A second case of genetic host races in Rhagoletis? A population genetic comparison of sympatric host populations in the European cherry fruit fly,Rhagoletis cerasi

Despite an increasing acceptance in the biological community for sympatric speciation as a mode of species formation, well documented examples of sympatrically evolved ‘incipient species’ remain rare. The sympatric host races of apple maggot, Rhagoletis pomonella (Walsh), represent one of the most prominent case studies for sympatric speciation via a host shift. The European cherry fruit fly, R. cerasi (L.), shows strong ecological similarities to R. pomonella: (1) infestation of two different host plants, Lonicera xylosteum L. and Prunus avium L., and (2) divergent phenological and behavioral adaptations of flies on different hosts. The population genetic study presented here addresses whether the host associated populations of R. cerasi also represent genetically differentiated true host races. Out of a total of 29 allozyme loci examined, six were polymorphic and used to analyze six sympatric pairs of R. cerasi populations on Lonicera and Prunus from Switzerland and Germany. A direct comparison of allele frequencies between sympatric sites showed no pattern indicative of host races in R. cerasi. However, the hierarchical F‐statistic for one locus, mannose 6‐phosphate isomerase (Mpi), showed significant population differentiation that was in accordance with host race differentiation. Mpi is one of several loci that are also diagnostic for host race differentiation in R. pomonella. Results from Mpi suggest the formation of sympatric host races in R. cerasi, but additional polymorphic markers are necessary.     

Host plant‐related genomic differentiation in the European cherry fruit fly,Rhagoletis cerasi

Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher F_ST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.     

Genetic differentiation on multiple spatial scales in an ecotype-forming marine snail with limited dispersal: Littorina saxatilis

The population genetic structure of marine species lacking free-swimming larvae is expected to be strongly affected by random genetic drift among populations, resulting in genetic isolation by geographical distance. At the same time, ecological separation over microhabitats followed by direct selection on those parts of the genome that affect adaptation might also be strong. Here, we address the question of how the relative importance of stochastic vs. selective structuring forces varies at different geographical scales. We use microsatellite DNA and allozyme data from samples of the marine rocky shore snail Littorina saxatilis over distance scales ranging from metres to 1000 km, and we show that genetic drift is the most important structuring evolutionary force at distances > 1 km. On smaller geographical scales (< 1 km), divergent selection between contrasting habitats affects population genetic structure by impeding gene flow over microhabitat borders (microsatellite structure), or by directly favouring specific alleles of selected loci (allozyme structure). The results suggest that evolutionary drivers of population genetic structure cannot a priori be assumed to be equally important at different geographical scales. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 31–40.     

Genetic differentiation and gene flow among populations of the alpine butterfly, Parnassius smintheus, vary with landscape connectivity

Levels of gene flow among populations vary both inter- and intraspecifically, and understanding the ecological bases of variation in levels of gene flow represents an important link between the ecological and evolutionary dynamics of populations. The effects of habitat spatial structure on gene flow have received considerable attention; however, most studies have been conducted at a single spatial scale and without background data on how individual movement is affected by landscape features. We examined the influence of habitat connectivity on inferred levels of gene flow in a high-altitude, meadow-dwelling butterfly, Parnassius smintheus. For this species, we had background data on the effects of landscape structure on both individual movement and on small-scale population genetic differentiation. We compared genetic differentiation and patterns of isolation by distance, based on variation at seven microsatellite loci, among three regions representing two levels of connectivity of high-altitude, nonforested habitats. We found that reduced connectivity of habitats, resulting from more forest cover at high altitudes, was associated with greater genetic differentiation among populations (higher estimated FST), a breakdown of isolation by distance, and overall lower levels of inferred gene flow. These observed differences were consistent with expectations based on our knowledge of the movement behaviour of this species and on previous population genetic analyses conducted at the smaller spatial scale. Our results indicate that the role of gene flow may vary among groups of populations depending on the interplay between individual movement and the structure of the surrounding landscape.     

