AFLP Genotypes Research Articles

Genetic polymorphism in waxweed (Red Book of the Russian Federation) in North-West Russia

BACKGROUND: Waxweed (Myrica gale L.) is a protected plant species found in the Russian Federation only in the Leningrad Region and Karelia. It is almost not studied from the genetic point of view. This species is presumably hexaploid; it propagates mainly vegetatively, and the role of sexual reproduction in the life cycle of waxweed is unclear. All waxweed populations in the Russian Federation are small and belong to the edge ones (occupy the easternmost positions in the range). AIM: The aim of the study is to investigate genomic DNA polymorphism in waxweed populations in the Russian Federation, and to evaluate the role of sexual reproduction in propagation and dispersal of this species. MATERIALS AND METHODS: AFLP-analysis of waxweed genomic DNA in 6 natural populations (5 populations in the Leningrad Region, 1 in Karelia). Using 3 pairs of primers, we studied waxweed genomic polymorphism for 22 DNA fragments. RESULTS: Each of the studied waxweed populations is genetically polymorphic. Among 182 analyzed plants we distinguished 27 different AFLP-genotypes, two of which were common in all populations studied. Most of others AFLP genotypes (20) were represented just by a single plant or a couple of plants. Some of these rare AFLP genotypes are likely the results of mutation and/or recombination processes affecting the common AFLP genotypes. CONCLUSIONS: The role of sexual reproduction in waxweed propagation, although minor, is noticeable.

New insights regarding the taxonomy and phylogeography of Onobrychis montana DC. subsp. transsilvanica (Fabaceae)

Onobrychis montana DC. Subsp. transsilvanica (Simonk.) Jáv. (Fabaceae) is a plant taxon, endemic to the South-Eastern Carpathians, whose taxonomic status is treated inconsistently by the classic taxonomy based on morphological traits. In a previous study, by sequencing several chloroplast DNA regions and AFLP genotyping, we tried to elucidate the controversy concerning its taxonomic status in relation to the more widespread O. montana DC., and determined its phylogeographic structure within the Carpathians. The present study, based on DNA fingerprinting by seven SSR markers, brings more insights on this problematic taxon by conferring higher resolution and sub-clustering previously identified phylogeographic groups. However, the newly SSR genetic data are in agreement with molecular evidence revealed by AFLP and chloroplastic SNPs and do not support O. montana DC. Subsp. transsilvanica (Simonk.) Jáv. As a distinct species from O. montana DC.

P257 Amplified fragment length polymorphism fingerprinting supports the absence of correlation of genotype with clinical phenotype or source of the isolate in Aspergillus flavus infections

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PMObjectives Aspergillus flavus accounts for ∼ 10% of bronchopulmonary aspergillosis and is the second leading etiological agent of invasive aspergillosis worldwide. It is the commonest cause of fungal rhinosinusitis and ocular mycoses in tropical countries including India. We report amplified fragment length polymorphism genotyping of a set of clinical and environmental isolates to unravel the genetic diversity of A. flavus in India and to further determine correlation between isolate genotype and the source/clinical phenotype of the Aspergillus infection.MethodsTwo sets of morphologically identified isolates of A. flavus from clinical (n = 71) and environmental sources (n = 22) were included in the study using a stratified random sampling method. Clinical strains were isolated from lower respiratory tract specimens (n = 22), sinus and sino-nasal biopsies (n = 25), corneal samples (n = 12), and others (n = 12). Environmental strains were isolated from different niches like air, soil, and infected crop samples. Aspergillus fumigatus F145 was used as an out-group. DNA was extracted from the fungal broth culture following the method of Lee et al. AFLP was done as per an earlier described method using HpyCH41V and Mse1 (New England BioLabs) for restriction digestion followed by selective amplification of restriction-digested products with 1 mm HpyCH4 IV primer with one selective residue (5-Flu-GTA-GACTGCGTACCCGTC-3’), 1 mm MseI primer with four selective residues (5-GATGAGTCCTGACTAATGAA). Fingerprint data was analyzed in BioNumerics software version 7.6 (Applied Maths, Belgium). The phylogenetic tree was constructed using Pearson's Correlation coefficient. An AFLP genotype was assigned to a cluster using an arbitrary cut-off value of ≥90% fingerprint similarity. The distribution of genotypes among different categories was analyzed by Fisher's exact test or Pearson's χ 2 goodness of fit test with Yates correction factor as appropriate and two-tailed P-values of <.05 were considered statistically significant.ResultsThe analyses revealed a total of 16 AFLP genotypes with 5 major clusters (≥ 5 isolates) reflecting the extent of genetic diversity in A. flavus. Genotype VIII encompassed predominantly clinical isolates (P <.01) and genotype XI with majority of isolates from environmental sources (P <.0001). The strains which were isolated from invasive and non-invasive forms or from different sites (pulmonary, sinus, and ocular) did not diverge into separate or unique clusters. Although the genotypes had an asymmetric distribution in different clinical presentations as revealed by the χ2 goodness of fit test, none of the genotypes was exclusively responsible for causing a particular infection. Isolates from the north zone of India shared genotypes with those from the southern region of the country. Three isolates formed a separate genotype XVI and diverged from the A. flavus cluster by 42% fingerprint similarity. Partial β-tubulin and calmodulin gene sequencing-based phylogeny reconstruction placed those three isolates in A. tamarii clade of the A. flavus species complex.Conclusions: This study suggests that every genotype of A. flavus has the potential of causing an allergic, non-invasive or invasive infection. Further, A. flavus sensu stricto was predominantly (97%) isolated from clinical specimens revealing the majority of infections/colonization are caused by this species compared to other members in the Flavi complex.

