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Diversity Estimates (diversity + estimate)
Selected AbstractsVegetative Compatibility Among Isolates of Colletotrichum gloeosporioides from Yam (Dioscorea spp.) in NigeriaJOURNAL OF PHYTOPATHOLOGY, Issue 1 2004M. M. Abang Abstract Isolates of Colletotrichum gloeosporioides obtained from yam-based cropping systems in Nigeria, previously characterized on the basis of morphology, virulence and rDNA internal transcribed spacer (ITS) sequence variation were further compared for vegetative compatibility (VC). Chlorate-resistant nitrate non-utilizing (nit) mutants were generated from the isolates and used in complementation (heterokaryon) tests. Tests of VC between complementary mutants from different isolates indicated the presence of several genotypes within a single field, suggesting limited clonal spread. In some cases, isolates obtained from the same lesion were observed to belong to different vegetative compatibility groups (VCGs). No compatibility was observed between isolates of the highly virulent slow-growing grey (SGG), the moderately virulent fast-growing salmon (FGS) and the avirulent/weakly virulent fast-growing grey (FGG) strains. Forty-one C. gloeosporioides isolates belonged to 28 VCGs, giving a genotype diversity estimate of 0.68. This diversity confirmed the high variability of the pathogen population as revealed by previous characterization studies, however, a correlation between VCGs and isolate groupings based on morphology and virulence was not found. The finding that an isolate from weed was compatible with yam isolates indicated that transfer of important traits, such as virulence, may take place between isolates from yam and non-yam hosts. The VCG diversity revealed by this study suggests that in addition to asexual reproduction, sexual reproduction may play an important role in the epidemiology of anthracnose on yam. [source] Isolation and characterization of microsatellite markers from guineagrass (Panicum maximum) for genetic diversity estimate and cross-species amplificationPLANT BREEDING, Issue 1 2010A. Chandra With 1 figure and 1 table Abstract Guineagrass (Panicum maximum Jacq.) is one of the major forage grasses in tropical and semitropical regions, largely apomictic and predominantly exist as tetraploid. Non-availability of polymorphic molecular markers has been a major limitation in its characterization and improvement. We report isolation and characterization of microsatellites in P. maximum and cross-species results with other five Panicum species. Based on microsatellite-motifs, 15 functional and polymorphic simple sequence repeat (SSR) primer-pairs were designed, validated and employed in estimating genetic relationship among 34 guineagrass accessions. Thirteen primer-pairs amplified single locus and remaining two generated more than two loci with an average of 3.57 bands per locus amounts to 63 bands with 34 guineagrass accessions. Average expected heterozygosity (HE) of 0.35 (maximum 0.97) and observed heterozygosity (HO) of 0.37 (maximum 0.91) established the efficiency of developed markers for discriminating guineagrass accessions. Dice's similarity coefficients-based unweighted pair group with arithmetic average method-clustering supported with high bootstrap values (,40) indicated its significance and distinguished all accessions except IG97-93 and IG97-6. Utility of these new SSR loci in genetic diversity study of P. maximum and other cross,amplified species is discussed. [source] Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimatesENVIRONMENTAL MICROBIOLOGY, Issue 1 2010Victor Kunin Summary Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that the extent of rare microbial populations in several environments, the ,rare biosphere', is orders of magnitude higher than previously thought. One important caveat with this method is that sequencing error could artificially inflate diversity estimates. Although the per-base error of 16S rDNA amplicon pyrosequencing has been shown to be as good as or lower than Sanger sequencing, no direct assessments of pyrosequencing errors on diversity estimates have been reported. Using only Escherichia coli MG1655 as a reference template, we find that 16S rDNA diversity is grossly overestimated unless relatively stringent read quality filtering and low clustering thresholds are applied. In particular, the common practice of removing reads with unresolved bases and anomalous read lengths is insufficient to ensure accurate estimates of microbial diversity. Furthermore, common and reproducible homopolymer length errors can result in relatively abundant spurious phylotypes further confounding data interpretation. We suggest that stringent quality-based trimming