Divergence times, historical biogeography, and shifts in speciation rates of Myrtales.

We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.

Molecular and morphological characterization of pomegranate (Punica granatum L.) genotypes sampled from Coruh Valley in Turkey.

The pomegranate is one of the oldest fruits that are traditionally consumed by the local inhabitants of the Coruh Valley, Turkey. In this study, the molecular and morphological characteristics of 19 promising pomegranate genotypes selected from the Coruh Valley were evaluated. For the morphological evaluation, 22 quantitative fruit characteristics were used. For the molecular evaluation, 47 random amplified polymorphic DNA (RAPD) primers were used for polymerase chain reaction analysis. The principle component analysis of 22 quantitative fruit characteristics revealed that fruit weight and skin color are dominant traits for genotype discrimination. The unweighted average distance cluster of fruit characteristics revealed 3 distinct groups. Among the 47 RAPD primers, 9 exhibited reliable polymorphic patterns, and generated a total of 63 RAPD bands, of which 49.2% were polymorphic. The similarity matrix showed that the highest (0.920) and lowest (0.556) genetic similarities occurred between the APS13 and APS28 genotypes and the APS12 and APS42 genotypes, respectively. We determined clear discrepancies between the morphological and molecular data; consequently, the differences obtained among genotypes for fruit characteristics did not support genetic relationships among genotypes. In conclusion, molecular data provided the most reliable results at the DNA level.

A novel strategy for identification of 47 pomegranate (Punica granatum) cultivars using RAPD markers.

DNA marker can be used for precise plant cultivar identification. However, DNA markers have often not been used effectively for the identification of plant cultivars due to a lack of an effective analysis strategy. We used a novel strategy for effective identification of plant individuals based on a new way of recording DNA fingerprints of the genotyped plants; a cultivar identification diagram can be manually generated and used as key reference information for quick identification of plant and/or seed samples. Forty-seven pomegranate varieties popularly cultivated in various provinces of China were subjected to RAPD marker analysis. Using the cultivar identification diagram strategy, they were clearly separated by the fingerprints of 11 RAPD primers. The utility and accuracy of the cultivar identification diagram analysis results were confirmed by the identification of three randomly chosen groups of cultivars among the 47 varieties.

Genetic relationships among wild pomegranate (Punica granatum) genotypes from Coruh Valley in Turkey.

The pomegranate has been used traditionally in Coruh Valley in Turkey for a long time; fruits are harvested from wild, semi-domesticated and cultivated trees. In the valley, it occurs in general along with olive trees. We sampled 23 wild-grown pomegranate genotypes sampled from different parts of Coruh Valley and compared them using RAPD primers to determine genetic variability. Eighty-six RAPD primers were used for molecular characterizations, among which 12 gave reliable polymorphic patterns. These primers generated 145 RAPD bands of which 91% were polymorphic. The highest polymorphism ratio was observed with primers OPY06, OPY13, OPBA03, OPBB03, OPBB07, and OPBB09 (100%), while the lowest was with OPBB09 and OPBB10 (75%). The band size was between 250 and 2400 bp. There were five main clusters in the dendrogram; the highest genetic similarity was 0.24 and the lowest was 0.08.

Genetic characterization of pomegranate (Punica granatum L.) genotypes by AFLP markers.

The Coruh Valley, located in Northeastern Turkey, is one of the most important centers of diversity in pomegranate in Turkey. In this study, we attempted to characterize 19 promising pomegranate genotypes originating from the Coruh Valley in using fluorescent dye AFLP markers and capillary electrophoresis. Four AFLP primer combinations were used, generating a total of 297 fragments, 213 of which were polymorphic (73.0%). Resolving powers of the AFLP primers ranged from 0.700 to 1.018, with a total of 3.440, while polymorphism information contents ranged from 0.707 to 0.837 with an average of 0.764. UPGMA clustering of the genotypes showed two major groups. Most of the fruit characteristics of the genotypes within the same group were variable. Therefore, the results showed that molecular characterization is necessary to get reliable relationships among pomegranate genotypes and AFLP markers can be used effectively in pomegranate.

Genetic characterization of pomegranate (Punica granatum L.) genotypes by AFLP markers

The Coruh Valley, located in Northeastern Turkey, is one of the most important centers of diversity in pomegranate in Turkey. In this study, we attempted to characterize 19 promising pomegranate genotypes originating from the Coruh Valley in using fluorescent dye AFLP markers and capillary electrophoresis. Four AFLP primer combinations were used, generating a total of 297 fragments, 213 of which were polymorphic (73.0%). Resolving powers of the AFLP primers ranged from 0.700 to 1.018, with a total of 3.440, while polymorphism information contents ranged from 0.707 to 0.837 with an average of 0.764. UPGMA clustering of the genotypes showed two major groups. Most of the fruit characteristics of the genotypes within the same group were variable. Therefore, the results showed that molecular characterization is necessary to get reliable relationships among pomegranate genotypes and AFLP markers can be used effectively in pomegranate.