Comparative Study of the Genetic and Biochemical Variability of Polyscias filicifolia (Araliaceae) Regenerants Obtained by Indirect and Direct Somatic Embryogenesis as a Source of Triterpenes.

Polyscias filicifolia (Araliaceae) is broadly used in traditional medicine in Southeast Asia due to its antimicrobial, immunomodulating and cytotoxic activities. The main groups of compounds responsible for pharmacological effects are believed to be oleanolic triterpene saponins. However, Polyscias plants demonstrate relatively slow growth in natural conditions, which led to applying a developing sustainable source of plant material via primary (PSE), secondary (DSE) and direct somatic embryogenesis from DSE (TSE). The AFLP and metAFLP genotyping resulted in 1277 markers, amplified by a total of 24 pairs of selective primers. Only 3.13% of the markers were polymorphic. The analysis of variance showed that the PSE and TSE regenerants differed only in terms of root number, while the DSE plantlets differed for all studied morphological characteristics. Further, the chemical analysis revealed that oleanolic acid (439.72 µg/g DW), ursolic acid (111.85 µg/g DW) and hederagenin (19.07 µg/g DW) were determined in TSE regenerants. Our results indicate that direct somatic embryogenesis ensures the production of homogeneous plant material, which can serve as a potential source of triterpene compounds. Plants obtained via somatic embryogenesis could also be reintroduced into the natural environment to protect and preserve its biodiversity.

Oceanographic heterogeneity influences an ecological radiation in elasmobranchs

AbstractAimDuring ecological speciation, reproductive isolation is predicted to evolve between populations adapted to different biotic or abiotic environments despite the absence of geographical isolation. Regions of oceanographic heterogeneity (e.g. current interfaces, habitat transition zones, ecological gradients) are strong candidates for the presence of ecologically divergent natural selection, but their role in the radiation of elasmobranch species is yet to be tested. We used an integrative framework to assess the relative influence of oceanographic heterogeneity and geological history on the diversification of an elasmobranch genus.LocationGulf of California (GC) and Baja California Peninsula (BCP), Mexico.TaxonShovelnose guitarfish (genus Pseudobatos).MethodsWe sampled 210 Pseudobatos specimens from four distinct but physically connected oceanographic regions within the GC and in the BCP. We used genetic (mtDNA sequences and AFLP genotypes) and environmental (six oceanographic variables) datasets to clarify phylogenetic relationships, demographic history and evolutionary divergence among populations, and to test for associations between ecologically driven selection and reproductive isolation.ResultsPhylogenetic and population genetic evidence exposed five distinct lineages of Pseudobatos in the region, including four cryptic lineages in the GC. Phylogeographic analyses indicate a recent history of ecologically driven diversification associated with the Gulf's young oceanographic environment and its four ecologically discrete regions. This hypothesis was supported by seascape genetics, ecological niche modelling and by tests of selection.Main conclusionsWe propose an adaptive radiation for the genus Pseudobatos linked with habitat heterogeneity of the GC. Our study likely represents the first assessment of an ecological radiation in the highly diverse elasmobranch group. It capitalizes on the environmental and biogeographic settings of the GC to offer a new perspective about the application of integrative approaches to study divergent natural selection and diversification in the sea.

