Amplified Fragment Length Polymorphism (AFLP) reveals no genetic divergence of the Eastern Alpine endemic Oxytropis campestris subsp. tiroliensis (Fabaceae) from widespread subsp. campestris

Applying Amplified Fragment Length Polymorphism, we explored genetic differences between widespread Oxytropis campestris subsp. campestris and O. campestris subsp. tiroliensis, a presumed glacial relict restricted to a small area along the main chain of the Eastern Alps. We could not find genetic differences between the two taxa. Neither do the morphological characters given in the literature discriminate between them. Therefore Oxytropis campestris subsp. tiroliensis is unlikely a glacial relict that survived Pleistocene glaciations on nunataks, but rather a genetically insignificantly differentiated phenotype that arose in the course of postglacial recolonisation. There is no phylogeographical structure in O. campestris s.l. in the Alps most probably due to the fact that the taxon did not survive the cold stages of the Pleistocene in the interior of the Alps but immigrated to that region at a later date.     

Regional population structure of a widely introduced estuarine invertebrate: Nematostella vectensis Stephenson in New England

Nematostella vectensis is an infaunal anemone occurring in salt marshes, lagoons and other estuarine habitats in North America and the United Kingdom. Although it is considered rare and receives protection in England, it is widely distributed and abundant in the United States, particularly along the Atlantic coast. Recent studies suggest that both anthropogenic dispersal and reproductive plasticity may significantly influence the genetic structure of N. vectensis populations. Amplified fragment length polymorphism (AFLP) fingerprinting of individuals from nine populations in the northeastern United States indicates that stable populations are maintained by both asexual and sexual reproduction; in some cases asexually reproducing lineages exist within sexually reproducing populations. F statistics reveal extraordinarily high degrees of genetic differentiation between populations, even those separated by very short distances (less than 100 m). Genetic distances show little to no correlation with geographical distances, consistent with a role for sporadic, geographically discontinuous dispersal coupled with limited gene flow. No single genotype was found at more than one site, despite apparent homogeneity of habitat. In contrast with reported genotypic distributions for Nematostella in the United Kingdom, where a single clonal genotype dominates at multiple sites through southern England, our data thus fail to support the hypothesis of a general-purpose genotype in the northeastern United States. However, they are consistent with important roles for reproductive plasticity, sporadic introductions and complex local population dynamics in determining the global and regional distribution of this species.     

Genetic structure of the forest herb Primula elatior in a changing landscape

To investigate whether changes in land use and associated forest patch turnover affected genetic diversity and structure of the forest herb Primula elatior, historical data on landscape changes were combined with a population genetic analysis using dominant amplified fragment length polymorphism markers. Based on nine topographic maps, landscape history was reconstructed and forest patches were assigned to two age classes: young (less than 35 years) and old (more than 35 years). The level of differentiation among Primula populations in recently established patches was compared with the level of differentiation among populations in older patches. Genetic diversity was independent of population size (P > 0.05). Most genetic variation was present within populations. Within-population diversity levels tended to be higher for populations located in older forests compared with those for populations located in young forests (Hj = 0.297 and 0.285, respectively). Total gene diversity was also higher for old than for young populations (Ht = 0.2987 and 0.2828, respectively). The global fixation index FST averaged over loci was low, but significant. Populations in older patches were significantly more differentiated from each other than were populations in recently established patches and they showed significant isolation by distance. In contrast, no significant correlations between pairwise geographical distance and FST were found for populations in recently established patches. The location of young and old populations in the studied system and altered gene flow because of increased population density and decreased inter-patch distances between extant populations may explain the observed lower genetic differentiation in the younger populations. This study exemplifies the importance of incorporating data on historical landscape changes in population genetic research at the landscape scale.     

Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods

Three different approaches were used to assess the kinship structure of two epiphytic bryophytes, Orthotrichum speciosum and O. obtusifolium, that have different dispersal strategies. The two species were sampled in a 200 ha landscape where species occurrence and host trees had been mapped previously. Local environmental conditions at sampled trees were recorded and kinship between individuals was calculated based on amplified fragment length polymorphism (AFLP)-marker data. We did not detect any association between AFLP-markers and investigated environmental conditions. In both species, significant kinship coefficients were found between individuals up to 300-350 m apart which shows that both species have a restricted dispersal range. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models (GAMs), but linear regression failed to detect any structure in O. speciosum. Although the dioecious O. obtusifolium is currently the more common species it may, none the less, due to its restricted dispersal range and reproduction mode, become threatened in the future by current silvicultural practices which enhance the distance between host trees and decrease their life span. Finally, GAMs seem most appropriate for analysing spatial genetic structure because the effects of local environmental conditions and spatial structure can be analysed simultaneously, no assumption of a parametric form between kinship coefficient and distance is required, and spatial data resolution is not lost in the arbitrary choice of distance classes characterizing autocorrelation analysis.     

