Assessing population genetic structure and variability with RAPD data: Application to <i>Vaccinium macrocarpon</i> (American Cranberry)

Stewart, C. N.; Excoffier, Laurent

doi:10.1046/j.1420-9101.1996.9020153.x

Cited by 231 publications

(233 citation statements)

References 23 publications

Supporting

Mentioning

223

Contrasting

Unclassified

Order By: Relevance

“…An analysis of molecular variance using the program WINAMOVA 1.55 (Excoffier et al, 1992;Stewart and Excoffier, 1996) was performed on the matrix of genetic distances for the estimation of the distribution of genetic variability within and among populations and ecological groups. The program also extracts analogs of F-statistics (so-called Φ-statistics: Φ ST (differentiation among populations), Φ CT (differentiation among ecological groups) and Φ SC (differentiation among populations within groups)).…”

Section: Discussionmentioning

confidence: 99%

Genetic structure of Tunisian natural carob tree (Ceratonia siliqua L.) populations inferred from RAPD markers

et al. 2008

View full text Add to dashboard Cite

Abstract• Seven RAPD markers were used to assess the genetic diversity and structure of ten Tunisian natural Ceratonia siliqua L. populations from different geographic and bioclimatic zones.• The species maintain a high diversity within population as estimated by the percentage of polymorphic loci and Shannon's index (P% = 76.31, H pop = 0.569). The range of variation between populations was large. Populations from the upper semi-arid bioclimates, with more continuous distribution area showed the highest level of variation.• A high genetic differentiation among populations (Φ ST = 0.250 and G ST = 0.347), as a result of population isolation was revealed. Nevertheless, the genetic structure is in accordance with bioclimate indicating that ecological factors also should influence differentiation. Populations from the sub-humid, upper semi-arid and mean semi-arid zones clustered together and were distinct from those of the lower semi-arid ones.• Conservation strategy should be made according to the level of polymorphism within population and bioclimate.Mots-clés : diversité génétique / RAPD / Ceratonia siliqua / populations naturelles / bioclimat / conservation Résumé -Structure génétique des populations naturelles du caroubier (Ceratonia siliqua L.) en Tunisie estimée par les marqueurs RAPD.• Sept marqueurs RAPD ont été utilisés pour analyser la diversité et la structure génétique de dix populations tunisiennes de caroubier (Ceratonia siliqua L.) prospectées dans différentes zones géo-graphiques et bioclimatiques.• L'espèce maintient une diversité génétique intra population importante (P% = 76.31 ; H pop = 0.569) et les niveaux de variation diffèrent selon les populations. Celles du subhumide et du semi-aride supérieur, à aire de distribution plus continue, ont montré la variation la plus importante.• Une forte différenciation (Φ ST = 0.250 et G ST = 0.347) entre les populations, due à leur fragmentation récente, est observée. Toutefois, cette différenciation concorde avec le bioclimat des sites témoi-gnant l'influence des facteurs écologiques dans cette différenciation. Les populations du subhumide, du semi-aride supérieur et du semi-aride moyen constituent un groupe distinct de celui représenté par les populations du semi-aride inférieur.• La conservation des populations doit tenir compte de leur niveau de diversité génétique intra population et du bioclimat.

show abstract

Section: Discussionmentioning

confidence: 99%

Genetic structure of Tunisian natural carob tree (Ceratonia siliqua L.) populations inferred from RAPD markers

et al. 2008

View full text Add to dashboard Cite

show abstract

“…The binomial matrix was also applied to an AMOVA in RAPD patterns by the program WINAMOVA 1.55 (Excoffier et al, 1992;Stewart and Excoffier, 1996). AMOVA was originally developed for RFLP haplotypes, but it is also appropriate for RAPD phenotypes (Huff et al, 1993).…”

Section: Discussionmentioning

confidence: 99%

Genetic differentiation among populations of Sesleria albicans Kit. ex Schultes (Poaceae) from ecologically different habitats in central Europe

