Amplified Fragment Length Polymorphism Data Research Articles

Disentangling Relationships among the Alpine Species of Luzula Sect. Luzula (Juncaceae) in the Eastern Alps

Polyploidisation, agmatoploidy and symploidy have driven the diversification of Luzula sect. Luzula. Several morphologically very similar species with different karyotypes have evolved, but their evolutionary origins and relationships are unknown. In this study, we used a combination of relative genome size and karyotype estimations as well amplified fragment length polymorphism (AFLP) fingerprinting to investigate the relationships among predominately (sub)alpine Luzula alpina, L. exspectata, L multiflora and L. sudetica in the Eastern Alps, including also some samples of L. campestris and L. taurica as outgroup. Our study revealed common co-occurrence of two or three different ploidies (di-, tetra- and hexaploids) at the same localities, and thus also common co-occurrence of different species, of which L. sudetica was morphologically, ecologically and genetically most divergent. Whereas agmatoploid L. exspectata likely originated only once from the Balkan L. taurica, and hexaploid L. multiflora once from tetraploid L. multiflora, the AFLP data suggest multiple origins of tetraploid L. multiflora, from which partly agmatoploid individuals of L. alpina likely originated recurrently by partial fragmentation of the chromosomes. In contrast to common recurrent formation of polyploids in flowering plants, populations of agmatoploids resulting by fission of complete chromosome sets appear to have single origins, whereas partial agmatoploids are formed recurrently. Whether this is a general pattern in Luzula sect. Luzula, and whether segregation of ecological niches supports the frequent co-occurrence of closely related cytotypes in mixed populations, remains the subject of ongoing research.

Molecular Characterization of Olive (Olea europaea L.) Cultivars in Duhok Governorate

The olive tree (Olea europaea L.) was considered one of the most cultivated crops in the Mediterranean region, and it had an economically important value due to it began consumed as a table olive and oil production. In this study, AFLP and SRAP techniques were used to identify 15 cultivars of olive plants that were collected from 12 different locations in the Duhok governorate, eleven primer combinations of sequence-related amplified polymorphism (SRAP) and ten primer combinations of amplified fragment length polymorphism (AFLP) were used to fingerprinting these cultivars. The results show that the SRAP marker had the least genetic distance 0.241between (Shtla falay olive and Khodeiri olive) and the highest value 0.946 was found between (Zawita olive and Sorani olive). While AFLP marker show the lowest value of 0.107 between (Nzarky olive and Dger olive) and the highest value of 0.916 between (Amedi olive and Shtla falay olive). Cluster analysis based on AFLP and SRAP combined data clearly differentiated the genotype and it showed it was a powerful tool to evaluate the genetic distance and fingerprinting of these tested cultivars. Establishing the genetic relationships between cultivars and species, and the construction of genetic maps, had the main aims for the researchers in plant breeding programs and to understand the plant evolution lingues, and as a conclusion, this study demonstrates that AFLP and SRAP markers both are powerful tools in plants tree genetics.

AFLP-Based Genetic Structure of Lithuanian Populations of Small Balsam (Impatiens parviflora DC.) in Relation to Habitat Characteristics

Currently, there is an increasing focus on understanding the interactions between genetic features of the invader and environmental factors that ensure the success of invasion. The objective of our study was to evaluate the genetic diversity of Lithuanian populations of highly invasive small balsam (Impatiens parviflora) by amplified fragment length polymorphism (AFLP) markers and to relate molecular data to biotope features defined by employing neighboring species of herbaceous plants. Low polymorphism of I. parviflora populations was observed at AFLP loci. Hierarchical analysis of molecular variance did not reveal differentiation of populations depending on biotope, geography, or road types. Bayesian analyses of AFLP data demonstrated many genetic clusters. Our results suggest multiple introductions of I. parviflora into Lithuania. The polymorphism of AFLP loci of populations significantly correlated with the total coverage by herbaceous plants in the sites. Defined by principal component analysis, the variability of study sites was most related to the coverage of herbaceous plants and least related to the molecular features of I. parviflora populations. The sites with I. parviflora were classified into agricultural scrubland, riparian forest, and urban forest biotopes. Of them, urban forest was distinguished by the highest coverage of I. parviflora and the lowest Ellenberg indicatory values for light, soil acidity, and richness in nutrients.