Genetic differentiation between individuals

I describe a method of analysis of genetic differentiation which is suitable for the comparison of genetic and demographic estimates of the ‘neighborhood size’– more precisely the product of density and second moment of dispersal distance σ²– in continuous populations sampled at the smallest scale. This method is based on results of models of isolation by distance common to a wide variety of dispersal distances. The performance of this method is tested by simulation for some highly leptokurtic dispersal distributions, and it is applied to a previous study of a kangaroo‐rat (Dipodomys spectabilis) population. In this case, genetic and demographic estimates are within a factor of two from each other. Thus, in line with some previous examples, this study shows that a better agreement may be attained than is usually recognized between genetic and demographic estimates.     

Genetic differentiation associated with commercial traffic in the Polynesian mosquito, Aedes polynesiensis Marks 1951

The population structure of the Polynesian mosquito Aedes polynesiensis was investigated using electrophoretic data from two polymorphic protein loci. Considerable differentiation was observed both within and between islands in different archipelagos (Society, Tuamotu, Austral). Gene flow evaluated by F_st estimates was independent of geographic distance between islands but related to commercial traffic intensity. The results are discussed in view of recent findings on the variability of susceptibility to insecticides and of suitability as a vector for the nematode Wuchereria bancrofti.     

Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.     

Genetic variability and level of differentiation among Brazilian pantanal wood stork populations

The Wood Stork (Mycteria americana) is a colonial wading bird of the tropical and lower subtropical zones. We assessed genetic structure within and among five stork colonies from the Brazilian Pantanal and compared our data with those from North American populations. Samples of 234 individuals were studied using protein electrophoresis to evaluate genetic variability and interpopulation differentiation. Of 22 loci examined, 7 were polymorphic (mean heterozygosity = 0.068). The low Fst value (0.005) indicated little intraspecific variation among breeding colonies. Estimated number of migrants per generation based on private alleles (Nm = 11.3) and on Fst (48.8) suggests high gene flow. Nei's genetic distance values among Pantanal colonies ranged from 0.0001 to 0.0034, demonstrating low genetic divergence among populations. Our data can be explained by supposing high gene flow levels among Pantanal colonies, and between North and South American populations, intermediated by a probable interbreeding population in Central America.     

It''s about time: the evidence for host plant-mediated selection in the apple maggot fly, Rhagoletis pomonella, and its implications for fitness trade-offs in phytophagous insects

The apple maggot fly, Rhagoletis pomonella, Walsh (Diptera: Tephritidae), provides a unique opportunity to address the issue of host-related fitness trade-offs for phytophagous insects. Rhagoletis pomonella has been controversial since the 1860's when Benjamin Walsh cited the fly's shift from hawthorn (Crataegus spp.) to apple (Malus pumila) as an example of an incipient sympatric speciation event. Allozyme and mark-release-recapture studies have subsequently confirmed the status of apple and hawthorn flies as partially reproductively isolated and genetically differentiated host races, the hypothesized initial stage in sympatric divergence. Here, we review the ecological and genetic evidence for host-plant mediated selection in R. pomonella. We reach the following three major conclusions: First, although developmental timing is not everything, it is a good deal of the story. Differences in the fruiting phenologies of apple and hawthorn trees exert different selection pressures on the diapause and eclosion time characteristics of the host races. In particular, the 3-week earlier mean fruiting phenology of apples in eastern North America appears to select for a slower rate of metabolism or deeper pupal diapause in apple than hawthorn flies. Second, host-related fitness trade-offs for R. pomonella may not be due to disruptive selection affecting any one specific life-history stage. Rather, it is the sum total of directional selection pressures acting across different life-stages that generates divergent selection on apple and hawthorn flies. For example, selection favors the alleles Me 100, Acon-2 95 and Mpi 37 (or linked genes) in the larval stage in both host races. However, these same alleles are disfavored in the pupal stage to follow, where they correlate with early adult eclosion, and by inference premature diapause termination. Because apple trees fruit an average of 3 weeks earlier than hawthorn trees, this counter-balancing selection is stronger on apple-fly pupae. The net result is that the balance of selective forces is different between apple and hawthorn flies, helping to maintain the genetic integrity of the host races in sympatry in the face of gene flow. Finally, natural R. pomonella populations harbor a good deal of genetic variation for development-related traits. This variation allows fly populations to rapidly respond to temporal vagaries in local environmental conditions across years, as well as to broad-scale geographic differences that exist across the range of the species. Perhaps most importantly, this variation gives R. pomonella the flexibility to explore and adapt to novel plants. Taken together, our results underscore how difficult it can be to document host plant-related fitness trade-offs for phytophagous insects due to the need to consider details of the entire life-cycle of a phytophagous insect. Our findings also show how reproductive isolation can arise as a by-product of host-associated adaptation in insects, a central theme for models of sympatric speciation via host shifts.     

