AFLP Genotypes Research Articles

Genetic Identity and Diversity of Perennial Pepperweed (Lepidium latifolium) in Its Native and Invaded Ranges

AbstractPerennial pepperweed is an invasive plant species in North America, native to temperate Eurasia and northern Africa. Effective biological control depends upon correct taxonomic identification. Therefore, we investigated morphological and genetic data (cpDNA sequences and amplified fragment length polymorphisms [AFLP]) in its native range, where the species is at times treated as multiple taxa (L. latifolium, L. affineandL. obtusum). We also analyzed genetic data to determine the number and distribution of haplotypes and genotypes in the invaded range. Using Bayesian analysis, we found three clusters of AFLP genotypes in the native range, but little correlation between these clusters and morphological characters used to distinguish taxa. Also, we found combinations of morphological character states within many native range plants that are incompatible with current species descriptions, offering no support for splittingL. latifoliumsensu lato into three species. In North America 97% of the genetic variation was among populations and there were only eight AFLP genotypes in 288 plants, suggesting few introductions or a severe bottleneck, and little or no creation of new genotypes since introduction. We found plants in the native range that are genetically similar (88 to 99%) to six of the eight invasive AFLP genotypes, suggesting that Kazakhstan and China are origins for much of the North American invasion.

The population structure of Hemileia vastatrix in Brazil inferred from AFLP

Efforts to obtain durable resistant cultivars to coffee leaf rust have a long history of disappointment because of the lack of information on the Hemileia vastatrix evolutionary potential. In this study, the AFLP marker was used to analyze the genetic structure of a field population of H. vastatrix from different coffee genotypes cultivated in a wide geographic region of Brazil’s main production areas. A total of 91 isolates were sampled from genotypes of Coffea arabica, C. canephora and Híbrido de Timor/Icatu derivatives. Each isolate exhibited unique multilocus AFLP genotypes with no identical isolates obtained from the same geographical and host origins. This finding was corroborated by a small correlation between genetic similarity and geographic distance (R xy = 0.31, P = 0.23). The analyses showed a low genetic differentiation (G ST = 0.026) between the populations defined by a host and AMOVA analysis, most of the genetic variance (99.56 %) was attributed to differences within populations. In addition, based on the index of association (IA), the random mating possibility was not rejected (IA = 0.225, P = 0.123) for the population of H. vastatrix derived from C. canephora. This result suggested that H. vastatrix in Brazil behaves as a large undifferentiated population with a high level of genotypic diversity that is unstructured with regard to its geographic and host origins.

The association between polyploidy and clonal reproduction in diploid and tetraploidChamerion angustifolium

Clonal reproduction is associated with the incidence of polyploidy in flowering plants. This pattern may arise through selection for increased clonality in polyploids compared to diploids to reduce mixed-ploidy mating. Here, we test whether clonal reproduction is greater in tetraploid than diploid populations of the mixed-ploidy plant, Chamerion angustifolium, through an analysis of the size and spatial distribution of clones in natural populations using AFLP genotyping and a comparison of root bud production in a greenhouse study. Natural tetraploid populations (N = 5) had significantly more AFLP genotypes (x¯ = 10.8) than diploid populations (x¯ = 6.0). Tetraploid populations tended to have fewer ramets per genotype and fewer genotypes with >1 ramet. In a spatial autocorrelation analysis, ramets within genotypes were more spatially aggregated in diploid populations than in tetraploid populations. In the greenhouse, tetraploids allocated 90.4% more dry mass to root buds than diploids, but tetraploids produced no more root buds and 44% fewer root buds per unit root mass than diploids. Our results indicate that clonal reproduction is significant in most populations, but tetraploid populations are not more clonal than diploids, nor are their clones more spatially aggregated. As a result, tetraploids may be less sheltered from mixed-ploidy mating and diploids more exposed to inbreeding, the balance of which could influence the establishment of tetraploids in diploid populations.