Impact of Quaternary climatic oscillations on phylogeographic patterns of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps

AbstractAimThe Balkan Peninsula has served as source for the colonisation of large parts of Europe after the Pleistocene, but the processes driving the intraspecific diversification within the Balkan Peninsula are much less understood. To fill this gap, we investigated the phylogeography and evolutionary history of three habitat‐segregated Cerastium taxa endemic to the Dinaric Alps and explored whether they responded differently to the Quaternary climatic oscillations in the Balkan Peninsula.LocationEurope, Balkan Peninsula, Dinaric Alps.TaxonCerastium (Caryophyllaceae, angiosperms).MethodsWe combined climatic niche comparisons and species distribution modelling (SDM) on the one hand, with cytological (relative genome size, RGS) and genetic / genomic approaches such as amplified fragment length polymorphism (AFLP) fingerprinting, phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and plastid (trnT–ndhJ) sequences on the other hand, in order to investigate how the Pleistocene glaciations and the Holocene warming influenced the phylogeographic structure of the studied taxa. SDM was used to reconstruct past, present and future habitat suitability.ResultsDespite nonequivalent climatic niches, we detected climatic niche similarity amongst the three Cerastium taxa. Nonhierarchical K‐means clustering of AFLP data revealed an optimal split into two geographically segregated groups in all three taxa. Genetic divergence between the northwestern and the southeastern populations can be explained by isolation in northern and southern refugia, as suggested by SDM. The ITS and plastid sequences revealed similar, although more complex, patterns of genetic differentiation, and RGS differentiation was mainly geography‐correlated.Main conclusionsDespite the pronounced habitat segregation amongst the studied taxa, their overall phylogeographic structure is similar, suggesting comparable underlying processes and similar responses to the same historical events. However, we anticipate that the three taxa will respond differently to ongoing climate warming.

Biogeography of amphi-adriatic Gentianella crispata (Gentianaceae): a northern refugium and recent trans-adriatic migration

The Balkan Peninsula as one of Europe’s biodiversity hotspots came into the focus of biogeographic research during the last decade, but the phylogeography of its mountain flora still remains widely unexplored. To investigate historical and future range dynamics within Gentianella crispata, a typical plant of mountainous grasslands sub-endemic to the Balkan Peninsula with a single known population in southern Italy, we combine molecular analyses based on cpDNA sequence and amplified fragment length polymorphism data with species distribution models. In the western Balkan, we found a distinctly separated cluster at the northern edge of the species’ distribution range. The split towards the less structured southern populations is located at the Neretva canyon, a pattern repeatedly reported before. This finding is clearly in line with the refugia-within-refugia hypothesis assuming more than one Pleistocene refugium on the Balkan Peninsula. The Italian population was found to be closely related to populations in the central to southern Dinaric mountains indicating a recent, possibly human-mediated migration event. Niche models for future climate scenarios forecast a severe loss of climatically suitable areas, especially in the southern parts of the range, pointing at deteriorating effects of climate warming for those mountainous grassland habitats in southern Europe, which harbour G. crispata.

Hybridization in the Temperate Bamboos (Poaceae: Bambusoideae: Arundinarieae): A Phylogenetic Study Using AFLPs and cpDNA Sequence Data

Abstract—The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis on Arundinaria of North America and its allies in East Asia (the Arundinaria clade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, including Hibanobambusa, Sasaella, and Semiarundinaria. Evidence also indicated that Pseudosasa japonica (the type species of Pseudosasa) is an intergeneric hybrid involving Pleioblastus and Sasamorpha. In addition, cryptic hybrids were detected within and among Pleioblastus, Sasa, and Sasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in the Arundinaria clade, including Pleioblastus sensu stricto, Sasa s. s., and Sasamorpha. AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.

