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ABSTRACT: • Premise of the Study: Known-age artificial-lake islands provide ideal model systems to elucidate the genetic and evolutionary consequences of anthropogenic habitat fragmentation on very recent time scales. Here, we studied a distylous herb, Hedyotis chrysotricha (Rubiaceae), in the artificially created Thousand-Island Lake (TIL) region of southeast China to explore the genetic consequences of islanding for this species. • Methods: Seven microsatellite loci were used to genotype 384 individuals of H. chrysotricha from 18 populations to estimate genetic diversity, population structure, and demographic parameters. • Key Results: Island populations had significantly lower mean genetic diversity than those from the western/eastern mainland (e.g., H(E) = 0.381 vs. 0.461) and also displayed higher mean subdivision (F(ST) = 0.12 vs. 0.042/0.051). BayesAss analyses indicated moderate levels of migration rates among most populations, whereas Bottleneck did not provide strong evidence for such effects. In consequence, 2MOD strongly favored a gene flow-drift model over a pure drift model in the study area, but concomitantly revealed a relatively greater influence of drift in the island populations as evidenced by their significantly higher probabilities of allelic coancestry (F = 0.184 vs. 0.085). • Conclusions: The observed genetic patterns in H. chrysotricha indicate that recent anthropogenic habitat fragmentation in the TIL region can lead to significant loss of genetic diversity in isolated fragments (islands) due to ongoing drift. By contrast, patterns of random mating, gene flow, and population connectivity have not greatly been modified yet, possibly owing to the species' fruit (seed) dispersal capabilities providing resilience in the face of habitat fragmentation.
American Journal of Botany 09/2012; 99(10):1715-25. · 2.66 Impact Factor
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ABSTRACT: • East Asia's temperate deciduous forests served as sanctuary for Tertiary relict trees, but their ages and response to past climate change remain largely unknown. To address this issue, we elucidated the evolutionary and population demographic history of Cercdiphyllum, comprising species in China/Japan (Cercdiphyllum japonicum) and central Japan (Cercdiphyllum magnificum). • Fifty-three populations were genotyped using chloroplast and ribosomal DNA sequences and microsatellite loci to assess molecular structure and diversity in relation to past (Last Glacial Maximum) and present distributions based on ecological niche modelling. • Late Tertiary climate cooling was reflected in a relatively recent speciation event, dated at the Mio-/Pliocene boundary. During glacials, the warm-temperate C. japonicum experienced massive habitat losses in some areas (north-central China/north Japan) but increases in others (southwest/-east China, East China Sea landbridge, south Japan). In China, the Sichuan Basin and/or the middle-Yangtze were source areas of postglacial northward recolonization; in Japan, this may have been facilitated through introgressive hybridization with the cool-temperate C. magnificum. • Our findings challenge the notion of relative evolutionary and demographic stability of Tertiary relict trees, and may serve as a guideline for assessing the impact of Neogene climate change on the evolution and distribution of East Asian temperate plants.
New Phytologist 07/2012; 196(2):617-630. · 6.64 Impact Factor
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ABSTRACT: • Premise of the study: Microsatellite markers were characterized in Platycrater arguta, a rare endemic shrub from eastern China and southern Japan, to investigate its population genetic structure, phylogeographic patterns, and breeding system. • Methods and Results: Using both the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol and the compound microsatellite marker technique, we developed 12 microsatellite markers. All primers showed polymorphism when assessed in 43 individuals from two populations in eastern China and southern Japan. Overall, the number of alleles ranged from five to 21, with an average of 14.91 alleles per locus. • Conclusions: These markers can be used in further studies on population genetics, phylogeography, and breeding system of P. arguta.
American Journal of Botany 07/2012; 99(8):e304-6. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: Microsatellite primers were developed for the endangered Davidia involucrata to assess the population genetics and infer its evolutionary history. • Methods and Results: Using both the modified magnetic bead hybridization method and the dual-suppression PCR method, we isolated and characterized 12 polymorphic microsatellite loci using 134 individuals from five populations in southwestern China. The number of alleles per locus ranged from six to 21 (mean = 10.8). The expected heterozygosity per locus ranged from 0.404 to 0.918 and observed heterozygosity ranged from 0.015 to 0.821. • Conclusions: All of the 12 microsatellite markers developed for D. involucrata are polymorphic, and lay a solid foundation for further studies of the population genetics of this famous tree.
