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.     

Experimental taxonomy of Silene section Elisanthe (Caryophyllaceae): crossing experiments

Silene section Elisanthe is a well-defined group containing (in Europe) the following species: S. alba, S. diclinis, S. dioica, S. heuffelii and S. marizii (dioecious perennials or biennials) and S. noctifloara (a self-compatible hermaphrodite annual). Crosses were attempted among these species, and between these species and members of other Silene sections.
Crosses among the first five species revealed partial cross-incompatibility with moderate hybrid fertility. S. alba proved especially incompatible with S. diclinis. S. noctiflora would not cross at all with other members of the section. It is suggested that S. noctiflora evolved from a dioecious precursor of S. alba , the species to which it is most similar in morphology, distribution and habitat; hybrid sterility, even without incompatibility, would have assured mutual isolation.
Crosses with species from other sections of Silene have usually either failed consistently or revealed high cross-incompatibility with hybrid sterility. Those crosses which were successful have all been within the boundaries of the old genus Melandrium , or with Lychnis species.     

Local genetic population structure in an endangered plant species, Silene tatarica (Caryophyllaceae)

Genetic substructuring in plant populations may evolve as a consequence of sampling events that occur when the population is founded or regenerated, or if gene dispersal by pollen and seeds is restricted within a population. Silene tatarica is an endangered, perennial plant species growing along periodically disturbed riverbanks in northern Finland. We investigated the mechanism behind the microspatial genetic structure of S. tatarica in four subpopulations using amplified fragment length polymorphism markers. Spatial autocorrelation revealed clear spatial genetic structure in each subpopulation, even though the pattern diminished in older subpopulations. Parentage analysis in an isolated island subpopulation indicated a very low level of selfing and avoidance of breeding between close relatives. The mean estimated pollen dispersal distance (24.10 m; SD = 10.5) was significantly longer and the mean seed dispersal distance (9.07 m; SD = 9.23) was considerably shorter than the mean distance between the individuals (19.20 m; SD = 13.80). The estimated indirect and direct estimates of neighbourhood sizes in this subpopulation were very similar, 32.1 and 37.6, respectively. Our results suggested that the local spatial genetic structure in S. tatarica was attributed merely to the isolation-by-distance process rather than founder effect, and despite free pollen movement across population, restricted seed dispersal maintains local genetic structure in this species.     

Duplicative transfer of a MADS box gene to a plant Y chromosome

Y chromosomes carry genes with functions in male reproduction and often have few other loci. Their evolution and the causes of genetic degeneration are of great interest. In addition to genetic degeneration, the acquisition of autosomal genes may be important in Y chromosome evolution. We here report that the dioecious plant Silene latifolia harbors a complete MADS box gene, SlAP3Y, duplicated onto the Y chromosome. This gene has no X-linked homologs but only an autosomal paralog, SlAP3A, and sequence divergence suggests that the duplication is a quite old event that occurred soon after the evolution of the sex chromosomes. Evolutionary sequence analyses using homologs of closely related species, including hermaphroditic Silene conica and dioecious Silene dioica and Silene diclinis, suggest that both SlAP3A and SlAP3Y genes encode functional proteins. Indeed, quantitative RT-PCR and in situ hybridization analyses showed that SlAP3A is expressed specifically in developing petals, but SlAP3Y is much more strongly expressed in developing stamens. The S. conica homolog, ScAP3A, is expressed in developing petals, suggesting subfunctionalization with evolution of male-specific functions, possibly due to evolutionary change in regulatory elements. Our results suggest that the acquisition of autosomal genes is an important event in the evolution of plant Y chromosomes.     

Species diversity and population density affect genetic structure and gene dispersal in a subtropical understory shrub