A New Variety of Dianthus anatolicus (Caryophyllaceae) from Turkey as Evidenced by Morphology and AFLP Data

Dianthus anatolicus var. afyonensis Ugurlu, M. Koch & Donmez var. nova is described from central Turkey (Cay, Afyonkarahisar). It is morphologically different from D. anatolicus by stem, leaf and calyx length, and the shape of epicalyx scales and petals. We also used amplified fragment length polymorphism (AFLP) data to identify and circumscribe the new variety. Habitat, ecology and the conservation status of the new variety are described.

Phylotype and sequevar determination and AFLP fingerprinting of Ralstonia solanacearum strains causing bacterial wilt of potato in southeastern Iran

Bacterial wilt of potato caused by Ralstonia solanacearum is a severe threat to potato cultivation in Kerman province, located in southeastern Iran and the third largest potato producer in the country. The present study intends to determine the precise phylogenetic position, sequevar, and genetic diversity of R. solanacearum strains associated with the disease. To this end, the major potato-growing regions of the province (Jiroft and Laleh Zaar) were surveyed to collect tuber samples from affected potato plants showing typical wilt symptoms. Twenty-three strains were collectively purified and subjected to phenotypic and genotypic characterization. Biochemical tests showed that all the strains belonged to R. solanacearum biovar 2A. Furthermore, phylotype-specific multiplex polymerase chain reaction results indicated that the strains belonged to phylotype II. For sequevar typing as well as the determination of the phylotype subcluster (IIA/IIB), polymerase chain reaction amplicons of the endoglucanase precursor gene of 11 representative strains were sequenced. In phylogenetic analysis, the strains were grouped with the reference strains of phylotype IIB-1 retrieved from the GenBank. Then, to assess genetic diversity, 19 selected strains were subjected to genomic fingerprinting, i.e., amplified fragment length polymorphism (AFLP) using seven primer pair combinations. The AFLP data showed heterogeneity among the strains of R. solanacearum and were grouped into four clusters. With our knowledge, this is the first report of the phylotype, and sequevar determination (i.e., IIB-1) in addition to AFLP-based genomic fingerprinting of R. solanaceraum strains causing potato wilt in southeastern Iran.

Massive introgression weakens boundaries between a regionally endemic allopolyploid and a widespread congener

Polyploidy is a significant driver of plant diversity and is, along with homoploid hybridisation, widely accepted as a common and important evolutionary force in plants. Here, we employed Amplified Fragment Length Polymorphism (AFLP) fingerprinting, ploidy level and genome size determination via flow cytometry and morphometry in order to disentangle origin and evolutionary history of tetraploid Knautia norica, endemic to the eastern Central Alps in Austria. Our data clearly support parapatric diploid K. carinthiaca, endemic to a single mountain slope, as one of the parental species. The AFLP data as well as morphological evidence suggest co-occurring and widespread diploid K. arvensis as second parent. Allopolyploidisation has thus obviously contributed to the greater evolutionary success of K. norica, compared with its stenoendemic progenitor K. carinthiaca. There is strong evidence for recent massive introgression of morphologically divergent K. drymeia into K. norica, which might present a threat to the long-term persistence of the latter species due to genetic erosion.

Investigation of Genetic Diversity in Afghan Bread Wheat Genotypes Using SSR and AFLP Markers