American Journal of Botany 04/2012; 99(5):e206-9. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: Compound microsatellite primers were developed for Emmenopterys henryi, an endangered deciduous tree endemic to China, to assess its genetic diversity and population structure as well as its evolutionary history. • Methods and Results: Using the compound microsatellite marker technique, 10 pairs of polymorphic microsatellite primers were isolated and characterized in E. henryi. Levels of polymorphism were tested across a total of 63 individuals from three natural populations. Allele numbers varied from 10 to 20 per locus, with an average of 14.50 alleles per locus. The observed heterozygosity per locus ranged from 0.125 to 0.962, and the expected heterozygosity ranged from 0.377 to 0.903. • Conclusions: The highly polymorphic markers developed and characterized in this study will facilitate evolutionary and population genetic studies in E. henryi.
American Journal of Botany 04/2012; 99(4):e179-81. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: Microsatellite primers were developed for a heterostylous herb, Hedyotis chrysotricha to investigate the effect of habitat fragmentation on its genetic diversity and population structure. • Methods and Results: Twelve primer sets were developed and their polymorphisms were tested on 47 individuals from two island populations of H. chrysotricha in Thousand Island Lake of China. The number of alleles per locus ranged from five to 10, with an average of seven alleles. Expected heterozygosity per locus ranged from 0.284 to 0.821 and observed heterozygosity ranged from 0.191 to 0.851. • Conclusions: We showed that all of the 12 microsatellite markers developed for H. chrysotricha are polymorphic within populations, which should provide a powerful tool for assessing population structure and genetic diversity across fragmented and continuous populations, and for studying the genetic effects of habitat fragmentation on this species.
American Journal of Botany 02/2012; 99(2):e43-5. · 2.66 Impact Factor
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ABSTRACT: Microsatellite markers were developed for Dipteronia dyerana, an endangered endemic species in China, to study the population genetics of this species.
Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 12 microsatellite markers that were successfully amplified showed polymorphism when tested on 31 individuals from two populations in the counties of Wenshan and Mengzi. Overall, the number of alleles per locus ranged between seven and 25, with an average of 12.3. Nine of these markers were able to be amplified in D. sinensis.
These microsatellite markers should facilitate further studies on the population genetics and the reproductive ecology of Dipteronia.
American Journal of Botany 10/2011; 98(10):e271-3. · 2.66 Impact Factor
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ABSTRACT: Microsatellite markers were developed for the common Mediterranean shrub Smilax aspera to study the population genetics of this species.
Using the compound microsatellite marker technique, a total of 14 pairs of primers were developed for S. aspera, of which 11 were polymorphic, and three were monomorphic. Levels of polymorphism in the 11 markers were checked in 43 individuals collected from two populations in Greece and Italy. The number of alleles per locus ranged from 10 to 26, with an average of 15.55 alleles per locus. All of these primers also could be amplified from a second species, S. hispida.
These microsatellite markers can be used for future studies of genetic diversity in S. aspera, as well as in other related taxa, and will help us to improve our understanding of the microevolutionary processes of this species in the Mediterranean region.
American Journal of Botany 03/2011; 98(3):e64-6. · 2.66 Impact Factor
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ABSTRACT: The Sino-Japanese Floristic Region (SJFR) of East Asia harbors the most diverse of the world's temperate flora, and was the most important glacial refuge for its Tertiary representatives ('relics') throughout Quaternary ice-age cycles. A steadily increasing number of phylogeographic studies in the SJFR of mainland China and adjacent areas, including the Qinghai-Tibetan-Plateau (QTP) and Sino-Himalayan region, have documented the population histories of temperate plant species in these regions. Here we review this current literature that challenges the oft-stated view of the SJFR as a glacial sanctuary for temperate plants, instead revealing profound effects of Quaternary changes in climate, topography, and/or sea level on the current genetic structure of such organisms. There are three recurrent phylogeographic scenarios identified by different case studies that broadly agree with longstanding biogeographic or palaeo-ecological hypotheses: (i) postglacial re-colonization of the QTP from (south-)eastern glacial refugia; (ii) population isolation and endemic species formation in Southwest China due to tectonic shifts and river course dynamics; and (iii) long-term isolation and species survival in multiple localized refugia of (warm-)temperate deciduous forest habitats in subtropical (Central/East/South) China. However, in four additional instances, phylogeographic findings seem to conflict with a priori predictions raised by palaeo-data, suggesting instead: (iv) glacial in situ survival of some hardy alpine herbs and forest trees on the QTP platform itself; (v) long-term refugial isolation of (warm-)temperate evergreen taxa in subtropical China; (vi) 'cryptic' glacial survival of (cool-)temperate deciduous forest trees in North China; and (vii) unexpectedly deep (Late Tertiary/early-to-mid Pleistocene) allopatric-vicariant differentiation of disjunct lineages in the East China-Japan-Korea region due to past sea transgressions. We discuss these and other consequences of the main phylogeographic findings in light of palaeo-environmental evidence, emphasize notable gaps in our knowledge, and outline future research prospects for disentangling the evolution and biogeographic history of the region's extremely diverse temperate flora.