PFGE and AFLP genotyping of Staphylococcus aureus subsp. anaerobius isolated from goats with Morel’s disease

Staphylococcus aureus subsp. anaerobius is the etiological agent of the Morel’s disease in sheep and goats. The disease presents with subcutaneous abscesses, located mainly in the superficial lymph nodes. Forty-one isolates of S. aureus subsp. anaerobius were collected from two outbreaks of the Morel’s disease in Poland in years 2006–2008. Analysis of DNA SmaI digests by PFGE showed that 35 of 41 isolates belonged to the same PFGE type, identical to the type strain of S. aureus subsp. anaerobius ATCC 35844, confirming high level of clonality of the species. The DNA patterns of the remaining identical 6 isolates, different from the reference strain only by two bands, were found closely related. Genotyping performed with AFLP technique revealed two clonal groups including 16 and 25 isolates, respectively. The study indicated that AFLP technique might be a better discriminatory tool for genetic analysis of S. aureus subsp. anaerobius isolates, when compared to PFGE.

An AFLP-based test of clonality in widespread, putatively asexual populations of Porphyra umbilicalis (Rhodophyta) in the Northwest Atlantic with an in silico analysis for bacterial contamination

Asexual reproduction often predominates in populations of species experiencing range expansion. Locally selected genotypes can lead to the establishment of clonal populations that accumulate genetic diversity through time. Sexual reproduction has never been observed in extensive field and culture studies of the red alga Porphyra umbilicalis from Maine, USA, even though sexual reproduction predominates in this species in the eastern Atlantic (Europe). This suggests that Maine populations are indeed asexual and might consist of one or only a few genetic clones; we have tested this using AFLPs. Individuals were sampled at two sites in Maine (Cobscook Bay [n = 25], Schoodic Point [n = 26]) and compared to sexual individuals from England (Sidmouth [n = 17]). The AFLP analysis determined that individuals at two sites in Maine containing putative asexuals were not strictly clonal; however, two multilocus lineages were sampled more than once. Two genetic clones, one at each Maine site, were comprised of 6 individuals each; the 39 additional Maine individuals had distinctive AFLP genotypes. However, when the individuals from Maine were compared with a known sexual population from Sidmouth, England, much greater genetic diversity was found within the sexual population in England. Finally, we examine how preparation of field-collected material for AFLP investigations can affect the inclusion of non-target DNA and demonstrate an in silico approach for removing some cryptic contaminants from analysis.

Bringing together evolution on serpentine and polyploidy: spatiotemporal history of the diploid-tetraploid complex of Knautia arvensis (Dipsacaceae).

Polyploidization is one of the leading forces in the evolution of land plants, providing opportunities for instant speciation and rapid gain of evolutionary novelties. Highly selective conditions of serpentine environments act as an important evolutionary trigger that can be involved in various speciation processes. Whereas the significance of both edaphic speciation on serpentine and polyploidy is widely acknowledged in plant evolution, the links between polyploid evolution and serpentine differentiation have not yet been examined. To fill this gap, we investigated the evolutionary history of the perennial herb Knautia arvensis (Dipsacaceae), a diploid-tetraploid complex that exhibits an intriguing pattern of eco-geographic differentiation. Using plastid DNA sequencing and AFLP genotyping of 336 previously cytotyped individuals from 40 populations from central Europe, we unravelled the patterns of genetic variation among the cytotypes and the edaphic types. Diploids showed the highest levels of genetic differentiation, likely as a result of long term persistence of several lineages in ecologically distinct refugia and/or independent immigration. Recurrent polyploidization, recorded in one serpentine island, seems to have opened new possibilities for the local serpentine genotype. Unlike diploids, the serpentine tetraploids were able to escape from the serpentine refugium and spread further; this was also attributable to hybridization with the neighbouring non-serpentine tetraploid lineages. The spatiotemporal history of K. arvensis allows tracing the interplay of polyploid evolution and ecological divergence on serpentine, resulting in a complex evolutionary pattern. Isolated serpentine outcrops can act as evolutionary capacitors, preserving distinct karyological and genetic diversity. The serpentine lineages, however, may not represent evolutionary ‘dead-ends’ but rather dynamic systems with a potential to further influence the surrounding populations, e.g., via independent polyplodization and hybridization. The complex eco-geographical pattern together with the incidence of both primary and secondary diploid-tetraploid contact zones makes K. arvensis a unique system for addressing general questions of polyploid research.