Aims The dispersal of pollen and seeds is spatially restricted and may vary among plant populations because of varying biotic interactions, population histories or abiotic conditions. Because gene dispersal is spatially restricted, it will eventually result in the development of spatial genetic structure (SGS), which in turn can allow insights into gene dispersal processes. Here, we assessed the effect of habitat characteristics like population density and community structure on small-scale SGS and estimate historical gene dispersal at different spatial scales.Methods In a set of 12 populations of the subtropical understory shrub Ardisia crenata, we assessed genetic variation at 7 microsatellite loci within and among populations. We investigated small-scale genetic structure with spatial genetic autocorrelation statistics and heterogeneity tests and estimated gene dispersal distances based on population differentiation and on within-population SGS. SGS was related to habitat characteristics by multiple regression.Important findings The populations showed high genetic diversity (H e = 0.64) within populations and rather strong genetic differentiation (F ′ ST = 0.208) among populations, following an isolation-by-distance pattern, which suggests that populations are in gene flow–drift equilibrium. Significant SGS was present within populations (mean Sp = 0.027). Population density and species diversity had a joint effect on SGS with low population density and high species diversity leading to stronger small-scale SGS. Estimates of historical gene dispersal from between-population differentiation and from within-population SGS resulted in similar values between 4.8 and 22.9 m. The results indicate that local-ranged pollen dispersal and inefficient long-distance seed dispersal, both affected by population density and species diversity, contributed to the genetic population structure of the species. We suggest that SGS in shrubs is more similar to that of herbs than to trees and that in communities with high species diversity gene flow is more restricted than at low species diversity. This may represent a process that retards the development of a positive species diversity–genetic diversity relationship.     

Genetic variability and founder effect in the pitcher plant Sarracenia purpurea (Sarraceniaceae) in populations introduced into Switzerland: from inbreeding to invasion

BACKGROUND AND AIMS: The long-lived and mainly outcrossing species Sarracenia purpurea has been introduced into Switzerland and become invasive. This creates the opportunity to study reactions to founder effect and how a species can circumvent deleterious effects of bottlenecks such as reduced genetic diversity, inbreeding and extinction through mutational meltdown, to emerge as a highly invasive plant. METHODS: A population genetic survey by random amplified polymorphism DNA markers (RAPD) together with historical insights and a field pollination experiment were carried out. KEY RESULTS: At the regional scale, S. purpurea shows low structure (thetast=0.072) due to a recent founder event and important subsequent growth. Nevertheless, multivariate statistical analyses reveal that, because of a bottleneck that shifted allele frequencies, most of the variability is independent among populations. In one population (Tenasses) the species has become invasive and genetic analysis reveals restricted gene flow and family structure (thetast=0.287). Although inbreeding appears to be high (Fis >0.410 from a Bayesian estimation), a field pollination experiment failed to detect significant inbreeding depression upon F1 seed number and seed weight fitness-traits. Furthermore, crosses between unrelated individuals produced F1 seeds with significantly reduced fitness, thus showing local outbreeding depression. CONCLUSIONS: The results suggest that, under restricted gene flow among families, the species may not only have rapidly purged deleterious alleles, but also have undergone some form of selection for inbreeding due to co-adaptation between loci.     

湖北3种药用淫羊藿植物等位酶多样性与居群遗传结构

采用超薄平板微型聚丙烯酰胺等电聚焦电泳方法对湖北3种淫羊藿属（Epimedium L．）药用植物：柔毛淫羊藿（E．pubescens Maxim．）、箭叶淫羊藿（Esagittatum（Sieb．＆Zucc．）Maxim．）和巫山淫羊藿（Ewushanense T.S．Ying）的11个自然居群进行了等位酶种内遗传多样性和居群遗传结构以及种间遗传关系的研究。6个酶系统在3种淫羊藿植物中检测到13个酶位点共45个等位基因,分析结果表明：1）3种淫羊藿均具有较高的遗传多样性水平（A=2．6-3．2,P=69．2％-84．6％,Ho=0．274-0．377,HE=0．282-0．369）,远高于多年生草本植物和依靠动物传粉植物的平均水平;2）所有居群都显著偏离Hardy—Weinberg平衡,大多数多态位点固定指数（F）明显偏离于0且正负值各半,暗示该属植物可能具有复杂的繁育系统;3）种内和种间的遗传分化度均较低,分别为GST=0．0246-0．0409和0．0495-0．1213,表明种内居群间存在较高的基因流和种间较近的遗传关系;4）聚类分析表明柔毛淫羊藿与箭叶淫羊藿的亲缘关系更近,这与形态学特征、花瓣演化趋势及系统发育分析等方面的研究的结果相吻合。讨论分析认为3种淫羊藿植物的遗传变异特性是由淫羊藿属植物异交与克隆繁殖的混合繁育系统、多年生的生活特性、古老的进化历史和种子的蚁播特性等多因素共同决定的。     

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.     