Genetic evidence of multiple introductions and mixed reproductive strategy in the peregrine earthworm Pontoscolex corethrurus

Pontoscolex corethrurus is a well-known invasive earthworm in tropical zone which is believed to have originated from the Guayana Shield in South America and was described as parthenogenetic. A recent phylogenetic study revealed four cryptic species in the P. corethrurus complex (L1, L2, L3 and L4), among them L1 was particularly widespread and was proposed as P. corethrurus sensu stricto. Here, our aims were to investigate the genetic variation of P. corethrurus L1 in its presumed native and introduced ranges and to examine its reproductive strategy. An extensive dataset of 478 cytochrome oxidase I gene (COI) sequences, obtained in specimens sampled all around the world, revealed a weak COI haplotype diversity with one major haplotype (H1) present in 76% of the specimens. Analyses of the genetic variation of 12 L1 populations were done using both nuclear (226 AFLP profiles) and mitochondrial (269 COI sequences) genetic information. The high AFLP genotype diversity at the worldwide scale and the fact that no genotype was shared among populations, allowed to reject the ‘super-clone’ invasion hypothesis. Moreover, a similar level of mean genetic diversity indices were observed between the introduced and native ranges, a pattern explained by a history of multiple introductions of specimens from different parts of the world. At last, occurrence of identical AFLPs genotypes (i.e. clones) in several population confirmed asexual reproduction, but recombination was also revealed by gametic equilibrium analysis in some populations suggesting that P. corethrurus L1 may have a mixed reproductive strategy.

The mitochondrial intergenic regions nad1-cob and cob-rps3 as molecular identification tools for pathogenic members of the genus Cryptococcus.

Cryptococcus spp. are fungal species belonging to Tremellomycetes, Agaricomycotina, Basidiomycota, and several members are responsible for cryptococcosis, one of the most ubiquitous human mycoses. Affecting mainly immunosuppressed patients, but also immunocompetent ones, the members of this genus present a high level of genetic diversity. In this study, two mitochondrial intergenic regions, i.e. nad1-cob and cob-rps3, were tested for the intra- or interspecies discrimination and identification of strains and species of the genus Cryptococcus. Phylogenetic trees were constructed based on individual and concatenated sequences from representative pathogenic strains of the Cryptococcus neoformans/Cryptococcus gattii complex, representing serotypes and AFLP genotypes of all newly introduced species of this complex. Using both intergenic regions, as well as the concatenated dataset, the strains clustered in accordance with the new taxonomy. These results suggest that identification of Cryptococcus strains is possible by employing these mitochondrial intergenic regions using PCR amplification as a quick and effective method to elucidate genotypic and taxonomic differences. Thus, these regions may be applicable to a broad range of clinical studies, leading to a rapid recognition of the clinical profiles of patients.

Distribution and tracking of Clostridium difficile and Clostridium perfringens in a free-range pig abattoir and processing plant

The presence and genetic diversity of Clostridium difficile and C. perfringens along the slaughtering process of pigs reared in a free-range system was assessed. A total of 270 samples from trucks, lairage, slaughter line and quartering were analyzed, and recovered isolates were toxinotyped and genotyped. C. difficile and C. perfringens were retrieved from 14.4% and 12.6% of samples, respectively. The highest percentage of positive samples for C. difficile was detected in trucks (80%) whereas C. perfringens was more prevalent in cecal and colonic samples obtained in the slaughter line (85% and 45%, respectively). C. difficile isolates (n = 105) were classified into 17 PCR ribotypes (including 010, 078, and 126) and 95 AFLP genotypes. C. perfringens isolates (n = 85) belonged to toxinotypes A (94.1%) and C (5.9%) and were classified into 80 AFLP genotypes. The same genotypes of C. difficile and C. perfringens were isolated from different pigs and occasionally from environmental samples, suggesting a risk of contaminated meat products.