Gene flow among Tetranychus urticae (Acari: Tetranychidae) populations in Greece

Polymorphism of four enzymatic loci has been examined in 27 populations of Tetranychus urticae in relation to their geographical distribution and to two ecological parameters: open field vs. greenhouse habitats, and species of the colonized host plant. Genetic differentiation was significantly correlated to geographical distance in both types of habitat. Mite density and distribution of infested plants appear to be important factors for the population structure of T. urticae . In open field, T. urticae specimens from citrus trees were genetically more similar to other 'citrus' samples collected in different localities than they were from mites collected in the same locality on other plant species.     

Genetic differentiation of the tephritid fly Urophora cardui in Europe as evidence for its biogeographical history

Gaps in the large-scale distribution of the tephritid fly Urophora cardui in Europe have been explained as the results of an ongoing re-immigration from Pleistocene refugia due to a very low dispersal capacity. Following evidence of a much greater dispersal capacity of U. cardui than previously assumed, the pattern of genetic differentiation of 41 populations from 16 European regions was studied using allozyme electrophoresis. In these analyses 18 enzyme systems were scored consistently providing 27 alleles. Allozyme variation indicated high gene flow and low levels of genetic differentiation within and between sampling regions as well as in recently colonized areas. No geographical pattern of heterozygosity or allozyme differentiation could be found matching the previously suggested recent immigration pattern. An observed south-north gradient in allozyme frequencies was interpreted as a geographical cline due to environmental factors. The results corroborate evidence from more recent studies that U. cardui is a highly mobile species which is likely to have repeatedly colonized some suboptimal European regions since the Pleistocene after retreats during 'little ice ages'. Patterns resulting from postglacial immigration processes are likely to have been long wiped out through high exchange rates.     

Genetic diversity and genetic structure of populations of Ranunculus japonicus Thunb. (Ranunculaceae)

Abstract In order to clarify the genetic diversity and population structure of Ranunculus japonicus , allozymic analysis was conducted on 60 populations in southwestern Japan. Considerable genetic variati ons were detected among the populations of R. japonicus . The genetic diversities within species ( H _es = 0.215) and within populations ( H _ep = 0.172) were slightly higher than those of other perennial herbs with widespread distribution and outcrossing plants. Significantly higher values of fixation index were detected in some populations, which might have arisen from restricted mating partners. The majority of genetic variation (approx. 80%) resided within a population and a moderate level of genetic differentiation ( G _ST = 0.203) was observed among populations. The F _ST value (0.203) suggests the existence of a substantial population structure in this species. The highly significant correlation between geographic distance and F _ST values indicates that isolation by distance has played an important role in the construction of the genetic structure of this species.     