Molecular Phylogenetics and Evolution 02/2011; 59(1):225-44. · 3.61 Impact Factor
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ABSTRACT: Molecular phylogeographic studies have recently begun to elucidate how plant species from the Qinghai-Tibetan Plateau (QTP) and adjacent regions responded to the Quaternary climatic oscillations. In this regard, however, far less attention has been paid to the southern and south-eastern declivities of the QTP, i.e. the Himalaya-Hengduan Mountains (HHM) region. Here, we report a survey of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA (cpDNA) sequence variation in the HHM endemic Sinopodophyllum hexandrum, a highly selfing alpine perennial herb with mainly gravity-dispersed berries (105 individuals, 19 localities). We specifically aimed to test a vicariant evolutionary hypothesis across the 'Mekong-Salween Divide', a known biogeographic and phytogeographic boundary of north-to-south trending river valleys separating the East Himalayas and Hengduan Mts. Both cpDNA and AFLPs identified two divergent phylogroups largely congruent with these mountain ranges. There was no genetic depauperation in the more strongly glaciated East Himalayas (AFLPs: H(E)=0.031; cpDNA: h(S)=0.133) compared to the mainly ice-free Hengduan Mts. (AFLPs: H(E)=0.037; cpDNA: h(S)=0.082), while population differentiation was consistently higher in the former region (AFLPs: Φ(ST)=0.522 vs. 0.312; cpDNA: Φ(ST)=0.785 vs. 0.417). Our results suggest that East Himalayan and Hengduan populations of S. hexandrum were once fragmented, persisted in situ during glacials in both areas, and have not merged again, except for a major instance of inter-lineage chloroplast capture identified at the MSD boundary. Our coalescent time estimate for all cpDNA haplotypes (c. 0.37-0.48 mya), together with paleogeological evidence, strongly rejects paleo-drainage formation as a mechanism underlying allopatric fragmentation, whereas mountain glaciers following the ridges of the MSD during glacials (and possible interglacials) could have been responsible. This study thus indicates an important role for mountain glaciers in driving (incipient) allopatric speciation across the MSD in the HHM region by causing vicariant lineage divergence and acting as barriers to post-divergence gene flow.
Molecular Phylogenetics and Evolution 02/2011; 59(2):412-24. · 3.61 Impact Factor
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ABSTRACT: • Premise of the study: The development of compound microsatellite markers was conducted in Neolitsea sericea to investigate genetic diversity and population genetic structure of this endangered insular species. • Methods and Results: Using the compound microsatellite marker technique, 10 compound microsatellite markers that were successfully amplified showed polymorphism when assessed in 55 individuals from two populations in East China and Japan. Overall, the number of alleles ranged from 3 to 17, with an average of 7.9 alleles per locus. In addition, these primers could be easily amplified in Neolitsea aurata var. paraciculata and N. aurata var. chekiangensis. • Conclusions: The highly polymorphic markers developed and characterized in this study will be useful for population genetic studies of N. sericea.
American Journal of Botany 12/2010; 97(12):e139-41. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: Microsatellite markers were developed for Cercidiphyllum japonicum to study population genetics of this endangered species native to both eastern China and Japan. • Methods and Results: Using the Fast Isolation by AFLP of Sequences Containing Repeats (FIASCO) protocol, 12 microsatellite markers that were successfully amplified showed polymorphism when tested on 33 individuals from two populations in eastern China and Japan. Overall, the number of alleles per locus ranged between 5 and 18. Eleven markers could be easily amplified and were polymorphic in C. magnificum. • Conclusions: These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure in Cercidiphyllum at fine and range-wide geographical scales.
American Journal of Botany 09/2010; 97(9):e82-4. · 2.66 Impact Factor
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ABSTRACT: • Premise of the study: Microsatellite markers were developed for Kirengeshoma palmata to assess the population genetics and mating pattern of this critically endangered species. • Methods and Results: A total of 24 microsatellite markers were developed for K. palmata using an enrichment protocol. These markers were screened in 37 individuals from four populations in China and Japan, and twelve were found to be polymorphic, with the number of alleles per locus ranging from two to eight. All of these primers also amplified in K. koreana. • Conclusions: These microsatellite markers provide a useful tool to investigate the mating system, gene flow, parentage, and population dynamics of Kirengeshoma.