QTL mapping of economically important traits in Silkworm (<Emphasis Type="Italic">Bombyx mori</Emphasis>)

A backcrossed population(BC1)was derived from a cross between C1AFLP technique was employed for mapping the QTLs.The QTLs for the whole cocoon weight,cocoon shell weight,ratio of cocoon shell,weight of pupae etc.Were analyzed and 11 QTLs were detected based on the constructed linkage map.Two QTLs for whole cocoon weight were localized on linkage group 6 and 19; three QTLs for cocoon shell weight were localized on linkage group 3,14 and 19; three QTLs for ratio of cocoon shell were localized on the linkage group 2,11and 15,and three QTLs for the weight of pupae were localized on linkage 2,14 and 19.All these have laid an important base for the marker assisted breeding of the silkworm.     

AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites

Individual-based population assignment tests have thus far mainly relied on the use of microsatellite loci. However, the logistic difficulty of screening large numbers of loci required to reach sufficient statistical power hampers the usefulness of microsatellites in situations of weak population structuring. Amplified fragment length polymorphisms (AFLP) represents an alternative for overcoming this logistical issue as the technique allows the user to characterize a much larger number of loci with a comparable analytical effort. In this study, an assignment test based on maximum likelihood for dominant markers was used to investigate the potential usefulness of AFLP for population assignment. We also compared assignment success achieved with AFLP with that obtained using microsatellites in a case study of low population differentiation involving whitefish (Coregonus clupeaformis) sympatric ecotypes. The analytical investigation showed that the minimum number of AFLP loci required to reach an assignment success of 95% stood within values that are easily achievable in many situations. This also showed how assignment success varied according to the number of AFLP loci used, their absolute frequency and their frequency differential and sampling errors, as well as the number of putative source populations. The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring.     

Hybridization and Rorippa austriaca (Brassicaceae) invasion in Germany

Introgressive hybridization between the invasive Rorippa austriaca and the native R. sylvestris in Germany has been studied using chloroplast DNA (trnL intron) and amplified fragment length polymorphism. Three hybrid zones between the invasive and native species were located in the Ruhr Valley (Mülheim) and at the River Main near Würzburg (Randersacker, Winterhausen). In each hybrid zone hybridization was indicated by additivity of region-specific amplified fragment length polymorphism markers proving independent hybridization events. The hybrids were either morphologically intermediate (R. x armoracioides) or were close to R. sylvestris. The trnL intron of R. austriaca is characterized by a species-specific deletion. This diagnostic chloroplast marker of R. austriaca was detected in three individuals of R. sylvestris providing evidence for introgression of the invasive chloroplast into the native species. Bidirectional introgression of R. austriaca markers into R. sylvestris and of R. sylvestris markers into R. austriaca was detected in the amplified fragment length polymorphism analysis. Some of the invasive R. austriaca populations showed high within-population variation. A possible association among introgression, within-population variation and invasion success is discussed. The morphologically intermediate hybrid R. x armoracioides is currently spreading in northern Germany. It forms large populations without its parent species R. austriaca and R. sylvestris. It is concluded that hybridization between invasive R. austriaca and native R. sylvestris may lead to the evolution of a new invasive species R. x armoracioides.     

Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers

A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy-Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full-sibs, and performs better than a previously developed estimator. When comparing marker-based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co-dominant markers (microsatellites) in studying microgeographic isolation-by-distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.     

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.     

Resistance or emigration: response of the high-alpine plant Eritrichium nanum (L.) Gaudin to the ice age within the Central Alps

Two main possibilities regarding glacial survival of the mountain flora of the Alps during the Quaternary have been discussed: the tabula rasa and the nunatak hypotheses. Eritrichium nanum (L.) Gaudin (Boraginaceae) is a perennial cushion plant, occurring at high elevations of the Central Alps and having a preference for extreme habitats. It belongs to a group of high-alpine plants, for which in situ glacial survival on nunataks is ecologically possible. By investigating 20 populations of E. nanum of potential nunatak and peripheral refugial regions using amplified fragment length polymorphism, considerable genetic differences between populations from the Central Alps and populations from peripheral refugia were detected; hence, the latter probably did not serve as potential sources for the re-colonization of the Central Alps after glaciation. Genetic variation was hierarchically structured (AMOVA), and three genetically distinct regions could be identified in the Central Alps. Two of these, the Penninic and Rhaetic Alps, correspond to nunatak regions proposed in the biogeographic literature. Populations from the Lepontic Alps formed a third genetic group. Genetic correlation (Mantel statistics) was highest within populations, with a modest decline among populations within specific nunatak regions and a negative correlation outside the genetic influence of specific nunatak regions. In situ glacial survival in E. nanum could be a model for the Quaternary history of other alpine plants, especially those that also occur at high elevations and in similar habitats.