Host-related genetic differentiation in the anther smut fungus Microbotryum violaceum in sympatric, parapatric and allopatric populations of two host species Silene latifolia and S. dioica

We investigated genetic diversity in West European populations of the fungal pathogen Microbotryum violaceum in sympatric, parapatric and allopatric populations of the host species Silene latifolia and S. dioica, using four polymorphic microsatellite loci. In allopatric host populations, the fungus was highly differentiated by host species, exhibiting high values of F(ST) and R(ST), and revealed clear and distinct host races. In sympatric and parapatric populations we found significant population differentiation as well, except for one sympatric population in which the two host species grew truly intermingled. The mean number of alleles per locus for isolates from each of the host species was significantly higher in sympatric/parapatric than in allopatric populations. This suggests that either gene flow between host races in sympatry, or in case of less neutral loci, selection in a more heterogeneous host environment can increase the level of genetic variation in each of the demes. The observed pattern of host-related genetic differentiation among these geographically spread populations suggest a long-term divergence between these host races. In sympatric host populations, both host races presumably come in secondary contact, and host-specific alleles are exchanged depending on the amount of fungal gene flow.     

Genetic structure of hybrid zones between Silene latifolia and Silene dioica (Caryophyllaceae): evidence for introgressive hybridization

Natural hybrid zones provide a valuable tool to study introgressive hybridization, because they can contain a wide variety of genotypes that result from many generations of recombination. Here we used molecular markers and morphological variation to describe the structure of two natural hybrid zones between Silene latifolia and Silene dioica in the Swiss Alps. Populations in both hybrid zones consisted of few intermediate hybrids and were dominated by backcross hybrids. The latter were also found in the parental populations at the margins of the hybrid zones. Out of 209 amplified fragment length polymorphism (AFLP) markers scored in 390 individuals, only 7 (3.3%) were species specific. These results indicate that introgression between S. dioica and S. latifolia is extensive, and that hybrid zones act as bridges to gene flow between these two species. Analysis of linkage disequilibrium identified few populations in which hybridization is ongoing, whereas in most populations linkage disequilibrium has eroded. Where hybridization is ongoing, strong changes in species-specific marker frequencies and morphological traits were observed. Plastid introgression into the hybrid zone was found to be bidirectional, but only the S. latifolia plastid haplotype was found in a nuclear S. dioica background. This unidirectional plastid introgression from S. latifolia into S. dioica is most likely due to pollen-flow from S. dioica onto S. latifolia, and results in plastid capture. Comparisons between the molecular and the morphological hybrid indices revealed that morphology in this study system is useful for identifying hybrids, but not for detailed analysis of hybrid zone structure.     

Differences in population structure of the anther smut fungus Microbotryum violaceum on two closely related host species, Silene latifolia and S. dioica

We investigated the genetic population structure of the sexually transmitted plant pathogen, the fungus Microbotryum violaceum, on the two closely related host species Silene latifolia and S. dioica using microsatellite markers. We found strong deviations from Hardy-Weinberg expectations, with significant heterozygote deficiency in almost all populations. Fungal strains from the two host species were differentiated, and these host races differed in amount of variation within populations and differentiation among populations. Anther smut from S. latifolia harboured significantly less microsatellite diversity and were more genetically differentiated from each other than those from S. dioica. Small effective population sizes, rapid population turnover, and less gene flow among populations could lead to this higher population differentiation and lower within population genetic diversity for anther smut populations on S. latifolia than on S. dioica. These results are in concordance with host ecology because S. latifolia grows in more disturbed habitats than S. dioica and may provide a shorter-lived host environment.     

