. These differences are not explained solely by environmentally-induced plasticity, but include heritable, nonallometric shifts in brain structure. We suggest these differences reflect divergence to meet the demands of contrasting sensory ecologies. This conclusion would support the hypothesis that the evolution of brain structure and function play an important role in facilitating the emergence of ecologically distinct species.

Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation.

The early stages of speciation are often characterized by the formation of partially reproductively isolated ecotypes, which evolve as a by-product of divergent selective forces that are endemic to different habitats. Identifying the genomic regions, genes and ultimately functional polymorphisms that are involved in the processes of ecotype formation is inherently challenging, as there are likely to be many different loci involved in the process. To localize candidate regions of the genome contributing to ecotype formation, we conducted whole-genome pooled sequencing (pool-seq) with 47 coastal perennial and 50 inland annual populations of the yellow monkeyflower, Mimulus guttatus. Coastal perennial and inland annual ecotypes of M.guttatus have previously been shown to be ecologically reproductively isolated and highly locally adapted to their respective habitats. Our pool-seq results found allelic differentiation between the ecotypes for two chromosomal inversions, suggesting that frequencies of inversion heterokaryotypes are strongly differentiated between the ecotypes. Further, there were elevated levels of nonsynonymous change across chromosomal inversions. Across the genome, we identified multiple strong candidate genes potentially driving the morphological, life history and salt tolerance differences between the ecotypes. Several candidate genes coincide with previously identified quantitative trait locus regions and also show a signature of recent natural selection. Overall, the results of our study add to growing support for a major role of chromosomal inversions in adaptation and speciation and provide new insights into the genetic mechanisms underlying classic plant ecotype adaptations to wet and dry habitats.