A virulent clone of Devriesea agamarum affects endangered Lesser Antillean iguanas (Iguana delicatissima)

Infectious diseases affecting wildlife are drivers of global biodiversity loss. Here we report a bacterial threat to endangered wild reptiles. Since April 2011, a severe skin disease has affected free-ranging, endangered Lesser Antillean iguanas (Iguana delicatissima) on the French Caribbean island of Saint Barthélemy and we identified Devriesea agamarum as the causative agent. The presence of this bacterium was also demonstrated in healthy lizards (anoles) co-inhabiting the island. All isolates from the iguanas corresponded to a single AFLP genotype that until now has exclusively been associated with infections in lizard species in captivity. The clonal relatedness of the isolates and recent emergence of the disease suggest recent arrival of a virulent D. agamarum clone on the island. The presence of healthy but infected lizards suggests the presence of asymptomatic reservoir hosts. This is the first description of a bacterial disease that poses a conservation threat towards free-ranging squamates.

Recreational sandboxes for children and dogs can be a source of epidemic ribotypes of Clostridium difficile.

Different studies have suggested that the sand of public playgrounds could have a role in the transmission of infections, particularly in children. Furthermore, free access of pets and other animals to the playgrounds might increase such a risk. We studied the presence of Clostridium difficile in 20 pairs of sandboxes for children and dogs located in different playgrounds within the Madrid region (Spain). Clostridium difficile isolation was performed by enrichment and selective culture procedures. The genetic (ribotype and amplified fragment length polymorphism [AFLP]) diversity and antibiotic susceptibility of isolates was also studied. Overall, 52.5% (21/40) of samples were positive for the presence of C.difficile. Eight of the 20 available isolates belonged to the toxigenic ribotypes 014 (n=5) and 106 (n=2), both regarded as epidemic, and CD047 (n=1). The other 12 isolates were non-toxigenic, and belonged to ribotypes 009 (n=5), 039 (n=4), and 067, 151 and CD048 (one isolate each). Nevertheless, all isolates (even those of a same ribotype) were classified into different AFLP genotypes indicating non-relatedness. In conclusion, our results revealed the presence of epidemic ribotypes of C.difficile in children's and dog's sandboxes located nearby, which constitutes a major health risk.

Genetic diversity of common carp (Cyprinus carpio L.) strains breed in Poland based on microsatellite, AFLP, and mtDNA genotype data

The common carp (Cyprinus carpio L.) has a long-standing history in Polish pond aquaculture, which has given rise to a great number of local breeds, strains and hatchery populations. They are well adapted to their local conditions, play an important role for fisherman's livelihoods and embody valuable genetics for future breeding programs. Proper maintenance of animal genetic resources (AnGR) requires an appropriate strategy based upon the precise knowledge of their genetic structure. This study genetically characterizes 20 common carp strains breed in Poland alongside with wild carp from Onuma Lake in Japan. We study three different types of genetic markers including the 963 AFLP markers, a set of 11 microsatellite loci (STR) and DNA sequences of the mitochondrial control region (D-loop). Bayesian clustering analysis of microsatellite loci divided the studied strains into 17 distinct clusters. Using population assignment test 92.4% of carp individuals were correctly assigned to their strain of origin. Microsatellite and AFLP marker analysis have shown the moderate but significant level of genetic variation between strains (AMOVA 23% and 18.2% respectively). AFLP and STR analysis of genetic distances gave equivalent values and were positively correlated with high values of the Mantel test (r=0.553, n=20, p=0.001). Only two mtDNA haplotypes (H5 and H2) were detected in all studied carp strains with H2 being the most prevalent.This is the first comprehensive genetic research of common carp strains breed in Poland which provided crucial data for the national conservation strategy. This study means that this resource can now be placed within the context of similar studies worldwide allowing the further improvement and breeding work.

Variation in genome size in the Valeriana officinalis complex resulting from multiple chromosomal evolutionary processes