Genetic and ecological differentiation in the hybridizing campions Silene dioica and S. latifolia

Ecological differentiation is a major contributor to the generation and maintenance of biological diversity. We investigated habitat differentiation between and within sites in the fully cross-fertile and hybridizing Silene dioica and S. latifolia using amplified fragment length polymorphisms (AFLP) profiles and corresponding vegetation relevés around individual plants. Nineteen study sites in the Swiss Alps included pure sites and contact sites (both taxa present within 30 m). In pure sites and at contact sites, the two taxa showed consistently differentiated AFLP banding patterns across regions but few discriminating bands. This indicates that although the two taxa are weakly differentiated, current introgression has not led to genome-wide admixture. Only three putative early generation hybrids were detected at contact sites. The habitats of the two taxa differed between pure sites with S. dioica occurring in moister, colder, and less-disturbed sites than S. latifolia. However, asymmetric habitat overlap was evident within contact sites found in intermediate conditions that were more similar to S. latifolia sites. This situation might favor introgression from S. dioica into S. latifolia. Evidence for habitat-genotype associations within contact sites was weak making habitat-mediated selection against intermediate phenotypes of hybrids unlikely in the contact sites investigated. We suggest that other reproductive barriers together with dispersal limitation contribute to the rarity of early generation hybrids.     

Intraspecific competition and mating between fungal strains of the anther smut Microbotryum violaceum from the host plants Silene latifolia and S. dioica

Abstract We studied intraspecific competition and assortative mating between strains of the anther smut fungus Microbotryum violaceum from two of its host species, Silene latifolia and S. dioica . Specifically, we investigated whether strains from allopatric host populations have higher competitive ability on their native host species and show positive assortative mating. In general, strains isolated from S. latifolia outcompeted strains isolated from S. dioica on both host species, but in female hosts, heterotypic dikaryons (i.e., dikaryons composed of a haploid strain originating from S. latifolia and a haploid strain originating from S. dioica ) were most successful in competition. Furthermore, the latency period was significantly shorter for heterokaryons that contained at least one strain originating from S. latifolia , compared to heterokaryons that only contained strains originating from S. dioica . The frequencies of conjugations between strains originating from S. latifolia were much higher than conjugation frequencies between strains originating from S. dioica . A significant positive correlation was detected between the relative success of strains in competition and in conjugation, suggesting that success of a strain in competition might be partly determined by its swiftness of mating. In addition, reciprocal differences within heterotypic crosses revealed a significant effect of fungal mating type, with mating type a₁ being the main determinant of mating pace. The observed differences in infection success, conjugation rate, and latency period in favor of strains from S. latifolia relative to strains from S. dioica on both host species are discussed in an evolutionary context of opportunities for the maintenance of differentiation between different formae speciales upon secondary contact.     

中华猕猴桃和美味猕猴桃自然居群遗传结构及其种间杂交渐渗

 利用9对SSR引物对中华猕猴桃（Actinidia chinensis）和美味猕猴桃（A. deliciosa）两近缘种的5个同域分布复合体和各自1个非同域分布居群进行了遗传多样性、居群遗传结构的分析以及种间杂交渐渗的探讨。结果表明：1）两物种共有等位基因比例高达81.13%,物种特有等位基因较少（中华猕猴桃：13.27%,美味猕猴桃：5.61%）,但共享等位基因表型频率在两近缘种间存在差异,而且与各同域复合体中两物种样本的交错程度或间距存在关联;2）两种猕猴桃均具有极高遗传多样性,美味猕猴桃的遗传多样性（H_o＝0 .749, PIC＝0.818）都略高于中华猕猴桃（H_o＝0.686,PIC＝0.799）;3）两猕 猴桃物种均具有较低的Nei’s居群遗传分化度,但AMOVA分析结果揭示种内异域居群间（F_ST=0.091 5）和同域复合体种间（F_ST=0.111 5）均存在一定程度的遗传分化;中华猕猴桃居群遗传分化（G_ST=0.086; F_ST=0.212 1）高于美味猕猴桃（G_ST= 0.080;F_ST=0.142 0）;4）同域分布复合体两物种间的遗传分化（G_ST=0.020）低于物种内异域居群间的遗传分化（中华猕猴桃：G_ST=0.086; 美味猕猴桃：G_ST=0.080）,同域复合体物种间的基因流（N_m＝7.89 -29.75）远远高于 同种异域居群间（中华猕猴桃：N_m =2.663; 美味猕猴桃：N_m=2.880）; 5）居群UPGMA聚类揭示在同一地域的居群优先聚类,个体聚类结果显示多数个体聚在各自居群组内,但各地理居群并不按地理距离的远近聚类,这与Mantel相关性检测所揭示的居群间遗传距离与地理距离没有显著性相关的结果一致。进一步分析表明两种猕猴桃的遗传多样性和居群遗传结构不仅受其广域分布、远交、晚期分化等生活史特性的影响,同时还与猕猴桃的染色体基数高 (x=29)、倍性复杂和种间杂交等因素密切相关,其中两种猕猴桃的共享祖先多态性和同域分布种间杂交基因渗透对两猕猴桃的居群遗传结构产生了重要影响。     