of 16S pyrotags and clustering thresholds no greater than 97% identity should be used to avoid overestimates of the rare biosphere. [source] Effect of PCR amplicon size on assessments of clone library microbial diversity and community structureENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Julie A. Huber Summary PCR-based surveys of microbial communities commonly use regions of the small-subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using operational taxonomic unit (OTU)- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of c. 100, 400 and 1000 base pairs (bp) from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias and mispriming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities. [source] Distribution and frequency of , -thalassemia mutations in northwestern and central GreeceEUROPEAN JOURNAL OF HAEMATOLOGY, Issue 2 2003I. Georgiou Abstract: Objectives : , -Thalassemia is a common autosomal recessive disorder resulting from over 200 different mutations of the , -globin genes. The spectrum of , -thalassemia mutations in Greece has been previously described in the population of the capital city of Athens, or in , -thalassemia patients having transfusion therapy. The aim of the present study was to identify the distribution of the most common , -thalassemia mutations in the population of northwestern and central Greece. Methods : The data for this study were derived from a total of 1130 unrelated subjects including 46 , -thalassemia major, three , -thalassemia intermedia and 1081 carriers identified in our antenatal screening program. , -Thalassemia mutations were identified by ARMS, DGGE and Reverse Dot Blot. Results : The most common mutation, IVS-I-110, is followed, in order of frequency, by the mutations Cd-39, IVS-I-1, IVS-II-1, Cd-6, IVS-I-6, IVS-I-5, IVS-II-745, Cd-5 and 44 bp del. IVS-I-110 and Cd-39 frequencies are similar with those found in other Balkan countries. Significant differences in regional distribution were observed. The results showed a clear drift of the distribution of the most frequent IVS-I-110 mutation in the south,north (29.4, 40.0, 44.6 and 61.7%) and the east,west axis (31.8 and 44.6%). Conclusions : Population screening and prenatal diagnosis are significantly facilitated by these data. Furthermore, the detailed distribution tables of , -thalassemia mutations are essential for counseling and extraction of genetic diversity estimates for population genetic studies in other inherited disorders. [source] Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stressFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006Lau Chui Yim Abstract We report an assessment of whole-community diversity for an extremely isolated geothermal location with considerable phylogenetic and phylogeographic novelty. We further demonstrate, using multiple statistical analyses of sequence data, that the response of community diversity is not monotonic to thermal stress along a gradient of 52,83°C. A combination of domain- and division-specific PCR was used to obtain a broad spectrum of community phylotypes, which were resolved by denaturing gradient gel electrophoresis. Among 58 sequences obtained from microbial mats and streamers, some 95% suggest novel archaeal and bacterial diversity at the species level or higher. Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified. Shannon,Wiener diversity estimates suggest that mats at 63°C supported highest diversity, but when alternate models were applied [Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD)] that also take into account the phylogenetic relationships between phylotypes, it is evident that greatest taxonomic diversity (AvTD) occurred in streamers at 65,70°C, whereas greatest phylogenetic distance between taxa (VarTD) occurred in streamers of 83°C. All models demonstrated that diversity is not related to thermal stress in a linear fashion. [source] Genetic diversity and phylogeographic analysis of Pinus leiophylla: a post-glacial range expansionJOURNAL OF BIOGEOGRAPHY, Issue 9 2009Abril Rodríguez-Banderas Abstract Aim, Mexico is a centre of diversity for species of the genus Pinus, most of which have restricted geographical distributions. An exception is Pinus leiophylla Schiede and Deppe, which is widely distributed throughout most of Mexico's mountainous regions. We attempt to reconstruct the phylogeographic history of this species, in order to determine if its current broad distribution is associated with major events of environmental change that occurred during the Quaternary. Location, Coniferous forests in Sierra Madre Occidental, Eje Volcánico Transversal and Sierra Montañosa del Norte de Oaxaca, Mexico. Methods, A total of 323 individuals of both