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J Provan

Publications and source records attributed to J Provan.

At least 19 recordsLinked to original sources
PubMed2003

High-resolution organellar genome analysis of Triticum and Aegilops sheds new light on cytoplasm evolution in wheat.

We have utilised polymorphic chloroplast microsatellites to analyse cytoplasmic relationships between accessions in the genera Triticum and Aegilops. Sequencing of PCR products revealed point mutations and insertions/deletions in addition to the standard repeat length expansion/contraction which most likely represent ancient synapomorphies. Phylogenetic analyses revealed three distinct groups of accessions. One of these contained all the non- Aegilops speltoides S-type cytoplasm species, another comprised almost exclusively A, C, D, M, N, T and U cytoplasm-type accessions and the third contained the polyploid Triticum species and all the Ae. speltoides accessions, further confirming that Ae. speltoides or a closely related but now extinct species was the original B-genome donor of cultivated polyploid wheat. Successive decreases in levels of genetic diversity due to domestication were also observed. Finally, we highlight the importance of elucidating longer-term evolutionary processes operating at microsatellite repeat loci.

Base Sequence↗
PubMed2003

Long-term population isolation in the endangered tropical tree species Caesalpinia echinata Lam. revealed by chloroplast microsatellites.

Habitat fragmentation represents the single most serious threat to the survival of tropical ecosystems. In formulating strategies to counteract the detrimental effects of fragmentation, knowledge of the levels and patterns of genetic diversity within and between natural populations is vital to the establishment of any conservation programme. We utilized polymorphic chloroplast microsatellite markers to analyse genetic diversity in populations of the endangered tropical tree Caesalpinia echinata Lam. representing the entire extant range of the species. Levels of within-population diversity were low, with only two of seven populations studied displaying any variation. The vast majority of the genetic variation was partitioned between geographical regions (36%) and between populations within regions (55%). These levels of genetic structuring, coupled with a calculated pollen-to-seed flow ratio of approximately 6.7:1, suggest that there has been little gene flow between the three major geographical regions over an extended period. Thus, the current tripartite distribution of the species is more consistent with the existence of separate glacial refugia, rather than reflecting any anthropogenic effects.

Brazil↗
PubMed2001

Chloroplast microsatellites: new tools for studies in plant ecology and evolution.

The nonrecombinant, uniparentally inherited nature of organelle genomes makes them useful tools for evolutionary studies. However, in plants, detecting useful polymorphism at the population level is often difficult because of the low level of substitutions in the chloroplast genome, and because of the slow substitution rates and intramolecular recombination of mtDNA. Chloroplast microsatellites represent potentially useful markers to circumvent this problem and, to date, studies have demonstrated high levels of intraspecific variability. Here, we discuss the use of these markers in ecological and evolutionary studies of plants, as well as highlighting some of the potential problems associated with such use.

Journal Article↗
PubMed2001

rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi.

In Europe, the last 20 years have seen a spectacular increase in accidental introductions of marine species, but it has recently been suggested that both the actual number of invaders and their impacts have been seriously underestimated because of the prevalence of sibling species in marine habitats. The red alga Polysiphonia harveyi is regarded as an alien in the British Isles and Atlantic Europe, having appeared in various locations there during the past 170 years. Similar or conspecific populations are known from Atlantic North America and Japan. To choose between three competing hypotheses concerning the origin of P. harveyi in Europe, we employed rbcL sequence analysis in conjunction with karyological and interbreeding data for samples and isolates of P. harveyi and various congeners from the Pacific and North Atlantic Oceans. All cultured isolates of P. harveyi were completely interfertile, and there was no evidence of polyploidy or aneuploidy. Thus, this biological species is both morphologically and genetically variable: intraspecific rbcL divergences of up to 2.1% are high even for red algae. Seven rbcL haplotypes were identified. The four most divergent haplotypes were observed in Japanese samples from Hokkaido and south-central Honshu, which are linked by hypothetical 'missing' haplotypes that may be located in northern Honshu. These data are consistent with Japan being the centre of diversity and origin for P. harveyi. Two non-Japanese lineages were linked to Hokkaido and Honshu, respectively. A single haplotype was found in all North Atlantic and Mediterranean accessions, except for North Carolina, where the haplotype found was the same as that invading in New Zealand and California. The introduction of P. harveyi into New Zealand has gone unnoticed because P. strictissima is a morphologically indistinguishable native sibling species. The sequence divergence between them is 4-5%, greater than between some morphologically distinct red algal species. Two different types of cryptic invasions of P. harveyi have therefore occurred. In addition to its introduction as a cryptic sibling species in New Zealand, P. harveyi has been introduced at least twice into the North Atlantic from presumed different source populations. These two introductions are genetically and probably also physiologically divergent but completely interfertile.

Fertility↗
PubMed2000

Postoperative tonsillectomy pain in pediatric patients: electrocautery (hot) vs cold dissection and snare tonsillectomy--a randomized trial.