A biogeographic genetic approach for testing the role of reinforcement: the case of Drosophila pseudoobscura and D. persimilis

Abstract.— The role of reinforcement in speciation can be explained by two distinct models. In model I, two diverged populations hybridize and produce fertile hybrids that successfully backcross (hybridization with gene flow). In model II, two populations hybridize but succeeding backcrosses are unproductive (hybridization without gene flow). Using Drosophila persimilis and D. pseudoobscura , we have tested model I by comparing the extent of heterospecific introgression in sympatric versus allopatric populations. We show that certain expectations of this particular model of reinforcement, which is based on hybridization and gene flow between divergent populations after secondary contact, are not realized in these two species. The evidence consists of the similarity of genetic distances as well as proportions of unique/rare alleles between sympatric and allopatric heterospecific populations and a negative correlation between genetic distance and geographical distance between heterospecific populations, which suggests ecological differentiation. This approach in quantifying differential gene flow has important consequences to studies that compare sympatric and allopatric isolation using genetic distance. Following model I, one would expect a pattern of higher prezygotic isolation in sympatric species compared to allopatric species of the same genetic distance simply as a result of an underestimation of genetic distance due to introgression between sympatric populations. We suggest more parsimonious explanations such as reinforcement without genetic exchange (model II) and ecological differentiation, which require high levels of preexisting reproductive isolation between populations.     

Dynamics of drift, gene flow, and selection during speciation in Silene

The mechanics of speciation with gene flow are still unclear. Disparity among genes in population differentiation (F(ST)) between diverging species is often interpreted as evidence for semipermeable species boundaries, with selection preventing "key" genes from introgressing despite ongoing gene flow. However, F(ST) can remain high before it reaches equilibrium between the lineage sorting of species divergence and the homogenizing effects of gene flow (via secondary contact). Thus, when interpreting F(ST), the dynamics of drift, gene flow, and selection need to be taken into account. We illustrate this view with a multigenic analyses of gene flow and selection in three closely related Silene species, S. latifolia, S. dioica, and S. diclinis. We report that although S. diclinis appears to have evolved in allopatry, isolation with (bidirectional) gene flow between S. latifolia and S. dioica is likely, perhaps as a result of parapatric speciation followed by more extensive sympatry. Interestingly, we detected the signatures of apparently independent instances of positive selection at the same locus in S. latifolia and S. dioica. Despite gene flow between the species, the adaptive alleles have not crossed the species boundary, suggesting that this gene has independently undergone species-specific (diversifying or parallel) selection.     

C-banded karyotypes of two Silene species with heteromorphic sex chromosomes.

Mitotic metaphase chromosomes of Silene latifolia (white campion) and Silene dioica (red campion) were studied and no substantial differences between the conventional karyotypes of these two species were detected. The classification of chromosomes into three distinct groups proposed for S. latifolia by Ciupercescu and colleagues was considered and discussed. Additionally, a new small satellite on the shorter arm of homobrachial chromosome 5 was found. Giemsa C-banded chromosomes of the two analysed species show many fixed and polymorphic heterochromatic bands, mainly distally and centromerically located. Our C-banding studies provided an opportunity to better characterize the sex chromosomes and some autosome types, and to detect differences between the two Silene karyotypes. It was shown that S. latifolia possesses a larger amount of polymorphic heterochromatin, especially of the centromeric type. The two Silene sex chromosomes are easily distinguishable not only by length or DNA amount differences but also by their Giemsa C-banding patterns. All Y chromosomes invariably show only one distally located band, and no other fixed or polymorphic bands on this chromosome were observed in either species. The X chromosomes possess two terminally located fixed bands, and some S. latifolia X chromosomes also have an extra-centric segment of variable length. The heterochromatin amount and distribution revealed by our Giemsa C-banding studies provide a clue to the problem of sex chromosome and karyotype evolution in these two closely related dioecious Silene species.     