Silene rothmaleri P. Silva (Caryophyllaceae), a rare, fragmented but genetically diverse species

Silene rothmaleri is an endemic Portuguese species considered extinct until 1992, when it was rediscovered in the wild with a highly fragmented distribution. These rare plants occur along the southwestern Portuguese coast in small populations, which in addition to phenological differences that occur along the north–south gradient could create a pattern of genetic isolation. To evaluate the degree of genetic diversity and estimate the relationship between population fragmentation and genetic variability, we analysed the five known populations of S. rothmaleri using random amplified polymorphic DNA. Degree of polymorphism and Shannon Index of phenotypic diversity revealed high levels of diversity, found mainly within populations. PCo and cluster analysis revealed a distinct north–south cline, which was confirmed by spatial autocorrelation (Mantel) analysis. This indicates the existence of gene flow between small nearby populations and its insufficiency between widely separated populations. Levels of gene flow (Nm) estimated from the Shannon Index reveal a pattern consistent with a larger past distribution that went through a period of contraction and lack of gene flow followed by population differentiation. The central and largest population probably acts as a core of genetic variability inherited as a relict from a larger and more diverse ancestral population.     

The role of gene flow in shaping genetic structures of the subtropical conifer species Araucaria angustifolia

The morphological features of pollen and seed of Araucaria angustifolia have led to the proposal of limited gene dispersal for this species. We used nuclear microsatellite and AFLP markers to assess patterns of genetic variation in six natural populations at the intra- and inter-population level, and related our findings to gene dispersal in this species. Estimates of both fine-scale spatial genetic structure (SGS) and migration rate suggest relatively short-distance gene dispersal. However, gene dispersal differed among populations, and effects of more efficient dispersal within population were observed in at least one stand. In addition, even though some seed dispersal may be aggregated in this principally barochorous species, reasonable secondary seed dispersal, presumably facilitated by animals, and overlap of seed shadows within populations is suggested. Overall, no correlation was observed between levels of SGS and inbreeding, density or age structure, except that a higher level of SGS was revealed for the population with a higher number of juvenile individuals. A low estimate for the number of migrants per generation between two neighbouring populations implies limited gene flow. We expect that stepping-stone pollen flow may have contributed to low genetic differentiation among populations observed in a previous survey. Thus, strategies for maintenance of gene flow among remnant populations should be considered in order to avoid degrading effects of population fragmentation on the evolution of A. angustifolia.     

Microsatellite diversity and genetic structure of fragmented populations of the rare,fire-dependent shrub Grevillea macleayana

Recent habitat loss and fragmentation superimposed upon ancient patterns of population subdivision are likely to have produced low levels of neutral genetic diversity and marked genetic structure in many plant species. The genetic effects of habitat fragmentation may be most pronounced in species that form small populations, are fully self-compatible and have limited seed dispersal. However, long-lived seed banks, mobile pollinators and long adult lifespans may prevent or delay the accumulation of genetic effects. We studied a rare Australian shrub species, Grevillea macleayana (Proteaceae), that occurs in many small populations, is self-compatible and has restricted seed dispersal. However, it has a relatively long adult lifespan (c. 30 years), a long-lived seed bank that germinates after fire and is pollinated by birds that are numerous and highly mobile. These latter characteristics raise the possibility that populations in the past may have been effectively large and genetically homogeneous. Using six microsatellites, we found that G. macleayana may have relatively low within-population diversity (3.2-4.2 alleles/locus; Hexp = 0.420-0.530), significant population differentiation and moderate genetic structure (FST = 0.218) showing isolation by distance, consistent with historically low gene flow. The frequency distribution of allele sizes suggest that this geographical differentiation is being driven by mutation. We found a lack mutation-drift equilibrium in some populations that is indicative of population bottlenecks. Combined with evidence for large spatiotemporal variation of selfing rates, this suggests that fluctuating population sizes characterize the demography in this species, promoting genetic drift. We argue that natural patterns of pollen and seed dispersal, coupled with the patchy, fire-shaped distribution, may have restricted long-distance gene flow in the past.     