AFLP data suggest a potential role for the low genetic diversity of acid lime (Citrus aurantifolia Swingle) in Oman in the outbreak of witches’ broom disease of lime

Acid lime (Citrus aurantifolia) is the fourth largest fruit crop in terms of cultivated area and production in Oman. However, over half a million lime trees were lost in Oman over the past 35 years due to witches’ broom disease of lime (WBDL) which is caused by Candidatus phytoplasma aurantifolia. This study was conducted to examine genetic diversity of acid lime in Oman. AFLP analysis of 143 acid lime samples from Oman, 2 from Brazil and one from Pakistan using 4 primer pair combinations produced 980 polymorphic loci (100 %) and 146 AFLP genotypes. Despite the long history of acid lime cultivation in Oman, populations of lime from different districts were found to have low levels of genetic diversity (0.0888–0.2284). AMOVA analysis indicated the existence of high level of genetic differentiation (FST = 0.271) among populations of acid lime from Oman and Brazil, which indicates that both populations have evolved independently for a considerably long period of time. On the other hand, AMOVA analysis showed that only 11 % of the genetic variation exists among populations from the 18 different districts in Oman. This suggests frequent exchange of acid lime planting material across geographical regions in Oman. Findings from this study suggest that the low level of genetic diversity of acid lime in Oman and frequent movement of acid lime planting material across districts are two main factors which contributed to the rapid spread and high susceptibility of acid limes to WBDL in the country.

Origins of early-flowering cherry cultivars, Prunus × kanzakura cv. Atami-zakura and Prunus × kanzakura cv. Kawazu-zakura, revealed by experimental crosses and AFLP analysis

Flowering cherry trees (Prunus subgenus Cerasus) are characterized by beautiful flowers along with the existence of hundreds of flower ornamental cultivars. The long history of cultivation of flowering cherries, however, has caused significant confusion over names and origins. We conducted experimental crosses and AFLP analysis to reveal the origins or parentages of early-flowering cherry cultivars, Prunus×kanzakura cv. Atami-zakura and Prunus×kanzakura cv. Kawazu-zakura. Multivariate analysis based on pairwise genetic similarity (principal coordinate analysis; PCoA), and Bayesian statistical methods to find genetic group (STRUCTURE analysis) and to classify samples into different hybrid classes (NewHybrids) clearly demonstrated that (1) Prunus×kanzakura cv. Atami-zakura is the F1 hybrid between P. jamasakura and P. campanulata, and (2) Prunus×kanzakura cv. Kawazu-zakura is the F1 hybrid between P. lannesiana var. speciosa and P. campanulata. The experimental crosses revealed the significant difficulty of generating these hybrids. In addition, 18 of 20 and six of six samples of Prunus×kanzakura cv. Atami-zakura and Prunus×kanzakura cv. Kawazu-zakura, respectively, are classified into a single AFLP genotype. It is apparent that the original trees or genets of these taxa have long been propagated by grafting over several tens to one hundred years.

A first-generation linkage map of the Pacific lion-paw scallop (Nodipecten subnodosus): Initial evidence of QTL for size traits and markers linked to orange shell color

The first genetic linkage maps of the Pacific lion-paw scallop were created using microsatellite and AFLP genotyping of a full-sibling family spawned from a single, pairwise mating. As an important step in the development of genomic resources for this species, the maps were then used in an effort to identify putative quantitative trait loci (QTL) for the size traits of shell length, height, and width, as well as total mass, soft tissue mass, muscle mass, and orange shell color. The female map contains 147 markers on 27 linkage groups, covering 919.7cM, while the male map contains 149 markers placed on 20 linkage groups spanning 963.7cM. Combining all available markers resulted in a consensus map of 320 loci (56 microsatellites and 264 AFLPs) on 22 linkage groups with an average spacing of 3.8cM and a total map distance of 1124.14cM. Non-parametric, Kruskal–Wallis tests found significant linkage at α=0.005 for two size traits: total biomass in the loci segregating in the female parent, and shell width in the male. Interval mapping showed chromosome-wide significance for many traits on two primary linkage groups in the female map and one in the male. Highly correlated, 91.7% of the variation among the six size phenotypes could be explained by the first principal component, which explained 9 and 7.8% of the variance in the female and male maps, respectively. With the exception of muscle mass mapped when maturation stage was considered as a covariate, no significant LOD scores for size traits were identified using the combined map. Finally, orange shell color was mapped to a 1cM region of linkage group Nsub9. The development of these maps and identification of linkage groups linked to size traits provide a foundation for future quantitative studies, which could ultimately result in marker assisted selection to improve scallop growth in aquaculture.