DNA diversity in sex-linked and autosomal genes of the plant species Silene latifolia and Silene dioica

The relatively recent origin of sex chromosomes in the plant genus Silene provides an opportunity to study the early stages of sex chromosome evolution and, potentially, to test between the different population genetic processes likely to operate in nonrecombining chromosomes such as Y chromosomes. We previously reported much lower nucleotide polymorphism in a Y-linked gene (SlY1) of the plant Silene latifolia than in the homologous X-linked gene (SlX1). Here, we report a more extensive study of nucleotide diversity in these sex-linked genes, including a larger S. latifolia sample and a sample from the closely related species Silene dioica, and we also study the diversity of an autosomal gene, CCLS37.1. We demonstrate that nucleotide diversity in the Y-linked genes of both S. latifolia and S. dioica is very low compared with that of the X-linked gene. However, the autosomal gene also has low DNA polymorphism, which may be due to a selective sweep. We use a single individual of the related hermaphrodite species Silene conica, as an outgroup to show that the low SlY1 diversity is not due to a lower mutation rate than that for the X-linked gene. We also investigate several other possibilities for the low SlY1 diversity, including differential gene flow between the two species for Y-linked, X-linked, and autosomal genes. The frequency spectrum of nucleotide polymorphism on the Y chromosome deviates significantly from that expected under a selective-sweep model. However, we detect population subdivision in both S. latifolia and S. dioica, so it is not simple to test for selective sweeps. We also discuss the possibility that Y-linked diversity is reduced due to highly variable male reproductive success, and we conclude that this explanation is unlikely.     

Population differentiation in plethodontid salamanders: divergence of allozymes and sexual compatibility among populations of Desmognathus imitator and D. ochrophaeus (Gaudata: Plethodontidae)

Plethodontid salamanders of the genus Desmognathus exhibit varying levels of genetic differentiation among and within both allopatric and sympatric taxa. This provides excellent opportunities to study population differentiation and speciation. Two morphologically similar species in this genus, D. imitator and D. ochrophaeus, are genetically well-differentiated from one another and occur in sympatry with no evidence of hybridization and introgression. We report that the degree of sexual isolation between these two species is very high, regardless of whether the populations under comparison are allopatric or sympatric with one another. Neither reinforcement nor reproductive character displacement are required to explain the evolution of sexual incompatibility in sympatry. Sexual behaviour apparently diverges while populations are allopatric with one another. Preliminary study indicates that D. imitator consists of populations among which there may be significant sexual isolation in the absence of detectable genetic differentiation.     

Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species

One of the challenges in evolutionary biology is to understand the evolution of speciation with incomplete reproductive isolation as many taxa have continued gene flow both during and after speciation. Comparison of population structure between sympatric and allopatric populations can reveal specific introgression and determine if introgression occurs in a unidirectional or bidirectional manner. Simple sequence repeat markers were used to characterize sympatric and allopatric population structure of plant species, Elymus alaskanus (Scribn. and Merr.) Löve, E. caninus L., E. fibrosus (Schrenk) Tzvel., and E. mutabilis (Drobov) Tzvelev. Our results showed that genetic diversity (H_E) at species level is E. caninus (0.5355) > E. alaskanus (0.4511) > E. fibrosus (0.3924) > E. mutabilis (0.3764), suggesting that E. caninus and E. alaskanus are more variable than E. fibrosus and E. mutabilis. Gene flow between species that occurs within the same geographic locations versus gene flow between populations within species was compared to provide evidence of introgression. Our results indicated that gene flow between species that occur within the same geographic location is higher than that between populations within species, suggesting that gene flow resulting from introgressive hybridization might have occurred among the sympatric populations of these species, and may play an important role in partitioning of genetic diversity among and within populations. The migration rate from E. fibrosus to E. mutabilis is highest (0.2631) among the four species studied. Asymmetrical rates of gene flow among four species were also observed. The findings highlight the complex evolution of these four Elymus species.     