OBJECTIVE: To determine the effect of the method of tonsillectomy on postoperative pain in pediatric patients. DESIGN: Prospective, randomized, single-blind, controlled clinical trial. SETTING: A university pediatric hospital in Aberdeen, Scotland. PATIENTS: A volunteer sample of 54 children, aged 3 to 12 years, with recurrent tonsillitis or symptomatic adenotonsillar hypertrophy. Two patients withdrew consent. INTERVENTIONS: Twenty-six children underwent a nonelectrical (ie, cold) dissection tonsillectomy with cold steel instruments, 5 of whom also had adenoidectomy by curettage. Monopolar diathermy forceps were used for tonsillar bed hemostasis. Twenty-four children had electrocautery (ie, hot) dissection tonsillectomy, 7 of whom underwent adenoidectomy by curettage without a suction coagulator. MAIN OUTCOME MEASURES: Postoperative analgesic consumption, time to regain normal diet and activity levels, and complications. RESULTS: Patients who underwent hot dissection tonsillectomy showed no difference in time to first drink or analgesic use within the first 24 postoperative hours compared with children undergoing cold nonelectrical dissection tonsillectomy. The hot dissection tonsillectomy group took 7.5 (95% confidence interval [CI], 1-14.1) more doses of analgesics than the cold dissection group over the next 12 days (P<.05). The hot dissection tonsillectomy group took 2.5 more days than the cold dissection tonsillectomy group to regain normal diet (P<.05). Thirteen children (54%; 95% CI, 34-74) in the hot dissection tonsillectomy group and 6 (23%; 95% CI, 7-39) in the cold dissection tonsillectomy group sought outpatient care for throat pain, otalgia, poor diet, pyrexia, and/or bleeding (P<.05). Throat pain delayed in onset or of prolonged duration affected 9 children (38%; 95% CI, 19-57) in the hot dissection tonsillectomy group as opposed to 3 children (12%; 95% CI, 0-24) in the cold dissection tonsillectomy group (P<.05). CONCLUSION: Hot dissection tonsillectomy increases morbidity in pediatric patients in the recovery period following hospital discharge.

Adenoidectomy↗
PubMed2000

Patterns of variation at a mitochondrial sequence-tagged-site locus provides new insights into the postglacial history of European Pinus sylvestris populations.

Due to their maternal mode of inheritance, mitochondrial markers can be regarded as almost 'ideal' tools in evolutionary studies of conifer populations. In the present study, polymorphism was analysed at one mitochondrial intron (nad 1, exon B/C) in 23 native European Pinus sylvestris populations. In a preliminary screening for variation using a polymerase chain reaction-restriction fragment length polymorphism approach, two length variants were identified. By fully sequencing the 2.5 kb region, the observed length polymorphism was found to result from the insertion of a 31 bp sequence, with no other mutations observed within the intron. A set of primers was designed flanking the observed mutation, which identified a novel sequence-tagged-site mitochondrial marker for P. sylvestris. Analysis of 747 trees from the 23 populations using these primers revealed the occurrence of two distinct haplotypes in Europe. Within the Iberian Peninsula, the two haplotypes exhibited extensive population differentiation (PhiST = 0.59; P < or = 0.001) and a marked geographical structuring. In the populations of central and northern Europe, one haplotype largely predominated, with the second being found in only one individual of one population.

Base Sequence↗
PubMed2000

Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis.

Heart-of-palm (Euterpe edulis Mart.) is a wild palm with a wide distribution throughout the Atlantic Rainforest. Populations of E. edulis represent important renewable natural resources but are currently under threat from predatory exploitation. Furthermore, because the species is indigenous to the Atlantic Rainforest, which is located in the most economically developed and populated region of Brazil, social and economic pressures have devastated heart-of-palm forests. In order to estimate the partitioning of genetic variation of endangered E. edulis populations, 429 AFLP markers were used to analyse 150 plants representing 11 populations of the species distribution range. Analysis of the genetic structure of populations carried out using analysis of molecular variance (AMOVA) revealed moderate genetic variation within populations (57. 4%). Genetic differentiation between populations (FST = 0.426) was positively correlated with geographical distance. These results could be explained by the historical fragmentation of the Atlantic coastal region, together with the life cycle and mating system. The data obtained in this work should have important implications for conservation and future breeding programmes of E. edulis.

Base Sequence↗
PubMed2000

Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.).

We have used eight pairs of simple sequence repeat (SSR) primers to analyse the genetic diversity in 130 individuals of coconut (Cocos nucifera L.) comprising 75 tall individuals and 55 dwarf individuals, representing 94 different coconut ecotypes throughout the world. A total of 51 alleles were detected, with an average of 6.4 alleles per locus. Fifty alleles were detected in tall coconuts (talls; mean alleles/locus 6.3) compared with only 26 (mean/locus 3.3) in dwarfs, and the average diversity value in talls (0.589) was also significantly higher than that in dwarfs (0.348). Using the eight SSRs we were able to uniquely discriminate 116 of the 130 individuals. A phenetic tree based on DAD (absolute distance) values clustered individuals into five groups, each mainly composed of either talls or dwarfs. These results provide evidence in support of previous hypotheses concerning the dissemination of coconut, as well as important new information for conservation and breeding purposes.