P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana sampled from 22 populations were screened for variation at six paternally inherited chloroplast DNA microsatellite markers (cpSSR). In addition to haplotypic diversity estimates and neutrality tests, the following clustering methods were employed: principal components analysis (PCA), analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), haplotype network and a technique similar to Croizat's panbiogeographical method of individual and generalized tracks. Results, The combination of mutations at the six microsatellites yielded a total of 92 different haplotypes. The percentage of shared haplotypes between varieties (P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana) was only 2.2%. The average haplotypic diversity for the species was H = 0.760. PCA and SAMOVA indicate the presence of four main genetic clusters. The estimated divergence time between the two most frequent haplotypes was between 75,000 and 110,000 years. Significantly large negative Fs values suggest that most of the sampled populations are currently expanding. Individual and generalized tracks identified three potential zones that may have harboured ancestral populations of P. leiophylla and from which the expansion of this species started, as well as two secondary contact zones between the two varieties. Main conclusions, The results indicate that one of the three potential areas hypothesized to have harboured ancestral populations of P. leiophylla may be related to the origin of P. leiophylla var. chihuahuana, while the other two may be related to the origin of P. leiophylla var. leiophylla. The current broad distribution of P. leiophylla is probably associated with its strong colonization ability. [source] Sampling within the genome for measuring within-population diversity: trade-offs between markersMOLECULAR ECOLOGY, Issue 7 2002S. Mariette Abstract Experimental results of diversity estimates in a set of populations often exhibit contradictory patterns when different marker systems are used. Using simulations we identified potential causes for these discrepancies. These investigations aimed also to detect whether different sampling strategies of markers within the genome resulted in different estimates of the diversity at the whole genome level. The simulations consisted in generating a set of populations undergoing various evolutionary scenarios which differed by population size, migration rate and heterogeneity of gene flow. Population diversity was then computed for the whole genome and for subsets of loci corresponding to different marker techniques. Rank correlation between the two measures of diversity were investigated under different scenarios. We showed that the heterogeneity of genetic diversity either between loci (genomic heterogeneity, GH) or among populations (population heterogeneity, PH) varied greatly according to the evolutionary scenario considered. Furthermore, GH and PH were major determinants of the level of rank correlation between estimates of genetic diversities obtained using different kinds of markers. We found a strong positive relationship between the level of the correlation and PH, whatever the marker system. It was also shown that, when GH values were constantly low during generations, a reduced number of microsatellites was enough to predict the diversity of the whole genome, whereas when GH increased, more loci were needed to predict the diversity and amplified fragment length polymorphism markers would be more recommended in this case. Finally the results are discussed to recommend strategies for gene diversity surveys. [source] Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism dataMOLECULAR ECOLOGY, Issue 5 2002M. M. Ribeiro Abstract We compared the genetic variation of Pinus pinaster populations using amplified fragment length polymorphism (AFLP) and chloroplast simple-sequence repeat (cpSSR) loci. Populations' levels of diversity within groups were found to be similar with AFLPs, but not with cpSSRs. The high interlocus variance associated with the AFLP loci could account for the lack of differences in the former. Although AFLPs revealed much lower genetic diversity than cpSSRs, the levels of among-population differentiation found with the two types of marker were similar, provided that loci showing fewer than four null-homozygotes, in any population, were pruned from the AFLP data. Moreover, the French and Portuguese populations were clearly differentiated from each other, with both markers. The Mantel test showed that the genetic distance matrix calculated using the AFLP data was correlated with the matrix derived from the cpSSRs. Because of the concordance found between markers we conclude that gene flow was indeed the predominant