Floral odour and reproductive isolation in two species of Silene

Mechanisms preventing interspecific pollination are important in closely related plant species, in particular when post-zygotic barriers are weak or absent. We investigated the role of floral odour in reproductive isolation between the two closely related species Silene latifolia and S. dioica. First, we tested whether floral odour composition and emission differed between the species. We found significant odour differences, but contrary to expectations, both species showed a rhythmic emission of the same compounds between day and night. Second, in a field experiment, odour of the two species was made more similar by applying phenylacetaldehyde to flowers. This manipulation led to higher pollen-analogue transfer between species, revealing that floral odour differences are important for maintaining reproductive isolation. We conclude that differences in single key compounds can reduce pollen transfer across species boundaries by pollinators and demonstrate that odour differences are an important component of premating floral isolation between closely related plant species.     

Reproductive character displacement and the genetics of gamete recognition in tropical sea urchins

Reproductive character displacement occurs when sympatric and allopatric populations of a species differ in traits crucial to reproduction, and it is commonly thought of as a signal of selection acting to limit hybridization. Most documented cases of reproductive character displacement involve characters that are poorly understood at the genetic level, and rejecting alternative hypotheses for biogeographic shifts in reproductive traits is often very difficult. In sea urchins, the gamete recognition protein bindin evolves under positive selection when species are broadly sympatric, suggesting character displacement may be operating in this system. We sampled sympatric and allopatric populations of two species in the sea urchin genus Echinometra for variation in bindin and for the mitochondrial cytochrome oxidase I to examine patterns of population differentiation and molecular evolution at a reproductive gene. We found a major shift in bindin alleles between central Pacific (allopatric) and western Pacific (sympatric) populations of E. oblonga. Allopatric populations of E. oblonga are polyphyletic with E. sp. C at bindin, whereas sympatric populations of the two species are reciprocally monophyletic. There is a strong signal of positive selection (P(N)/P(S) = 4.5) in the variable region of the first exon of bindin, which is associated with alleles found in sympatric populations of E. oblonga. These results indicate that there is a strong pattern of reproductive character displacement between E. oblonga and E. sp. C and that the divergence is driven by selection. There is much higher population structure in sympatric populations at the bindin locus than at the neutral mitochondrial locus, but this difference is not seen in allopatric populations. These data suggest a pattern of speciation driven by selection for local gamete coevolution as a result of interactions between sympatric species. Although this pattern is highly suggestive of speciation by reinforcement, further research into hybrid fitness and egg-sperm interactions is required to address this potential mechanism for character displacement.     

Indirect evidence from DNA sequence diversity for genetic degeneration of the Y-chromosome in dioecious species of the plant Silene: the SlY4/SlX4 and DD44-X/DD44-Y gene pairs

The action of natural selection is expected to reduce the effective population size of a nonrecombining chromosome, and this is thought to be the chief factor leading to genetic degeneration of Y-chromosomes, which cease recombining during their evolution from ordinary chromosomes. Low effective population size of Y chromosomes can be tested by studying DNA sequence diversity of Y-linked genes. In the dioecious plant, Silene latifolia, which has sex chromosomes, one comparison (SlX1 vs. SlY1) indeed finds lower Y diversity compared with the homologous X-linked gene, and one Y-linked gene with no X-linked homologue has lower species-wide diversity than a homologous autosomal copy (SlAp3Y vs. SlAp3A). To test whether this is a general pattern for Y-linked genes, we studied two further recently described X and Y homologous gene pairs in samples from several populations of S. latifolia and S. dioica. Diversity is reduced for both Y-linked genes, compared with their X-linked homologues. Our new data are analysed to show that the low Y effective size cannot be explained by different levels of gene flow for the X vs. the Y chromosomes, either between populations or between these closely related species. Thus, all four Y-linked genes that have now been studied in these plants (the two studied here, and two previously studied genes, have low diversity). This supports other evidence for an ongoing degeneration process in these species.     