Genetic population structure of the Dakota skipper (Lepidoptera: Hesperia dacotae): A North American native prairie obligate

A range-wide survey of Dakotaskipper (Hesperia dacotae) populationsassessed levels of genetic variability andgeographic scale of population structure inthis species of conservation concern. Thisspecies exists on isolated patches of nativetall- and mixed-grass prairie within a highlymodified landscape dominated by agriculture. It has been extirpated from the southernportion of its range and has sufferedrange-wide declines. Nine populations weresampled from western Minnesota, eastern SouthDakota, and southern Manitoba. Starch gelelectrophoresis was used to resolve 21 isozymeloci in 278 Dakota skippers. Dakota skipperpopulations were approximately as variable asother lepidopterans found in isolated habitats. Genetic distances indicated that Manitobapopulations were somewhat distinct from ones inMinnesota and South Dakota. Isolation-by-distance was detected range-wideand among the seven southern-most populations. Genetically effective immigration rates weresmall at both range-wide and regional scalesand effective populations sizes were lowsuggesting that Dakota skipper populations aregenetically isolated from one another, althoughthey were likely more connected in the recentpast. Genotype assignment tests revealed twoclusters of populations in Minnesota and SouthDakota that were not apparent from theisolation-by-distance results. Significantheterozygote deficiencies relative toHardy-Weinberg expectations and high inbreedingcoefficients suggest structure within samplelocations. Management recommendations includethe maximization of effective population sizein each Dakota skipper population to offset theeffects of drift and habitat corridors in somecases. Habitat management should consider thewithin-site population structure and possibletemporal population structure detected in thisstudy.     

Genetic differentiation and speciation among four Phyllotreta species (Coleoptera: Chrysomelidae)

Among the four closely related Phyllotreta species P. dilatata Thomson, 1866, P. flexuosa (Illiger, 1794), P. ochripes (Curtis, 1837) and P. tetrastigma (Comolli, 1837) several systematic problems occur due to the existence of colour pattern variation and morphological similarity. All four species feed on Brassicaceae, but P. tetrastigma , P. flexuosa and P. dilatata are monophagous in the field, whereas P. ochripes is oligophagous. Genetic differentiation and systematic relationships of the four species are studied by means of allozyme electrophoresis of 10 variable loci, with a total of 30 allelomorphs. Of the six alleles that are present only in a single species, none is diagnostic. Rogers modified genetic distance and Cavalli-Sforza & Edwards arc distance between all populations are calculated and Distance Wagner trees are constructed, revealing three major groups. P. ochripes is separated first, being the most distant species. The three other species are more closely related, and within this group P. dilatata is separated from the other two. The last group contains the populations of P. tetrastigma and P. flexuosa. In the differentiation between the different species host plant shifts and consequent genetic differentiation have been important.     

Hawthorn-infesting populations of Rhagoletis pomonella in Mexico and speciation mode plurality

Categorizing speciation into dichotomous allopatric versus nonallopatric modes may not always adequately describe the geographic context of divergence for taxa. If some of the genetic changes generating inherent barriers to gene flow between populations evolved in geographic isolation, whereas others arose in sympatry, then the mode of divergence would be mixed. The apple maggot fly, Rhagoletis pomonella, has contributed to this emerging concept of a mixed speciation mode "plurality." Genetic studies have implied that a source of diapause life-history variation associated with inversions and contributing to sympatric host race formation and speciation for R. pomonella in the United States may have introgressed from the Eje Volcanico Trans Mexicano (EVTM; a.k.a. the Altiplano) in the past. A critical unresolved issue concerning the introgression hypothesis is how past gene flow occurred given the current 1200-km disjunction in the ranges of hawthorn-infesting flies in the EVTM region of Mexico and the southern extreme of the U.S. population in Texas. Here, we report the discovery of a hawthorn-infesting population of R. pomonella in the Sierra Madre Oriental Mountains (SMO) of Mexico. Sequence data from 15 nuclear loci and mitochondrial DNA imply that the SMO flies are related to, but still different from, U.S. and EVTM flies. The host affiliations, diapause characteristics, and phylogeography of the SMO population are consistent with it having served as a conduit for gene flow between Mexico and the United States. We also present evidence suggesting greater permeability of collinear versus rearranged regions of the genome to introgression, in accord with recent models of chromosomal speciation. We discuss the implications of the results in the context of speciation mode plurality. We do not argue for abandoning the terms sympatry or allopatry, but caution that categorizing divergence into either/or geographic modes may not describe the genetic origins of all species. For R. pomonella in the United States, the proximate selection pressures triggering race formation and speciation stem from sympatric host shifts. However, some of the phenological variation contributing to host-related ecological adaptation and reproductive isolation in sympatry at the present time appears to have an older history, having originated and become packaged into inversion polymorphism in allopatry.     