Extensive Genetic Diversity within the Dutch Clinical Cryptococcus neoformans Population

A set of 300 Dutch Cryptococcus neoformans isolates, obtained from 237 patients during 1977 to 2007, was investigated by determining the mating type, serotype, and AFLP and microsatellite genotype and susceptibility to seven antifungal compounds. Almost half of the studied cases were from HIV-infected patients, followed by a patient group of individuals with other underlying diseases and immunocompetent individuals. The majority of the isolates were mating type α and serotype A, followed by αD isolates and other minor categories. The most frequently observed genotype was AFLP1, distantly followed by AFLP2 and AFLP3. Microsatellite typing revealed a high genetic diversity among serotype A isolates but a lower diversity within the serotype D set of isolates. One patient was infected by multiple AFLP genotypes. Fluconazole and flucytosine had the highest geometric mean MICs of 2.9 and 3.5 μg/ml, respectively, while amphotericin B (0.24 μg/ml), itraconazole (0.08 μg/ml), voriconazole (0.07 μg/ml), posaconazole (0.06 μg/ml), and isavuconazole (0.03 μg/ml) had much lower geometric mean MICs. One isolate had a high flucytosine MIC (>64 μg/ml), while decreased susceptibility (≥16 μg/ml) for flucytosine and fluconazole was found in 9 and 10 C. neoformans isolates, respectively.

Does a shift in host plants trigger speciation in the Alpine leaf beetle Oreina speciosissima (Coleoptera, Chrysomelidae)?

BackgroundWithin the Coleoptera, the largest order in the animal kingdom, the exclusively herbivorous Chrysomelidae are recognized as one of the most species rich beetle families. The evolutionary processes that have fueled radiation into the more than thirty-five thousand currently recognized leaf beetle species remain partly unresolved. The prominent role of leaf beetles in the insect world, their omnipresence across all terrestrial biomes and their economic importance as common agricultural pest organisms make this family particularly interesting for studying the mechanisms that drive diversification. Here we specifically focus on two ecotypes of the alpine leaf beetle Oreina speciosissima (Scop.), which have been shown to exhibit morphological differences in male genitalia roughly corresponding to the subspecies Oreina speciosissima sensu stricto and Oreina speciosissima troglodytes. In general the two ecotypes segregate along an elevation gradient and by host plants: Oreina speciosissima sensu stricto colonizes high forb vegetation at low altitude and Oreina speciosissima troglodytes is found in stone run vegetation at higher elevations. Both host plants and leaf beetles have a patchy geographical distribution. Through use of gene sequencing and genome fingerprinting (AFLP) we analyzed the genetic structure and habitat use of Oreina speciosissima populations from the Swiss Alps to examine whether the two ecotypes have a genetic basis. By investigating a wide range of altitudes and focusing on the structuring effect of habitat types, we aim to provide answers regarding the factors that drive adaptive radiation in this phytophagous leaf beetle.ResultsWhile little phylogenetic resolution was observed based on the sequencing of four DNA regions, the topology and clustering resulting from AFLP genotyping grouped specimens according to their habitat, mostly defined by plant associations. A few specimens with intermediate morphologies clustered with one of the two ecotypes or formed separate clusters consistent with habitat differences. These results were discussed in an ecological speciation framework.ConclusionsThe question of whether this case of ecological differentiation occurred in sympatry or allopatry remains open. Still, the observed pattern points towards ongoing divergence between the two ecotypes which is likely driven by a recent shift in host plant use.