Polyploidy, aneuploidy and change in DNA content of monoploid genomes or chromosomes are the principal causes of the variation in genome size. We studied these phenomena in central-European populations of the Valeriana officinalis complex in order to identify mechanisms or forces driving its evolution. The complex comprises di-, tetra- and octoploid morphologically defined so-called taxonomic “types”. Within the study area there are also intermediate “transitional types” the existence of which hampers the application of traditional taxonomic concepts. We thus chose AFLP genotyping and admixture analyses to identify the genetic structuring of the material studied. Di- (2x), tetra- (4x) and octoploidy (8x) were confirmed as major ploidy levels. Major genetic clusters roughly corresponded to these ploidy levels (for K = 2: 2x- and 8x-clusters, for K = 4 with nearly identical probability: 2x-, 4x-, 8x- and unspecific clusters were identified), which further more significantly differed from each other in monoploid absolute genome size (mean 1Cx for 2x = 1.48 pg, 4x 1.29 pg, 8x 1.10 pg). Several individuals of all ploidy levels were admixed, particularly tetraploids. Relative genome size (the sample: standard DAPI fluorescence) was positively correlated with the proportion of the diploid genetic cluster shared by the tetraploids, indicating that hybridization caused the variation in genome size. This result is in accordance with the significant negative correlation of the genome size of tetraploids with their geographic distance to the diploids. However, remarkable intra-ploidy variation in relative genome size was recorded for all ploidy levels (1.14-fold in diploids, 1.28-fold in tetraploids, 1.19-fold in octoploids). We identified aneuploidy as an additional source of variation in genome size in the di- and tetraploids. The contribution of extra chromosomes to absolute genome size exceeded the observed variation within euploids in the diploids, whereas it was included in the regular variability in genome size recorded for the eutetraploids. Variation in monoploid genome size was recorded in polyploids but not in diploids, indicating that polyploids experienced higher dynamics in the evolution of their genomes. Finally, 38.0–63.2% of the total intra-ploidy variation in relative genome size occurred within populations. In conclusion, the Valeriana officinalis complex provides an example of variation in genome size due to four principal evolutionary forces: polyploidization, change in chromosome number and in DNA content of chromosomes and (secondarily) hybridization, but their relative importance differed among ploidy levels. Although the stability in the size of the monoploid genome in species is considered to be the standard case, we found great variability within populations suggesting that genome size is variable even within narrowly defined taxa.

Population Structure of a Widespread Species under Balancing Selection: The Case of Arbutus unedo L.

Arbutus unedo L. is an evergreen shrub with a circum-Mediterranean distribution that also reaches the Eurosiberian region in northern Iberia, Atlantic France, and a disjunct population in southern Ireland. Due to the variety of climatic conditions across its distribution range, the populations of A. unedo were expected to display local adaptation. Conversely, common garden experiments revealed that diverse genotypes from a range of provenances produce similar phenotypes through adaptive plasticity, suggesting the action of stabilizing selection across its climatically heterogeneous range. Nonetheless, since a uniform response might also result from extensive gene flow, we have inferred the population structure of A. unedo and assessed whether its extended and largely one-dimensional range influences gene flow with the help of AFLP genotypes for 491 individuals from 19 populations covering the whole range of the species. As we had anticipated, gene flow is restricted in A. unedo, providing further support to the hypothesis that stabilizing selection is the most likely explanation for the homogeneous phenotypes along the range. The Euro-Siberian populations were not particularly isolated from the Mediterranean. Instead, there was a distinct genetic divide between the populations around the Mediterranean Sea and those sampled along Atlantic coasts from northern Africa up to Ireland. This genetic structure suggests the action of historic rather than biogeographic factors as it seems consistent with a scenario of independent glacial refugia in the Atlantic and Mediterranean portions of the range of A. unedo. Genetic exchange was likewise restricted within each set of populations. Nevertheless, isolation-by-distance (IBD) was stronger, and FST increased faster with distance, along the Atlantic, suggesting that gene flow might be larger among Mediterranean populations. Genetic diversity was significantly lower in NW Iberia and Ireland than in other populations whereas Ireland was more closely related to populations in NW Iberia than to a population in Atlantic France, suggesting a postglacial stepping-stone colonization of the Atlantic coast. Altogether, our results show that stabilizing selection is able to homogenize the phenotypic response even when population structure is strong, gene flow is constrained, and the phylogeographic past is complex.

Social and environmental influences on tartary buckwheat (Fagopyrum tataricum Gaertn.) varietal diversity in Yunnan, China

Effective conservation strategies aimed to protect crop genetic resources require multiple sources of information. We used a combination of AFLP genotyping and farmer surveys to understand the extent, distribution and management of tartary buckwheat (Fagopyrum tataricum Gaertn.) diversity in its center of origin in Yunnan Province, China. We found genetic evidence of gene flow in tartary buckwheat throughout the study area, with small but statistically significant regional and village-level components. We also found genetic differentiation by seed color. Although most farmers reported exchanging seed in localized kinship networks, our results imply homogenizing gene flow is occurring. Yi ethnic farmers tend to plant more buckwheat than non-Yi farmers, and we found that in some communities, Yi farmers serve as seed sources for farmers of other ethnicities. Different tartary buckwheat varieties did not have different end uses; rather farmers maintained varietal diversity in order to protect crop yield and quality. Individual farmers’ seed exchange practices reflect their ideas about components of seed quality, as well as priorities in protecting buckwheat yield. From the standpoint of genetic resources conservation, the presence of a culturally rich farmer exchange network and hierarchical structuring of tartary buckwheat genetic diversity demonstrates the importance of maintaining an interlinked community of tartary buckwheat farmers in Yunnan.