Genetic differentiation among the sympatric brown trout (Salmo trutta) populations of Lough Melvin, Ireland

Three morphotypes of brown trout have been described from Lough Melvin in north-west Ireland: gillaroo; sonaghen; ferox. The extensive genetic differences among the three types indicate that they are reproductively isolated, i.e. separate stocks of trout. For example, only gillaroo possess the Ldh -1(n) allele. Ferox show a high frequency of the Ldh -5(100) allele and this allele does not exceed a frequency of 0.02 in the other two types. Sonaghen are characterized by relatively much higher frequencies for Ck -2(115) and Gpi- 2(135) alleles. Sampling over a period of 7 years and experiments with artificial stocks of gillaroo and sonaghen have demonstrated that these differences are temporally stable. On the basis of observation of mature adults and the genetic composition of fry samples, it has been shown that the three types maintain their genetic integrity as the result of their distinctive spawning habits with gillaroo spawning in the lake and outflowing river, sonaghen in the smaller inflowing rivers and ferox in the deep downstream section of the largest inflowing river. The ferox is a relict population of an early post-glacial trout colonist while gillaroo and sonaghen are representative of a more recent independent colonization. However, it cannot be determined at present whether or not gillaroo and sonaghen were already differentiated prior to colonizing Melvin although the weight of evidence favours a sympatric split. It is proposed that the three types of trout be designated as separate subspecies to highlight the need for independent management and urgent requirement for conservation action.     

Latitudinal variability of Drosophila melanogaster: Allozyme frequencies divergence between European and Afrotropical populations

Allelic frequencies at five polymorphic loci were determined in seven European and six Afrotropical populations of Drosophila melanogaster. African populations, which may be considered as ancestral for the species, showed a greater genetic diversity as measured by the number of alleles found. Within each geographic group (Europe or tropical Africa) genetic distances between local populations were very small (D=0.027). By contrast, the average distance between European and African populations (D=0.389) was more than 12 times bigger. It was previously known that various morphological or physiological differences, which probably reflect genetic adaptations to different environments, exist between these temperate and tropical populations. Data presented here suggest that the divergence in allozyme frequencies also reflects some selective mechanisms.     

Population genetic structure of the western cherry fruit fly Rhagoletis indifferens (Diptera: Tephritidae) in British Columbia,Canada

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Gene flow between nascent species: geographic,genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens

Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible, yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths, respectively. Using 79 SNP loci, we genotyped nearly 1000 individuals from populations of both species in close proximity to each other and from putative hybrid zones. The species shared all but one SNP polymorphism, and on average, allele frequencies differed by only 0.14. However, the species were clearly differentiated using Structure, and admixed individuals were primarily identified at putative hybrid zones. PopGraph identified a highly integrated network among all populations, but populations of each species and hybrid zones occupied distinct regions in the network. Using either conditional graph distance (cGD) or Fst/(1‐Fst), we found significant isolation by distance (IBD) among populations. Within species, IBD was strong, indicating high historic gene flow. IBD extended approximately 100 km in A. pubescens and 30 km in A. formosa. However, IBD between the species was very weak and extended only a few km beyond hybrid zones, suggesting little recent gene flow. The extensive sharing of SNP polymorphisms between these species suggests that they are very early in the speciation process while the low signal of IBD suggests that they have largely ceased gene exchange.     

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata . Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics ( AMOVA ) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (Φ_ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata , culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.