Diversity of S-alk(en)yl cysteine sulphoxide content within a collection of garlic ( Allium sativum L.) and its association with the morphological and genetic background assessed by AFLP

Garlic ( Allium sativum L.) is a vegetatively propagated species that has been used as a culinary and medicinal plant and it is a source of sulphur-containing compounds. Our objectives are to assess S-alk(en)yl cysteine sulphoxide (SACS) content and to characterise genotypically, a set of 135 accessions, which have previously been assigned standard morphological descriptors. HPLC was used to assay the amount of sulphur-containing compounds, while AFLP was used as the genotyping platform. The 286 different informative AFLP fragments identified across the collection were subjected to principal component analysis. Eight clusters were obtained: two consisted exclusively of A. sativum L. var. ophioscorodon clones; four clusters grouped together both non-bolting and semi-bolting clones (all classified as var. sativum); the remaining two contained only non-bolting types. AFLP genotyping successfully differentiated var. ophioscorodon from var. sativum clones. Semi-bolters were not distinguished from the non-bolting clones. A K-clustering analysis generated similar outcomes. However, a model-based approach identified some heterogeneity within bolting accessions. Strict correlation between the geographical origin of clones and the clusters to which they belonged was not observed. The SACS content, important for the taste and the protective health benefits of the bulbs, was analysed for the whole set. Clones of two non-bolting clusters contained significantly greater amounts of SACSs than the remaining ones. The non-bolter and semi-bolter clusters produced low amounts of SACS, so they are not locally adopted genotypes. This is the first report on variation between alliin:methiin ratio. The ratio varied between clusters too. The analysis of SACS content provided some insight into the genetic basis of this important end-use trait, and this can be further used for efficient conservation of garlic genotypes.

Genetic structure of Eurasian and North American Leymus (Triticeae) wildryes assessed by chloroplast DNA sequences and AFLP profiles

Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve phylogenetic relationships between closely related species, with a curvilinear relationship expected between the proportion of shared bands and nucleotide substitution rate (D), up to about 0.100 D. The objective of this study was to compare D and phylogenetic relationships among 16 Leymus taxa, based on chloroplast DNA sequences and multi-locus AFLP genotypes. Estimates of chloroplast D between taxa were 0.002 and 0.013 within and among continental regions, respectively. Estimates of AFLP D between taxa were 0.076 and 0.093 compared within and between continental regions, respectively, versus 0.024 within taxa. Bayesian and neighbor-joining cluster analyses effectively separated all AFLP genotypes by species, but showed that North American L. ambiguus is a hybrid species with nearly equal contributions from sympatric L. cinereus and L. salinus taxa. Two hierarchical AFLP clades, containing six North American taxa and four Eurasian taxa, had more than 98% bootstrap confidence with 0.071 and 0.055 D among taxa. Three other Eurasian taxa clustered with 79% and 89% confidence, with up to 0.79 D between taxa. These estimates provide benchmarks for phylogenetic comparisons of AFLP profiles, but three taxa could not be reliably grouped, which may reflect concurrent radiation of multiple lineages or lack of homologous AFLP characters caused by a high D.

A cryptic heterogametic transition revealed by sex‐linked DNA markers in Palearctic green toads

In sharp contrast to birds and mammals, most cold-blooded vertebrates have homomorphic (morphologically undifferentiated) sex chromosomes. This might result either from recurrent X-Y recombination (occurring e.g. during occasional events of sex reversal) or from frequent turnovers (during which sex-determining genes are overthrown by new autosomal mutations). Evidence for turnovers is indeed mounting in fish, but very few have so far been documented in amphibians, possibly because of practical difficulties in identifying sex chromosomes. Female heterogamety (ZW) has long been established in Bufo bufo, based on sex reversal and crossing experiments. Here, we investigate a sex-linked marker identified from a laboratory cross between Palearctic green toads (Bufo viridis subgroup). The F(1) offspring produced by a female Bufo balearicus and a male Bufo siculus were phenotypically sexed, displaying an even sex ratio. A sex-specific marker detected in highly reproducible AFLP genotypes was cloned. Sequencing revealed a noncoding, microsatellite-containing fragment. Reamplification and genotyping of families of this and a reciprocal cross showed B.siculus to be male heterogametic (XY) and suggested the same system for B.balearicus. Our results thus reveal a cryptic heterogametic transition within bufonid frogs and help explain patterns of hybrid fitness within the B.viridis subgroup. Turnovers of genetic sex-determination systems may be more frequent in amphibians than previously thought and thus contribute to the prevalence of homomorphic sex chromosomes in this group.