Microevolution in Solatopupa landsnails (Pulmonata Chondrinidae): genetic diversity and founder effects

Enzyme variability at 28 presumptive gene loci was studied, by standard starch gel electrophoresis, in 30 populations belonging to the five recognized species of the landsnail Solatopupa from its entire NW Mediterranean range.
Six genetically differentiated groups can be identified among the 30 populations sampled. These are distinguished by two to 19 diagnostic loci, different levels of genetic variability and populations genetics. They are also significantly different as far as the D values are considered. There is no evidence of gene flow among them. Genetically inferred groups correspond in four cases to morphologically distinguished species. In contrast, S. similis , as identified by morphological features, is likely to be a complex of at least two cryptic species.
Populations and species of Solatopupa are characterized by: high fixation of alternative alleles both within and between species; medium-lo-low levels of genie variation; heterozygote deficiency; sharp genetic differentiation among population within species; restricted gene flow; and high genetic distances. Genetic variability is partly associated with climatic factors related to moisture.
Both deterministic and stochastic processes may play a part in the genetic differentiation of Solatopupa snails. Founder events seem to be the main factor affecting the genetic structure of populations and perhaps also speciation. Solatopupa populations display many attributes of populations that may be expected to undergo speciation events involving reorganization of the whole genome after a founder event.     

Local adaptation, patterns of selection, and gene flow in the Californian serpentine sunflower (Helianthus exilis)

The traditional view of the species as the fundamental unit of evolution has been challenged by observations that in heterogeneous environments, gene flow may be too restricted to overcome the effects of local selection. Whether a species evolves as a cohesive unit depends critically on the dynamic balance between homogenizing gene flow among populations and potentially disruptive local adaptation. To examine this evolutionary balance between "global" gene flow and local selection, we studied northern Californian populations of Helianthus exilis, the serpentine sunflower, within a mosaic of contrasting serpentine and nonserpentine areas that differ considerably in soil chemistry and water availability. Local adaptation to riparian and serpentine habitats was studied in Helianthus exilis along with an analysis of gene flow patterns among populations within these habitats. Local adaptation was assessed in H. exilis during 2002 and 2003 using reciprocal transplant experiments at multiple locations within serpentine and riparian habitats. Effects of competition and germination date on the expression of local adaptation were also examined within the reciprocal transplant experiments. Local adaptation was detected in both years at the local site level and at the level of habitat. The analysis of the transplanted populations indicated that the patterns of selection differed considerably between riparian and serpentine sites. Differential survivorship occurred in serpentine habitats, whereas selection on reproductive output predominated in riparian habitats. Local adaptation was expressed only in the absence of competition. Local adaptation in terms of survivorship was most strongly expressed in treatments with delayed seed germination. Microsatellite markers were used to quantify population genetic parameters and examine the patterns of gene flow among sampled populations. Analysis of molecular markers revealed a system of population patches that freely exchange genes with each other. Strong selection seems to maintain ecotypic variation within this endemic sunflower species, while extensive gene flow among populations prevents local speciation between serpentine and riparian ecotypes.     

Genetic structure in the species-pair Silene vulgaris and S. uniflora (Caryophyllaceae) on the Baltic island of Öland

Allozyme data were used to assess the genetic structure between 37 sympatric populations of the species-pair Stlene vulgaris and S uniflora ssp petraea, and to infer levels of intra- and interspecific gene flow in the two species Silene vulgaris is a geographically widespread weed of disturbed habitats whereas S uniflora ssp petraea is endemic to the Baltic islands of Oland and Gotland On Oland, Silene vulgaris forms extensive linear populations along roads while S uniflora ssp petraea occurs in sparse and spatially-separated populations in open limestone habitats Despite the differences in population size and structure between the two species, both species show extremely low levels of between-population differentiation Between-site differences account for <2% of the total allozyme diversity within Oland in S vulgaris, and < 1% in S uniflora ssp petraea Indirect estimates of gene flow are high for both species (Nm = 11 and 27, respectively) There is no relationship between genetic distance and geographic distance within either species, and the lack of genetic structure is consistent with the pollination biology of the species - both of which are predominantly moth-pollinated The two species hybridize in intermediate habitats, and the geographic distribution of species-characteristic alleles indicates a potential for spatially extensive interspecific gene flow Nevertheless, there are significant differences in allele frequencies between the two species and multivariate analyses show no overlap between populations of the two species The species are ecologically separated by their different habitat preferences and by differences in their flowering phenology There is no evidence that the endemic S uniflora ssp petraea is threatened by genetic contamination or assimilation by the widespread weed, S vulgaris     

Genetic structure and gene flow among Komodo dragon populations inferredby microsatellite loci analysis