Glacial survival in northern refugia? Phylogeography of the temperate shrubRosa pendulinaL. (Rosaceae): AFLP vs. chloroplast DNA variation

Identification of postglacial migration patterns and localization of possible glacial refugia are the main tasks of phylogeographical studies. Analyses of AFLPs in the European temperate shrub Rosa pendulina L. provided an insight into this issue. Similarly to a previous study of chloroplast DNA (cpDNA) haplotype variation in this species, we detected two widely distributed groups of AFLP genotypes that probably contributed to the postglacial colonization of Central Europe. The first group comprises populations from most of the Alps, the Balkans, and the Apennines. The second group includes populations from the Carpathians, the Bohemian Massif, and part of the Alps. However, geographical delimitation of the contact zone between these two lineages was situated slightly southward from the zone defined by cpDNA haplotypes. This might reflect different dispersal abilities of seeds and pollen. Populations from the Iberian Peninsula represent a separate genetic subgroup within the Alpine–Balkan group that apparently did not contribute to the most recent postglacial expansion of the species. Indications for glacial survival (defined by higher-than-average frequency-down-weighted marker values) were identified in the Balkan Peninsula and in the Southern Alps. However, one population at the northern edge of the Alps and one in the Western Carpathians also possessed very high values. This finding might be an indication of full-glacial survival in these regions and points out the importance of the Carpathians for the historical distributional changes of R. pendulina.

Environmental sampling reveals that Pythium insidiosum is ubiquitous and genetically diverse in North Central Florida.

Pythiosis is a deadly disease of horses, dogs, and other mammals, including humans, in tropical and subtropical regions. In the United States, the disease has been reported in the Southeast as well as in the temperate North and the dry Southwest. The causal agent of pythiosis is Pythium insidiosum, one of few mammalian pathogens in the fungus-like Oomycetes. P. insidiosum has not been studied in the environment in the United States. Given anecdotal reports of pythiosis in Gainesville, Florida dogs, we hypothesized that warm standing water in lakes and ponds in North Central Florida is suitable habitat for P. insidiosum. We sampled 19 lakes or ponds to examine the environmental distribution of P. insidiosum and to determine which of the three previously described genetic clusters of P. insidiosum are present. We found P. insidiosum in 11 of the sampled lakes and ponds. Sequencing of the ITS region separated isolates into three genetic clusters, including a distinct group previously represented by a single isolate from South Carolina. AFLP genotyping of isolates showed genetic variation in Cluster I, which is the group associated with the majority of characterized clinical isolates from the Americas. Our results indicate that animal exposure to P. insidiosum in North Central Florida is common. This study provides the first evidence that P. insidiosum may be more widely distributed in freshwater lakes and ponds in the Southeastern United States than previously appreciated.

Population Structure and Development of Resistance to Hymexazol Among Fusarium solani Populations from Date Palm, Citrus and Cucumber

AbstractA study was conducted to investigate genetic diversity and sensitivity to hymexazol among 80 isolates of Fusarium solani complex obtained from date palm (30), citrus (31) and cucumber (19). Characterization based on sequences of the EF1α and ITS rRNA showed that isolates belong to F. solani complex MLST type 3 + 4. AFLP analysis produced 980 polymorphic loci, 80 AFLP genotypes and moderate levels of genetic diversity (H = 0.2494). Clustering of the isolates was not related to the host or the geographical origin of the isolates. Analysis of molecular variance (amova) indicated the existence of a low level of genetic differentiation among populations obtained from different hosts (Fst = 0.0162) and regions (Fst = 0.0066). This may provide evidence for frequent movement of inoculum among hosts and regions in Oman, which could be attributed to cultural practices employed by farmers. Isolates of F. solani displayed variation in sensitivity to hymexazol, with EC50 values ranging from 2 to 5745 μg/ml (mean = 878 μg/ml); 19% of the isolates have an EC50 value of more than 1000 μg/ml. Findings are discussed in terms of the factors that affect diversity in F. solani isolates. The study reports for the first time the development of resistance to hymexazol among F. solani isolates from date palm, citrus and cucumber.