2003

View full text Add to dashboard Cite

As observed for many other plant species, the populations of Sesleria albicans in Central Europe are located in habitats, which differ to a high degree from each other with regard to ecological factors such as nutrients, light and water as well as in type of land use. The species colonizes limestone cliffs, pavements, screes, grazed and mown grasslands, heaths, fens and open woodlands. In this study, we used random amplified polymorphic DNA (RAPD) analysis to investigate the genetic differentiation among 25 populations of S. albicans from six different types of habitat (beech forests, alpine and lowland rocky ridges, lowland screes, fens, calcareous grasslands). With RAPD analysis, 344 fragments could be amplified, of which 95.9% were polymorphic. The level of polymorphism ranged from 29.7 to 56.7% polymorphic bands per population and was correlated with population size. In an analysis of molecular variance (AMOVA), used to detect variation among individuals within populations, among populations from the same habitat and among different habitats, most of the genetic variation was found within populations (62.06%) and among populations from the same habitat (33.36%). In contrast, only a very low level of differentiation could be observed among different habitats (4.58%). The results of our study give only little evidence for an ecotypic differentiation of Sesleria albicans. This differentiation is principally conceivable, but obviously not related to the investigated RAPD loci.

show abstract

“…The libraries were considered significantly different if the P value was b 0.05. Analysis of molecular variance (AMOVA) (Anderson, 2001;Excoffier et al, 1992;Martin, 2002) and Homogeneity of molecular variance (HOMOVA) (Stewart and Excoffier, 1996) was used to test whether population genetic heterogeneicity is significantly different be-tween populations (Schloss, 2008). With an error rate of 0.05 and taking into account a Bonferroni's correction for multiple comparisons, the libraries were considered significantly different if the P value was b 0.0167.…”

Section: Statistical Comparisons Between Librariesmentioning

confidence: 99%

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Riquelme

Câmara

Dapkevicius

et al. 2015

International Journal of Food Microbiology

View full text Add to dashboard Cite

This work presents the first study on the bacterial communities in Pico cheese, a traditional cheese of the Azores (Portugal), made from raw cow's milk. Pyrosequencing of tagged amplicons of the V3-V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.Pyrosequencing revealed a high bacterial diversity in Pico cheese. Four phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) and 54 genera were identified. The predominant genus was Lactococcus (77% of the sequences). Sequences belonging to major cheese-borne pathogens were not found. Staphylococcus accounted for 0.5% of the sequences. Significant differences in bacterial community composition were observed between cheese-maker B and the other two units that participated in the study. However, OTU analysis identified a set of taxa (Lactococcus, Streptococcus, Acinetobacter, Enterococcus, Lactobacillus, Staphylococcus, Rothia, Pantoea and unclassified genera belonging to the Enterobacteriaceae family) that would represent the core components of artisanal Pico cheese microbiota. A diverse bacterial community was present at early maturation, with an increase in the number of phylotypes up to 2 weeks, followed by a decrease at the end of ripening. The most remarkable trend in abundance patterns throughout ripening was an increase in the number of sequences belonging to the Lactobacillus genus, with a concomitant decrease in Acinetobacter, and Stenotrophomonas. Microbial rank abundance curves showed that Pico cheese's bacterial communities are characterized by a few dominant taxa and many low-abundance, highly diverse taxa that integrate the socalled "rare biosphere".2

show abstract

Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry)

Cited by 231 publications

References 23 publications

Genetic structure of Tunisian natural carob tree (Ceratonia siliqua L.) populations inferred from RAPD markers

Genetic structure of Tunisian natural carob tree (Ceratonia siliqua L.) populations inferred from RAPD markers

Genetic differentiation among populations of Sesleria albicans Kit. ex Schultes (Poaceae) from ecologically different habitats in central Europe

Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Contact Info

Product

Resources

About