American Journal of Botany 06/2010; 97(6):e48-51. · 2.66 Impact Factor
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ABSTRACT: To evaluate the role of Quaternary refugial isolation in allopatric (incipient) speciation of East Asian temperate forest biotas, we analyzed amplified fragment length polymorphisms (AFLPs) and the breeding system in Dysosma versipellis. The study revealed that D. versipellis is mostly self-incompatible, genetically highly subdivided and depauperate at the population level (e.g., Φ(ST) = 0.572/H(E) = 0.083), and characterized by a low pollen-to-seed migration ratio (r ≈ 4.0). The latter outcome likely reflects limited pollen flow in a low-seed disperser whose hypothesized "sapromyophilous" flowers undergo scarce, inefficient, and likely specialized cross-pollination by small Anoplodera beetles, rather than carrion flies as assumed previously. In consequence, fruit set in D. versipellis was strongly pollen-limited. Our AFLP data support the hypothesis of a long-standing cessation of gene flow between western and central eastern populations, consistent with previous chloroplast DNA data. This phylogeographic pattern supports the role of the Sichuan Basin as a floristic boundary separating the Sino-Himalayan vs. Sino-Japanese Forest subkingdoms. Our genetic data of D. versipellis also imply that temperate deciduous forest elements to the west and the east of this basin responded differently to Quaternary climate change, which may have triggered or is leading to allopatric (incipient) speciation.
American Journal of Botany 01/2010; 97(1):111-22. · 2.66 Impact Factor
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ABSTRACT: Kirengeshoma comprises two species inhabiting warm temperate-deciduous forests in East China/South Japan (Kirengeshoma palmata) and South Korea (Kirengeshoma koreana). A survey of chloroplast (cp) DNA and inter-simple sequence repeats (ISSRs) variation in Kirengeshoma was carried out to determine the population history of a plant taxon around the East China Sea (ECS). CpDNA and ISSRs revealed lower genetic divergence between China and Japan relative to the other contrasts, in line with intrageneric classification. Molecular dating suggests that K. koreana diverged at the Plio-Pleistocene boundary from the Japanese populations, whereas the latter migrated into China during the early-to-mid Pleistocene via the ECS basin. Vicariant segregation of Chinese and Japanese populations likely occurred during the mid-Pleistocene. Mismatch distributions and neutrality tests indicated that Chinese populations expanded their range during the Late Pleistocene, probably during a cold period, whereas those from Japan showed no significant population growth. We conclude that the current distribution and differentiation of components of presently isolated warm temperate-deciduous forests in China, Japan and Korea likely resulted from a combination of relatively ancient vicariant and immigration events, and those from Japan were particularly sensitive to range fragmentation and long-term refugial isolation throughout the Late Pleistocene.
New Phytologist 07/2009; 183(2):480-95. · 6.64 Impact Factor
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ABSTRACT: To explore the evolutionary consequences of climate-induced fluctuations in presently fragmented temperate forest habitats in continental East Asia we investigated the phylogeography and demographic history of the temperate-deciduous forest endemic Dysosma versipellis from disjunct montane sites in Central-Southeast China. Based on a survey of chloroplast (cp) DNA sequence variation, our analyses show that this perennial herb consists of morphologically indistinguishable western and central/eastern cpDNA lineages. Coalescent analyses under the ‘isolation with migration’ (IM) model support an ancient (Mid-Pleistocene) divergence between these lineages, with the western lineage having persisted without significant population growth in a long-term refuge just east of the Tibetan (Qinghai-Xizang) Plateau. In contrast, for the central/eastern lineage, we found strong evidence for population expansion from a refuge located south of the middle and lower reaches of the Yangtze River, and likely coinciding with the last or penultimate interglacial, followed by considerable population isolation and divergence in situ over (at least) the latest glacial–interglacial cycle. In line with recent evidence from palaeomodeling of East Asian forest biomes, our results suggest that the same vicariance factor, i.e. climate-induced eco-geographic isolation through (a)biotic displacement of temperate-deciduous forested habitats, promoted the divergence of D. versipellis lineages and populations at different spatial–temporal scales and over glacial and interglacial periods. Thus, there is no evidence that populations of D. versipellis merged at lower elevations during the last glacial(s). As such, D. versipellis accords with the premise that Late Quaternary refugial isolation is likely to have enhanced allopatric (incipient) species formation of temperate plants in East Asia.
Molecular Phylogenetics and Evolution 03/2009; · 3.61 Impact Factor
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ABSTRACT: To investigate the genetic diversity of main germplasm of Atractylodes macrocephala in China and the genetic differentiation of the germplasm of A. macrocephala.
A molecular marker ISSR was used to analyze the genetic diversity of 7 populations of A. macrocephala and a population of A. lancea.