force shaping nuclear and chloroplastic genetic variation of the populations within regions, at the geographical scale studied. [source] Population genetic studies of Alouatta belzebul from the Amazonian and Atlantic ForestsAMERICAN JOURNAL OF PRIMATOLOGY, Issue 5 2008F.F. Nascimento Abstract Cytochrome b DNA sequence data (ca. 1,140,bp) of 66 Alouatta belzebul from the Amazonian and the Atlantic Forests of Brazil were used for phylogenetic reconstructions and population studies. Our sample consisted of 60 specimens from the Amazonian Forest (captured in 1984 and 1998 in Pará-PA state) and six specimens from the Atlantic Forest (Paraíba-PB state). We found 32 haplotypes, 23 in PA-1984 (with 12 present in more than one individual), 11 in PA-1998 (with two present in more than one individual), and a single haplotype in the PB sample. Animals from PA-1984 and PA-1998 shared three haplotypes while animals from Pará and Paraíba did not share any haplotype. We found 57 variable sites, consisting of 53 transitions and four transversions, with most replacements occurring at third codon position (77.19%) and less frequently at first and second positions (10.53 and 12.28%, respectively). Genetic distance between all haplotypes varied between 0 and 1.2%. Nucleotide diversity estimates between PA-1984 haplotypes and PA-1998 haplotypes were the same (,=0.01), and haplotype diversity estimates were very similar (h=0.96 and 0.93 for PA-1984 and PA-1998, respectively). Maximum parsimony, median-joining, split decomposition, and TCS showed that PA and PB haplotypes had not drastically diverged and that subsequent radiation within these regions was not apparent. No temporal structure was found between PA-1984 and PA-1998. The sum of square deviation estimate for PA-1984 equaled 0.01 (P=0.23), in agreement with a hypothetical model of sudden expansion contrary to PA-1998 whose sum of square deviation estimate (0.40; P=0.04) was not compatible with this model, although the small sample size of PA-1998 as well as the smaller area of capture could have also accounted for this result. Fu's Fs and R2 statistical neutrality tests corroborated these propositions. Lack of drastic differentiation was attributable to the once existing connection between the Atlantic and the Amazonian forests at a non-distant past. Am. J. Primatol. 70:423,431, 2008. © 2007 Wiley-Liss, Inc. [source] Population genetic studies of Alouatta caraya (Alouattinae, Primates): inferences on geographic distribution and ecologyAMERICAN JOURNAL OF PRIMATOLOGY, Issue 10 2007Fabrícia F. Do Nascimento Abstract Cytochrome b DNA sequence data (ca. 1,140,bp) of 44 Alouatta caraya, including 42 specimens from three localities of Brazil and two from Bolivia, were used for phylogenetic reconstructions and population studies. Seventeen haplotypes were identified, eight of which were present in more than one individual. Seven of these eight haplotypes were shared by individuals from a same locality and one by individuals from two localities. We found 26 variable sites along the entire gene, consisting of 18 transitions and eight transversions; most replacements occurring at the third codon position (65.39%) in contrast to first and second positions (26.92 and 7.69%, respectively). In the sample collected at Chapada dos Guimarães (Brazil), nucleotide and haplotype diversity estimates were ,=0.002325 and h=0.8772, respectively. Maximum parsimony analysis grouped all haplotypes in two clades, separating Bolivian haplotypes from Brazilian haplotypes, the grouping of which did not show a straightforward correspondence with geographic distribution. Median-joining and TCS network pointed to haplotypes 11 or 12 as the most likely ancestral ones. Mismatch distribution and the goodness-of-fit test (SSD estimate=0.0027; P=0.6999) indicated that the population from Chapada dos Guimarães experienced a demographic expansion, in agreement with the median-joining star-like pattern, although this finding could not be confirmed by Fu's Fs test. Am. J. Primatol. 69:1093,1104, 2007. © 2007 Wiley-Liss, Inc. [source] Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markersANNALS OF APPLIED BIOLOGY, Issue 2 2009A.A.J. Raji Abstract Molecular-marker-aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within-population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within-population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (He) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base. [source] Persea americana (avocado): bringing ancient flowers to fruit in the genomics eraBIOESSAYS, Issue 4 2008André S. Chanderbali The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms. BioEssays 30:386,396, 2008. © 2008 Wiley Periodicals, Inc. [source] | ||||||||||