Human disturbance causes the formation of a hybrid swarm between two naturally sympatric fish species

Most evidence for hybrid swarm formation stemming from anthropogenic habitat disturbance comes from the breakdown of reproductive isolation between incipient species, or introgression between allopatric species following secondary contact. Human impacts on hybridization between divergent species that naturally occur in sympatry have received considerably less attention. Theory predicts that reinforcement should act to preserve reproductive isolation under such circumstances, potentially making reproductive barriers resistant to human habitat alteration. Using 15 microsatellites, we examined hybridization between sympatric populations of alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) to test whether the frequency of hybridization and pattern of introgression have been impacted by the construction of a dam that isolated formerly anadromous populations of both species in a landlocked freshwater reservoir. The frequency of hybridization and pattern of introgression differed markedly between anadromous and landlocked populations. The rangewide frequency of hybridization among anadromous populations was generally 0–8%, whereas all landlocked individuals were hybrids. Although neutral introgression was observed among anadromous hybrids, directional introgression leading to increased prevalence of alewife genotypes was detected among landlocked hybrids. We demonstrate that habitat alteration can lead to hybrid swarm formation between divergent species that naturally occur sympatrically, and provide empirical evidence that reinforcement does not always sustain reproductive isolation under such circumstances.     

Importance of Silene latifolia ssp. alba and S. dioica (Caryophyllaceae) as host plants of the parasitic pollinator Hadena bicruris (Lepidoptera, Noctuidae)

With regards to pollination there exist several mutualistic relationships between Hadena -species and Caryophyllaceae. As mutualists have both negative and positive effects on their partners, mutualism is often betoken as reciprocative exploitation which may shift to parasitism if the exploitation of one partner becomes prevalent.
Several Silene - and Saponaria -species are considered to be larval host plants of Hadena bicruris . Although Silene latifolia ssp. alba and S. dioica are frequently cited as hosts of the seed eating larvae, field and laboratory observations at Ulm were suggestive for only S. latifolia ssp. alba being a suitable host. Records of the oviposition behavior of H. bicruris made it evident that in fact a considerable number of eggs could be found in planted stands of both species. On the other hand, phenological data of the flowering periods and of the oviposition behavior of H. bicruris showed that S. latifolia ssp. alba is clearly preferred for oviposition if host selection is possible due to contemporaneous flowering of individuals of both plant species growing at close range. In addition, the flowering periods of S. latifolia ssp. alba and the periods of moth activity overlap to a large extent. This is not the case in S. dioica . Feeding experiences first indicated that the caterpillars may not prefer one of the species to the other, but comparison of the pupal weight of the animals reared on fruits of exclusively one of the species showed that the seeds of S. latifolia ssp. alba were more profitable for nutrition than those of S. dioica ; the pupal weight of animals reared on seeds of the former species significantly exceeded that of animals reared on seeds of the latter one. The question arises if the symbiosis of H. bicruris and its hosts constitutes a stable situation or if an evolutionary shift to mutualism or parasitism will take place.     

Searching for the genetic footprint of ancient and recent hybridization

Determining the long‐term consequences of hybridization remains a central quest for evolutionary biologists. A particular challenge is to establish whether and to what extent widespread hybridization results in gene flow (introgression) between parental taxa. In this issue of Molecular Ecology, Jordan et al. ( 2018 ) search for evidence of gene flow between two closely related species of Geum (Rosaceae), which hybridize readily in contemporary populations and where hybrid swarms have been recorded for at least 200 years (Ruhsam, Hollingsworth, & Ennos, 2013 ). The authors find mixed evidence of ancient introgression when analysing allopatric populations. Intriguingly, when analysing populations of a region where the two species occur either mixed in the same population or in close proximity, and where hybrids are presently common, Jordan and colleagues find that the majority of randomly sampled individuals analysed (92/96) show no evidence of introgression (defined as individuals with admixture coefficients of <1%). The few individuals identified as hybrids are shown to likely be F1 or early‐generation backcrosses, indicating that even in sympatric regions, hybridization does not penetrate beyond a few generations. Based on their findings, Geum seems to be an example of little to no introgression despite contemporary hybridization.