Does sex make a difference? Genetic diversity and spatial genetic structure in two co-occurring species of Gagea (Liliaceae) with contrasting reproductive strategies

Gagea lutea and G. spathacea are spring geophytes naturally co-occurring in woodlands, characterised by contrasting reproductive strategies probably caused by divergent ploidy levels. The hexaploid G. lutea relies on vegetative reproduction by subterranean bulbils in young stages but completely switches to sexual reproduction once a certain bulb size is attained. The nonaploid G. spathacea seems to be sterile and reproduces only vegetatively; the plants continue to form bulbils even in the rare event of flowering. This study used AFLP genotyping to investigate the consequences of these reproductive strategies for genetic diversity. For 150 and 100 samples from three Western Pomeranian populations of G. lutea and G. spathacea, respectively, AFLP fingerprints were analysed for three different spatial scales, the patch, the transect, and the region. Applying a threshold for genotypic identity of <0.05 simple matching distance, 22–30 genets were detected in the three G. lutea populations, with all genets confined to single populations. Clonal genets consisted of 2–9 samples and extended over up to 28 m, but never occupied the whole length of a transect; 67–75% of all patches had different genets. Genetic distances between genets within populations were similar to those recorded between populations. Genotyping of G. spathacea revealed a single clonal genet for all three populations sampled within a distance of 30 km. The absent genetic diversity confirms the suspected sexual sterility. Gagea spathacea seems to be one of the few non-apomictic, fully clonal vascular plants able to occupy a significant range solely by dispersal of vegetative diaspores.

Antifungal susceptibility, serotyping, and genotyping of clinicalCryptococcus neoformansisolates collected during 18 years in a single institution in Madrid, Spain

We studied the serotypes, mating-types, AFLP genotypes, and antifungal susceptibility of 58 Cryptococcus neoformans strains causing 56 episodes of cryptococcosis in 55 patients over an 18-year period in a single institution. The underlying conditions of the patients were classified as HIV infection (n = 48) or non-HIV-related immunodeficiency (n = 7). Serotype A (n = 34; 58.9%) predominated, but serotype AD was involved in 23.2% of episodes. Most of the episodes were caused by mating-type α (n = 41; 73.2%) or α/a strains (n = 12; 21.5%). The most common genotype was AFLP1 (n = 26; 44.8%), followed by AFLP3 (n = 21; 36.2%), and AFLP2 (n = 11; 19.0%). In two different patients, we showed the coexistence of different serotypes and/or genotypes in the same episode (AFLP1 and 3). The new triazoles voriconazole, posaconazole and isavuconazole showed high and similar antifungal activity (MICs ≤ 0.125 μg/ml). Fluconazole also had good antifungal activity, but two strains from patients with HIV-infections had an MIC of 16 μg/ml (3.4%). However, these two isolates remained very susceptible to the new triazoles (MICs ≤ 0.062 μg/ml). The remaining strains always showed MICs ≤ 8 μg/ml.

Host resistance mediated inter-genotype competition and temporal variation in Fusarium oxysporum f. sp. vasinfectum