Twelve primers were used in the PCR amplification of 86 samples of A. macrocephala and 5 samples of A. lancea. Sixty-three bands with sizes ranged from 100 to 2500 bp were generated from 12 primers. Of all the 63 bands, 55 bands were polymorphic among 86 individuals of A. macrocephala, the percentage of polymorphic bands were 87.30% at the species level. The percentage of polymorphic bands (PPL) for a single population ranged from 58.73% to 71.43% (mean, 64.85%). Among the 7 populations, a population from Panan, GM exhibited highest variability (PPL =71.43%; HE = 0.2835; I = 0.4267). A dendrogram constructed by an unweighted pair group method of cluster analysis showed that populations from Panan constructed one branch and separated from other populations. In the AMOVA analysis, low level of genetic differentiation among populations was detected, 90.52% of the variability existed in population.
The genetic diversity of cultivated A. macrocephala in China is high, which is good for the production of high quality herb medicine.
Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica 01/2009; 33(23):2756-60.
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ABSTRACT: Rhizoma Corydalis is an important Chinese medicinal herb. In this paper, we employed ISSR data to explore the genetic variation in domesticated populations and wild populations of the species. The average of within-population ISSR diversity in cultivated populations (PPF=25.32%, Hpop=0.094) was lower than that in wild populations (PPF=47.70%, Hpop=0.144). Cultivated populations (PhiST=0.515, GST=0.429) have a greater proportion of their genetic variability distributed among populations than wild populations (PhiST=0.277, GST=0.226). Based on hierarchical estimates of variance components, significant statistical differences (57.77%, P<0.001) were found between the wild and cultivated groups. The low levels of genetic diversity within cultivated populations and high levels of genetic differentiation among populations/groups may result from artificial selection, the mode of clonal propagation, and only limited exchange of material among localities. Finally, some suggestions for conservation and efficient management of the genetic resources of this important medicinal herb are proposed.
Planta Medica 12/2008; 75(1):94-8. · 2.15 Impact Factor
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ABSTRACT: The genus Croomia (Stemonaceae) comprises three herbaceous perennial species that are distributed in temperate-deciduous forests in Southeastern North America (C.pauciflora) and East Asia (C. japonica, C. heterosepala). The two Asian species have abutting ranges in South Japan, but C. japonica also occurs disjunctively on the adjacent Asiatic mainland in East China. In our phylogenetic analysis of Croomia, based on chloroplast (cp) DNA sequence variation of the trnL-F region, and rooted with Stemona spp., the two Asian species are identified as sister that likely diverged in the Mid-to-Late Pleistocene (0.84-0.13 mya), whereas the divergence of C. pauciflora dates back to the Late Plio-/Pleistocene (<2.6 mya). Phylogeographical analysis of the two East Asian species detected seven cpDNA (trnL-F) haplotypes across 16 populations surveyed, and all of those were fixed for a particular cpDNA haplotype (H(E)=0.0, G(ST)=1). A survey of inter-simple sequence repeats (ISSRs) markers also detected remarkably low levels of within-population diversity (C. japonica: H(E)=0.085; C. heterosepala: H(E)=0.125), and high levels of inter-population differentiation (C. japonica: Phi(ST)=0.736; C. heterosepala: Phi(ST)=0.550), at least partly due to pronounced regional genetic substructure within both species. Non-overlapping distributions of cpDNA haplotypes and strong genetic (cpDNA/ISSR) differentiation among populations and/or regions accord with findings of a nested clade analysis, which inferred allopatric fragmentation as the major process influencing the spatial haplotype distribution of the two species. Based on mismatch distribution analysis and neutrality tests, we do not find evidence of population expansion in both species. Overall, we conclude that components of temperate-deciduous forest types in South Japan and East China are particularly sensitive to range fragmentation, isolation, and enhanced (incipient) species formation through climate-induced expansions of other forest types over glacial and interglacial periods of the (Late) Quaternary.
Molecular Phylogenetics and Evolution 09/2008; 49(3):702-14. · 3.61 Impact Factor
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ABSTRACT: Dysosma versipellis (Berberidaceae) is an important threatened medicinal plant (TMP) species. Here we isolated nine polymorphic microsatellite
loci from D. versipellis using a modified biotin-capture method. Our isolated loci provided SSR markers with polymorphism of 2–7 alleles per locus.
The expected and observed heterozygosities ranged from 0.507 to 0.864 and from 0.360 to 0.720, respectively. These markers
would be the useful tools for analyzing questions concerning population genetic structure and mating system of D. versipellis.
Conservation Genetics 05/2008; 9(3):783-785. · 1.61 Impact Factor