Genetic diversity assessment is the principle component for conservation and characterization of germplasm. Genetic diversity study of Afghan bread wheat genotypes is a first step to identify and to select high performance genotypes and distribute to wheat breeding programs. The main objective of this study is to investigate of genetic diversity in 35 Afghan bread wheat genotypes by using Simple Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers. DNA extraction according to Cetyl Trimethyl Ammonium Bromide (CTAB) method was conducted and the total genomic DNA was isolated from each variety. Sixty-four SSR primer markers were used and eighteen EcoRI+(N)/MseI+(N) primer combinations with their primer sequences were used for selective polymerase chain reaction (PCR) amplification. Every SSR and AFLP fragment was scored as present (1) or absent (0) within all genotypes under study. Marker/ Value ratio of pairwise genetic distance between genotypes according to the SSRs data was from 0.508 to 0.691 with an average distance of 0.599. Relatively different grouping pattern in comparison to AFLP data observed through cluster analysis. Both types of molecular markers (AFLP and SSR) used in this research proved to be suitable for investigating genetic diversity in the genotypes of Afghan bread wheat, however, AFLP markers gave better view of genetically relationships among genotypes than the SSR markers. The grouping generated by AFLP data showed a special agreement with the origin regions of genotypes (Ariana-07 and Mazar-99 originating from the north of Afghanistan, Lalmi-03 and Kabul-02. Large number of DNA bands identified with AFLP markers might provide a better estimation of genetic similarity than those of SSR markers.

Polyphasic Discrimination of Trichophyton tonsurans and T. equinum from Humans and Horses.

The anthropophilic dermatophyte Trichophyton tonsurans and its zoophilic counterpart T. equinum are phylogenetically closely related. The barcoding marker rDNA internal transcribed spacer (ITS) shows limited variation between these two species. In the current study, we combined molecular approaches with phenotypic data to determine the species boundaries between T. tonsurans (n = 52) and T. equinum (n = 15) strains originating from humans (n = 40), horses (n = 26), and a mouse (n = 1). Culture characteristics and physiology on Trichophyton agar media 1 and 5 were evaluated. Multi-locus sequencing involving ITS, partial large rDNA subunit (LSU), β-tubulin (TUB), 60S ribosomal protein (RPB), and translation elongation factor-3 (TEF3) genes, and the mating-type (MAT) locus was performed. Amplified fragment length polymorphism data were added. None of the test results showed complete mutual correspondence. With the exception of strains from New Zealand, strains of equine origin required niacin for growth, whereas most strains from human origin did not show this dependence. It is concluded that T. tonsurans and T. equinum incompletely diverged from a common lineage relatively recently. MAT1-1 and MAT1-2 are the main distinguishing genes between the two species.

Genetic diversity and population structure in Cary’s Beardtongue Penstemon caryi (Plantaginaceae), a rare plant endemic to the eastern Rocky Mountains of Wyoming and Montana

Penstemon caryi is a narrow-range endemic angiosperm found primarily on sparsely vegetated limestone outcrops in the Bighorn and Pryor Mountains of north-central Wyoming and south-central Montana. A former candidate for listing under the Endangered Species Act, and currently a species of concern in these states, P. caryi is potentially threatened by habitat loss due to encroaching anthropogenic activities, such as limestone quarrying and road construction. In an effort to assess the capacity of P. caryi to withstand habitat loss and degradation, we used simple sequence repeats (SSRs) and amplified fragment length polymorphism (AFLP) markers to examine genetic diversity and differentiation of P. caryi populations from the Pryor Mountains of Montana and the southern Bighorn Mountains of Wyoming. Our analyses revealed overall moderate to high levels of genetic diversity in P. caryi, but with relatively lower levels of diversity in populations from the Pryor Mountains. There are fewer known individuals of Penstemon caryi in Montana, and because the examined populations from Montana exhibited less genetic diversity than those from Wyoming, populations from Montana may face an increased risk of population decline and extirpation. Both the AFLP and SSR data sets found population structure between different regions (Montana vs. Wyoming), while AFLP markers identified further subdivision between Wyoming populations. Despite moderate to high levels of genetic diversity, P. caryi is still a species at risk due to impending environmental stresses such as global climate change and human encroachment, which may be especially troublesome given its narrow distribution and the specificity of its habitat preferences.

AFLP protocol comparison for microbial diversity fingerprinting.