Phylogenetic relationships in the extreme polyploid complex of the New Zealand genus Leptinella (Compositae: Anthemideae) based on AFLP data

AbstractAFLP fingerprinting for 236 individuals from 75 populations and 31 taxa of the Southern Hemisphere genus Leptinella (Compositae: Anthemideae) was carried out in order to infer the evolutionary relationships among the New Zealand representatives of the genus and to compare the results with sequence–based phylogenetic reconstructions for the genus. The New Zealand–based clade of the genus is characterised by the formation of an impressive polyploid complex with ploidy levels reaching from 4x to 24x. We observe a tripartition of taxa into species groups that correspond to species assemblages also found in the sequence–based reconstructions: A basal, presumably paraphyletic stock of tetraploid species (AFLP cluster A) corresponding to the morphologically defined Leptinella subg. Radiata is connected through one of its sub–clusters (A1, the L. minor group) with a monophyletic group of two clusters (B and C) with a sister–group relationship. While AFLP cluster B remained on the tetraploid level, clusters A and C form ploidy series reaching the levels of 16x and 24x, respectively. The lack of intermediate AFLP genotypes demonstrates that polyploidisation has occurred independently in the two clusters forming the L. pectinata/L. pyrethrifolia assemblage (cluster A2) in L. subg. Radiata and the L. dioica assemblage (clusters C1 and C2) in L. subg. Leptinella. The joint consideration of sequence–based reconstructions and AFLP fingerprint patterns further allows the formulation of an evolutionary hypothesis for the genus that tries to explain differentiation processes in a temporal and geographic framework: The available data argue for a Late Miocene (ca. 5–10 Ma) establishment of Leptinella in New Zealand and its further differentiation on the tetraploid level throughout the Pliocene and the Early Pleistocene, followed by extensive polyploidisation cycles caused by the climatic oscillations of the Pleistocene.

Influence of Neighbouring Tree Species on AFLP Variants of EndangeredPicea chihuahuanaMartínez Populations on the Sierra Madre Occidental, North-Western Mexico

ABSTRACT: Plant-plant interactions, which are defined as the effect of one plant on another of the same or different species, are inherently local in nature. Plants interact in both positive and negative ways, which are governed by the same underlying ecological dynamic processes. The Mexican endemic Picea chihuahuana Martinez is a largely untouched tree species and it is therefore an excellent model for estimating genetic potential of plant-plant interactions under natural conditions. Because of the scarce research examining plant-plant interactions at the genetic level, we tested the hypothesis that specific genetic variants of P. chihuahuana are associated with (and likely selected by) the presence of particular neighbouring tree species. To explore this question, we applied AFLP genotyping to five P. chihuahuana populations in the State of Durango, North-western Mexico. Under the assumption that the variables genetic variant of P. chihuahuana and nearest-neighbour tree species are directly related to ...

Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish

Phylogenetic analyses of rapid radiations are particularly challenging as short basal branches and incomplete lineage sorting complicate phylogenetic inference. Multilocus data of presence-absence polymorphisms such as obtained by AFLP genotyping overcome some of the difficulties, but also present their own intricacies. Here we analyze >1000 AFLP markers to address the evolutionary history of the Limnochromini, a cichlid fish lineage endemic to Lake Tanganyika, and to test for potential effects of outgroup composition on tree topology. The data support previous mitochondrial evidence on the tribe’s taxonomy by confirming the polyphyly of the genus Limnochromis and – in contradiction to a recent taxonomic revision – nesting the genus Greenwoodochromis within the Limnochromini. Species relationships suggest that ecological segregation occurred during the rapid basal radiation of the Limnochromini. The large phylogenetic distance between candidate outgroup taxa and the Limnochromini radiation caused random outgroup effects. Bootstrap support for ingroup nodes was lower in outgroup-rooted than in midpoint-rooted trees, and root positions and ingroup tree topologies varied in response to the composition of the outgroup. These observations suggest that the predisposition for homoplastic evolution makes AFLP-based phylogenetic analyses particularly susceptible to random biases introduced by too-distant outgroup taxa.