Cocos↗
PubMed1999

Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum

In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum, which includes cultivated barley (H. vulgare ssp. vulgare) and its wild progenitor H. vulgare ssp. spontaneum. Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many corp species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.

Journal Article↗
PubMed1999

Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam

Moringa oleifera is an important multipurpose tree introduced to Africa from India at the turn of this century. Despite limited knowledge of the levels of genetic diversity and relatedness of introduced populations, their utilization as a source of seed for planting is widespread. In order to facilitate reasoned scientific decisions on its management and conservation and prepare for a selective breeding programme, genetic analysis of seven populations was performed using amplified fragment length polymorphism (AFLP) markers. The four pairs of AFLP primers (PstI/MseI) generated a total of 236 amplification products of which 157 (66.5%) were polymorphic between or within populations. Analysis of molecular variance (AMOVA) revealed significant differences between regions and populations, even though outcrossing perennial plants are expected to maintain most variation within populations. A phenetic tree illustrating relationships between populations suggested at least two sources of germplasm introductions of Kenya. The high levels of population differentiation detected suggest that provenance source is an important factor in the conservation and exploitation of M. oleifera genetic resources.

Journal Article↗
PubMed1999

A low mutation rate for chloroplast microsatellites.

We used chloroplast simple sequence repeats (cpSSRs) to examine whether there is any variation present in the chloroplast genome of Pinus torreyana (Parry ex Carrière) that may previously not have been detected using RFLPs. Analysis of 17 cpSSR loci showed no variation, which is consistent with previous cpRFLP work and confirms that the species is descended from an original, highly monomorphic population following a bottleneck. This lack of biological variation in the chloroplast genome of P. torreyana allowed us to estimate the mutation rates at cpSSR loci as between 3. 2 x 10(-5) and 7.9 x 10(-5). This estimate is lower than published mutation rates at nuclear SSR loci but higher than substitution rates elsewhere in the chloroplast genome.

Chloroplasts↗
PubMed1999

An example of microsatellite length variation in the mitochondrial genome of conifers.

In the present study, the intergenic region between the mitochondrial genes encoding subunit 3 of NADH dehydrogenase (nad3) and ribosomal protein S12 (rps12) was shown to contain a Gn mononucleotide microsatellite repeat. This region was analysed in 15 species belonging to the genus Pinus and interspecific variation was detected in the form of repeat length polymorphism. Sequence analysis of a 576-bp region containing the microsatellite confirmed that the variability was due to expansion and contraction of the repeat motif and that no point mutations were present in the coding regions of the two genes. This is the first report of the occurrence of a microsatellite polymorphism in plant mitochondria.

Base Sequence↗
PubMed1998

Gene-pool variation in caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple-sequence repeats.

We have used polymorphic chloroplast simple-sequence repeats to analyse levels of genetic variation within and between seven native Scottish and eight mainland European populations of Scots pine (Pinus sylvestris L.). Diversity levels for the Scottish populations based on haplotype frequency were far in excess of those previously obtained using monoterpenes and isozymes and confirmed lower levels of genetic variation within the derelict population at Glen Falloch. The diversity levels were higher than those reported in similar studies in other Pinus species. An analysis of molecular variance (AMOVA) showed that small (3.24-8.81%) but significant (p < or = 0.001) portions of the variation existed between the populations and that there was no significant difference between the Scottish and the mainland European populations. Evidence of population substructure was found in the Rannoch population, which exhibited two subgroups. Finally, one of the loci studied exhibited an allele distribution uncharacteristic of the stepwise mutation model of evolution of simple-sequence repeats, and sequencing of the PCR products revealed that this was due to a duplication rather than slippage in the repeat region. An examination of the distribution of this mutation suggests that it may have occurred fairly recently in the Wester Ross region or that it may be evidence of a refugial population.

Alleles↗
PubMed1997

Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats.

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 +/- 0.0845 (SE) to 0.8298 +/- 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.

Chloroplasts↗
PubMed1996

DNA fingerprints of rice (Oryza sativa) obtained from hypervariable chloroplast simple sequence repeats.

The aim of this research was to develop a convenient polymerase chain reaction-based assay that would allow intraspecific chloroplast variability to be detected. Our approach is based on the detection of length polymorphism within chloroplast mononucleotide microsatellite loci. Information from the fully sequenced rice chloroplast genome was used to identify 12 regions with a minimum of ten uninterrupted mononucleotide repeats. Primers flanking these repeats were used in conjunction with polymerase chain reaction to examine levels of polymorphism in six wild and 14 cultivated rice accessions. A total of six of the primer pairs revealed length polymorphism with between two and five size variants being detected. Diversity indices varied between 0.07 and 0.72. The length variation detected at multiple, physically linked sites was used to identify 15 unique haplotypes with an overall diversity index of 0.90. This level of polymorphism is sufficiently high to allow chloroplast variability to be studied at the intraspecific level. An additional 47 Oryza sativa accessions were also assayed with 31 unique chloroplast haplotypes being detected. The distribution of these haplotypes is described in relation to isozyme groupings and subspecies differentiation. The relevance and implications of these results for plant population genetics and the management of germplasm collections is discussed.

Chloroplasts↗