Over the last decade, several methods based on genomic DNA have been developed for the identification and genotyping of prokaryotic and eukaryotic organisms. These genomic methods differ regarding taxonomic range, discriminatory power, reproducibility, and ease of interpretation and standardization. The amplified fragment length polymorphism (AFLP) technique is a very powerful DNA fingerprinting technique for DNA of any source or complexity, varying in both size and base composition. In addition, this method shows high discriminatory power and good reproducibility allowing it to be efficient in discriminating at both the species and strain levels. The development and application of AFLP have allowed significant progress in the study of biodiversity and taxonomy of microorganisms. In the last years, the Applied Biosystems AFLP Microbial Fingerprinting Kit, now out of production, was widely used in various studies to perform AFLP characterization of selected bacteria strains (described by Vos et al. (Nucleic Acids Res 23(21):4407-4414, 1995)). Its replacement gives the possibility for laboratories to continue the use of the previous AFLP data as a reference for bacteria genetic fingerprinting analysis in biodiversity studies. To overcome this issue a result comparison, by using an improved AFLP protocol and the AFLP commercial kit, was performed. In particular, previous results on different species (Listeria monocytogenes, Lactobacillus plantarum, and Streptococcus thermophilus) obtained with the commercial kit were compared with the improved AFLP procedure to validate the protocol. When compared with the AFLP Microbial Fingerprinting Kit, the improved protocol shows high reproducibility, resolution, and overall, is a faster method with lower costs.

Distribution and Genetic Diversity of the Rare Plant Veratrum woodii (Liliales: Melanthiaceae) in Georgia: A Preliminary Study with AFLP Fingerprint Data

Veratrum woodii, a long-lived herbaceous perennial species, has a fragmented distribution with populations scattered in the southeastern and lower midwestern USA. In Georgia, the species has a protection status of rare. This preliminary study focused on verifying historic and/or unvouchered populations in Georgia and characterizing variation and genetic structure within and among all populations in the state. We analyzed AFLP (amplified fragment length polymorphism) data as dominantly inherited markers for 16 populations sampled from Georgia, Florida, and Missouri. Our results suggest that this species overall has relatively low levels of genetic diversity and that differentiation among populations is comparable to species with similar life history traits. Measures of genetic diversity, such as mean He, indicate that variation of populations has some partitioning between disjunct northern and southern Georgia (and Florida) populations. However, our analyses imply that watershed assignment, rather than geographic distance, provides a better explanation for variation and population structure. We hypothesize that southern relict populations in Georgia may have served as refugia during Pleistocene glaciations. We conclude that life-history characteristics, low levels of genetic variation, and suppression of ecological disturbance collectively jeopardize populations of Veratrum woodii in Georgia.

Phylogeography of western Mediterranean Cymbalaria (Plantaginaceae) reveals two independent long-distance dispersals and entails new taxonomic circumscriptions

The Balearic Islands, Corsica and Sardinia (BCS) constitute biodiversity hotspots in the western Mediterranean Basin. Oligocene connections and long distance dispersal events have been suggested to cause presence of BCS shared endemic species. One of them is Cymbalaria aequitriloba, which, together with three additional species, constitute a polyploid clade endemic to BCS. Combining amplified fragment length polymorphism (AFLP) fingerprinting, plastid DNA sequences and morphometrics, we inferred the phylogeography of the group and evaluated the species’ current taxonomic circumscriptions. Based on morphometric and AFLP data we propose a new circumscription for C. fragilis to additionally comprise a group of populations with intermediate morphological characters previously included in C. aequitriloba. Consequently, we suggest to change the IUCN category of C. fragilis from critically endangered (CR) to near threatened (NT). Both morphology and AFLP data support the current taxonomy of the single island endemics C. hepaticifolia and C. muelleri. The four species had a common origin in Corsica-Sardinia, and two long-distance dispersal events to the Balearic Islands were inferred. Finally, plastid DNA data suggest that interspecific gene flow took place where two species co-occur.

Analysis of Genetic Variation and Enhancement of Salt Tolerance in French Pea (Pisum Sativum L.).

