Amplified fragment length polymorphism analysis reveals high genetic variation in the Ouachita Mountain endemic Carex latebracteata (Cyperaceae)

Botany ◽  
2009 ◽  
Vol 87 (8) ◽  
pp. 770-779
Author(s):  
Bruce A. Ford ◽  
Anne C. Worley ◽  
Robert F. C. Naczi ◽  
Habibollah Ghazvini

Species with limited geographic ranges are often of conservation concern because they may possess low levels of genetic variability and thus have a reduced ability to respond to stochastic events. As a consequence, an important conservation strategy is to maximize a species’ adaptive potential by preserving natural levels of genetic variation. With this goal in mind, we assessed genetic variation within and among six populations of the Ouachita Mountain endemic Carex latebracteata Waterfall using 653 amplified fragment length polymorphism (AFLP) loci. Indices of genetic variation [% polymorphic loci, expected heterozygosity (HE), population differentiation (ΦPT)] were most consistent with an outcrossing or mixed mating system despite an inflorescence morphology that seems conducive to self-pollination. An analysis of molecular variance (AMOVA) showed that >80% of the variation occurred within populations, suggesting high levels of gene flow. The close geographic proximity of most populations, which are often adjacent to streams, may facilitate long-distance seed dispersal and help to maintain high intra-population genetic variation. Conservation strategies focused on maintaining the ecological integrity of rivers and streams, and the provision of naturally vegetated buffers would likely assist in the conservation of this and other Ouachita Mountain endemics.

1999 ◽  
Vol 37 (6) ◽  
pp. 1948-1952 ◽  
Author(s):  
Meeta Desai ◽  
Androulla Efstratiou ◽  
Robert George ◽  
John Stanley

We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise “identical” M1 isolates as members of a clone complex.


1999 ◽  
Vol 181 (15) ◽  
pp. 4469-4475 ◽  
Author(s):  
Adam Meijer ◽  
Servaas A. Morré ◽  
Adriaan J. C. Van Den Brule ◽  
Paul H. M. Savelkoul ◽  
Jacobus M. Ossewaarde

ABSTRACT The genomic relatedness of 19 Chlamydia pneumoniaeisolates (17 from respiratory origin and 2 from atherosclerotic origin), 21 Chlamydia trachomatis isolates (all serovars from the human biovar, an isolate from the mouse biovar, and a porcine isolate), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and 1 Chlamydia pecorum isolate was studied by analyzing genomic amplified fragment length polymorphism (AFLP) fingerprints. The AFLP procedure was adapted from a previously developed method for characterization of clinical C. trachomatis isolates. The fingerprints of all C. pneumoniae isolates were nearly identical, clustering together at a Dice similarity of 92.6% (± 1.6% standard deviation). The fingerprints of the C. trachomatis isolates of human, mouse, and swine origin were clearly distinct from each other. The fingerprints of the isolates from the human biovar could be divided into at least 12 different types when the presence or absence of specific bands was taken into account. The C. psittacifingerprints could be divided into a parakeet, a pigeon, and a feline type. The fingerprint of C. pecorum was clearly distinct from all others. Cluster analysis of selected isolates from all species revealed groups other than those based on sequence data from single genes (in particular, omp1 and rRNA genes) but was in agreement with available DNA-DNA hybridization data. In conclusion, cluster analysis of AFLP fingerprints of representatives of all species provided suggestions for a grouping of chlamydiae based on the analysis of the whole genome. Furthermore, genomic AFLP analysis showed that the genome of C. pneumoniae is highly conserved and that no differences exist between isolates of respiratory and atherosclerotic origins.


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