A general concern for the conservation of endangered species is the maintenance of genetic variation within populations, particularly when they become isolated and reduced in size. Estimates of gene flow and effective population size are therefore important for any conservation initiative directed to the long-term persistence of a species in its natural habitat. In the present study, 10 microsatellite loci were used to assess the level of genetic variability among populations of the Komodo dragon Varanus komodoensis. Effective population size was calculated and gene flow estimates were compared with palaeogeographic data in order to assess the degree of vulnerability of four island populations. Rinca and Flores, currently separated by an isthmus of about 200 m, retained a high level of genetic diversity and showed a high degree of genetic similarity, with gene flow values close to one migrant per generation. The island of Komodo showed by far the highest levels of genetic divergence, and its allelic distinctiveness was considered of great importance in the maintenance of genetic variability within the species. A lack of distinct alleles and low levels of gene flow and genetic variability were found for the small population of Gili Motang island, which was identified as vulnerable to stochastic threats. Our results are potentially important for both the short- and long-term management of the Komodo dragon, and are critical in view of future re-introduction or augmentation in areas where the species is now extinct or depleted.     

Islands of water in a sea of dry land: hydrological regime predicts genetic diversity and dispersal in a widespread fish from Australia's arid zone, the golden perch (Macquaria ambigua)

Rivers provide an excellent system to study interactions between patterns of biodiversity structure and ecological processes. In these environments, gene flow is restricted by the spatial hierarchy and temporal variation of connectivity within the drainage network. In the Australian arid zone, this variability is high and rivers often exist as isolated waterholes connected during unpredictable floods. These conditions cause boom/bust cycles in the population dynamics of taxa, but their influence on spatial genetic diversity is largely unknown. We used a landscape genetics approach to assess the effect of hydrological variability on gene flow, spatial population structure and genetic diversity in an Australian freshwater fish, Macquaria ambigua. Our analysis is based on microsatellite data of 590 samples from 26 locations across the species range. Despite temporal isolation of populations, the species showed surprisingly high rates of dispersal, with population genetic structure only evident among major drainage basins. Within drainages, hydrological variability was a strong predictor of genetic diversity, being positively correlated with spring-time flow volume. We propose that increases in flow volume during spring stimulate recruitment booms and dispersal, boosting population size and genetic diversity. Although it is uncertain how the hydrological regime in arid Australia may change under future climate scenarios, management strategies for arid-zone fishes should mitigate barriers to dispersal and alterations to the natural flow regime to maintain connectivity and the species' evolutionary potential. This study contributes to our understanding of the influence of spatial and temporal heterogeneity on population and landscape processes.     

Isolation and characterization of microsatellite loci from Silene tatarica

Five new microsatellite loci were isolated from the perennial plant, Silene tatarica. We characterized S. tatarica individuals originating from two riverbank populations in northern Finland and observed between four and nine alleles per locus. Observed heterozygosity was consistently lower than gene diversity (H_O: 0.0450–0.2385, H_E: 0.1919–0.6187). This deficiency of heterozygous genotypes was observed in most locus/population combinations, and is presumably caused by spatial genetic structuring due to restricted seed flow within subpopulations. The markers presented here are the first microsatellites reported for S. tatarica.     

Allopolyploid origin and population genetics of the rare orchid Spiranthes diluvialis

The process of becoming and the attributes of being polyploid play a major role in the development and maintenance of genetic variation in allopolyploid species. A genetic survey employing protein electrophoresis on 12 populations of S. diluvialis, as well as on populations of eight congeneric species, was conducted to assess the putative allopolyploid origin of S. diluvialis and to determine the genetic variability within and among populations. Genetic identity values indicated S. diluvialis was more similar to S. magnicamporum (0.619) and S. romanzoffiana (0.727) than to any of the other congeneric species assayed. Similar to most allopolyploids, S. diluvialis showed high levels of fixed, or nearly fixed, heterozygosity and a high percentage of polymorphic loci (57.1-71.4%). The mean number of alleles per polymorphic locus in populations of S. diluvialis (2.6-3.3), however, was similar to mean values for both animal-pollinated, outcrossing, diploid species, and geographically restricted, diploid species (2.6 and 2.5, respectively). Genetic divergence among populations (mean Fst = 0.083) was low, leading to relatively high estimates of interpopulational gene flow (mean Nm = 5.41). Thus, each population harbors most of the genetic variability found within the species. The genetic variation observed within S. diluvialis supports the occurrence of at least two separate hybridization events giving rise to S. diluvialis.     

Genetic structure and gene flow in a metapopulation of an endangered plant species,Silene tatarica

We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.