Pisum sativum L. (field pea) is a crop of a high nutritional value and seed oil content. The characterization of pea germplasm is important to improve yield and quality. This study aimed at using fatty acid profiling and amplified fragment length polymorphism (AFLP) markers to evaluate the variation and relationships of 25 accessions of French pea. It also aimed to conduct a marker-trait associations analysis using the crude oil content as the target trait for this analysis, and to investigate whether 5-aminolevulinic acid (ALA) could enhance salt tolerance in the pea germplasm. The percentage of crude oil of the 25 pea genotypes varied from 2.6 to 3.5%, with a mean of 3.04%. Major fatty acids in all of the accessions were linoleic acid. Moreover, the 12 AFLP markers used were polymorphic. The cluster analysis based on fatty acids data or AFLP data divided the 25 pea germplasm into two main clusters. The gene diversity of the AFLP markers varied from 0.21 to 0.58, with a mean of 0.41. Polymorphic information content (PIC) of pea germplasm varied from 0.184 to 0.416 with a mean of 0.321, and their expected heterozygosity (He) varied from 0.212 to 0.477 with a mean of 0.362. The AFLP results revealed that the Nain Ordinaire cultivar has the highest level of genetic variability, whereas Elatius 3 has the lowest level. Three AFLP markers (E-AAC/M-CAA, E-AAC/M-CAC, and E-ACA/M-CAG) were significantly associated with the crude oil content trait. The response of the Nain Ordinaire and Elatius 3 cultivars to high salinity stress was studied. High salinity (150 mM NaCl) slightly reduced the photosynthetic pigments contents in Nain Ordinaire leaves at a non-significant level, however, the pigments contents in the Elatius 3 leaves were significantly reduced by high salinity. Antioxidant enzymes (APX—ascorbate peroxidase; CAT—catalase; and POD—peroxidase) activities were significantly induced in the Nain Ordinaire cultivar, but non-significantly induced in Elatius 3 by high salinity. Priming the salt-stressed Nain Ordinaire and Elatius 3 plants with ALA significantly enhanced the pigments biosynthesis, antioxidant enzymes activities, and stress-related genes expression, as compared to the plants stressed with salt alone. In conclusion, this study is amongst the first investigations that conducted marker-trait associations in pea, and revealed a sort of correlation between the diversity level and salt tolerance.

Analysis of genetic diversity evaluation of Lysiphyllum strychnifolium (Craib) A. Schmitz in Thailand using amplified fragment length polymorphism markers

Lysiphyllum strychnifolium (Craib) A. Schmitz, a Leguminosae-Caesalpiniodeae species, is colloquially known in Thai as Ya Nang Daeng. In Thai traditional medicine, the leaves, stems and roots have been used to relieve fever and alcohol toxication. The stem has also been used for anti-HIV-1 integrase, anti-allergy and anti-cancer treatment. Confusion over herbal drugs has arisen from the homonymity and morphological characteristics, which present many similarities within its family. Thus, germplasm collection and genetic diversity analysis are prerequisites for a breeding program. In this study, the amplified fragment length polymorphism (AFLP) marker was used to identify and elucidate the phylogenetic relationships among 98 accessions of Ya Nang Daeng throughout Thailand. Thirteen AFLP primer combinations generated 379 bands, of which 359 were polymorphic. The value of the similarity coefficient varied from 0.52 to 0.93, with a mean of 0.73. A phylogenetic tree was constructed using the unweighted major clusters at a cut-off genetic mean (UPGMA) clustering method. The phylogenetic tree derived from the AFLP data showed that the Ya Nang Daeng accessions could be divided into two clusters. Cluster 1 could be further classified into five subgroups, while a similarity coefficient of 0.23 could be used to separate an outgroup from Ya Nang Daeng. The result of principal coordinate analysis and morphological grouping corresponded to the UPGMA clustering. This study showed that the AFLP technique is a useful tool for estimating DNA polymorphism of the genetic diversity and differentiation of related plants. This genetic information will provide useful information for a breeding program in the future.