Temporal variation in Fusarium oxysporum f. sp. vasinfectum (Fov) populations was determined by comparing the genetic diversity of pathogen isolates recovered from three consecutive cotton crops (2002, 2004 and 2006) in the Boggabilla area of New South Wales, Australia. A total of 288 isolates were collected, among which 25 distinct AFLP genotypes were identified. These genotypes were classified into two main groups corresponding to known vegetative compatibility groups (VCG)—01111 and 01112. The Fov populations were dominated by four genotypes (I-A, I-B, II-A, II-B) that accounted for 87.5% of the isolates. Significant temporal variation was observed in both sampled fields with 6.8% and 10.7% of total genetic variation being attributed to differences among collections in different years. Genetic diversity based on Nei’s gene diversity and the Shannon-Wiener index increased over time. Significant changes in the frequency of the dominant Fov genotypes were observed in one field, where genotype I-A declined from 84.8% to 40.0% over the study period (2002–2006), while genotype I-B increased from 7.6% to 35.4%. Strong inter-genotype competition was detected in glasshouse bioassays with 93.4% of symptomatic plants sampled from dual inoculation trials being infected by single genotypes. Competition was differentially mediated by cotton cultivars as the competitive ability of pathogen genotype I-B was enhanced on the resistant cultivar Sicot 189 relative to the susceptible cultivar Siokra 1–4. This suggests that host-mediated inter-genotype competition may play an important role in temporal variation in Fov populations in the field.

Biochemical and molecular characterization of Cronobacter spp. (formerly Enterobacter sakazakii) isolated from foods

The aim of this study was to identify and characterize Cronobacter spp. isolated from a range of foods. A total of 71 Cronobacter strains were isolated from 602 foods in our laboratory. The highest contamination was observed in foods of plant origin, e.g. spices, teas, chocolate, nuts, pastries and vegetables. On the basis of genus and species identification performed using genus-specific PCR, 16SrRNA sequencing and AFLP genotyping, most of the strains belonged to Cronobacter sakazakii. Biochemical profiling by the tests included in API20E, complemented with relevant additional tests, classified the strains into 13 biogroups. AFLP genotyping facilitated discrimination of six main groups at the 70% similarity level and strain grouping correlated clearly with species identification. Our results indicate that molecular typing by AFLP may be applied as a useful tool not only for direct comparison of Cronobacter isolates, providing traceability, but also for the reliable species classification. Moreover, tracing of these bacteria in a wider variety of foods should be important to enhance the knowledge of their transmission.

Extended and global phylogenetic view of the Bacillus cereus group population by combination of MLST, AFLP, and MLEE genotyping data

The Bacillus cereus group of bacteria includes species that can cause food-poisoning or spoilage, such as B. cereus, as well as Bacillus anthracis, the cause of anthrax. In the present report we have conducted a multi-datatype analysis using tools from the HyperCAT database ( http://mlstoslo.uio.no/) that we recently developed, combining data from multilocus sequence typing ( Tourasse et al., 2010), amplified fragment length polymorphism, and multilocus enzyme electrophoresis typing techniques. We provide a comprehensive snapshot of the B. cereus group population, incorporating 2213 isolates including 450 from food and dairy products, in the form of both phylogenetic supertrees and superclusters of genetically closely related isolates. Our main findings include the detection of phylogenetically separated groups of isolates possibly representing novel evolutionary lineages within the B. cereus group, a putative new branch of B. anthracis, as well as new groups of related strains containing both environmental and clinical isolates. In addition, the multi-datatype analysis revealed to a larger extent than previously recognized that food-borne isolates can share identical genotyping profiles with strains from various other origins. Altogether, the global analysis confirms and extends the results underlining the opportunistic nature of B. cereus group organisms, and the fact that isolates responsible for disease outbreaks and contamination of foodstuffs can originate from various genetic backgrounds.

Divergent selection in trailing- versus leading-edge populations of Biscutella laevigata

Knowledge on how climate-induced range shifts might affect natural selection is crucial to understand the evolution of species ranges. Using historical demographic perspectives gathered from regional-scale phylogeography on the alpine herb Biscutella laevigata, indirect inferences on gene flow and signature of selection based on AFLP genotyping were compared between local populations persisting at the trailing edge and expanding at the leading edge. Spatial autocorrelation revealed that gene flow was two times more restricted at the trailing edge and genome scans indicated divergent selection in this persisting population. In contrast, no pattern of selection emerged in the expanding population at the leading edge. Historical effects may determine different architecture of genetic variation and selective patterns within local populations, what is arguably important to understand evolutionary processes acting across the species ranges.