Ommatissus lybicus(Hemiptera: Tropiduchidae), an economically important pest of date palm (Arecaceae) with highly divergent populations

AbstractOmmatissus lybicusde Bergevin (Hemiptera: Tropiduchidae) is a key pest of date palm (Phoenix dactyliferaLinnaeus; Arecaceae) with worldwide distribution and various management strategies. To study genetic diversity of date palm hopper, a series of experiments was conducted on genetic structure and genetic diversity of 15 geographic populations ofO.lybicus(Abu Musa, Bam, Bushehr, Behbahan, Tezerj, Fin, Jiroft, Shahdad, Jahrom, Ghire Karzin, Ghasre Shirin, Iran; Pakistan; Oman; Egypt; and Tunisia) by amplified fragment length polymorphism, cytochromecoxidase subunit I (COI), and 28S rRNA markers. Analysis of molecular variance analysis of amplified fragment length polymorphism data and COI sequences revealed a significant variation amongO.lybicuspopulations (94.12% and 65.08% similarities for amplified fragment length polymorphism and COI, respectively). The 28S rDNA sequences from different populations were identical. Phylogenetic network inferred from amplified fragment length polymorphism data and COI sequences grouped two geographically close populations (Tezerj and Bam) in the two distinct clades while far apart geographical populations bunched in the same or close clades. These two populations experience repeated exposure to heavy pesticide applications annually. In conclusion, study of the genetic structure revealed a considerable variation betweenO.lybicuspopulations under intensive chemical strategies.

Genetic Differentiation and Population Genetic Structure of the Chinese Endemic Dipteronia Oliv. Revealed by cpDNA and AFLP Data

Dipteronia Oliv. is an endangered genus found in China with two species, D. sinensis and D. dyeriana. Previous morphological, cytogenetic, and molecular studies have suggested that D. dyeriana is a species related to D. sinensis. However, it is unclear how the two species diverged and whether gene flow exists between these two species. Here, we performed a molecular study at the population level to characterize genetic differentiation and decipher the phylogeographic history for Dipteronia species based on newly sequenced chloroplast DNA (cpDNA) and amplified fragment length polymorphisms (AFLP) date retrieved from our previous studies. No haplotype was shared between the two species in the cpDNA network. However, the phylogenetic analysis suggested that a haplotype found in D. sinensis (H4) showed a closer relationship with haplotypes of D. dyeriana. Based on our estimated time of divergence, these two cpDNA haplotype lineages of Dipteronia diverged at about 31.19 Ma. Furthermore, two genetic clusters with asymmetric gene flow were supported based on the structure analysis, which corresponded with the two Dipteronia species, and we also detected a low level of asymmetric gene flow between these two species according to the MIGRATE analysis using AFLP data. During the Last Glacial Maximum (LGM, c.21 kya BP), the genus’ predicted distribution was more or less similar to that at present, which was also supported by the mismatch analyses that showed no population expansion of the two Dipteronia populations after the LGM. The combined cpDNA and AFLP data revealed significant genetic differentiation between the two Dipteronia species with asymmetric gene flow, which can be explained by the varying phylogeographical histories of these two species.

Molecular diversity and allergenic profiles of Alternaria spp. from desert environments in Arizona

This study examined the genetic diversity of small-spored Alternaria species in the southwest desert of the USA by sampling 552 isolates from different habitats (soil and plant debris) in different locations (urban and an undisturbed desert). To estimate the genetic diversity, Amplified Fragment Length Polymorphism (AFLP) fingerprinting analysis was performed for all isolates. Strains representative of the sampled genotypic diversity (n = 125) were further characterized according their sporulation pattern and the capability to produce allergens. Morphological characterization assigned the majority of the strains to the Alternaria alternata and Alternaria tenuissima morpho-groups with only two isolates assigned to the Alternaria arborescens morpho-group. AFLP fingerprinting differentiated the A. arborescens morpho-groups, but could not distinguish between the A. alternata and A. tenuissima morpho-groups. Western blot analysis showed that a large number of allergenic proteins were produced by strains. These proteins were not specific for any morpho-group nor source of isolation. A hierarchical analysis of molecular variance was performed on the AFLP data to quantify molecular variation and partition this variation among sampled locations and habitat. No statistically significant differentiation among locations and habitat was detected indicating a lack of population structure across environments.